A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

A - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
abort() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
This method is called if the LoginContext's overall authentication failed.
absolute - Variable in class org.biomage.Measurement.Measurement.Type
 
ABSTRACT - Static variable in class org.biomage.tools.generate_er.CreateMageER
the object (table) is abstract
AbstractDataExternalTxtReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Reader for tab-delimited txt files imported via caAMEL.
AbstractDataFileReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Base class for all data file readers.
AbstractIlluminaCsvReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Reader for both row and column oriented Illumina CSV data.
AbstractSessionBean - Class in gov.nih.nci.caarray.services.util
Warning: This class doesn't implement SessionBean intentionally as to force the subclasses to implement it so that the remote interface can be generated properly by the ejbdoclet task.
AbstractSessionBean() - Constructor for class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
AbstractUseCase - Class in gov.nih.nci.caarray.services.fileparse.test.usecases
 
AbstractUseCase() - Constructor for class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
AbstractUseCase constructor comment.
AbstractUseCase - Class in gov.nih.nci.caarray.services.security.test.usecases
 
AbstractUseCase() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
AbstractUseCase constructor comment.
AbstractUseCase - Class in gov.nih.nci.caarray.services.test.usecases
 
AbstractUseCase() - Constructor for class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
AbstractUseCase constructor comment.
AbstractUseCase - Class in gov.nih.nci.caarray.services.util.netcdf.test.usecases
 
AbstractUseCase() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
AbstractUseCase constructor comment.
acceptableFileTypes_ - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
ACCESS_DENIED_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
AccessDeniedException - Exception in gov.nih.nci.caarray.services.exception
 
AccessDeniedException() - Constructor for exception gov.nih.nci.caarray.services.exception.AccessDeniedException
Creates a new default AccessDeniedException
AccessDeniedException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.AccessDeniedException
Creates an AccessDeniedException with the specified message.
accessionNumber - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
accessions - Variable in class org.biomage.BQS.BibliographicReference
References in publications, eg Medline and PubMed, for this BibliographicReference.
ACTION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
action - Variable in class org.biomage.BioMaterial.Treatment
The event that occurred (e.g.
Action2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Action2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Action2StringFieldConversion
 
ACTION_ADD - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
ACTION_LABELING - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ACTION_POOLING - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ACTION_SETUP - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
ACTION_SPLITTING - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
actionMeasurement - Variable in class org.biomage.BioMaterial.Treatment
Measures events like duration, centrifuge speed, etc.
actionPerformed(ActionEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
This ActionListener method is invoked when the user double-clicks on an entry or clicks on one of the buttons.
actionPerformed(ActionEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.HelpFrame
 
actionPerformed(ActionEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.ResultFrame
 
actionPerformed(ActionEvent) - Method in class gov.nih.nci.caarray.ui.experiment.UploadApplet
This ActionListener method is invoked when the user double-clicks on an entry or clicks on one of the buttons.
ActionProtocolTypeMap - Class in org.biomage.BioMaterial
 
ActionProtocolTypeMap() - Constructor for class org.biomage.BioMaterial.ActionProtocolTypeMap
 
ActionProtocolTypeMapData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
ActionProtocolTypeMapData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData
 
ActionUtils - Class in gov.nih.nci.caarray.ui.core
 
ActionUtils() - Constructor for class gov.nih.nci.caarray.ui.core.ActionUtils
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
Handles the results display when returning from an add or update action
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
add(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
add(Container, Component, int, int, int, int) - Method in class org.biomage.tools.apps.annot.GuiSet
Description: Place a component to a container at certain location.
add(Container, Component, int, int, int, int, int, int, int, int) - Method in class org.biomage.tools.apps.annot.GuiSet
Description: Place a component to a container at certain location.
add(Container, Component, int, int, int, int, int, int, int, int, Insets, int, int) - Method in class org.biomage.tools.apps.annot.GuiSet
Description: Place a component to a container at certain location.
add(Container, Component, int, int, int, int, int, int, int, int, int, int, int, int) - Method in class org.biomage.tools.apps.annot.GuiSet
Description: Place a component to a container at certain location.
add(Container, Component, int, int, int, int, int, int, int, int, int, int, int, int, int, int) - Method in class org.biomage.tools.apps.annot.GuiSet
Description: Place a component to a container at certain location.
addAdditionalDataProcessing(long, AdditionalDataProcessingData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addAdditionalDataProcessing(long, AdditionalDataProcessingData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addAdditionalDataProcessing(long, AdditionalDataProcessing) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addAdditionalQualifier(long, AdditionalQualifierData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addAdditionalQualifier(long, AdditionalQualifierData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addAdditionalQualifier(long, OntologyEntry) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addAdditionalUploadedFile(long, AdditionalUploadedFileData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addAdditionalUploadedFile(long, AdditionalUploadedFileData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addAdditionalUploadedFile(long, AdditionalUploadedFile) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addArrayDesign(ArrayDesignData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
addArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Adds the specified ArrayDesign to the persistence store
addArrayDesign(ArrayDesignData) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Add the specified ArrayDesign to the persistence store
addArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addArrayDesignFileUploadEntry(ArrayDesignFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
Deprecated. no longer used
addArrayDesignFileUploadEntry(ArrayDesignFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
Deprecated. no longer used
addArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addArrayDesignFileUploadGroup(ArrayDesignFileUploadGroupData) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
addArrayDesignFileUploadGroup(ArrayDesignFileUploadGroupData) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
addArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
addArrayGroup(ArrayGroup) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
Adds the specified ArrayGroup to the persistence store.
addArrayGroup(long, String) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
Adds an ArrayGroup that has one Array that has the specified arrayName as its name and references to the specified ArrayDesign.
addArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
Adds the specified ArrayGroup to the persistence store
addArrayGroup(ArrayGroupData, ArrayManagerDB, SessionContext) - Static method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
This method is shared by ExperimentManagerEJB.
addAssociation(CreateFile.AssociationAttrInformation, Integer) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Creates an association from the input association, using as rank the passed in parameter.
addAssociation(CreateFile.AssociationAttrInformation, Integer, int, int, int, int, boolean, boolean) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Creates an association from the input association, using as rank, minCard and maxCard the passed in parameters.
addAssociation(String, String, String, String, int, int, int, int, int, boolean, Integer, boolean, boolean, boolean, boolean) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Creates an association from the input parameters.
addAttribute(String, String, String, String, String, boolean) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Adds an attribute to this create file.
addAttributeComments(Vector, StringBuffer, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Adds the documentation for the attributes passed in.
addBibliographicReference(long, BibliographicReference) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addBioSample(BioSampleData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
addBioSample(BioSample) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
addBioSample(BioSampleData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Adds the specified Biosample to the persistence store
AddBioSampleTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
AddBioSampleTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.AddBioSampleTest
 
addBioSource(BioSourceData, VocabData[]) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
addBioSource(BioSource) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
addBioSource(BioSourceData, VocabData[]) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Adds the specified BioSource to the persistence store
AddBioSourceTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
AddBioSourceTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.AddBioSourceTest
 
addCAFileUploadEntry(CAFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
addCAFileUploadEntry(CAFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
addCAFileUploadEntry(CAFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addClassMapper(ClassMapper) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository
 
addColumnOrder(String) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method addColumnOrder.
addCompositeGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Add the specified CompositeGroup to the specified ArrayDesign.
addCompositeGroup(CompositeGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Add a new CompositeGroup.
addCompositeGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
addCompositeSequence(CompositeGroup, CompositeSequence) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
 
addCompositeSequence(CompositeGroup, CompositeSequence) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Adds a composite sequence to the given group.
addCompositeSequence(CompositeGroup, CompositeSequence) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
addCompositeSequence(CompositeGroup, CompositeSequence) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
addCompound(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
addCompound(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
 
addConvertField(ClassMapperRepository.ConvertField) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.TargetClass
 
addDataRow(GprDataRow) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDataMatrix
Adds a data row
addDesignProviderRole(long, DesignProviderRoleData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
addDesignProviderRole(long, DesignProviderRole) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Associate specified provider that has a role with the specified array design
addDesignProviderRole(long, DesignProviderRoleData) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Associates a provider with an ArrayDesign
addEntryToList(long, HttpServletRequest, Class<? extends BioMaterialDesc>) - Static method in class gov.nih.nci.caarray.ui.biomaterial.BioMaterialUIUtils
 
addExperiment(ExperimentData, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addExperiment(ExperimentData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addExperiment(ExperimentData, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Adds a new experiment.
addExperiment(Experiment) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
Add the specified Experiment to the persistence store
addExperimentalFactor(long, ExperimentalFactor) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addExperimentalFactors(long, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addExperimentalFactors(long, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addExperimentalFactors(long, ExperimentalFactor[]) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
AddExperimentFactorAction - Class in gov.nih.nci.caarray.ui.experiment
 
AddExperimentFactorAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.AddExperimentFactorAction
 
addExperimentId(long) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
AddExperimentPublicationAction - Class in gov.nih.nci.caarray.ui.experiment
 
AddExperimentPublicationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.AddExperimentPublicationAction
 
addFactorValue(long, FactorValueData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addFactorValue(long, FactorValueData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addFactorValue(long, FactorValue) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addFactorValue(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
addFactorValues(long, FactorValue[]) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addFeatureGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Add the specified FeatureGroup to the specified ArrayDesign.
addFeatureGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
addFeatureGroup(FeatureGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Adds a new FeatureGroup.
addFieldMapper(FieldMapper) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
addFile(String, FileType, String, String, String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
 
addFile(String, HybridizationFileType, String, String, String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
addFile(UploadFile) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
addFile(Long, String, UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
addFile(String, UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
addFileByGuessingType(String, String, String, String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
Adds a file which type is to be discovered based on its extension.
addFileByGuessingType(String, String, String, String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
Adds a file which type is to be discovered based on its original file's extension or the zipped version's extension.
addFileParameter(FileItem) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Adds a file parameter to the set of file parameters for this request and also to the list of all parameters.
addFiles(UploadFile[]) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
addFileType(String) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
addFileUploadEntry(ArrayDesignFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
addFileUploadEntry(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
addGroup(GroupData) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
addGroup(GroupData) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
addGroup(GroupData) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Adds a new caArray Group to the persistence store with the specified data.
addHardware(HardwareData) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
addHardware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
addHardware(HardwareData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
addHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
addHardware(Hardware) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Add a new hardware.
addHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Adds the specified Hardware to the specified Protocol.
addHardware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
addHardwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
addHardwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
addHardwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Associates a software with a hardware.
addHttp(String) - Static method in class gov.nih.nci.caarray.ui.core.FormUtils
 
addHybridization(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAddAdditionalHybPageAction
 
addHybridization(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAddHybPageAction
 
addHybridization(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationDetailDoneAction
 
addHybridizationFileParsingEntry(HybridizationFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addHybridizationFileParsingEntryToFileUploadEntry(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addHybridizationFileUpload(long, HybridizationFileUploadData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addHybridizationFileUpload(long, HybridizationFileUploadData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup
addHybridizationFileUpload(long, HybridizationFileUpload) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
This method performs the following: Add caARRAY-specific HybridizationFileUpload to the persistence store.
addHybridizationFileUploadEntry(HybridizationFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
addHybridizationFileUploadEntry(HybridizationFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
addHybridizationFileUploadEntry(HybridizationFileUploadEntry, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addHybridizationFileUploadGroup(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
addHybridizationFileUploadGroup(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
addHybridizationFileUploadGroup(HybridizationFileUploadGroup) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addHybridizationFileUploads(long, HybridizationFileUploadData[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addHybridizationFileUploads(long, HybridizationFileUploadData[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup
addHybridizationFileUploads(long, HybridizationFileUpload[]) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addHybridizationRow(HybridizationRowWrapper) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.DataMatrix
Adds a data row
AdditionalDataProcessing - Class in org.biomage.Experiment
 
AdditionalDataProcessing() - Constructor for class org.biomage.Experiment.AdditionalDataProcessing
 
AdditionalDataProcessingData - Class in gov.nih.nci.caarray.common.data.experiment
 
AdditionalDataProcessingData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
AdditionalQualifierData - Class in gov.nih.nci.caarray.common.data.experiment
 
AdditionalQualifierData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
additionalReporterFileLocation - Variable in class org.biomage.ArrayDesign.ArrayDesign
 
AdditionalUploadedFile - Class in org.biomage.Experiment
 
AdditionalUploadedFile() - Constructor for class org.biomage.Experiment.AdditionalUploadedFile
 
AdditionalUploadedFileData - Class in gov.nih.nci.caarray.common.data.experiment
 
AdditionalUploadedFileData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
addLabeledExtract(LabeledExtract) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
addMAGEMLFileUploadEntry(MAGEMLFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
addMAGEMLFileUploadEntry(MAGEMLFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
addMAGEMLFileUploadEntry(MAGEMLFileUploadEntry, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
addMatrix(ParsingDataMatrix) - Method in class gov.nih.nci.caarray.services.fileparse.CubeCreator
Adds a data matrix to the cube
addMatrix(DataMatrix) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.BioDataCubeCreator
Adds a data matrix to the cube
addMessage(String) - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionResult
 
addNewFactor(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
addNewType(String, String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
addNewType(String, String, long) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
addNonNumericAssociation(String, Integer) - Method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypes
Adds items to the hashes
addOntology(OntologyEntry) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
addOntology(OntologyEntry, long) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
addOrganization(OrganizationData) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
addOrganization(Organization) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
addOrganization(OrganizationData) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Adds a new organization to the persistence store with the specified data.
addOrSyncAnnotations(Describable) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Adds or synchronizes the vocabularies that represent the annotations of the specified Describable object.
addOrUpdateActionProtocolTypeMap(ActionProtocolTypeMapData) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
addOrUpdateActionProtocolTypeMap(ActionProtocolTypeMapData) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
addOrUpdateActionProtocolTypeMap(ActionProtocolTypeMap) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Adds or updates the association object between an action represented by an OntologyEntry and one or more protocol types represented by OntologyEntry's.
addOrUpdateMeasurement(Measurement) - Method in class gov.nih.nci.caarray.services.protocol.MeasurementManagerDB
 
addOrUpdateProtocolApplication(ProtocolApplication) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
addParameter(long, ParameterData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
addParameter(long, Parameter) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Add a new parameter to an existing hardware.
addParameter(long, Parameter) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Adds the specified Parameter to the specified Protocol.
addParameter(long, Parameter) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Add the new parameter to the specified software.
addParameterToForward(ActionForward, String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
Utility method that add request parameters to an already-defined forward.
addPerson(PersonData) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
addPerson(Person) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
addPerson(PersonData) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Adds a new person to the persistence store with the specified data.
addProblem(String) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
addProtectionGroup(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.security.RoleAssignmentData
 
addProtocol(ProtocolData) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
addProtocol(ProtocolData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
Add the specified Protocol to the persistence store
addProtocol(Protocol) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Adds a Protocol to the persistence store.
addProtocolApplication(long, ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
addProtocolApplication(long, ProtocolApplication) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
addProtocolApplication(long, ProtocolApplicationData) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
addProtocolApplication(ProtocolApplication) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
addProvider(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
addPublication(long, PublicationData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addPublication(long, PublicationData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addQualityControl(long, QualityControlData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
addQualityControl(long, QualityControlData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
addQualityControl(long, Description) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
addQualityControl(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
addReporterGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Add the specified ReporterGroup to the specified ArrayDesign.
addReporterGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
addReporterGroup(ReporterGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Adds a new ReporterGroup.
addRoleName(String, int, int) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Adds the role name to the tree.
addRow(LocalDynaBean) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Method addRow.
addRow(LocalDynaBean) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method addRow.
addRow(Object) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method addRow.
addSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
addSoftware(SoftwareData) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
addSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
addSoftware(SoftwareData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
addSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Adds the specified Software to the specified Protocol.
addSoftware(Software) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Add a new software.
addSoftware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
addSoftwareToHardware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
addSoftwareToHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
addSoftwareToHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Associates a hardware with a software.
addSoftwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
addSoftwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
addSoftwareToSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Associates a software with another software.
addStatus(String) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
addTextParameter(HttpServletRequest, FileItem) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Adds a regular text parameter to the set of text parameters for this request and also to the list of all parameters.
addToAccessions(DatabaseEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to add DatabaseEntry to Accessions_list
addToAccessions(int, DatabaseEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to add DatabaseEntry at position to Accessions_list
addToAccessions(DatabaseEntry) - Method in interface org.biomage.Interface.HasAccessions
Method to add DatabaseEntry to Accessions_list
addToAccessions(int, DatabaseEntry) - Method in interface org.biomage.Interface.HasAccessions
Method to add DatabaseEntry at position to Accessions_list
addToAdjustments(ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add ZoneDefect to Adjustments_list
addToAdjustments(int, ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add ZoneDefect at position to Adjustments_list
addToAdjustments(ZoneDefect) - Method in interface org.biomage.Interface.HasAdjustments
Method to add ZoneDefect to Adjustments_list
addToAdjustments(int, ZoneDefect) - Method in interface org.biomage.Interface.HasAdjustments
Method to add ZoneDefect at position to Adjustments_list
addToAnalysisResults(BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssayDataCluster to AnalysisResults_list
addToAnalysisResults(int, BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssayDataCluster at position to AnalysisResults_list
addToAnalysisResults(BioAssayDataCluster) - Method in interface org.biomage.Interface.HasAnalysisResults
Method to add BioAssayDataCluster to AnalysisResults_list
addToAnalysisResults(int, BioAssayDataCluster) - Method in interface org.biomage.Interface.HasAnalysisResults
Method to add BioAssayDataCluster at position to AnalysisResults_list
addToAnnotations(OntologyEntry) - Method in class org.biomage.Description.Description
Method to add OntologyEntry to Annotations_list
addToAnnotations(int, OntologyEntry) - Method in class org.biomage.Description.Description
Method to add OntologyEntry at position to Annotations_list
addToAnnotations(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to add OntologyEntry to Annotations_list
addToAnnotations(int, OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to add OntologyEntry at position to Annotations_list
addToAnnotations(OntologyEntry) - Method in interface org.biomage.Interface.HasAnnotations
Method to add OntologyEntry to Annotations_list
addToAnnotations(int, OntologyEntry) - Method in interface org.biomage.Interface.HasAnnotations
Method to add OntologyEntry at position to Annotations_list
addToArray_list(Array) - Method in class org.biomage.Array.Array_package
Method to add Array to Array_list
addToArray_list(int, Array) - Method in class org.biomage.Array.Array_package
Method to add Array at position to Array_list
addToArrayDesign_list(ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add ArrayDesign to ArrayDesign_list
addToArrayDesign_list(int, ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add ArrayDesign at position to ArrayDesign_list
addToArrayGroup_list(ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to add ArrayGroup to ArrayGroup_list
addToArrayGroup_list(int, ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to add ArrayGroup at position to ArrayGroup_list
addToArrayManufacture_list(ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to add ArrayManufacture to ArrayManufacture_list
addToArrayManufacture_list(int, ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to add ArrayManufacture at position to ArrayManufacture_list
addToArrayManufactureDeviations(ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list
addToArrayManufactureDeviations(int, ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list
addToArrayManufactureDeviations(ArrayManufactureDeviation) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list
addToArrayManufactureDeviations(int, ArrayManufactureDeviation) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list
addToArrayManufacturers(Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to add Contact to ArrayManufacturers_list
addToArrayManufacturers(int, Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to add Contact at position to ArrayManufacturers_list
addToArrayManufacturers(Contact) - Method in interface org.biomage.Interface.HasArrayManufacturers
Method to add Contact to ArrayManufacturers_list
addToArrayManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasArrayManufacturers
Method to add Contact at position to ArrayManufacturers_list
addToArrays(Array) - Method in class org.biomage.Array.ArrayGroup
Method to add Array to Arrays_list
addToArrays(int, Array) - Method in class org.biomage.Array.ArrayGroup
Method to add Array at position to Arrays_list
addToArrays(Array) - Method in class org.biomage.Array.ArrayManufacture
Method to add Array to Arrays_list
addToArrays(int, Array) - Method in class org.biomage.Array.ArrayManufacture
Method to add Array at position to Arrays_list
addToArrays(Array) - Method in interface org.biomage.Interface.HasArrays
Method to add Array to Arrays_list
addToArrays(int, Array) - Method in interface org.biomage.Interface.HasArrays
Method to add Array at position to Arrays_list
addToAssociationMap(Map, Element, Element, Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains the association and the current end and places the information on a map keyed by the model element id.
addToAssociations(OntologyEntry) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Method to add OntologyEntry to Associations_list
addToAssociations(int, OntologyEntry) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Method to add OntologyEntry at position to Associations_list
addToAssociations(OntologyEntry) - Method in class org.biomage.Description.OntologyEntry
Method to add OntologyEntry to Associations_list
addToAssociations(int, OntologyEntry) - Method in class org.biomage.Description.OntologyEntry
Method to add OntologyEntry at position to Associations_list
addToAssociations(OntologyEntry) - Method in interface org.biomage.Interface.HasAssociations
Method to add OntologyEntry to Associations_list
addToAssociations(int, OntologyEntry) - Method in interface org.biomage.Interface.HasAssociations
Method to add OntologyEntry at position to Associations_list
addToAuditTrail(Audit) - Method in class org.biomage.Common.Describable
Method to add Audit to AuditTrail_list
addToAuditTrail(int, Audit) - Method in class org.biomage.Common.Describable
Method to add Audit at position to AuditTrail_list
addToAuditTrail(Audit) - Method in interface org.biomage.Interface.HasAuditTrail
Method to add Audit to AuditTrail_list
addToAuditTrail(int, Audit) - Method in interface org.biomage.Interface.HasAuditTrail
Method to add Audit at position to AuditTrail_list
addToBibliographicReferences(BibliographicReference) - Method in class org.biomage.Description.Description
Method to add BibliographicReference to BibliographicReferences_list
addToBibliographicReferences(int, BibliographicReference) - Method in class org.biomage.Description.Description
Method to add BibliographicReference at position to BibliographicReferences_list
addToBibliographicReferences(BibliographicReference) - Method in interface org.biomage.Interface.HasBibliographicReferences
Method to add BibliographicReference to BibliographicReferences_list
addToBibliographicReferences(int, BibliographicReference) - Method in interface org.biomage.Interface.HasBibliographicReferences
Method to add BibliographicReference at position to BibliographicReferences_list
addToBioAssay_list(BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
Method to add BioAssay to BioAssay_list
addToBioAssay_list(int, BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
Method to add BioAssay at position to BioAssay_list
addToBioAssayData(BioAssayData) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssayData to BioAssayData_list
addToBioAssayData(int, BioAssayData) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssayData at position to BioAssayData_list
addToBioAssayData(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayData
Method to add BioAssayData to BioAssayData_list
addToBioAssayData(int, BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayData
Method to add BioAssayData at position to BioAssayData_list
addToBioAssayData_list(BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayData to BioAssayData_list
addToBioAssayData_list(int, BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayData at position to BioAssayData_list
addToBioAssayDataCluster_list(BioAssayDataCluster) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Method to add BioAssayDataCluster to BioAssayDataCluster_list
addToBioAssayDataCluster_list(int, BioAssayDataCluster) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Method to add BioAssayDataCluster at position to BioAssayDataCluster_list
addToBioAssayDataSources(BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
Method to add BioAssayData to BioAssayDataSources_list
addToBioAssayDataSources(int, BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
Method to add BioAssayData at position to BioAssayDataSources_list
addToBioAssayDataSources(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Method to add BioAssayData to BioAssayDataSources_list
addToBioAssayDataSources(int, BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Method to add BioAssayData at position to BioAssayDataSources_list
addToBioAssayDimension_list(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayDimension to BioAssayDimension_list
addToBioAssayDimension_list(int, BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayDimension at position to BioAssayDimension_list
addToBioAssayFactorValues(FactorValue) - Method in class org.biomage.BioAssay.BioAssay
Method to add FactorValue to BioAssayFactorValues_list
addToBioAssayFactorValues(int, FactorValue) - Method in class org.biomage.BioAssay.BioAssay
Method to add FactorValue at position to BioAssayFactorValues_list
addToBioAssayFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Method to add FactorValue to BioAssayFactorValues_list
addToBioAssayFactorValues(int, FactorValue) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Method to add FactorValue at position to BioAssayFactorValues_list
addToBioAssayMap_list(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayMap to BioAssayMap_list
addToBioAssayMap_list(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add BioAssayMap at position to BioAssayMap_list
addToBioAssayMaps(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
Method to add BioAssayMap to BioAssayMaps_list
addToBioAssayMaps(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
Method to add BioAssayMap at position to BioAssayMaps_list
addToBioAssayMaps(BioAssayMap) - Method in interface org.biomage.Interface.HasBioAssayMaps
Method to add BioAssayMap to BioAssayMaps_list
addToBioAssayMaps(int, BioAssayMap) - Method in interface org.biomage.Interface.HasBioAssayMaps
Method to add BioAssayMap at position to BioAssayMaps_list
addToBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
Method to add BioAssay to BioAssays_list
addToBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
Method to add BioAssay at position to BioAssays_list
addToBioAssays(BioAssay) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssay to BioAssays_list
addToBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.Experiment
Method to add BioAssay at position to BioAssays_list
addToBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasBioAssays
Method to add BioAssay to BioAssays_list
addToBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasBioAssays
Method to add BioAssay at position to BioAssays_list
addToBioAssayTreatments(BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to add BioAssayTreatment to BioAssayTreatments_list
addToBioAssayTreatments(int, BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to add BioAssayTreatment at position to BioAssayTreatments_list
addToBioAssayTreatments(BioAssayTreatment) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Method to add BioAssayTreatment to BioAssayTreatments_list
addToBioAssayTreatments(int, BioAssayTreatment) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Method to add BioAssayTreatment at position to BioAssayTreatments_list
addToBioAssayTuples(BioAssayTuple) - Method in class org.biomage.BioAssayData.BioDataTuples
Method to add BioAssayTuple to BioAssayTuples_list
addToBioAssayTuples(int, BioAssayTuple) - Method in class org.biomage.BioAssayData.BioDataTuples
Method to add BioAssayTuple at position to BioAssayTuples_list
addToBioAssayTuples(BioAssayTuple) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Method to add BioAssayTuple to BioAssayTuples_list
addToBioAssayTuples(int, BioAssayTuple) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Method to add BioAssayTuple at position to BioAssayTuples_list
addToBiologicalCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add BioSequence to BiologicalCharacteristics_list
addToBiologicalCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add BioSequence at position to BiologicalCharacteristics_list
addToBiologicalCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Method to add BioSequence to BiologicalCharacteristics_list
addToBiologicalCharacteristics(int, BioSequence) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Method to add BioSequence at position to BiologicalCharacteristics_list
addToBioMaterial_list(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to add BioMaterial to BioMaterial_list
addToBioMaterial_list(int, BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to add BioMaterial at position to BioMaterial_list
addToBioSequence_list(BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to add BioSequence to BioSequence_list
addToBioSequence_list(int, BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to add BioSequence at position to BioSequence_list
addToChannel_list(Channel) - Method in class org.biomage.BioAssay.BioAssay_package
Method to add Channel to Channel_list
addToChannel_list(int, Channel) - Method in class org.biomage.BioAssay.BioAssay_package
Method to add Channel at position to Channel_list
addToChannels(Channel) - Method in class org.biomage.BioAssay.BioAssay
Method to add Channel to Channels_list
addToChannels(int, Channel) - Method in class org.biomage.BioAssay.BioAssay
Method to add Channel at position to Channels_list
addToChannels(Channel) - Method in class org.biomage.BioAssay.Image
Method to add Channel to Channels_list
addToChannels(int, Channel) - Method in class org.biomage.BioAssay.Image
Method to add Channel at position to Channels_list
addToChannels(Channel) - Method in interface org.biomage.Interface.HasChannels
Method to add Channel to Channels_list
addToChannels(int, Channel) - Method in interface org.biomage.Interface.HasChannels
Method to add Channel at position to Channels_list
addToCharacteristics(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
addToCharacteristics(OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add OntologyEntry to Characteristics_list
addToCharacteristics(int, OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add OntologyEntry at position to Characteristics_list
addToCharacteristics(OntologyEntry) - Method in interface org.biomage.Interface.HasCharacteristics
Method to add OntologyEntry to Characteristics_list
addToCharacteristics(int, OntologyEntry) - Method in interface org.biomage.Interface.HasCharacteristics
Method to add OntologyEntry at position to Characteristics_list
addToComponentCompounds(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Compound
Method to add CompoundMeasurement to ComponentCompounds_list
addToComponentCompounds(int, CompoundMeasurement) - Method in class org.biomage.BioMaterial.Compound
Method to add CompoundMeasurement at position to ComponentCompounds_list
addToComponentCompounds(CompoundMeasurement) - Method in interface org.biomage.Interface.HasComponentCompounds
Method to add CompoundMeasurement to ComponentCompounds_list
addToComponentCompounds(int, CompoundMeasurement) - Method in interface org.biomage.Interface.HasComponentCompounds
Method to add CompoundMeasurement at position to ComponentCompounds_list
addToCompositeCompositeMap_list(CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add CompositeCompositeMap to CompositeCompositeMap_list
addToCompositeCompositeMap_list(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add CompositeCompositeMap at position to CompositeCompositeMap_list
addToCompositeCompositeMaps(CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add CompositeCompositeMap to CompositeCompositeMaps_list
addToCompositeCompositeMaps(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
addToCompositeCompositeMaps(CompositeCompositeMap) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Method to add CompositeCompositeMap to CompositeCompositeMaps_list
addToCompositeCompositeMaps(int, CompositeCompositeMap) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
addToCompositeGroup_list(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add CompositeGroup to CompositeGroup_list
addToCompositeGroup_list(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add CompositeGroup at position to CompositeGroup_list
addToCompositeGroups(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add CompositeGroup to CompositeGroups_list
addToCompositeGroups(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add CompositeGroup at position to CompositeGroups_list
addToCompositeGroups(CompositeGroup) - Method in interface org.biomage.Interface.HasCompositeGroups
Method to add CompositeGroup to CompositeGroups_list
addToCompositeGroups(int, CompositeGroup) - Method in interface org.biomage.Interface.HasCompositeGroups
Method to add CompositeGroup at position to CompositeGroups_list
addToCompositePositionSources(CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Method to add CompositePosition to CompositePositionSources_list
addToCompositePositionSources(int, CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Method to add CompositePosition at position to CompositePositionSources_list
addToCompositePositionSources(CompositePosition) - Method in interface org.biomage.Interface.HasCompositePositionSources
Method to add CompositePosition to CompositePositionSources_list
addToCompositePositionSources(int, CompositePosition) - Method in interface org.biomage.Interface.HasCompositePositionSources
Method to add CompositePosition at position to CompositePositionSources_list
addToCompositeSequence_list(CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add CompositeSequence to CompositeSequence_list
addToCompositeSequence_list(int, CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add CompositeSequence at position to CompositeSequence_list
addToCompositeSequences(CompositeSequenceData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
addToCompositeSequences(CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
Method to add CompositeSequence to CompositeSequences_list
addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
Method to add CompositeSequence at position to CompositeSequences_list
addToCompositeSequences(CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Method to add CompositeSequence to CompositeSequences_list
addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Method to add CompositeSequence at position to CompositeSequences_list
addToCompositeSequences(CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequences
Method to add CompositeSequence to CompositeSequences_list
addToCompositeSequences(int, CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequences
Method to add CompositeSequence at position to CompositeSequences_list
addToCompound_list(Compound) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to add Compound to Compound_list
addToCompound_list(int, Compound) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to add Compound at position to Compound_list
addToCompoundIndices(OntologyEntry) - Method in class org.biomage.BioMaterial.Compound
Method to add OntologyEntry to CompoundIndices_list
addToCompoundIndices(int, OntologyEntry) - Method in class org.biomage.BioMaterial.Compound
Method to add OntologyEntry at position to CompoundIndices_list
addToCompoundIndices(OntologyEntry) - Method in interface org.biomage.Interface.HasCompoundIndices
Method to add OntologyEntry to CompoundIndices_list
addToCompoundIndices(int, OntologyEntry) - Method in interface org.biomage.Interface.HasCompoundIndices
Method to add OntologyEntry at position to CompoundIndices_list
addToCompoundMeasurements(CompoundMeasurementData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
addToCompoundMeasurements(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to add CompoundMeasurement to CompoundMeasurements_list
addToCompoundMeasurements(int, CompoundMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to add CompoundMeasurement at position to CompoundMeasurements_list
addToCompoundMeasurements(CompoundMeasurement) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Method to add CompoundMeasurement to CompoundMeasurements_list
addToCompoundMeasurements(int, CompoundMeasurement) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Method to add CompoundMeasurement at position to CompoundMeasurements_list
addToConfidenceIndicators(ConfidenceIndicator) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Method to add ConfidenceIndicator to ConfidenceIndicators_list
addToConfidenceIndicators(int, ConfidenceIndicator) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Method to add ConfidenceIndicator at position to ConfidenceIndicators_list
addToConfidenceIndicators(ConfidenceIndicator) - Method in class org.biomage.QuantitationType.QuantitationType
Method to add ConfidenceIndicator to ConfidenceIndicators_list
addToConfidenceIndicators(int, ConfidenceIndicator) - Method in class org.biomage.QuantitationType.QuantitationType
Method to add ConfidenceIndicator at position to ConfidenceIndicators_list
addToContact_list(Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add Contact to Contact_list
addToContact_list(int, Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add Contact at position to Contact_list
addToContacts(Contact) - Method in class org.biomage.Description.Database
Method to add Contact to Contacts_list
addToContacts(int, Contact) - Method in class org.biomage.Description.Database
Method to add Contact at position to Contacts_list
addToContacts(Contact) - Method in interface org.biomage.Interface.HasContacts
Method to add Contact to Contacts_list
addToContacts(int, Contact) - Method in interface org.biomage.Interface.HasContacts
Method to add Contact at position to Contacts_list
addToContainedFeatures(Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
Method to add Feature to ContainedFeatures_list
addToContainedFeatures(int, Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
Method to add Feature at position to ContainedFeatures_list
addToContainedFeatures(Feature) - Method in interface org.biomage.Interface.HasContainedFeatures
Method to add Feature to ContainedFeatures_list
addToContainedFeatures(int, Feature) - Method in interface org.biomage.Interface.HasContainedFeatures
Method to add Feature at position to ContainedFeatures_list
addToControlFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
Method to add Feature to ControlFeatures_list
addToControlFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature
Method to add Feature at position to ControlFeatures_list
addToControlFeatures(Feature) - Method in interface org.biomage.Interface.HasControlFeatures
Method to add Feature to ControlFeatures_list
addToControlFeatures(int, Feature) - Method in interface org.biomage.Interface.HasControlFeatures
Method to add Feature at position to ControlFeatures_list
addToControlledFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
Method to add Feature to ControlledFeatures_list
addToControlledFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature
Method to add Feature at position to ControlledFeatures_list
addToControlledFeatures(Feature) - Method in interface org.biomage.Interface.HasControlledFeatures
Method to add Feature to ControlledFeatures_list
addToControlledFeatures(int, Feature) - Method in interface org.biomage.Interface.HasControlledFeatures
Method to add Feature at position to ControlledFeatures_list
addToDatabase_list(Database) - Method in class org.biomage.Description.Description_package
Method to add Database to Database_list
addToDatabase_list(int, Database) - Method in class org.biomage.Description.Description_package
Method to add Database at position to Database_list
addToDatabaseReferences(DatabaseEntry) - Method in class org.biomage.Description.Description
Method to add DatabaseEntry to DatabaseReferences_list
addToDatabaseReferences(int, DatabaseEntry) - Method in class org.biomage.Description.Description
Method to add DatabaseEntry at position to DatabaseReferences_list
addToDatabaseReferences(DatabaseEntry) - Method in interface org.biomage.Interface.HasDatabaseReferences
Method to add DatabaseEntry to DatabaseReferences_list
addToDatabaseReferences(int, DatabaseEntry) - Method in interface org.biomage.Interface.HasDatabaseReferences
Method to add DatabaseEntry at position to DatabaseReferences_list
addToDerivedBioAssayData(DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to add DerivedBioAssayData to DerivedBioAssayData_list
addToDerivedBioAssayData(int, DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
addToDerivedBioAssayData(DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Method to add DerivedBioAssayData to DerivedBioAssayData_list
addToDerivedBioAssayData(int, DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
addToDerivedBioAssayMap(BioAssayMap) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to add BioAssayMap to DerivedBioAssayMap_list
addToDerivedBioAssayMap(int, BioAssayMap) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to add BioAssayMap at position to DerivedBioAssayMap_list
addToDerivedBioAssayMap(BioAssayMap) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Method to add BioAssayMap to DerivedBioAssayMap_list
addToDerivedBioAssayMap(int, BioAssayMap) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Method to add BioAssayMap at position to DerivedBioAssayMap_list
addToDescriptions(Description) - Method in class org.biomage.Common.Describable
Method to add Description to Descriptions_list
addToDescriptions(int, Description) - Method in class org.biomage.Common.Describable
Method to add Description at position to Descriptions_list
addToDescriptions(Description) - Method in interface org.biomage.Interface.HasDescriptions
Method to add Description to Descriptions_list
addToDescriptions(int, Description) - Method in interface org.biomage.Interface.HasDescriptions
Method to add Description at position to Descriptions_list
addToDesignElementDimension_list(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add DesignElementDimension to DesignElementDimension_list
addToDesignElementDimension_list(int, DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add DesignElementDimension at position to DesignElementDimension_list
addToDesignElementMaps(DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
Method to add DesignElementMap to DesignElementMaps_list
addToDesignElementMaps(int, DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
Method to add DesignElementMap at position to DesignElementMaps_list
addToDesignElementMaps(DesignElementMap) - Method in interface org.biomage.Interface.HasDesignElementMaps
Method to add DesignElementMap to DesignElementMaps_list
addToDesignElementMaps(int, DesignElementMap) - Method in interface org.biomage.Interface.HasDesignElementMaps
Method to add DesignElementMap at position to DesignElementMaps_list
addToDesignElementTuples(DesignElementTuple) - Method in class org.biomage.BioAssayData.BioAssayTuple
Method to add DesignElementTuple to DesignElementTuples_list
addToDesignElementTuples(int, DesignElementTuple) - Method in class org.biomage.BioAssayData.BioAssayTuple
Method to add DesignElementTuple at position to DesignElementTuples_list
addToDesignElementTuples(DesignElementTuple) - Method in interface org.biomage.Interface.HasDesignElementTuples
Method to add DesignElementTuple to DesignElementTuples_list
addToDesignElementTuples(int, DesignElementTuple) - Method in interface org.biomage.Interface.HasDesignElementTuples
Method to add DesignElementTuple at position to DesignElementTuples_list
addToDesignProviderRoles(DesignProviderRole) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add Contact to DesignProviders_list
addToDesignProviderRoles(int, DesignProviderRole) - Method in class org.biomage.ArrayDesign.ArrayDesign
Adds a provider of this experiment that has a role
addToDesignProviders(Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add Contact to DesignProviders_list
addToDesignProviders(int, Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add Contact at position to DesignProviders_list
addToDesignProviders(Contact) - Method in interface org.biomage.Interface.HasDesignProviders
Method to add Contact to DesignProviders_list
addToDesignProviders(int, Contact) - Method in interface org.biomage.Interface.HasDesignProviders
Method to add Contact at position to DesignProviders_list
addToExperiment_list(Experiment) - Method in class org.biomage.Experiment.Experiment_package
Method to add Experiment to Experiment_list
addToExperiment_list(int, Experiment) - Method in class org.biomage.Experiment.Experiment_package
Method to add Experiment at position to Experiment_list
addToExperimentalFactors(ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add ExperimentalFactor to ExperimentalFactors_list
addToExperimentalFactors(int, ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add ExperimentalFactor at position to ExperimentalFactors_list
addToExperimentalFactors(ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactors
Method to add ExperimentalFactor to ExperimentalFactors_list
addToExperimentalFactors(int, ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactors
Method to add ExperimentalFactor at position to ExperimentalFactors_list
addToExperimentDesigns(ExperimentDesign) - Method in class org.biomage.Experiment.Experiment
Method to add ExperimentDesign to ExperimentDesigns_list
addToExperimentDesigns(int, ExperimentDesign) - Method in class org.biomage.Experiment.Experiment
Method to add ExperimentDesign at position to ExperimentDesigns_list
addToExperimentDesigns(ExperimentDesign) - Method in interface org.biomage.Interface.HasExperimentDesigns
Method to add ExperimentDesign to ExperimentDesigns_list
addToExperimentDesigns(int, ExperimentDesign) - Method in interface org.biomage.Interface.HasExperimentDesigns
Method to add ExperimentDesign at position to ExperimentDesigns_list
addToExperimentProviderRoles(ExperimentProviderRoleData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
addToFactorValues(FactorValueData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
addToFactorValues(FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to add FactorValue to FactorValues_list
addToFactorValues(int, FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to add FactorValue at position to FactorValues_list
addToFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasFactorValues
Method to add FactorValue to FactorValues_list
addToFactorValues(int, FactorValue) - Method in interface org.biomage.Interface.HasFactorValues
Method to add FactorValue at position to FactorValues_list
addToFailTypes(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
Method to add OntologyEntry to FailTypes_list
addToFailTypes(int, OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
Method to add OntologyEntry at position to FailTypes_list
addToFailTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasFailTypes
Method to add OntologyEntry to FailTypes_list
addToFailTypes(int, OntologyEntry) - Method in interface org.biomage.Interface.HasFailTypes
Method to add OntologyEntry at position to FailTypes_list
addToFeatureDefects(FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add FeatureDefect to FeatureDefects_list
addToFeatureDefects(int, FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to add FeatureDefect at position to FeatureDefects_list
addToFeatureDefects(FeatureDefect) - Method in interface org.biomage.Interface.HasFeatureDefects
Method to add FeatureDefect to FeatureDefects_list
addToFeatureDefects(int, FeatureDefect) - Method in interface org.biomage.Interface.HasFeatureDefects
Method to add FeatureDefect at position to FeatureDefects_list
addToFeatureGroups(FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add FeatureGroup to FeatureGroups_list
addToFeatureGroups(int, FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add FeatureGroup at position to FeatureGroups_list
addToFeatureGroups(FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroups
Method to add FeatureGroup to FeatureGroups_list
addToFeatureGroups(int, FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroups
Method to add FeatureGroup at position to FeatureGroups_list
addToFeatureInformationSources(FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
Method to add FeatureInformation to FeatureInformationSources_list
addToFeatureInformationSources(int, FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
Method to add FeatureInformation at position to FeatureInformationSources_list
addToFeatureInformationSources(FeatureInformation) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Method to add FeatureInformation to FeatureInformationSources_list
addToFeatureInformationSources(int, FeatureInformation) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Method to add FeatureInformation at position to FeatureInformationSources_list
addToFeatureLIMSs(ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to add ManufactureLIMS to FeatureLIMSs_list
addToFeatureLIMSs(int, ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to add ManufactureLIMS at position to FeatureLIMSs_list
addToFeatureLIMSs(ManufactureLIMS) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Method to add ManufactureLIMS to FeatureLIMSs_list
addToFeatureLIMSs(int, ManufactureLIMS) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Method to add ManufactureLIMS at position to FeatureLIMSs_list
addToFeatureReporterMap_list(FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add FeatureReporterMap to FeatureReporterMap_list
addToFeatureReporterMap_list(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add FeatureReporterMap at position to FeatureReporterMap_list
addToFeatureReporterMaps(FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
Method to add FeatureReporterMap to FeatureReporterMaps_list
addToFeatureReporterMaps(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
Method to add FeatureReporterMap at position to FeatureReporterMaps_list
addToFeatureReporterMaps(FeatureReporterMap) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Method to add FeatureReporterMap to FeatureReporterMaps_list
addToFeatureReporterMaps(int, FeatureReporterMap) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Method to add FeatureReporterMap at position to FeatureReporterMaps_list
addToFeatures(Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
Method to add Feature to Features_list
addToFeatures(int, Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
Method to add Feature at position to Features_list
addToFeatures(Feature) - Method in interface org.biomage.Interface.HasFeatures
Method to add Feature to Features_list
addToFeatures(int, Feature) - Method in interface org.biomage.Interface.HasFeatures
Method to add Feature at position to Features_list
addToFiducials(Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to add Fiducial to Fiducials_list
addToFiducials(int, Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to add Fiducial at position to Fiducials_list
addToFiducials(Fiducial) - Method in interface org.biomage.Interface.HasFiducials
Method to add Fiducial to Fiducials_list
addToFiducials(int, Fiducial) - Method in interface org.biomage.Interface.HasFiducials
Method to add Fiducial at position to Fiducials_list
addToHardware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
addToHardware_list(Hardware) - Method in class org.biomage.Protocol.Protocol_package
Method to add Hardware to Hardware_list
addToHardware_list(int, Hardware) - Method in class org.biomage.Protocol.Protocol_package
Method to add Hardware at position to Hardware_list
addToHardwareApplications(HardwareApplicationData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
addToHardwareApplications(HardwareApplication) - Method in interface org.biomage.Interface.HasHardwareApplications
Method to add HardwareApplication to HardwareApplications_list
addToHardwareApplications(int, HardwareApplication) - Method in interface org.biomage.Interface.HasHardwareApplications
Method to add HardwareApplication at position to HardwareApplications_list
addToHardwareApplications(HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add HardwareApplication to HardwareApplications_list
addToHardwareApplications(int, HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add HardwareApplication at position to HardwareApplications_list
addToHardwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Method to add Contact to HardwareManufacturers_list
addToHardwareManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Method to add Contact at position to HardwareManufacturers_list
addToHardwareManufacturers(Contact) - Method in class org.biomage.Protocol.Hardware
Method to add Contact to HardwareManufacturers_list
addToHardwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Hardware
Method to add Contact at position to HardwareManufacturers_list
addToHardwares(HardwareData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
addToHardwares(Hardware) - Method in interface org.biomage.Interface.HasHardwares
Method to add Hardware to Hardwares_list
addToHardwares(int, Hardware) - Method in interface org.biomage.Interface.HasHardwares
Method to add Hardware at position to Hardwares_list
addToHardwares(Hardware) - Method in class org.biomage.Protocol.Protocol
Method to add Hardware to Hardwares_list
addToHardwares(int, Hardware) - Method in class org.biomage.Protocol.Protocol
Method to add Hardware at position to Hardwares_list
addToImages(Image) - Method in class org.biomage.BioAssay.ImageAcquisition
Method to add Image to Images_list
addToImages(int, Image) - Method in class org.biomage.BioAssay.ImageAcquisition
Method to add Image at position to Images_list
addToImages(Image) - Method in interface org.biomage.Interface.HasImages
Method to add Image to Images_list
addToImages(int, Image) - Method in interface org.biomage.Interface.HasImages
Method to add Image at position to Images_list
addToImmobilizedCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.Reporter
Method to add BioSequence to ImmobilizedCharacteristics_list
addToImmobilizedCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.Reporter
Method to add BioSequence at position to ImmobilizedCharacteristics_list
addToImmobilizedCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Method to add BioSequence to ImmobilizedCharacteristics_list
addToImmobilizedCharacteristics(int, BioSequence) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Method to add BioSequence at position to ImmobilizedCharacteristics_list
addToInstances(OntologyHelper.InstanceInformation) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
addToLabels(Compound) - Method in class org.biomage.BioAssay.Channel
Method to add Compound to Labels_list
addToLabels(int, Compound) - Method in class org.biomage.BioAssay.Channel
Method to add Compound at position to Labels_list
addToLabels(Compound) - Method in class org.biomage.BioMaterial.LabeledExtract
Method to add Compound to Labels_list
addToLabels(int, Compound) - Method in class org.biomage.BioMaterial.LabeledExtract
Method to add Compound at position to Labels_list
addToLabels(Compound) - Method in interface org.biomage.Interface.HasLabels
Method to add Compound to Labels_list
addToLabels(int, Compound) - Method in interface org.biomage.Interface.HasLabels
Method to add Compound at position to Labels_list
addToList(Object) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
Add a meta data object HttpUploadedFileData into the fileList container.
addToList(Object) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
Add a meta data object HttpUploadedFileData into the fileList container.
addToMeasuredBioAssayData(MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
addToMeasuredBioAssayData(int, MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
addToMeasuredBioAssayData(MeasuredBioAssayData) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
addToMeasuredBioAssayData(int, MeasuredBioAssayData) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
addToMembers(Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Method to add Contact to Members_list
addToMembers(int, Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Method to add Contact at position to Members_list
addToMembers(Contact) - Method in interface org.biomage.Interface.HasMembers
Method to add Contact to Members_list
addToMembers(int, Contact) - Method in interface org.biomage.Interface.HasMembers
Method to add Contact at position to Members_list
addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
Method to add MismatchInformation to MismatchInformation_list
addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
Method to add MismatchInformation at position to MismatchInformation_list
addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
Method to add MismatchInformation to MismatchInformation_list
addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
Method to add MismatchInformation at position to MismatchInformation_list
addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
Method to add MismatchInformation to MismatchInformation_list
addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
Method to add MismatchInformation at position to MismatchInformation_list
addToMismatchInformation(MismatchInformation) - Method in interface org.biomage.Interface.HasMismatchInformation
Method to add MismatchInformation to MismatchInformation_list
addToMismatchInformation(int, MismatchInformation) - Method in interface org.biomage.Interface.HasMismatchInformation
Method to add MismatchInformation at position to MismatchInformation_list
addToNodeContents(NodeContents) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add NodeContents to NodeContents_list
addToNodeContents(int, NodeContents) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add NodeContents at position to NodeContents_list
addToNodeContents(NodeContents) - Method in interface org.biomage.Interface.HasNodeContents
Method to add NodeContents to NodeContents_list
addToNodeContents(int, NodeContents) - Method in interface org.biomage.Interface.HasNodeContents
Method to add NodeContents at position to NodeContents_list
addToNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Method to add Node to Nodes_list
addToNodes(int, Node) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Method to add Node at position to Nodes_list
addToNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add Node to Nodes_list
addToNodes(int, Node) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add Node at position to Nodes_list
addToNodes(Node) - Method in interface org.biomage.Interface.HasNodes
Method to add Node to Nodes_list
addToNodes(int, Node) - Method in interface org.biomage.Interface.HasNodes
Method to add Node at position to Nodes_list
addToNodeValue(NodeValue) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add NodeValue to NodeValue_list
addToNodeValue(int, NodeValue) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to add NodeValue at position to NodeValue_list
addToNodeValue(NodeValue) - Method in interface org.biomage.Interface.HasNodeValue
Method to add NodeValue to NodeValue_list
addToNodeValue(int, NodeValue) - Method in interface org.biomage.Interface.HasNodeValue
Method to add NodeValue at position to NodeValue_list
addToOntologyEntries(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add OntologyEntry to OntologyEntries_list
addToOntologyEntries(int, OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add OntologyEntry at position to OntologyEntries_list
addToOntologyEntries(OntologyEntry) - Method in interface org.biomage.Interface.HasOntologyEntries
Method to add OntologyEntry to OntologyEntries_list
addToOntologyEntries(int, OntologyEntry) - Method in interface org.biomage.Interface.HasOntologyEntries
Method to add OntologyEntry at position to OntologyEntries_list
addToOwner(Contact) - Method in class org.biomage.AuditAndSecurity.Security
Method to add Contact to Owner_list
addToOwner(int, Contact) - Method in class org.biomage.AuditAndSecurity.Security
Method to add Contact at position to Owner_list
addToOwner(Contact) - Method in interface org.biomage.Interface.HasOwner
Method to add Contact to Owner_list
addToOwner(int, Contact) - Method in interface org.biomage.Interface.HasOwner
Method to add Contact at position to Owner_list
addToParameters(ParameterData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
addToParameters(ParameterData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
addToParameters(OntologyEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to add OntologyEntry to Parameters_list
addToParameters(int, OntologyEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to add OntologyEntry at position to Parameters_list
addToParameters(OntologyEntry) - Method in interface org.biomage.Interface.HasParameters
Method to add OntologyEntry to Parameters_list
addToParameters(int, OntologyEntry) - Method in interface org.biomage.Interface.HasParameters
Method to add OntologyEntry at position to Parameters_list
addToParameterTypes(Parameter) - Method in interface org.biomage.Interface.HasParameterTypes
Method to add Parameter to ParameterTypes_list
addToParameterTypes(int, Parameter) - Method in interface org.biomage.Interface.HasParameterTypes
Method to add Parameter at position to ParameterTypes_list
addToParameterTypes(Parameter) - Method in class org.biomage.Protocol.Parameterizable
Method to add Parameter to ParameterTypes_list
addToParameterTypes(int, Parameter) - Method in class org.biomage.Protocol.Parameterizable
Method to add Parameter at position to ParameterTypes_list
addToParameterValues(ParameterValue) - Method in interface org.biomage.Interface.HasParameterValues
Method to add ParameterValue to ParameterValues_list
addToParameterValues(int, ParameterValue) - Method in interface org.biomage.Interface.HasParameterValues
Method to add ParameterValue at position to ParameterValues_list
addToParameterValues(ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
Method to add ParameterValue to ParameterValues_list
addToParameterValues(int, ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
Method to add ParameterValue at position to ParameterValues_list
addToParentNames(String) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
addToParents(OntologyHelper.ClassInformation) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
addToPerformers(Person) - Method in interface org.biomage.Interface.HasPerformers
Method to add Person to Performers_list
addToPerformers(int, Person) - Method in interface org.biomage.Interface.HasPerformers
Method to add Person at position to Performers_list
addToPerformers(Person) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add Person to Performers_list
addToPerformers(int, Person) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add Person at position to Performers_list
addToPhysicalBioAssayData(Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to add Image to PhysicalBioAssayData_list
addToPhysicalBioAssayData(int, Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to add Image at position to PhysicalBioAssayData_list
addToPhysicalBioAssayData(Image) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Method to add Image to PhysicalBioAssayData_list
addToPhysicalBioAssayData(int, Image) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Method to add Image at position to PhysicalBioAssayData_list
addToProperties(OntologyHelper.PropertyInformation) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
addToPropertySets(NameValueType) - Method in class org.biomage.Common.Extendable
Method to add NameValueType to PropertySets_list
addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.Extendable
Method to add NameValueType at position to PropertySets_list
addToPropertySets(NameValueType) - Method in class org.biomage.Common.NameValueType
Method to add NameValueType to PropertySets_list
addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.NameValueType
Method to add NameValueType at position to PropertySets_list
addToPropertySets(NameValueType) - Method in interface org.biomage.Interface.HasPropertySets
Method to add NameValueType to PropertySets_list
addToPropertySets(int, NameValueType) - Method in interface org.biomage.Interface.HasPropertySets
Method to add NameValueType at position to PropertySets_list
addToProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
addToProtocol_list(Protocol) - Method in class org.biomage.Protocol.Protocol_package
Method to add Protocol to Protocol_list
addToProtocol_list(int, Protocol) - Method in class org.biomage.Protocol.Protocol_package
Method to add Protocol at position to Protocol_list
addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to add ProtocolApplication at position to ProtocolApplications_list
addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add ProtocolApplication at position to ProtocolApplications_list
addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to add ProtocolApplication at position to ProtocolApplications_list
addToProtocolApplications(ProtocolApplication) - Method in interface org.biomage.Interface.HasProtocolApplications
Method to add ProtocolApplication to ProtocolApplications_list
addToProtocolApplications(int, ProtocolApplication) - Method in interface org.biomage.Interface.HasProtocolApplications
Method to add ProtocolApplication at position to ProtocolApplications_list
addToProviderRoles(DesignProviderRole) - Method in class org.biomage.ArrayDesign.ArrayDesign
Adds a provider of this experiment that has a role
addToProviderRoles(ExperimentProviderRole) - Method in class org.biomage.Experiment.Experiment
Adds a provider of this experiment that has a role
addToProviderRoles(int, ExperimentProviderRole) - Method in class org.biomage.Experiment.Experiment
Adds a provider of this experiment that has a role
addToProviders(Contact) - Method in class org.biomage.Experiment.Experiment
Method to add Contact to Providers_list
addToProviders(int, Contact) - Method in class org.biomage.Experiment.Experiment
Method to add Contact at position to Providers_list
addToProviders(Contact) - Method in interface org.biomage.Interface.HasProviders
Method to add Contact to Providers_list
addToProviders(int, Contact) - Method in interface org.biomage.Interface.HasProviders
Method to add Contact at position to Providers_list
addToQualityControlStatistics(NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to add NameValueType to QualityControlStatistics_list
addToQualityControlStatistics(int, NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to add NameValueType at position to QualityControlStatistics_list
addToQualityControlStatistics(NameValueType) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add NameValueType to QualityControlStatistics_list
addToQualityControlStatistics(int, NameValueType) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add NameValueType at position to QualityControlStatistics_list
addToQualityControlStatistics(NameValueType) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Method to add NameValueType to QualityControlStatistics_list
addToQualityControlStatistics(int, NameValueType) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Method to add NameValueType at position to QualityControlStatistics_list
addToQuantitationType_list(QuantitationType) - Method in class org.biomage.QuantitationType.QuantitationType_package
Method to add QuantitationType to QuantitationType_list
addToQuantitationType_list(int, QuantitationType) - Method in class org.biomage.QuantitationType.QuantitationType_package
Method to add QuantitationType at position to QuantitationType_list
addToQuantitationTypeDimension_list(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add QuantitationTypeDimension to QuantitationTypeDimension_list
addToQuantitationTypeDimension_list(int, QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list
addToQuantitationTypeMap_list(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add QuantitationTypeMap to QuantitationTypeMap_list
addToQuantitationTypeMap_list(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to add QuantitationTypeMap at position to QuantitationTypeMap_list
addToQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Method to add QuantitationTypeMap to QuantitationTypeMaps_list
addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list
addToQuantitationTypeMaps(QuantitationTypeMap) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Method to add QuantitationTypeMap to QuantitationTypeMaps_list
addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list
addToQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.QuantitationType.QuantitationType
Method to add QuantitationTypeMap to QuantitationTypeMaps_list
addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in class org.biomage.QuantitationType.QuantitationType
Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list
addToQuantitationTypes(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Method to add QuantitationType to QuantitationTypes_list
addToQuantitationTypes(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Method to add QuantitationType at position to QuantitationTypes_list
addToQuantitationTypes(QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationTypes
Method to add QuantitationType to QuantitationTypes_list
addToQuantitationTypes(int, QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationTypes
Method to add QuantitationType at position to QuantitationTypes_list
addToQuantitationTypeTuples(QuantitationTypeTuple) - Method in class org.biomage.BioAssayData.DesignElementTuple
Method to add QuantitationTypeTuple to QuantitationTypeTuples_list
addToQuantitationTypeTuples(int, QuantitationTypeTuple) - Method in class org.biomage.BioAssayData.DesignElementTuple
Method to add QuantitationTypeTuple at position to QuantitationTypeTuples_list
addToQuantitationTypeTuples(QuantitationTypeTuple) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Method to add QuantitationTypeTuple to QuantitationTypeTuples_list
addToQuantitationTypeTuples(int, QuantitationTypeTuple) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Method to add QuantitationTypeTuple at position to QuantitationTypeTuples_list
addToRegions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to add SeqFeatureLocation to Regions_list
addToRegions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to add SeqFeatureLocation at position to Regions_list
addToRegions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasRegions
Method to add SeqFeatureLocation to Regions_list
addToRegions(int, SeqFeatureLocation) - Method in interface org.biomage.Interface.HasRegions
Method to add SeqFeatureLocation at position to Regions_list
addToReporter_list(Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add Reporter to Reporter_list
addToReporter_list(int, Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add Reporter at position to Reporter_list
addToReporterCompositeMap_list(ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add ReporterCompositeMap to ReporterCompositeMap_list
addToReporterCompositeMap_list(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to add ReporterCompositeMap at position to ReporterCompositeMap_list
addToReporterCompositeMaps(ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add ReporterCompositeMap to ReporterCompositeMaps_list
addToReporterCompositeMaps(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
addToReporterCompositeMaps(ReporterCompositeMap) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Method to add ReporterCompositeMap to ReporterCompositeMaps_list
addToReporterCompositeMaps(int, ReporterCompositeMap) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
addToReporterGroup_list(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add ReporterGroup to ReporterGroup_list
addToReporterGroup_list(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to add ReporterGroup at position to ReporterGroup_list
addToReporterGroups(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add ReporterGroup to ReporterGroups_list
addToReporterGroups(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to add ReporterGroup at position to ReporterGroups_list
addToReporterGroups(ReporterGroup) - Method in interface org.biomage.Interface.HasReporterGroups
Method to add ReporterGroup to ReporterGroups_list
addToReporterGroups(int, ReporterGroup) - Method in interface org.biomage.Interface.HasReporterGroups
Method to add ReporterGroup at position to ReporterGroups_list
addToReporterPositionSources(ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Method to add ReporterPosition to ReporterPositionSources_list
addToReporterPositionSources(int, ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Method to add ReporterPosition at position to ReporterPositionSources_list
addToReporterPositionSources(ReporterPosition) - Method in interface org.biomage.Interface.HasReporterPositionSources
Method to add ReporterPosition to ReporterPositionSources_list
addToReporterPositionSources(int, ReporterPosition) - Method in interface org.biomage.Interface.HasReporterPositionSources
Method to add ReporterPosition at position to ReporterPositionSources_list
addToReporters(Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
Method to add Reporter to Reporters_list
addToReporters(int, Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
Method to add Reporter at position to Reporters_list
addToReporters(Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
Method to add Reporter to Reporters_list
addToReporters(int, Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
Method to add Reporter at position to Reporters_list
addToReporters(Reporter) - Method in interface org.biomage.Interface.HasReporters
Method to add Reporter to Reporters_list
addToReporters(int, Reporter) - Method in interface org.biomage.Interface.HasReporters
Method to add Reporter at position to Reporters_list
addToRoles(OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
Method to add OntologyEntry to Roles_list
addToRoles(int, OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
Method to add OntologyEntry at position to Roles_list
addToRoles(OntologyEntry) - Method in interface org.biomage.Interface.HasRoles
Method to add OntologyEntry to Roles_list
addToRoles(int, OntologyEntry) - Method in interface org.biomage.Interface.HasRoles
Method to add OntologyEntry at position to Roles_list
addToSecurity_list(Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add Security to Security_list
addToSecurity_list(int, Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add Security at position to Security_list
addToSecurityGroup_list(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add SecurityGroup to SecurityGroup_list
addToSecurityGroup_list(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to add SecurityGroup at position to SecurityGroup_list
addToSecurityGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
Method to add SecurityGroup to SecurityGroups_list
addToSecurityGroups(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
Method to add SecurityGroup at position to SecurityGroups_list
addToSecurityGroups(SecurityGroup) - Method in interface org.biomage.Interface.HasSecurityGroups
Method to add SecurityGroup to SecurityGroups_list
addToSecurityGroups(int, SecurityGroup) - Method in interface org.biomage.Interface.HasSecurityGroups
Method to add SecurityGroup at position to SecurityGroups_list
addToSeqFeatures(SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to add SeqFeature to SeqFeatures_list
addToSeqFeatures(int, SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to add SeqFeature at position to SeqFeatures_list
addToSeqFeatures(SeqFeature) - Method in interface org.biomage.Interface.HasSeqFeatures
Method to add SeqFeature to SeqFeatures_list
addToSeqFeatures(int, SeqFeature) - Method in interface org.biomage.Interface.HasSeqFeatures
Method to add SeqFeature at position to SeqFeatures_list
addToSequenceDatabases(DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add DatabaseEntry to SequenceDatabases_list
addToSequenceDatabases(int, DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to add DatabaseEntry at position to SequenceDatabases_list
addToSequenceDatabases(DatabaseEntry) - Method in interface org.biomage.Interface.HasSequenceDatabases
Method to add DatabaseEntry to SequenceDatabases_list
addToSequenceDatabases(int, DatabaseEntry) - Method in interface org.biomage.Interface.HasSequenceDatabases
Method to add DatabaseEntry at position to SequenceDatabases_list
addToSoftware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
addToSoftware_list(Software) - Method in class org.biomage.Protocol.Protocol_package
Method to add Software to Software_list
addToSoftware_list(int, Software) - Method in class org.biomage.Protocol.Protocol_package
Method to add Software at position to Software_list
addToSoftwareApplications(SoftwareApplicationData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
addToSoftwareApplications(SoftwareApplication) - Method in interface org.biomage.Interface.HasSoftwareApplications
Method to add SoftwareApplication to SoftwareApplications_list
addToSoftwareApplications(int, SoftwareApplication) - Method in interface org.biomage.Interface.HasSoftwareApplications
Method to add SoftwareApplication at position to SoftwareApplications_list
addToSoftwareApplications(SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add SoftwareApplication to SoftwareApplications_list
addToSoftwareApplications(int, SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to add SoftwareApplication at position to SoftwareApplications_list
addToSoftwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Method to add Contact to SoftwareManufacturers_list
addToSoftwareManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Method to add Contact at position to SoftwareManufacturers_list
addToSoftwareManufacturers(Contact) - Method in class org.biomage.Protocol.Software
Method to add Contact to SoftwareManufacturers_list
addToSoftwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Software
Method to add Contact at position to SoftwareManufacturers_list
addToSoftwares(SoftwareData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
addToSoftwares(Software) - Method in interface org.biomage.Interface.HasSoftwares
Method to add Software to Softwares_list
addToSoftwares(int, Software) - Method in interface org.biomage.Interface.HasSoftwares
Method to add Software at position to Softwares_list
addToSoftwares(Software) - Method in class org.biomage.Protocol.Hardware
Method to add Software to Softwares_list
addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Hardware
Method to add Software at position to Softwares_list
addToSoftwares(Software) - Method in class org.biomage.Protocol.Protocol
Method to add Software to Softwares_list
addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Protocol
Method to add Software at position to Softwares_list
addToSoftwares(Software) - Method in class org.biomage.Protocol.Software
Method to add Software to Softwares_list
addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Software
Method to add Software at position to Softwares_list
addToSourceBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
Method to add BioAssay to SourceBioAssays_list
addToSourceBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
Method to add BioAssay at position to SourceBioAssays_list
addToSourceBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasSourceBioAssays
Method to add BioAssay to SourceBioAssays_list
addToSourceBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasSourceBioAssays
Method to add BioAssay at position to SourceBioAssays_list
addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
addToSourceContact(Contact) - Method in class org.biomage.BioMaterial.BioSource
Method to add Contact to SourceContact_list
addToSourceContact(int, Contact) - Method in class org.biomage.BioMaterial.BioSource
Method to add Contact at position to SourceContact_list
addToSourceContact(Contact) - Method in interface org.biomage.Interface.HasSourceContact
Method to add Contact to SourceContact_list
addToSourceContact(int, Contact) - Method in interface org.biomage.Interface.HasSourceContact
Method to add Contact at position to SourceContact_list
addToSourcesQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Method to add QuantitationType to SourcesQuantitationType_list
addToSourcesQuantitationType(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Method to add QuantitationType at position to SourcesQuantitationType_list
addToSourcesQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Method to add QuantitationType to SourcesQuantitationType_list
addToSourcesQuantitationType(int, QuantitationType) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Method to add QuantitationType at position to SourcesQuantitationType_list
addToSubClasses(OntologyHelper.ClassInformation) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
addToSubregions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to add SeqFeatureLocation to Subregions_list
addToSubregions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to add SeqFeatureLocation at position to Subregions_list
addToSubregions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasSubregions
Method to add SeqFeatureLocation to Subregions_list
addToSubregions(int, SeqFeatureLocation) - Method in interface org.biomage.Interface.HasSubregions
Method to add SeqFeatureLocation at position to Subregions_list
addToSummaryStatistics(NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
Method to add NameValueType to SummaryStatistics_list
addToSummaryStatistics(int, NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
Method to add NameValueType at position to SummaryStatistics_list
addToSummaryStatistics(NameValueType) - Method in interface org.biomage.Interface.HasSummaryStatistics
Method to add NameValueType to SummaryStatistics_list
addToSummaryStatistics(int, NameValueType) - Method in interface org.biomage.Interface.HasSummaryStatistics
Method to add NameValueType at position to SummaryStatistics_list
addToTopLevelBioAssays(BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add BioAssay to TopLevelBioAssays_list
addToTopLevelBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add BioAssay at position to TopLevelBioAssays_list
addToTopLevelBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Method to add BioAssay to TopLevelBioAssays_list
addToTopLevelBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Method to add BioAssay at position to TopLevelBioAssays_list
addToTopLevelBioMaterials(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add Treatment to Treatments_list
addToTopLevelBioMaterials(int, BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add Treatment at position to Treatments_list
addToTopLevelBioMaterials(BioMaterial) - Method in interface org.biomage.Interface.HasTopBioMaterial
Method to add BioMaterial to TopLevelBioMaterials_list
addToTopLevelBioMaterials(int, BioMaterial) - Method in interface org.biomage.Interface.HasTopBioMaterial
Method to add BioMaterial at position to TopLevelBioMaterials_list
addToTreatments(TreatmentData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
addToTreatments(Treatment) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add Treatment to Treatments_list
addToTreatments(int, Treatment) - Method in class org.biomage.BioMaterial.BioMaterial
Method to add Treatment at position to Treatments_list
addToTreatments(Treatment) - Method in interface org.biomage.Interface.HasTreatments
Method to add Treatment to Treatments_list
addToTreatments(int, Treatment) - Method in interface org.biomage.Interface.HasTreatments
Method to add Treatment at position to Treatments_list
addToTypes(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData
 
addToTypes(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Method to add OntologyEntry to Types_list
addToTypes(int, OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Method to add OntologyEntry at position to Types_list
addToTypes(OntologyEntry) - Method in class org.biomage.Description.Ontology.ChromosomalAberration
 
addToTypes(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add OntologyEntry to Types_list
addToTypes(int, OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
Method to add OntologyEntry at position to Types_list
addToTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasTypes
Method to add OntologyEntry to Types_list
addToTypes(int, OntologyEntry) - Method in interface org.biomage.Interface.HasTypes
Method to add OntologyEntry at position to Types_list
addToZoneGroups(ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Method to add ZoneGroup to ZoneGroups_list
addToZoneGroups(int, ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Method to add ZoneGroup at position to ZoneGroups_list
addToZoneGroups(ZoneGroup) - Method in interface org.biomage.Interface.HasZoneGroups
Method to add ZoneGroup to ZoneGroups_list
addToZoneGroups(int, ZoneGroup) - Method in interface org.biomage.Interface.HasZoneGroups
Method to add ZoneGroup at position to ZoneGroups_list
addToZoneLocations(Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
Method to add Zone to ZoneLocations_list
addToZoneLocations(int, Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
Method to add Zone at position to ZoneLocations_list
addToZoneLocations(Zone) - Method in interface org.biomage.Interface.HasZoneLocations
Method to add Zone to ZoneLocations_list
addToZoneLocations(int, Zone) - Method in interface org.biomage.Interface.HasZoneLocations
Method to add Zone at position to ZoneLocations_list
addTreatment(long, Class, Treatment) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Adds the specified treatment to the specified BioMaterial.
addTreatmentToBioSample(long, TreatmentData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
addTreatmentToBioSample(long, TreatmentData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
addTreatmentToLabeledExtract(long, TreatmentData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
addTreatmentToLabeledExtract(long, TreatmentData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
addType(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
addUser(UserData) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
addUser(UserData) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
addUser(UserData) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Adds a new caArray user to the persistence store with the specified data.
addValidation() - Method in class org.biomage.tools.apps.annot.pages.ArrayPage
Description: checks if all entries get right data one be one.
addValue(Object, Object) - Static method in class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
 
addVocabulary(VocabData) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
addVocabulary(VocabData, long) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
addVocabulary(VocabData) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
addVocabulary(VocabData, long) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
addWarning(String) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
addZoneGroup(ZoneGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.ZoneGroupManagerDB
Add a new ZoneGroup.
addZoneLocation(Zone) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
addZoneLocation(Integer, Integer, Float, Float) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
addZoneLocation(Zone) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
addZoneLocation(Integer, Integer, Float, Float) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
addZoneLocation(Zone) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
addZoneLocation(Integer, Integer, Float, Float) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
adjustments - Variable in class org.biomage.Array.ArrayManufactureDeviation
Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
AdminData - Class in gov.nih.nci.caarray.common.data.useradmin
 
AdminData() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.AdminData
 
AdminManagementTest - Class in gov.nih.nci.caarray.services.useradmin.test
 
AdminManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
AdminManagerDB - Class in gov.nih.nci.caarray.services.useradmin
 
AdminManagerDB() - Constructor for class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
AdminManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
AdminManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
AdminManagerEJB - Class in gov.nih.nci.caarray.services.useradmin.ejb
This class contains the implemention of the AdminManagerEJB.
AdminManagerEJB() - Constructor for class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
 
AdminUtils - Class in gov.nih.nci.caarray.services.useradmin
 
affiliation - Variable in class org.biomage.AuditAndSecurity.Person
The organization a person belongs to.
AFFY_CEL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
AFFY_CEL_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
AFFY_CEL_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
AFFY_CHP_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
AFFY_CHP_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
AFFY_CHP_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
AFFY_EXP_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
AFFY_EXP_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
AFFY_TXT_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
AFFY_TXT_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
AffyCelFileParser - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
This class parses an Affymetrix's .cel data file.
AffyCelFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.AffyCelFileParser
 
AffyChpFileParser - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
 
AffyChpFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.AffyChpFileParser
 
AffymetrixArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix
Creates a new PhysicalArrayDesign from an Affymetrix .CDF file.
AffymetrixCdfLocatorUtil - Class in gov.nih.nci.caarray.services.arraydesign
Utility class used to lookup Affymetrix CDF files.
afterDelete(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
afterDelete(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerAbstractClassPKPersistence
 
afterInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementUpdateListener
 
afterInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
afterInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerCompoundResolver
 
afterInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerDescriptorModifier
 
afterInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerOntologyEntryResolver
 
afterLookup(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
afterUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementUpdateListener
 
afterUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
afterUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerCompoundResolver
 
afterUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerOntologyEntryResolver
 
Age - Class in org.biomage.Description.Ontology
 
Age() - Constructor for class org.biomage.Description.Ontology.Age
 
Age(Attributes) - Constructor for class org.biomage.Description.Ontology.Age
 
age_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
AGE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
AgeData - Class in gov.nih.nci.caarray.common.data.vocab
 
AgeData() - Constructor for class gov.nih.nci.caarray.common.data.vocab.AgeData
 
ageMax_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageMaxUnitId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageMaxUnitName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageMin_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageMinUnitId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageMinUnitName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageUnitId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageUnitName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ageUnits_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
AGGREGATE - Static variable in class org.biomage.tools.generate_classes.XMIParseHelpers
Is Co-owned by one or more objects
AgilentTxtArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.agilent
Loads an array design from an Agilent text data file.
AgilentTxtFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.agilent
Indicates an error in an Agilent txt data file.
AgilentTxtFormatException() - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtFormatException
 
AgilentTxtFormatException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtFormatException
 
AgilentTxtFormatException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtFormatException
 
AgilentTxtFormatException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtFormatException
 
AgilentTxtReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Reader for Agilent gene expression data files.
aLine - Static variable in class org.biomage.tools.generate_er.CreateMageER
a line for seperation
ALL_EXPRESSION_TYPES - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
allChar(String) - Method in class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
Description: checks if a string contains only characters.
allele_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ALLELE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
alphabetLinkingTabelName(String, String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: compare two strings and link them alphabetically if string1 < string2: negative number
amol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
analysisResults - Variable in class org.biomage.Experiment.Experiment
The results of analyzing the data, typically with a clustering algorithm.
annotations - Variable in class org.biomage.Description.Description
Allows specification of ontology entries related to the instance being described.
annotations - Variable in class org.biomage.Experiment.ExperimentalFactor
Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #.
appendChars(char[], int, int) - Method in interface org.biomage.tools.xmlutils.PCData
 
appendChars(char[], int, int) - Method in class org.biomage.tools.xmlutils.PCDataImpl
 
AppendInputStream - Class in gov.nih.nci.caarray.services.fileparse2.parsers
This InputStream appends 2 inputStreams together like JSDK's SequenceInputStream but also supports mark() and reset().
AppendInputStream(InputStream, InputStream) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
AppletValidatorCodeGenerator - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
AppletValidatorCodeGenerator() - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.AppletValidatorCodeGenerator
 
APPLICATION - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
Security constants
apply() - Method in class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
perform this use case
apply() - Method in class gov.nih.nci.caarray.services.fileparse.test.usecases.CanParseFiles
Perform this use case
apply() - Method in interface gov.nih.nci.caarray.services.fileparse.test.usecases.UseCase
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElement
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItf
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItfPG
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CreateSecuredElement
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetElementProtectionGroups
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetProtectionGroups
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetUserRole
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.IsUsrElementOwner
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.RemoveSecuredElement
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementOwner
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementProtectionGroups
Perform this use case
apply() - Method in interface gov.nih.nci.caarray.services.security.test.usecases.UseCase
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
perform this use case
apply() - Method in class gov.nih.nci.caarray.services.test.usecases.ExportMAGEML
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistArrayDesign
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistExperiment
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistProtocol
Perform this use case
apply() - Method in interface gov.nih.nci.caarray.services.test.usecases.UseCase
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
perform this use case
apply() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetBioAssayDatum
Perform this use case
apply() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetByQuantitationType
Perform this use case
apply() - Method in interface gov.nih.nci.caarray.services.util.netcdf.test.usecases.UseCase
Perform this use case
applyCharacteristics(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
applyProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
This method is called after a forward from the ApplyProtocol actions it gets the previously stored treatmentFormTwo that contains all the previous treatment information that was input before the "Apply Protocol" button was pressed.
applyProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
This method is called after a forward from the ApplyProtocol actions it gets the previously stored treatmentFormTwo that contains all the previous treatment information that was input before the "Apply Protocol" button was pressed.
applyProtocolSetting(ExperimentDetailForm) - Static method in class gov.nih.nci.caarray.ui.experiment.ExperimentUtils
 
applyProtocolToArray(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
applyProtocolToArrayDesign(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
applyProtocolToLabeledExtract(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
applyProtocolToTreatmentEvent(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
applyUpdateCharacteristics(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
args - Variable in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: The command line arguments.
Array - Class in org.biomage.Array
The physical substrate along with its features and their annotation
Array() - Constructor for class org.biomage.Array.Array
Default constructor.
Array(Attributes) - Constructor for class org.biomage.Array.Array
Attribute constructor.
array - Variable in class org.biomage.BioAssay.BioAssayCreation
The array used in the BioAssayCreation event.
ARRAY_DESIGN - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
ARRAY_DESIGN - Static variable in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
ARRAY_DESIGN - Static variable in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
ARRAY_DESIGN_FTP_DIR - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
ARRAY_DESIGN_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
ARRAY_DESIGN_MESSAGE - Static variable in class gov.nih.nci.caarray.services.fileparse.FileMessageTypes
 
array_list - Variable in class org.biomage.Array.Array_package
The physical substrate along with its features and their annotation
Array_package - Class in org.biomage.Array
Describes the process of creating arrays from array designs.
Array_package() - Constructor for class org.biomage.Array.Array_package
Default constructor.
Array_package(Attributes) - Constructor for class org.biomage.Array.Array_package
Attribute constructor.
array_package - Variable in class org.biomage.Common.MAGEJava
Describes the process of creating arrays from array designs.
Array_package.Array_list - Class in org.biomage.Array
Inner list class for holding multiple entries for attribute array.
Array_package.Array_list() - Constructor for class org.biomage.Array.Array_package.Array_list
 
Array_package.ArrayGroup_list - Class in org.biomage.Array
Inner list class for holding multiple entries for attribute arrayGroup.
Array_package.ArrayGroup_list() - Constructor for class org.biomage.Array.Array_package.ArrayGroup_list
 
Array_package.ArrayManufacture_list - Class in org.biomage.Array
Inner list class for holding multiple entries for attribute arrayManufacture.
Array_package.ArrayManufacture_list() - Constructor for class org.biomage.Array.Array_package.ArrayManufacture_list
 
ArrayAddUpdateAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
ArrayAddUpdateForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm
 
ArrayBaseForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayBaseForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
ArrayConstants - Class in gov.nih.nci.caarray.common.data.array
 
ArrayConstants() - Constructor for class gov.nih.nci.caarray.common.data.array.ArrayConstants
 
ArrayCopyAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayCopyAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyAction
 
ArrayCopyForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayCopyForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
ArrayData - Class in gov.nih.nci.caarray.common.data.array
 
ArrayData() - Constructor for class gov.nih.nci.caarray.common.data.array.ArrayData
 
arrayDesign - Variable in class org.biomage.Array.Array
The association of a physical array with its array design.
ArrayDesign - Class in org.biomage.ArrayDesign
Describes the design of an gene expression layout.
ArrayDesign() - Constructor for class org.biomage.ArrayDesign.ArrayDesign
Default constructor.
ArrayDesign(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign
Attribute constructor.
arrayDesign_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
Describes the design of an gene expression layout.
ArrayDesign_package - Class in org.biomage.ArrayDesign
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.
ArrayDesign_package() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package
Default constructor.
ArrayDesign_package(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package
Attribute constructor.
arrayDesign_package - Variable in class org.biomage.Common.MAGEJava
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.
ArrayDesign_package.ArrayDesign_list - Class in org.biomage.ArrayDesign
Inner list class for holding multiple entries for attribute arrayDesign.
ArrayDesign_package.ArrayDesign_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list
 
ArrayDesign_package.CompositeGroup_list - Class in org.biomage.ArrayDesign
Inner list class for holding multiple entries for attribute compositeGroup.
ArrayDesign_package.CompositeGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list
 
ArrayDesign_package.ReporterGroup_list - Class in org.biomage.ArrayDesign
Inner list class for holding multiple entries for attribute reporterGroup.
ArrayDesign_package.ReporterGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list
 
ArrayDesignAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAction
 
ArrayDesignAddAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignAddAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
ArrayDesignAddUpdateForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
ArrayDesignBaseForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignBaseForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
ArrayDesignCleaner - Class in gov.nih.nci.caarray.services.arraydesign.loader
Utility class used to remove elements from array designs.
ArrayDesignConstants - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignConstants() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
ArrayDesignData - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ArrayDesignData() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
ArrayDesignDataSetMapper - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
ArrayDesignDataSetMapper() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataSetMapper
 
ArrayDesignDataSource - Interface in gov.nih.nci.caarray.services.arraydesign
Retrieves various MAGE objects needed to populate array designs.
ArrayDesignDataSourceException - Exception in gov.nih.nci.caarray.services.arraydesign
Indicates that an error occurred accessing the data source.
ArrayDesignDataSourceException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSourceException
 
ArrayDesignDataSourceException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSourceException
 
ArrayDesignDataTableMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
ArrayDesignDataTableMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
ArrayDesignDelimitedFileParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
ArrayDesignDelimitedFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDelimitedFileParser
 
ArrayDesignDesc - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ArrayDesignDesc() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
ArrayDesignDetailAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignDetailAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
ArrayDesignDetailForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignDetailForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
ArrayDesignFileHandler - Interface in gov.nih.nci.caarray.services.arraydesign.loader.handler
Interface to array design parsing subsystem.
ArrayDesignFileHandlerFactory - Class in gov.nih.nci.caarray.services.arraydesign.loader.handler
Factory used to access array design file handler subsystem instance.
ArrayDesignFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
ArrayDesignFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
ArrayDesignFileHeaderParserItf - Interface in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
ArrayDesignFileParserMDB - Class in gov.nih.nci.caarray.services.fileparse2.mdb
 
ArrayDesignFileParserMDB() - Constructor for class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB
 
ArrayDesignFileParsingEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
ArrayDesignFileParsingEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileParsingEntry
 
ArrayDesignFileParsingEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
ArrayDesignFileParsingEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileParsingEntryData
 
ArrayDesignFileParsingException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.handler
Indicates an error parsing an array design file.
ArrayDesignFileParsingException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileParsingException
 
ArrayDesignFileParsingException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileParsingException
 
ArrayDesignFileParsingJob - Class in gov.nih.nci.caarray.services.arraydesign.loader
Contains the necessary data to load an array design from a data file.
ArrayDesignFileParsingJob(CAFileUploadEntry, String) - Constructor for class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignFileParsingJob
 
ArrayDesignFileParsingJobHandlerImpl - Class in gov.nih.nci.caarray.services.fileupload2
 
ArrayDesignFileParsingJobHandlerImpl() - Constructor for class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileParsingJobHandlerImpl
 
ArrayDesignFileParsingService - Class in gov.nih.nci.caarray.services.fileparse2
 
ArrayDesignFileParsingService() - Constructor for class gov.nih.nci.caarray.services.fileparse2.ArrayDesignFileParsingService
 
ArrayDesignFileProcessAction - Class in gov.nih.nci.caarray.ui.arraydesign
This action class is responsible for starting file parsing service, forwarding to a designated page upon user's request and cleaning up uploaded files when user requests a stop action.
ArrayDesignFileProcessAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignFileProcessAction
 
ArrayDesignFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
ArrayDesignFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
 
ArrayDesignFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
ArrayDesignFileUploadEntryData(String, FileType, String, String) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadEntryData
 
ArrayDesignFileUploadGroup - Class in gov.nih.nci.caarray.services.fileupload2
 
ArrayDesignFileUploadGroup() - Constructor for class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
ArrayDesignFileUploadGroupData - Class in gov.nih.nci.caarray.common.data.fileupload2
This class groups one or more files that belong to one type, e.g.
ArrayDesignFileUploadGroupData(FileType[]) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
Constructs an instance of this class with an array of FileTypes which can be accepted for the files to be uploaded.
ArrayDesignFinder - Class in gov.nih.nci.caarray.services.fileupload
 
ArrayDesignFinder() - Constructor for class gov.nih.nci.caarray.services.fileupload.ArrayDesignFinder
Default Constructor
ArrayDesignFixer - Class in gov.nih.nci.caarray.services.mageloader.test
 
ArrayDesignFixer() - Constructor for class gov.nih.nci.caarray.services.mageloader.test.ArrayDesignFixer
 
arrayDesignId - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
ArrayDesignLoaderClient - Class in gov.nih.nci.caarray.loader
Reloads the existing array designs.
ArrayDesignLoaderClient() - Constructor for class gov.nih.nci.caarray.loader.ArrayDesignLoaderClient
 
ArrayDesignManagementTest - Class in gov.nih.nci.caarray.services.arraydesign.test
 
ArrayDesignManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
ArrayDesignManager - Interface in gov.nih.nci.caarray.services.arraydesign
Interface to the ArrayDesignManager subsytem.
ArrayDesignManagerDB - Class in gov.nih.nci.caarray.services.arraydesign
 
ArrayDesignManagerDB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Default Constructor
ArrayDesignManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
ArrayDesignManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
ArrayDesignManagerEJB - Class in gov.nih.nci.caarray.services.arraydesign.ejb
ArrayDesignManagerEJB
ArrayDesignManagerEJB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
ArrayDesignManagerFactory - Class in gov.nih.nci.caarray.services.arraydesign
Allows clients access to an ArrayDesignManager interface instance.
ArrayDesignRetrievalException - Exception in gov.nih.nci.caarray.services.arraydesign
Indicates that there was an error retrieving an array design.
ArrayDesignSaveException - Exception in gov.nih.nci.caarray.services.arraydesign.loader
Indicates a problem storing array design annotation.
ArrayDesignSaveException() - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaveException
 
ArrayDesignSaveException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaveException
 
ArrayDesignSaveException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaveException
 
ArrayDesignSaveException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaveException
 
ArrayDesignSaver - Class in gov.nih.nci.caarray.services.arraydesign.loader
Efficiently stores large array designs by saving the enclosing objects and then directly storing design elements and their associations using SQL batch execution.
ArrayDesignSaver() - Constructor for class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
ArrayDesignSearchAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignSearchAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
ArrayDesignSearchCriteria - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ArrayDesignSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
ArrayDesignSearchForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignSearchForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
ArrayDesignSecurityHelper - Interface in gov.nih.nci.caarray.services.arraydesign
Provides secured element handling for array designs.
ArrayDesignTextFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
ArrayDesignTextFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
ArrayDesignTextFileHeaderParser(DataSetMapper, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
ArrayDesignType - Enum in gov.nih.nci.caarray.services.arraydesign
Enumerates the different array design types known to the system.
ArrayDesignUpdateAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
ArrayDesignUploadDelegate - Class in gov.nih.nci.caarray.services.fileupload
 
ArrayDesignUploadDelegate() - Constructor for class gov.nih.nci.caarray.services.fileupload.ArrayDesignUploadDelegate
 
ArrayDesignUploadedFileData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
ArrayDesignUploadedFileData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
ArrayDesignUploadManagerMDB - Class in gov.nih.nci.caarray.services.fileparse.mdb
 
ArrayDesignUploadManagerMDB() - Constructor for class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB
 
ArrayDesignUtils - Class in gov.nih.nci.caarray.services.arraydesign
 
ArrayDesignUtils - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDesignUtils() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
ArrayDesignValues - Class in gov.nih.nci.caarray.services.fileupload
 
ArrayDesignValues(ArrayDesignDesc, String, UploadFileTypes.MICROARRAY_FILE_TYPE) - Constructor for class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
Constructor with required values
ArrayDesignView - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ArrayDesignView() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
ArrayDetailAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDetailAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailAction
 
ArrayDetailForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayDetailForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
arrayGroup - Variable in class org.biomage.Array.Array
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
ArrayGroup - Class in org.biomage.Array
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
ArrayGroup() - Constructor for class org.biomage.Array.ArrayGroup
Default constructor.
ArrayGroup(Attributes) - Constructor for class org.biomage.Array.ArrayGroup
Attribute constructor.
ArrayGroup.OrientationMarkPosition - Class in org.biomage.Array
Inner class for the enumeration values that the attribute orientationMarkPosition can assume.
arrayGroup_list - Variable in class org.biomage.Array.Array_package
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
ArrayGroupData - Class in gov.nih.nci.caarray.common.data.array
 
ArrayGroupData() - Constructor for class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
ArrayGroupDesc - Class in gov.nih.nci.caarray.common.data.array
 
ArrayGroupDesc() - Constructor for class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
ArrayGroupManagementTest - Class in gov.nih.nci.caarray.services.array.test
 
ArrayGroupManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
ArrayManagerDB - Class in gov.nih.nci.caarray.services.array
 
ArrayManagerDB() - Constructor for class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
ArrayManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
ArrayManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
ArrayManagerEJB - Class in gov.nih.nci.caarray.services.array.ejb
ArrayManagerEJB
ArrayManagerEJB() - Constructor for class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
ArrayManufacture - Class in org.biomage.Array
Describes the process by which arrays are produced.
ArrayManufacture() - Constructor for class org.biomage.Array.ArrayManufacture
Default constructor.
ArrayManufacture(Attributes) - Constructor for class org.biomage.Array.ArrayManufacture
Attribute constructor.
arrayManufacture_list - Variable in class org.biomage.Array.Array_package
Describes the process by which arrays are produced.
ArrayManufactureDeviation - Class in org.biomage.Array
Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g.
ArrayManufactureDeviation() - Constructor for class org.biomage.Array.ArrayManufactureDeviation
Default constructor.
ArrayManufactureDeviation(Attributes) - Constructor for class org.biomage.Array.ArrayManufactureDeviation
Attribute constructor.
arrayManufactureDeviations - Variable in class org.biomage.Array.Array
Association to classes to describe deviations from the ArrayDesign.
ArrayManufacturerFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
ArrayManufacturerFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ArrayManufacturerFieldMapper
 
arrayManufacturers - Variable in class org.biomage.Array.ArrayManufacture
The person or organization to contact for information concerning the ArrayManufacture.
arrayName - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
ArrayPage - Class in org.biomage.tools.apps.annot.pages
 
ArrayPage() - Constructor for class org.biomage.tools.apps.annot.pages.ArrayPage
Description: defaul contructor that calls a method to initialize an interface.
arrays - Variable in class org.biomage.Array.ArrayGroup
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
arrays - Variable in class org.biomage.Array.ArrayManufacture
Association between the manufactured array and the information on that manufacture.
ArraySearchAction - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArraySearchAction() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
ArraySearchCriteria - Class in gov.nih.nci.caarray.common.data.array
 
ArraySearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
ArraySearchForm - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArraySearchForm() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
ArrayUtils - Class in gov.nih.nci.caarray.services.array
 
ArrayUtils - Class in gov.nih.nci.caarray.ui.arraydesign
 
ArrayUtils() - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
AssemblerFactory - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
This class is an abstract factory for creating and updating of an object which data is provided by one or more source objects.
AssemblerFactory() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
AssemblerNotAvailableException - Exception in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
AssemblerNotAvailableException() - Constructor for exception gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerNotAvailableException
 
AssemblerNotAvailableException(String) - Constructor for exception gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerNotAvailableException
 
AssemblerNotAvailableException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerNotAvailableException
 
AssemblerNotAvailableException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerNotAvailableException
 
assessDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
assessDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
assignableValues - Variable in class org.biomage.tools.helpers.MGEDOntologyEntry
 
assignElementToRole(long, String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Assign a protection element to a role.
assignIdentifier(Identifiable) - Static method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerMAGEIdentifierAssigner
Assign the Identifier value to an MAGE object using the format :::
assignValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyClassEntry
 
assignValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
assignValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyPropertyEntry
 
associateHardware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
associateSoftware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
associateSoftware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
associationAttrInformation(Vector, Element) - Method in class org.biomage.tools.generate_classes.CreateMAGEFile
Description: Puts together the information on the class associations.
associationAttrInformation(Element, Element, Map) - Method in class org.biomage.tools.generate_classes.CreatePackageFile
Description: Puts together the information on the class associations.
AssociationColumn - Class in org.biomage.tools.generate_er
 
AssociationColumn() - Constructor for class org.biomage.tools.generate_er.AssociationColumn
Description: Constructor for the AssociationColumn object.
associationInfo - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on the class association attributes for this class.
associationInformation(Element, Map, Map, Map, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Puts together the information on the class associations.
associationInformation() - Method in class org.biomage.tools.generate_classes.CreateInterfaceFile
Description: Puts together the information on the interface associations.
associationInformation(Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains the association and the current end and places the information on a map keyed by the model element id.
associationStack - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
associationStack - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
associationType - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
 
atmosphere_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ATMOSPHERE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ATTACHMENT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
Audit - Class in org.biomage.AuditAndSecurity
Tracks information on the contact that creates or modifies an object.
Audit() - Constructor for class org.biomage.AuditAndSecurity.Audit
Default constructor.
Audit(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Audit
Attribute constructor.
Audit.Action - Class in org.biomage.AuditAndSecurity
Inner class for the enumeration values that the attribute action can assume.
AuditAndSecurity_package - Class in org.biomage.AuditAndSecurity
Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
AuditAndSecurity_package() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Default constructor.
AuditAndSecurity_package(Attributes) - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Attribute constructor.
auditAndSecurity_package - Variable in class org.biomage.Common.MAGEJava
Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
AuditAndSecurity_package.Contact_list - Class in org.biomage.AuditAndSecurity
Inner list class for holding multiple entries for attribute contact.
AuditAndSecurity_package.Contact_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list
 
AuditAndSecurity_package.Security_list - Class in org.biomage.AuditAndSecurity
Inner list class for holding multiple entries for attribute security.
AuditAndSecurity_package.Security_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list
 
AuditAndSecurity_package.SecurityGroup_list - Class in org.biomage.AuditAndSecurity
Inner list class for holding multiple entries for attribute securityGroup.
AuditAndSecurity_package.SecurityGroup_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list
 
authenticateUser(String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecurityServiceItf
Returns the result of the user authentication.
authenticateUser(String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the result of the user authentication.
AuthenticationDAItf - Interface in gov.nih.nci.caarray.services.security.intf
An interface defines the generic properties of an authentication data service object.
AuthorizationDAItf - Interface in gov.nih.nci.caarray.services.security.intf
An interface defines the generic properties of an authorization data service object.
authorizeUser(String, Role[], String, String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecurityServiceItf
Returns the given user or role's access permission to a protection element.
authorizeUser(Role[], String, String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecurityServiceItf
Returns the roles' access permission to a protection element.
authorizeUser(String, String[], String, SecuredElementItf) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Overloaded to support isEditable.
authorizeUser(String, String[], String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the given users with role's access permission to a protection element.
authorizeUser(String, String[], String, SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the given users with role's access permission to a collection of protection element.
authorizeUser(String, String[], String, SecuredElementItf[], ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the given users with role's access permission to a collection of protection element.
authorizeUser(Role[], String, String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
place holders for to support interface.
authorizeUser(String, Role[], String, String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
 
authorizeUserOwner(String, String, SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the given users with role's access permission to a collection of protection element.
authorizeUserOwnerOnly(String, String, SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns the given users with role's access permission to a collection of protection element.
available() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 

B

B - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
back - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
back_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
backhome(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
BARRIER_FACILITY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
barrierFacility_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BaseAction - Class in gov.nih.nci.caarray.ui.core
 
BaseAction() - Constructor for class gov.nih.nci.caarray.ui.core.BaseAction
 
baseClassCreateFile - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Class, if any, that is the base class for this class.
baseClassID - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The element node for the base class.
baseClassName - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Class, if any, that is the base class for this class.
BaseDispatchAction - Class in gov.nih.nci.caarray.ui.core
This DispatchAction class is intended for use just like Struts's DispatchAction with the additional of cache and general exception handling.
BaseDispatchAction() - Constructor for class gov.nih.nci.caarray.ui.core.BaseDispatchAction
 
BaseForm - Class in gov.nih.nci.caarray.ui.core
 
BaseForm() - Constructor for class gov.nih.nci.caarray.ui.core.BaseForm
 
BaseHttpUnitTest - Class in gov.nih.nci.caarray.ui.test
 
BaseHttpUnitTest(String) - Constructor for class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
BaseInContainerTest - Class in gov.nih.nci.caarray.services.test
 
BaseInContainerTest() - Constructor for class gov.nih.nci.caarray.services.test.BaseInContainerTest
 
BaseMicroarrayFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
BaseMicroarrayFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
BaseMicroarrayFileParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
BaseMicroarrayFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
BaseSearchCriteria - Class in gov.nih.nci.caarray.common.data.util
 
BaseSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.util.BaseSearchCriteria
 
BaseSecuredElement - Class in gov.nih.nci.caarray.services.util
 
BaseSecuredElement() - Constructor for class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
Basis2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Basis2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Basis2StringFieldConversion
 
BCELCalls - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
 
BCELCalls() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.BCELCalls
 
BDQ - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
BeanConversionTest - Class in gov.nih.nci.caarray.services.fileparse2.parsers.test
 
BeanConversionTest() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
BeanConversionTest(String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
BeanProvider - Class in gov.nih.nci.caarray.services.fileparse2
 
bedding_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BEDDING_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
beforeDelete(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerAbstractClassPKPersistence
 
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerCompoundResolver
 
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerDescriptorModifier
Toggle the cascade store approriately for ReporterPosition before SeqFeatureLocation is inserted, so that the referenced Reporter object is stored when the referencing object is BioSequence (via SeqFeatureLocation), and only its primary key is stored otherwise.
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerMAGEIdentifierAssigner
 
beforeInsert(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerOntologyEntryResolver
 
beforeUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
beforeUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerCompoundResolver
 
beforeUpdate(PBLifeCycleEvent) - Method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerOntologyEntryResolver
 
begin() - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
beginTransaction() - Method in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
BibliographicReference - Class in org.biomage.BQS
Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference.
BibliographicReference() - Constructor for class org.biomage.BQS.BibliographicReference
Default constructor.
BibliographicReference(Attributes) - Constructor for class org.biomage.BQS.BibliographicReference
Attribute constructor.
BibliographicReferenceAccessionFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
BibliographicReferenceAccessionFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BibliographicReferenceAccessionFieldMapper
 
BibliographicReferenceAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
BibliographicReferenceAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.BibliographicReferenceAssembler
 
bibliographicReferences - Variable in class org.biomage.Description.Description
References to existing literature.
BIO_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
BioAssay - Class in org.biomage.BioAssay
An abstract class which represents both physical and computational groupings of arrays and biomaterials.
BioAssay() - Constructor for class org.biomage.BioAssay.BioAssay
Default constructor.
BioAssay(Attributes) - Constructor for class org.biomage.BioAssay.BioAssay
Attribute constructor.
bioAssay - Variable in class org.biomage.BioAssayData.BioAssayTuple
The BioAssay associated with the value of the BioAssayDatum.
bioAssay_list - Variable in class org.biomage.BioAssay.BioAssay_package
An abstract class which represents both physical and computational groupings of arrays and biomaterials.
BioAssay_package - Class in org.biomage.BioAssay
Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images.
BioAssay_package() - Constructor for class org.biomage.BioAssay.BioAssay_package
Default constructor.
BioAssay_package(Attributes) - Constructor for class org.biomage.BioAssay.BioAssay_package
Attribute constructor.
bioAssay_package - Variable in class org.biomage.Common.MAGEJava
Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images.
BioAssay_package.BioAssay_list - Class in org.biomage.BioAssay
Inner list class for holding multiple entries for attribute bioAssay.
BioAssay_package.BioAssay_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.BioAssay_list
 
BioAssay_package.Channel_list - Class in org.biomage.BioAssay
Inner list class for holding multiple entries for attribute channel.
BioAssay_package.Channel_list() - Constructor for class org.biomage.BioAssay.BioAssay_package.Channel_list
 
BioAssayCreation - Class in org.biomage.BioAssay
The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
BioAssayCreation() - Constructor for class org.biomage.BioAssay.BioAssayCreation
Default constructor.
BioAssayCreation(Attributes) - Constructor for class org.biomage.BioAssay.BioAssayCreation
Attribute constructor.
bioAssayCreation - Variable in class org.biomage.BioAssay.PhysicalBioAssay
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
BioAssayData - Class in org.biomage.BioAssayData
Represents the dataset created when the BioAssays are created.
BioAssayData() - Constructor for class org.biomage.BioAssayData.BioAssayData
Default constructor.
BioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayData
Attribute constructor.
bioAssayData - Variable in class org.biomage.Experiment.Experiment
The collection of BioAssayDatas for this Experiment.
bioAssayData_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
Represents the dataset created when the BioAssays are created.
BioAssayData_package - Class in org.biomage.BioAssayData
The classes defined here provide data and the information and annotation on the derivation of that data.
BioAssayData_package() - Constructor for class org.biomage.BioAssayData.BioAssayData_package
Default constructor.
BioAssayData_package(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayData_package
Attribute constructor.
bioAssayData_package - Variable in class org.biomage.Common.MAGEJava
The classes defined here provide data and the information and annotation on the derivation of that data.
BioAssayData_package.BioAssayData_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute bioAssayData.
BioAssayData_package.BioAssayData_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list
 
BioAssayData_package.BioAssayDimension_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute bioAssayDimension.
BioAssayData_package.BioAssayDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list
 
BioAssayData_package.BioAssayMap_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute bioAssayMap.
BioAssayData_package.BioAssayMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list
 
BioAssayData_package.DesignElementDimension_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute designElementDimension.
BioAssayData_package.DesignElementDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list
 
BioAssayData_package.QuantitationTypeDimension_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute quantitationTypeDimension.
BioAssayData_package.QuantitationTypeDimension_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list
 
BioAssayData_package.QuantitationTypeMap_list - Class in org.biomage.BioAssayData
Inner list class for holding multiple entries for attribute quantitationTypeMap.
BioAssayData_package.QuantitationTypeMap_list() - Constructor for class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list
 
BioAssayDataCluster - Class in org.biomage.HigherLevelAnalysis
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
BioAssayDataCluster() - Constructor for class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Default constructor.
BioAssayDataCluster(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Attribute constructor.
bioAssayDataCluster_list - Variable in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.
BioAssayDataInfo - Class in gov.nih.nci.caarray.services.bioassaydata
Provides access to all necessary information to parse an experiment hybridization file.
BioAssayDataInfo(BioAssayData, BioAssay, File, SourceType, Array, Experiment, String) - Constructor for class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
Creates a new instance.
BioAssayDataLoader - Interface in gov.nih.nci.caarray.services.bioassaydata
Interface to the BioAssayDataLoader subsystem, allows clients to parse BioDataCubes from existing DataInternal or DataExternal sources.
BioAssayDataLoaderException - Exception in gov.nih.nci.caarray.services.bioassaydata
Indicates an error in the BioAssayDataLoader subsystem.
BioAssayDataLoaderFactory - Class in gov.nih.nci.caarray.services.bioassaydata
Factory that allows clients to get an instance of the BioAssayDataLoader subsystem.
bioAssayDataSources - Variable in class org.biomage.BioAssayData.Transformation
The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
bioAssayDimension - Variable in class org.biomage.BioAssayData.BioAssayData
The BioAssays of the BioAssayData.
BioAssayDimension - Class in org.biomage.BioAssayData
An ordered list of bioAssays.
BioAssayDimension() - Constructor for class org.biomage.BioAssayData.BioAssayDimension
Default constructor.
BioAssayDimension(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayDimension
Attribute constructor.
bioAssayDimension - Variable in class org.biomage.HigherLevelAnalysis.NodeContents
The relevant BioAssays for this NodeContents from the BioAssayData.
bioAssayDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
An ordered list of bioAssays.
bioAssayFactorValues - Variable in class org.biomage.BioAssay.BioAssay
The values that this BioAssay is associated with for the experiment.
BioAssayMap - Class in org.biomage.BioAssayData
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
BioAssayMap() - Constructor for class org.biomage.BioAssayData.BioAssayMap
Default constructor.
BioAssayMap(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayMap
Attribute constructor.
bioAssayMap_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
BioAssayMapping - Class in org.biomage.BioAssayData
Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
BioAssayMapping() - Constructor for class org.biomage.BioAssayData.BioAssayMapping
Default constructor.
BioAssayMapping(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayMapping
Attribute constructor.
bioAssayMapping - Variable in class org.biomage.BioAssayData.Transformation
The collection of mappings for the BioAssays.
bioAssayMaps - Variable in class org.biomage.BioAssayData.BioAssayMapping
The maps for the BioAssays.
bioAssayMapTarget - Variable in class org.biomage.BioAssayData.BioAssayMap
The DerivedBioAssay that is produced by the sources of the BioAssayMap.
bioAssays - Variable in class org.biomage.BioAssayData.BioAssayDimension
The BioAssays for this Dimension
bioAssays - Variable in class org.biomage.Experiment.Experiment
The collection of BioAssays for this Experiment.
BioAssayService - Class in gov.nih.nci.caarray.services.fileparse
 
BioAssayService() - Constructor for class gov.nih.nci.caarray.services.fileparse.BioAssayService
 
BioAssayTreatment - Class in org.biomage.BioAssay
The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
BioAssayTreatment() - Constructor for class org.biomage.BioAssay.BioAssayTreatment
Default constructor.
BioAssayTreatment(Attributes) - Constructor for class org.biomage.BioAssay.BioAssayTreatment
Attribute constructor.
bioAssayTreatments - Variable in class org.biomage.BioAssay.PhysicalBioAssay
The set of treatments undergone by this PhysicalBioAssay.
BioAssayTuple - Class in org.biomage.BioAssayData
Transformed container to specify a BioAssay and the Design Elements and their data for that BioAssay.
BioAssayTuple() - Constructor for class org.biomage.BioAssayData.BioAssayTuple
Default constructor.
BioAssayTuple(Attributes) - Constructor for class org.biomage.BioAssayData.BioAssayTuple
Attribute constructor.
BioDataCube - Class in org.biomage.BioAssayData
A three-dimensional cube representation of the data.
BioDataCube() - Constructor for class org.biomage.BioAssayData.BioDataCube
Default constructor.
BioDataCube(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataCube
Attribute constructor.
BioDataCube.Order - Class in org.biomage.BioAssayData
Inner class for the enumeration values that the attribute order can assume.
BioDataCubeCreator - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
A class used to create cubes from data matrices
BioDataCubeCreator(SimpleQuantitationType[], SimpleDesignElement[], int) - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.BioDataCubeCreator
Constructor to initialize the cube to it's needed values
BioDataTuples - Class in org.biomage.BioAssayData
A relational, tuple representation of the data.
BioDataTuples() - Constructor for class org.biomage.BioAssayData.BioDataTuples
Default constructor.
BioDataTuples(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataTuples
Attribute constructor.
bioDataValues - Variable in class org.biomage.BioAssayData.BioAssayData
The data values of the BioAssayData.
BioDataValues - Class in org.biomage.BioAssayData
The actual values for the BioAssayCube.
BioDataValues() - Constructor for class org.biomage.BioAssayData.BioDataValues
Default constructor.
BioDataValues(Attributes) - Constructor for class org.biomage.BioAssayData.BioDataValues
Attribute constructor.
BioEvent - Class in org.biomage.BioEvent
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
BioEvent() - Constructor for class org.biomage.BioEvent.BioEvent
Default constructor.
BioEvent(Attributes) - Constructor for class org.biomage.BioEvent.BioEvent
Attribute constructor.
BioEvent_package - Class in org.biomage.BioEvent
An abstract class representing an event that takes sources of some type to produce a target of some type.
BioEvent_package() - Constructor for class org.biomage.BioEvent.BioEvent_package
Default constructor.
BioEvent_package(Attributes) - Constructor for class org.biomage.BioEvent.BioEvent_package
Attribute constructor.
bioEvent_package - Variable in class org.biomage.Common.MAGEJava
An abstract class representing an event that takes sources of some type to produce a target of some type.
bioMaterial - Variable in class org.biomage.Array.ManufactureLIMS
The BioMaterial used for the feature.
BioMaterial - Class in org.biomage.BioMaterial
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
BioMaterial() - Constructor for class org.biomage.BioMaterial.BioMaterial
Default constructor.
BioMaterial(Attributes) - Constructor for class org.biomage.BioMaterial.BioMaterial
Attribute constructor.
bioMaterial - Variable in class org.biomage.BioMaterial.BioMaterialMeasurement
A source BioMaterial for a treatment.
bioMaterial_list - Variable in class org.biomage.BioMaterial.BioMaterial_package
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
BioMaterial_package - Class in org.biomage.BioMaterial
The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay.
BioMaterial_package() - Constructor for class org.biomage.BioMaterial.BioMaterial_package
Default constructor.
BioMaterial_package(Attributes) - Constructor for class org.biomage.BioMaterial.BioMaterial_package
Attribute constructor.
bioMaterial_package - Variable in class org.biomage.Common.MAGEJava
The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay.
BioMaterial_package.BioMaterial_list - Class in org.biomage.BioMaterial
Inner list class for holding multiple entries for attribute bioMaterial.
BioMaterial_package.BioMaterial_list() - Constructor for class org.biomage.BioMaterial.BioMaterial_package.BioMaterial_list
 
BioMaterial_package.Compound_list - Class in org.biomage.BioMaterial
Inner list class for holding multiple entries for attribute compound.
BioMaterial_package.Compound_list() - Constructor for class org.biomage.BioMaterial.BioMaterial_package.Compound_list
 
BiomaterialAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiomaterialAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiomaterialAction
 
BiomaterialBaseForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiomaterialBaseForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BioMaterialCharacteristic - Class in org.biomage.Description.Ontology
 
BioMaterialCharacteristic() - Constructor for class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
BioMaterialCharacteristic(Attributes) - Constructor for class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
biomaterialCharacteristics_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BiomaterialCharacteristicsAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiomaterialCharacteristicsAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
BiomaterialCharacteristicsForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiomaterialCharacteristicsForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
BiomaterialConstants - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiomaterialConstants() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
BioMaterialData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioMaterialData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
BioMaterialDesc - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioMaterialDesc() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
biomaterialId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BioMaterialManagerDB - Class in gov.nih.nci.caarray.services.biomaterial
 
BioMaterialManagerDB() - Constructor for class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Default Constructor
BioMaterialManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
BioMaterialManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
BioMaterialManagerEJB - Class in gov.nih.nci.caarray.services.biomaterial.ejb
BioMaterialManagerEJB
BioMaterialManagerEJB() - Constructor for class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
BioMaterialMeasurement - Class in org.biomage.BioMaterial
A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial.
BioMaterialMeasurement() - Constructor for class org.biomage.BioMaterial.BioMaterialMeasurement
Default constructor.
BioMaterialMeasurement(Attributes) - Constructor for class org.biomage.BioMaterial.BioMaterialMeasurement
Attribute constructor.
BioMaterialParentsFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
BioMaterialParentsFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BioMaterialParentsFieldMapper
 
biomaterials - Static variable in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
biomaterials - Static variable in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
BioMaterialSearchCriteria - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioMaterialSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
BioMaterialUIUtils - Class in gov.nih.nci.caarray.ui.biomaterial
 
BioMaterialUIUtils() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BioMaterialUIUtils
 
BioMaterialUtils - Class in gov.nih.nci.caarray.services.biomaterial
 
BioMaterialView - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioMaterialView() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
biometricHeight_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricHeightUnitId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricHeightUnitName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricHeightUnits_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
Biometrics - Class in org.biomage.Description.Ontology
 
Biometrics() - Constructor for class org.biomage.Description.Ontology.Biometrics
 
BIOMETRICS_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
BiometricsData - Class in gov.nih.nci.caarray.common.data.vocab
 
BiometricsData() - Constructor for class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
biometricWeight_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricWeightUnitId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricWeightUnitName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
biometricWeightUnits_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
BioSample - Class in org.biomage.BioMaterial
BioSamples are products of treatments that are of interest.
BioSample() - Constructor for class org.biomage.BioMaterial.BioSample
Default constructor.
BioSample(Attributes) - Constructor for class org.biomage.BioMaterial.BioSample
Attribute constructor.
BIOSAMPLE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
BioSampleComparator - Class in gov.nih.nci.caarray.ui.core
 
BioSampleComparator() - Constructor for class gov.nih.nci.caarray.ui.core.BioSampleComparator
 
BioSampleData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSampleData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSampleData
 
bioSampleData - Variable in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
BioSampleDesc - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSampleDesc() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSampleDesc
 
BioSampleManagementTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
BioSampleManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
BioSampleView - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSampleView() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView
 
BioSequence - Class in org.biomage.BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence.
BioSequence() - Constructor for class org.biomage.BioSequence.BioSequence
Default constructor.
BioSequence(Attributes) - Constructor for class org.biomage.BioSequence.BioSequence
Attribute constructor.
bioSequence_list - Variable in class org.biomage.BioSequence.BioSequence_package
A BioSequence is a representation of a DNA, RNA, or protein sequence.
BioSequence_package - Class in org.biomage.BioSequence
Describes a known gene or sequence.
BioSequence_package() - Constructor for class org.biomage.BioSequence.BioSequence_package
Default constructor.
BioSequence_package(Attributes) - Constructor for class org.biomage.BioSequence.BioSequence_package
Attribute constructor.
bioSequence_package - Variable in class org.biomage.Common.MAGEJava
Describes a known gene or sequence.
BioSequence_package.BioSequence_list - Class in org.biomage.BioSequence
Inner list class for holding multiple entries for attribute bioSequence.
BioSequence_package.BioSequence_list() - Constructor for class org.biomage.BioSequence.BioSequence_package.BioSequence_list
 
BioSource - Class in org.biomage.BioMaterial
The BioSource is the original source material before any treatment events.
BioSource() - Constructor for class org.biomage.BioMaterial.BioSource
Default constructor.
BioSource(Attributes) - Constructor for class org.biomage.BioMaterial.BioSource
Attribute constructor.
BIOSOURCE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
BiosourceAddUpdateAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
BiosourceAddUpdateForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
BiosourceBaseForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceBaseForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
BioSourceData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSourceData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData
 
bioSourceData - Variable in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
BioSourceDesc - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSourceDesc() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSourceDesc
 
BiosourceDetailAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceDetailAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailAction
 
BiosourceDetailForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceDetailForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
BioSourceManagementTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
BioSourceManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
biosourceName - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
BioSourceProviderFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
BioSourceProviderFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BioSourceProviderFieldMapper
 
BiosourceSearchAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceSearchAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
BiosourceSearchForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
BiosourceSearchForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
biosourceType - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
BioSourceView - Class in gov.nih.nci.caarray.common.data.biomaterial
 
BioSourceView() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
bodyIndent - Static variable in class org.biomage.tools.generate_cpp.CreateCPPFile
 
Boolean2IntFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Boolean2IntFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Boolean2IntFieldConversion
 
both - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
bottom - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
BQD - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
BQS_package - Class in org.biomage.BQS
Allows a reference to an article, book or other publication to be specified for searching repositories.
BQS_package() - Constructor for class org.biomage.BQS.BQS_package
Default constructor.
BQS_package(Attributes) - Constructor for class org.biomage.BQS.BQS_package
Attribute constructor.
bQS_package - Variable in class org.biomage.Common.MAGEJava
Allows a reference to an article, book or other publication to be specified for searching repositories.
breaker - Static variable in class gov.nih.nci.caarray.ui.StringFormatter
 
build(Properties) - Method in class gov.nih.nci.caarray.services.security.test.MAGEMLImportSecuredElementBuilder
 
build(Properties) - Method in interface gov.nih.nci.caarray.services.security.test.SecuredElementBuilder
 
buildSecuredElement(SessionContext, String, long) - Static method in class gov.nih.nci.caarray.services.util.SecurityUtils
Creates a SecuredElementData with PROTECTION_GROUP_PRIVATE as a default group.
buildSecuredElement(String, String, long) - Static method in class gov.nih.nci.caarray.services.util.SecurityUtils
Creates a SecuredElementData with PROTECTION_GROUP_PRIVATE as a default group.
buildTables(String, Vector) - Method in class org.biomage.tools.generate_er.CreateMageER
 
bundle - Variable in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
bytesTransferred(long, int) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
callback method for copy util.

C

C - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
CAAMEL_CAARRAY_SERVERKEY - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CAAMEL_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CAARRAY_ADMIN_EMAIL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CAARRAY_DATASOURCE - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CAARRAY_DATASOURCE_PASSWORD - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CAARRAY_DATASOURCE_USER - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CaArrayArrayDesignSecurityHelper - Class in gov.nih.nci.caarray.services.arraydesign
Integrates with the caArray security subsystem.
CaArrayArrayDesignSecurityHelper() - Constructor for class gov.nih.nci.caarray.services.arraydesign.CaArrayArrayDesignSecurityHelper
 
CaArrayCache - Class in gov.nih.nci.caarray.services.util.cache
 
CaArrayCache() - Constructor for class gov.nih.nci.caarray.services.util.cache.CaArrayCache
 
CaArrayCache(String) - Constructor for class gov.nih.nci.caarray.services.util.cache.CaArrayCache
 
CaArrayCache2 - Class in gov.nih.nci.caarray.services.util.cache
 
CaArrayCache2(Cache) - Constructor for class gov.nih.nci.caarray.services.util.cache.CaArrayCache2
 
CaarrayCallBackHandler - Class in gov.nih.nci.caarray.services.security
 
CaarrayCallBackHandler(String, char[]) - Constructor for class gov.nih.nci.caarray.services.security.CaarrayCallBackHandler
 
CaArrayConstants - Class in gov.nih.nci.caarray.common.util
 
CaArrayConstants() - Constructor for class gov.nih.nci.caarray.common.util.CaArrayConstants
 
CaarrayDecorator - Class in gov.nih.nci.caarray.ui
CaarrayDecorator enables a table to have a column displaying well formated value.
CaarrayDecorator() - Constructor for class gov.nih.nci.caarray.ui.CaarrayDecorator
Default Constructor
CAArrayDesignFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
CAArrayDesignFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
CAArrayDesignFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
CAArrayDesignFileUploadEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
CaArrayLoginModule - Class in gov.nih.nci.caarray.services.security
This Custom Login module extends AbstractServerLogin Module.
CaArrayLoginModule() - Constructor for class gov.nih.nci.caarray.services.security.CaArrayLoginModule
 
CaArrayPrincipal - Class in gov.nih.nci.caarray.services.security
This class implements the Principal interface and represents a Sample user.
CaArrayPrincipal(String) - Constructor for class gov.nih.nci.caarray.services.security.CaArrayPrincipal
Create a CaArrayPrincipal with a Sample username.
CaArrayProperties - Class in gov.nih.nci.caarray.services.util.properties
 
CaArraySequenceManagerHighLowImpl - Class in gov.nih.nci.caarray.services.util.ojb
 
CaArraySequenceManagerHighLowImpl(PersistenceBroker) - Constructor for class gov.nih.nci.caarray.services.util.ojb.CaArraySequenceManagerHighLowImpl
 
CaArrayToMageConversion - Class in gov.nih.nci.caarray.services.fileparse
 
CaArrayToMageConversion() - Constructor for class gov.nih.nci.caarray.services.fileparse.CaArrayToMageConversion
 
CaArrayTransactionHandler - Class in gov.nih.nci.caarray.services.util.transaction
Integrates with the caArray transaction handling system.
CaArrayTransactionHandler() - Constructor for class gov.nih.nci.caarray.services.util.transaction.CaArrayTransactionHandler
 
cache(Identity, Object) - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
makes object obj persistent to the Objectcache under the key oid.
CAFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
CAFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
CAFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
CAFileUploadEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
CAFileUploadHistory - Class in gov.nih.nci.caarray.services.fileupload2
Uploaded file history bean Title: caArray Description: MicroArray data repository and application Copyright: (c) 2005 NCICB.
CAFileUploadHistory() - Constructor for class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Default Constructor
CAFileUploadHistoryData - Class in gov.nih.nci.caarray.common.data.fileupload2
Uploaded file history bean Title: caArray Description: MicroArray data repository and application Copyright: (c) 2005 NCICB.
CAFileUploadHistoryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Default Constructor
CAMagemlFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
CAMagemlFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
CAMagemlFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
CAMagemlFileUploadEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.AddExperimentFactorAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentAdditionalQualifierAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentContactAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentFactorAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentGeneralInfoAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentPublicationAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentQualityAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAdditionalUploadFileAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAddPublicationAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentDataProcessingAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentImportMageMLAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewAdditionalQualifierAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
cancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
cancelFileUpload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
cancelFileUpload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method is called upon cancel button press by the user to cancel upload process.
cancelModification(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
cancelModification(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
cancelModification(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
cancelModification(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
cancelThree(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
cancelToo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
cancelUpdateDetail(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
CanGetBioAssayDatum - Class in gov.nih.nci.caarray.services.util.netcdf.test.usecases
 
CanGetBioAssayDatum() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetBioAssayDatum
 
CanGetByQuantitationType - Class in gov.nih.nci.caarray.services.util.netcdf.test.usecases
 
CanGetByQuantitationType() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetByQuantitationType
 
CanParseFiles - Class in gov.nih.nci.caarray.services.fileparse.test.usecases
 
CanParseFiles() - Constructor for class gov.nih.nci.caarray.services.fileparse.test.usecases.CanParseFiles
 
canUserAccessElement(String, String, String[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Deprecated.  
canUserAccessElement(SecuredElementItf, String[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user can access the securedElemet for this Object.
canUserAccessElement(String, SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Deprecated.  
canUserAccessElement(SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessElement(SecuredElementItf[], String[], ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessElement(String, String, String[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Deprecated.  
canUserAccessElement(SecuredElementItf, String[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user can access the securedElemet for this Object.
canUserAccessElement(String, SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Deprecated.  
canUserAccessElement(SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessElement(SecuredElementItf[], String[], ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessElement(String, String, String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Deprecated.  
canUserAccessElement(SecuredElementItf, String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessElement(String, SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElemet for this Object.
canUserAccessElement(SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessElement(SecuredElementItf[], String[], ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessElement(String, String, String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Deprecated.  
canUserAccessElement(SecuredElementItf, String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessElement(String, SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElemet for this Object.
canUserAccessElement(SecuredElementItf[], String[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessElement(SecuredElementItf[], String[], ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElement for this Object.
CanUserAccessElement - Class in gov.nih.nci.caarray.services.security.test.usecases
 
CanUserAccessElement() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElement
 
CanUserAccessElementItf - Class in gov.nih.nci.caarray.services.security.test.usecases
 
CanUserAccessElementItf() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItf
 
CanUserAccessElementItfPG - Class in gov.nih.nci.caarray.services.security.test.usecases
 
CanUserAccessElementItfPG() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItfPG
 
canUserAccessOwnerElement(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElement(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElement(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElement(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElementOnly(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElementOnly(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElementOnly(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user can access the securedElement for this Object.
canUserAccessOwnerElementOnly(SecuredElementItf[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user can access the securedElement for this Object.
card - Variable in class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
CASCADE_LINK - Static variable in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
CASCADE_NONE - Static variable in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
CASCADE_OBJECT - Static variable in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
CaSecurityManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
Delegate class for security manager.
CaSecurityManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
 
CaSecurityManagerDelegate(int) - Constructor for class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Overloaded contructor to support Local/Remote EJB lookups.
CaSecurityManagerEJB - Class in gov.nih.nci.caarray.services.security.ejb
This class contains the implemention of the CaSecurityManager EJB.
CaSecurityManagerEJB() - Constructor for class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
 
CaSecurityManagerHelper - Class in gov.nih.nci.caarray.services.security
 
category - Variable in class org.biomage.Experiment.ExperimentalFactor
The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).
CATEGORY_ARRAY_DESIGN - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type that is to be parsed as an ArrayDesign.
CATEGORY_DERIVED_BIOASSAY - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type that is to be parsed as a DerivedBioAssay.
CATEGORY_MAGEML - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type that is to be parsed as MAGE-ML.
CATEGORY_MEASURED_BIOASSAY - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type that is to be parsed as a MeasuredBioAssay.
CATEGORY_NON_PARSEABLE - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type that is not be parseable but has a file extension to compare to given a file name.
CATEGORY_OTHER - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Represents a file type for those files which have a file extension that don't match any of the file types's extensions from other categories.
cc - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
CdfFileNotFoundException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix
Indicates that the Affymetrix CDF file couldn't be found at the expected location.
CdfFileNotFoundException(File) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.CdfFileNotFoundException
 
CEL_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
CELL_LINE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
CELL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
cellLine_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
CELLLINE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
cellLineId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
cellLines_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
cellType_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
CELLTYPE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
cellTypeId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
cellTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
cfgInfo - Variable in class org.biomage.tools.generate_classes.CreateMageDTDClasses
 
change - Variable in class org.biomage.Measurement.Measurement.Type
 
changeButtonOn(boolean, boolean) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
 
Channel - Class in org.biomage.BioAssay
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
Channel() - Constructor for class org.biomage.BioAssay.Channel
Default constructor.
Channel(Attributes) - Constructor for class org.biomage.BioAssay.Channel
Attribute constructor.
channel - Variable in class org.biomage.QuantitationType.QuantitationType
The optional channel associated with the QuantitationType.
channel_list - Variable in class org.biomage.BioAssay.BioAssay_package
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
channels - Variable in class org.biomage.BioAssay.BioAssay
Channels can be non-null for all subclasses.
channels - Variable in class org.biomage.BioAssay.Image
The channels captured in this image.
characteristics - Variable in class org.biomage.BioMaterial.BioMaterial
Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.
characteristics_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
characters(char[], int, int) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
characters(char[], int, int) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
charList_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
checkAdminRole(String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
 
checkBatchDownloadFile(long, String) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
checkBatchDownloadFile(long, String) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Check Batch Download Files are existing or not.
checkEntryName(String, String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
checkFileExtension(FormFile, int) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
checkHardwareInUse(long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
 
CheckRelationship(Vector, String, boolean) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: check to see if there is the case that A has two one_to_many relationships with B and get the same name
checkSecurity(Extendable, String[]) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
Check if the user is authorized to access this object
checkSecurityForUpdate(long, Class, String[], ManagerDB) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
checkSecurityForUpdate(Object, String[]) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
checkSelectedItem() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.ProcessDuplicatedFileName
 
checkSoftwareInUse(long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
 
childIdentifier - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
 
childType - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
 
CHP_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
CHROMOSOMAL_ABERRATION_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
CHROMOSOMAL_ABERRATION_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ChromosomalAberration - Class in org.biomage.Description.Ontology
 
ChromosomalAberration() - Constructor for class org.biomage.Description.Ontology.ChromosomalAberration
 
ChromosomalAberrationData - Class in gov.nih.nci.caarray.common.data.vocab
 
ChromosomalAberrationData() - Constructor for class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData
 
chromosomalAberrationDescription_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
chromosomalAberrations_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
chromosomalAberrationTypeId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
chromosomalAberrationTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
CLASS - Static variable in class gov.nih.nci.caarray.services.security.test.SecurityTester
 
classConstructorMap - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
classConstructorMap - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
classDoc - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Documentation for this class.
classExists(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
ClassGenerator - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
ClassGenerator.DirectLoader - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
Simple loader for constructed classes.
ClassGenerator.DirectLoader() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.ClassGenerator.DirectLoader
 
classInfo - Variable in class org.biomage.tools.helpers.OntologyHelper.InstanceInformation
 
ClassMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
This class performs the mapping of a source object to a target object.
ClassMapper(ClassMapperRepository, Class, Class) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
ClassMapperRepository - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
ClassMapperRepository.ConvertField - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
ClassMapperRepository.ConvertField() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
ClassMapperRepository.DTOClass - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
ClassMapperRepository.DTOClass() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.DTOClass
 
ClassMapperRepository.TargetClass - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
ClassMapperRepository.TargetClass() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.TargetClass
 
className - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Class name.
className - Variable in class org.biomage.tools.helpers.OntologyHelper.InstanceInformation
 
clean() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
empty the list of files selected.
cleanLog() - Static method in class org.biomage.tools.apps.annot.MageXMLConverter
 
cleanUp(Vector) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
This method is called to removed all temporary zip files after they have been uploaded from the temp directory.
cleanUp() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
This method is the actual implementation of the cleanup process.
cleanUp() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
Delete temp zip files
clear() - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
clear the ObjectCache.
clear() - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCachePerClassImpl
Clears the cache
clear() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
Used by the action classes to clear the form attributes
clear() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm
 
clearBiomaterialFromCache(BioMaterial) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Recursively removes a biomaterial and all it's parents from the cache, to be used after copying to make sure you get the latest copy from the database
clearBioMatSearchPage(HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
clearCache() - Method in class gov.nih.nci.caarray.services.hybridization.DbFileUploadEntrySaver
 
clearCache() - Method in interface gov.nih.nci.caarray.services.hybridization.FileUploadEntrySaver
 
clearCache() - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
Flushes the OJB cache so that any updated data may be found after a caAMEL MAGE-ML import is performed.
clearCache() - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
clears the cache Fix for TT13110
clearFileUploadEntries() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
Clear the file upload entry data from the session Clear the list for next batch of file upload
clearList(String, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
clearList(Class, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
clearList() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
Upon calling file parsing service, the content of the fileList is passed to the parsing object, and this list is cleared for accepting next batch of file upload.
clearList() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
Upon calling file parsing service, the content of the fileList is passed to the parsing object, and this list is cleared for accepting next batch of file upload.
clearOldLists(HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
clearOldLists(HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
clearOldLists(HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
CLINICAL_HISTORY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
CLINICAL_TEST_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
CLINICAL_TREATMENT_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
clinicalHistory_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
clinicalTest_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
clinicalTreatment_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
close() - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Close persistence resources.
close() - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Close persistence resources.
close() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
close() - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Close persistence resources.
close() - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
close() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileWriter
Close the output file stream and finish writing.
close() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
close() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Close persistence resources.
close() - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
 
close() - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Close database connection.
closeRequest() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
closeStream() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
 
clusterBioAssayData - Variable in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
The BioAssayData whose values were used by the cluster algorithm.
cm - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
CollectionField - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
CollectionField(String, Class, List, Class) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.CollectionField
 
columnDelimiter_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTableMap
 
COMMA_SEPARATED - Static variable in interface gov.nih.nci.caarray.services.util.file.LineSplitter
 
commit() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
This method is called if the LoginContext's overall authentication succeeded (the relevant REQUIRED, REQUISITE, SUFFICIENT and OPTIONAL LoginModules succeeded).
commit() - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
commitTransaction() - Method in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
commitTransaction() - Method in class gov.nih.nci.caarray.services.util.transaction.CaArrayTransactionHandler
 
commitTransaction() - Method in interface gov.nih.nci.caarray.services.util.transaction.TransactionHandler
 
compare(BioMaterial, BioMaterialData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
compare(BioMaterial, BioMaterialDesc) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
compare(Contact, ContactData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
compare(Person, PersonData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
compare(Experiment, ExperimentData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(Experiment, ExperimentView) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(OntologyEntry, AdditionalQualifierData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(BibliographicReference, PublicationData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(Description, QualityControlData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(ExperimentalFactor, ExperimentalFactorData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
compare(Parameter, ParameterData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
compare(Measurement, MeasurementData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
compare(ProtocolApplication, ProtocolApplicationData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
compare(Treatment, TreatmentData) - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestTreatmentConversion
 
compare(OntologyEntry, VocabData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
compare(Object, Object) - Method in class gov.nih.nci.caarray.ui.core.BioSampleComparator
 
compare(Object, Object) - Method in class gov.nih.nci.caarray.ui.core.DatabaseComparator
 
compare(Object, Object) - Method in class gov.nih.nci.caarray.ui.core.OrganizationComparator
 
compare(Object, Object) - Method in class gov.nih.nci.caarray.ui.core.PersonComparator
 
compare(Object, Object) - Method in class gov.nih.nci.caarray.ui.core.VisibilityComparator
 
compare(Object, Object) - Method in class org.biomage.tools.generate_java.CreateJavaFile.rankComparator
 
compareTo(Object) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
compareTo(Object) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
compareTo(Object) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
compareTo(Object) - Method in class org.biomage.BioMaterial.BioSample
equal method to be used by a set for comparison.
compareTo(Object) - Method in class org.biomage.BioMaterial.BioSource
equal method to be used by a set for comparison.
compareTo(Object) - Method in class org.biomage.BioMaterial.LabeledExtract
equal method to be used by a set for comparison.
componentCompounds - Variable in class org.biomage.BioMaterial.Compound
The Compounds and their amounts used to create this Compound.
composite - Variable in class org.biomage.DesignElement.CompositePosition
A source CompositeSequence that is part of a target CompositeSequence
COMPOSITE - Static variable in class org.biomage.tools.generate_classes.XMIParseHelpers
Is solely owned by a containing object
CompositeCompositeMap - Class in org.biomage.DesignElement
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
CompositeCompositeMap() - Constructor for class org.biomage.DesignElement.CompositeCompositeMap
Default constructor.
CompositeCompositeMap(Attributes) - Constructor for class org.biomage.DesignElement.CompositeCompositeMap
Attribute constructor.
compositeCompositeMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence.
CompositeGroup - Class in org.biomage.ArrayDesign
Allows specification of the type of Composite Design Element.
CompositeGroup() - Constructor for class org.biomage.ArrayDesign.CompositeGroup
Default constructor.
CompositeGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.CompositeGroup
Attribute constructor.
compositeGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
Allows specification of the type of Composite Design Element.
CompositeGroupData - Class in gov.nih.nci.caarray.common.data.arraydesign
 
CompositeGroupData() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
CompositeGroupDesc - Class in gov.nih.nci.caarray.common.data.arraydesign
 
CompositeGroupDesc() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
CompositeGroupManagerDB - Class in gov.nih.nci.caarray.services.arraydesign
 
CompositeGroupManagerDB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
 
compositeGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
The grouping of like CompositeSequence together.
CompositeGroupSearchCriteria - Class in gov.nih.nci.caarray.common.data.arraydesign
 
CompositeGroupSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
CompositePosition - Class in org.biomage.DesignElement
The location in the compositeSequence target's sequence to which a source compositeSequence maps.
CompositePosition() - Constructor for class org.biomage.DesignElement.CompositePosition
Default constructor.
CompositePosition(Attributes) - Constructor for class org.biomage.DesignElement.CompositePosition
Attribute constructor.
compositePositionSources - Variable in class org.biomage.DesignElement.CompositeCompositeMap
Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.
compositeSequence - Variable in class org.biomage.DesignElement.CompositeCompositeMap
A map to the compositeSequences that compose this CompositeSequence.
CompositeSequence - Class in org.biomage.DesignElement
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
CompositeSequence() - Constructor for class org.biomage.DesignElement.CompositeSequence
Default constructor.
CompositeSequence(Attributes) - Constructor for class org.biomage.DesignElement.CompositeSequence
Attribute constructor.
compositeSequence - Variable in class org.biomage.DesignElement.ReporterCompositeMap
A map to the reporters that compose this CompositeSequence.
compositeSequence_list - Variable in class org.biomage.DesignElement.DesignElement_package
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
CompositeSequenceData - Class in gov.nih.nci.caarray.common.data.designelement
 
CompositeSequenceData() - Constructor for class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceData
 
CompositeSequenceDesc - Class in gov.nih.nci.caarray.common.data.designelement
 
CompositeSequenceDesc() - Constructor for class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
CompositeSequenceDimension - Class in org.biomage.BioAssayData
Specialized DesignElementDimension to hold CompositeSequences.
CompositeSequenceDimension() - Constructor for class org.biomage.BioAssayData.CompositeSequenceDimension
Default constructor.
CompositeSequenceDimension(Attributes) - Constructor for class org.biomage.BioAssayData.CompositeSequenceDimension
Attribute constructor.
compositeSequences - Variable in class org.biomage.ArrayDesign.CompositeGroup
The compositeSequences that belong to this group.
compositeSequences - Variable in class org.biomage.BioAssayData.CompositeSequenceDimension
The CompositeSequences for this Dimension.
Compound - Class in org.biomage.BioMaterial
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
Compound() - Constructor for class org.biomage.BioMaterial.Compound
Default constructor.
Compound(Attributes) - Constructor for class org.biomage.BioMaterial.Compound
Attribute constructor.
compound - Variable in class org.biomage.BioMaterial.CompoundMeasurement
A Compound to be used to create another Compound.
compound_list - Variable in class org.biomage.BioMaterial.BioMaterial_package
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate).
CompoundAttrsProperties - Class in gov.nih.nci.caarray.services.util.properties
 
CompoundAttrsProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.CompoundAttrsProperties
 
compoundIndices - Variable in class org.biomage.BioMaterial.Compound
Indices into common Compound Indices, such as the Merck Index, for this Compound.
CompoundMeasurement - Class in org.biomage.BioMaterial
A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.
CompoundMeasurement() - Constructor for class org.biomage.BioMaterial.CompoundMeasurement
Default constructor.
CompoundMeasurement(Attributes) - Constructor for class org.biomage.BioMaterial.CompoundMeasurement
Attribute constructor.
CompoundMeasurementData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
CompoundMeasurementData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData
 
compoundMeasurements - Variable in class org.biomage.BioMaterial.Treatment
The compounds and their amounts used in the treatment.
compressHybridizationFiles(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
computational - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
concentration - Variable in class org.biomage.Measurement.Measurement.KindCV
 
ConcentrationUnit - Class in org.biomage.Measurement
Concentration
ConcentrationUnit() - Constructor for class org.biomage.Measurement.ConcentrationUnit
Default constructor.
ConcentrationUnit(Attributes) - Constructor for class org.biomage.Measurement.ConcentrationUnit
Attribute constructor.
ConcentrationUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
concreteSubClassNames - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Vector of the instantiable subclass names.
ConfidenceIndicator - Class in org.biomage.QuantitationType
Indication of some measure of confidence for a standard quantitation type.
ConfidenceIndicator() - Constructor for class org.biomage.QuantitationType.ConfidenceIndicator
Default constructor.
ConfidenceIndicator(Attributes) - Constructor for class org.biomage.QuantitationType.ConfidenceIndicator
Attribute constructor.
confidenceIndicators - Variable in class org.biomage.QuantitationType.QuantitationType
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
ConfigurationException - Exception in gov.nih.nci.caarray.services.exception
 
ConfigurationException() - Constructor for exception gov.nih.nci.caarray.services.exception.ConfigurationException
 
ConfigurationException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.ConfigurationException
 
ConfigurationException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.ConfigurationException
 
ConfigurationException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.ConfigurationException
 
configure(InputStream) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
CONNECTION_FACTORY_NAME - Static variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
CONNECTION_FACTORY_NAME - Static variable in class gov.nih.nci.caarray.services.security.mageom.SecuredElementUpdateListener
 
conref(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
conrefVectorize(String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
constraintInformation(Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains constraint information and puts it on a map keyed by the association end element id.
Contact - Class in org.biomage.AuditAndSecurity
A contact is either a person or an organization.
Contact() - Constructor for class org.biomage.AuditAndSecurity.Contact
Default constructor.
Contact(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Contact
Attribute constructor.
Contact - Class in org.biomage.tools.apps.annot.pages
 
Contact() - Constructor for class org.biomage.tools.apps.annot.pages.Contact
 
contact_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
A contact is either a person or an organization.
ContactData - Class in gov.nih.nci.caarray.common.data.contact
 
ContactData() - Constructor for class gov.nih.nci.caarray.common.data.contact.ContactData
 
ContactManagementTest - Class in gov.nih.nci.caarray.services.contact.test
 
ContactManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
ContactManagerDB - Class in gov.nih.nci.caarray.services.contact
 
ContactManagerDB() - Constructor for class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
ContactManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
ContactManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
ContactManagerEJB - Class in gov.nih.nci.caarray.services.contact.ejb
This class contains the implemention of the ContactManagerEJB.
ContactManagerEJB() - Constructor for class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
contacts - Variable in class org.biomage.Description.Database
Information on the contacts for the database
ContactsAction - Class in gov.nih.nci.caarray.ui.contact
 
ContactsAction() - Constructor for class gov.nih.nci.caarray.ui.contact.ContactsAction
 
ContactUtils - Class in gov.nih.nci.caarray.services.contact
 
containedFeatures - Variable in class org.biomage.BioAssayData.FeatureDimension
The features for this dimension.
containsFile(HybridizationFileUploadEntrySummaryData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
containsKey(Object) - Static method in class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
 
containsValue(Object) - Method in class org.biomage.tools.xmlutils.MultiHashMap
containsValue(Object) - Method in class org.biomage.tools.xmlutils.MultiHashtable
context() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
contextDestroyed(ServletContextEvent) - Method in class gov.nih.nci.caarray.services.util.db.OjbInitializer
 
contextInitialized(ServletContextEvent) - Method in class gov.nih.nci.caarray.services.util.db.OjbInitializer
 
controlType - Variable in class org.biomage.DesignElement.DesignElement
If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
convertFactorValueMeasurementsToValues(Experiment) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
convertSizeToBytes(String, long) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Converts a size value from a string representation to its numeric value.
coordinate - Variable in class org.biomage.BioSequence.SeqFeatureLocation
At which base pairs or amino acid this SeqFeature begins and ends.
copied - Variable in class org.biomage.BioMaterial.BioMaterial
caARRAY internal flag to indicate if this BioMaterial is generated by copy of existing biomaterial.
copy(ArrayData, Array) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(Array, ArrayData) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(ArrayGroupData, ArrayGroup) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(ArrayGroupData, Array) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy DTO ArrayGroupData to MAGE Array.
copy(ArrayGroup, ArrayGroupData) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(ArrayGroup, ArrayGroupDesc) - Static method in class gov.nih.nci.caarray.services.array.ArrayUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(ArrayDesignData, PhysicalArrayDesign) - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(PhysicalArrayDesign, ArrayDesignData) - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(PhysicalArrayDesign, ArrayDesignDesc) - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignUtils
 
copy(DesignProviderRole, DesignProviderRoleData) - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignUtils
 
copy(DesignProviderRoleData, DesignProviderRole) - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignUtils
 
copy(BioSourceData, BioSource) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSource, BioSourceData) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSource, BioSourceView) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSource, BioSourceDesc) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSampleData, BioSample) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSample, BioSampleData) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSample, BioSampleDesc) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(BioSample, BioSampleView) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(LabeledExtractData, LabeledExtract) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(LabeledExtract, LabeledExtractDesc) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(LabeledExtract, LabeledExtractData) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(LabeledExtract, LabeledExtractView) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(TreatmentData, Treatment) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(Treatment, TreatmentData) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(Measurement, MeasurementData) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(MeasurementData, Measurement) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
copy(Organization, OrganizationData) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(Organization, OrganizationDesc) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(OrganizationData, Organization) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(Person, PersonData) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(Person, PersonDesc) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(PersonData, Person) - Static method in class gov.nih.nci.caarray.services.contact.ContactUtils
 
copy(ExperimentData, Experiment) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(Experiment, ExperimentData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(Experiment, ExperimentDesc) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(Experiment, ExperimentShortDesc) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(PublicationData, BibliographicReference) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(BibliographicReference, PublicationData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(AdditionalQualifierData, OntologyEntry) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(OntologyEntry, AdditionalQualifierData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(QualityControlData, Description) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(Description, QualityControlData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(ExperimentalFactorData, ExperimentalFactor) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(ExperimentalFactor, ExperimentalFactorData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(FactorValueData, FactorValue) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(FactorValue, FactorValueData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(Experiment, ExperimentView) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(AdditionalDataProcessing, AdditionalDataProcessingData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(AdditionalDataProcessingData, AdditionalDataProcessing) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(AdditionalUploadedFile, AdditionalUploadedFileData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(AdditionalUploadedFileData, AdditionalUploadedFile) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(HybridizationFileUpload, HybridizationFileUploadData) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(HybridizationFileUploadData, HybridizationFileUpload) - Static method in class gov.nih.nci.caarray.services.experiment.ExperimentUtils
 
copy(HybridizationFileUploadGroupData, HybridizationFileUploadGroup) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileUploadGroup, HybridizationFileUploadGroupData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileUploadGroupData, HybridizationFileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
Use the same conversion mapping to populate HybridizationFileUploadEntry.measuredBioAssay with attributes from HybridizationFileUploadGroupData (not HybridizationFileUploadEntry) as the group defines common attributes of the entries
copy(MAGEMLFileUploadEntry, MAGEMLFileUploadEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(MAGEMLFileUploadEntryData, MAGEMLFileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileUploadEntryData, HybridizationFileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(FileUploadEntryData, FileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(FileUploadEntry, FileUploadEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(FileUploadHistory, FileUploadHistoryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileUploadEntry, HybridizationFileUploadEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileUploadEntry, HybridizationFileUploadEntrySummaryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileParsingEntryData, HybridizationFileParsingEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(HybridizationFileParsingEntry, HybridizationFileParsingEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileUploadGroupData, ArrayDesignFileUploadGroup) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileUploadGroup, ArrayDesignFileUploadGroupData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileUploadGroupData, ArrayDesignFileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileUploadEntryData, ArrayDesignFileUploadEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileUploadEntry, ArrayDesignFileUploadEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileParsingEntryData, ArrayDesignFileParsingEntry) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ArrayDesignFileParsingEntry, ArrayDesignFileParsingEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
copy(ProtocolData, Protocol) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(Protocol, ProtocolData) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types.
copy(Protocol, ProtocolDesc) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(HardwareData, Hardware) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(Hardware, HardwareData) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(Hardware, HardwareDesc) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(SoftwareData, Software) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(Software, SoftwareData) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(Software, SoftwareDesc) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(ParameterData, Parameter) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(Parameter, ParameterData) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(ProtocolApplication, ProtocolApplicationData) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(ProtocolApplicationData, ProtocolApplication) - Static method in class gov.nih.nci.caarray.services.protocol.ProtocolUtils
 
copy(OntologyEntry, VocabData) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(OntologyEntry, VocabDesc) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(VocabData, OntologyEntry) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(ActionProtocolTypeMapData, ActionProtocolTypeMap) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(ActionProtocolTypeMap, ActionProtocolTypeMapData) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(Database, DatabaseData) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copy(DatabaseData, Database) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
copyArray(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyAction
 
copyBioMaterial(long, Class, String, String) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
copyBioMaterial(BioMaterial, Class, String, String) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Recursively copies the whole biomaterial tree Move heirarchicaly fromtop down.
copyFromData(CAArrayDesignFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
copyFromData(CAFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
copyFromData(CAFileUploadHistoryData) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
 
copyFromData(CAMagemlFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
copyLabeledExtract(long, String) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
copyLabeledExtract(long, String) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Makes a copy of the given biomaterial including all the associated parent objects and treatments recursively.
countHybridizationFileUploadEntries(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
countHybridizationFileUploadEntries(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
countHybridizationFileUploads(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
Deprecated. This method was replaced by countHybridizationFileUploadEntries for the redesigned
countMessages(String) - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
countObjects(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Count the number of objects that match the specified Query.
countObjects(Query, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Count the number of objects that match the specified Query.
countOntologies(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
countProtocolApplications(long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Counts how many ProtocolApplication are using the specified Protocol.
countVocabDropdownItems(String, boolean) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
countVocabularies(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
countVocabularies(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
Counts the number of vocabularies that have the specified category.
cppBodyIndent - Static variable in class org.biomage.tools.helpers.StringOutputHelpers
 
create(PhysicalArrayDesign, String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Saves a new array design to the database.
create(PhysicalArrayDesign, String) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
create(String, ArrayDesignDataSource) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.AffymetrixArrayDesignLoader
 
create(File, ArrayDesignDataSource) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.AffymetrixArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGalArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGprArrayDesignLoader
 
create(File, ArrayDesignDataSource) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGalArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprArrayDesignLoader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractIlluminaCsvReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.TabDelimitedTxtReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
create(File) - Static method in class gov.nih.nci.caarray.services.bioassaydata.reader.WhiteSpaceDelimitedTxtReader
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
Create an object which properties has the value provided by the specified objects as mapped by mapper-repository.xml
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.BibliographicReferenceAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.DefaultAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.ExperimentAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadEntryAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.MeasuredBioAssayAssembler
 
create(Object[]) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.TreatmentAssembler
 
create(Object[], Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
Create an object of the specified class which data is provided by the specified source objects.
create(Object, Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
 
create(Element, Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
 
createAccess(Class, Method, Method, String) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.BCELCalls
Create access class for getting and setting a bean-style property value.
createAccess(Class, Method, Method, String) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.JavassistCalls
Create access class for getting and setting a bean-style property value.
createAccess(Class, Method, Method, String) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls
Create access class for getting and setting a bean-style property value.
createArrayDesign(ArrayDesignType, String, String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Creates a new array design.
createArrayDesignFileUploadGroup(String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
createArrayDesignFileUploadGroup(String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
createArrayDesignFileUploadGroupData(String) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
createAssociationStack() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the Associations Stack.
createAssociationStack() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the Associations Stack.
createAttrs(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the attribute entity for the class.
createAttrsEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the attribute entity for the class.
createBasicDynaBeanClass(String, String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
 
createBioAssayData(Long, Long, DesignElement[], QuantitationType[], Long) - Method in class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
createBioAssayData(long, long, long, DesignElement[], QuantitationType[]) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationManagerDB
 
createChoices(StringBuffer, Vector, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates all the possibilities of ordering the vector of choices.
createClassConstructorMap() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the Class->Constructor Map.
createClassConstructorMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the Class->Constructor Map.
createClassesEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the classes entity and, if not owned, the ref entity.
createClassesOrRefEntity(StringBuffer, String) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates either classes entity or the ref entity, depending on adornment parameter.
CreateClassFile - Class in org.biomage.tools.generate_classes
Description: Class that is resposible for generating a java file for the class represented by the class node passed into the constructor.
CreateClassFile(Element, Element, Map, Map, Map, Map, Map, Map) - Constructor for class org.biomage.tools.generate_classes.CreateClassFile
Description: Constructor for the class file generator.
CreateClassFile(String, String, String, int) - Constructor for class org.biomage.tools.generate_classes.CreateClassFile
Description: Constructor for the class file generator.
CreateClassFile() - Constructor for class org.biomage.tools.generate_classes.CreateClassFile
Description: Default Constructor for the class file generator.
CreateClassFile.DataTypeAttrInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold datatype attribute information.
CreateClassFile.DataTypeAttrInformation(String, String, String, String, String, boolean) - Constructor for class org.biomage.tools.generate_classes.CreateClassFile.DataTypeAttrInformation
Description: C'tor for class.
CreateClassFile.MethodInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold method information.
CreateClassFile.MethodInformation(Element, Map, Map, Map, Map) - Constructor for class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: C'tor for class.
CreateClassFile.MethodInformation.ParamInfo - Class in org.biomage.tools.generate_classes
Description: Inner class to hold parameter information.
CreateClassFile.MethodInformation.ParamInfo(Element, Map, Map, Map, Map) - Constructor for class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation.ParamInfo
Description: C'tor for class.
createClassFiles(Element, Map, Map, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: For each class in the XMI, will create a CreateClassFile object and place it on the return Vector.
createComment() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the documentation for the class.
createContainer(CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the name of the container for the association passed in.
createContent(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the content entity for the class.
createContentEntity(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the content entity for the class.
CreateCPPFile - Class in org.biomage.tools.generate_cpp
 
CreateCPPFile() - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile
 
CreateCPPFile.AssignmentWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the Assignment operator to the CPP file.
CreateCPPFile.AssignmentWriter(FileWriter, CreateFile) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
CreateCPPFile.ClassDeclWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the class declaration out to the file.
CreateCPPFile.ClassDeclWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.ClassDeclWriter
 
CreateCPPFile.ConstructorBodyWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the copy constructor body needed into the CPP file.
CreateCPPFile.ConstructorBodyWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorBodyWriter
 
CreateCPPFile.ConstructorWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the copy constructor header needed into the CPP file.
CreateCPPFile.ConstructorWriter(FileWriter, CreateFile) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
CreateCPPFile.DataMemberWriter - Class in org.biomage.tools.generate_cpp
Description: Writes out the data members of the Class in the Header File.
CreateCPPFile.DataMemberWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
CreateCPPFile.EquivalenceWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the =='s operator to the CPP file.
CreateCPPFile.EquivalenceWriter(FileWriter, CreateFile) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
CreateCPPFile.GetAndSetWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the attribute set and get methods to the C++ header file.
CreateCPPFile.GetAndSetWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
CreateCPPFile.ImportWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the correct includes needed in the header files.
CreateCPPFile.ImportWriter(FileWriter, CreateFile) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
CreateCPPFile.IncludeWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the includes that we need into the CPP file.
CreateCPPFile.IncludeWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.IncludeWriter
 
CreateCPPFile.RemoveFromWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the RemoveFrom function to the CPP file.
CreateCPPFile.RemoveFromWriter(FileWriter) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.RemoveFromWriter
 
CreateCPPFile.specificWriter - Class in org.biomage.tools.generate_cpp
Description: An abstract class used to in conjuction with the LoopNames function that reads through all the attributes and assocations.
CreateCPPFile.specificWriter() - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
CreateCPPFile.TemplateWriter - Class in org.biomage.tools.generate_cpp
Description: Writes the correct template needed in the header files.
CreateCPPFile.TemplateWriter(FileWriter, CreateFile) - Constructor for class org.biomage.tools.generate_cpp.CreateCPPFile.TemplateWriter
 
createDataHandlerDataSourceManagerDB() - Method in class gov.nih.nci.caarray.services.bioassaydata.IlluminaDbDataHanderDataSource
 
createDataTableRowBeanClass() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
createDerivedBioAssay(Long, Long) - Method in class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
createDerivedBioAssay(long, long) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationManagerDB
Creates a DerivedBioAssay that is derived from the specified MeasuredBioAssay.
createDesignElementDimension(Long, UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in class gov.nih.nci.caarray.services.bioassaydata.DesignElementDimensionCreator
 
CreateDocFile - Class in org.biomage.tools.generate_doc
 
CreateDocFile(Vector, String, String) - Constructor for class org.biomage.tools.generate_doc.CreateDocFile
Description: Constructor for the Doc file generator.
createElementAndAttlist(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: If not owned, creates the *_ref element and attlist then creates the element and attlist declarations for the class.
createElementAndAttlists() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the different element and attlist declarations for the class.
createEntities() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the different entities for the class.
createFieldMapper(ClassMapper, Class, String, Class, List, Class, String, Class, List, Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
CreateFile - Class in org.biomage.tools.generate_classes
Description: Base Class for other classes to generate files.
CreateFile() - Constructor for class org.biomage.tools.generate_classes.CreateFile
 
CreateFile.AssociationAttrInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold association attribute information.
CreateFile.AssociationAttrInformation(String, String, String, String, int, int, int, int, int, boolean, Integer, boolean, boolean, boolean, boolean) - Constructor for class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: C'tor for class.
CreateFile.AssociationAttrInformation(CreateFile.AssociationAttrInformation, Integer) - Constructor for class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: C'tor for class.
CreateFile.AssociationAttrInformation(CreateFile.AssociationAttrInformation, Integer, int, int, int, int, boolean, boolean) - Constructor for class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: C'tor for class.
CreateFile.AttrInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold attribute information.
CreateFile.AttrInformation(String, String, String, String) - Constructor for class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: C'tor for class.
CreateFile.IdentifierAttrInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold association attribute information.
CreateFile.IdentifierAttrInformation(CreateFile, boolean) - Constructor for class org.biomage.tools.generate_classes.CreateFile.IdentifierAttrInformation
Description: C'tor for class.
CreateFile.RoleInformation - Class in org.biomage.tools.generate_classes
 
CreateFile.RoleInformation(int, int) - Constructor for class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
createHybridizationFileUploadGroup(String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
createHybridizationFileUploadGroup(String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
createHybridizationFileUploadGroupData(String) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
createIdentifierMap() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the String->Object (identifiers->identified objects) Map.
createIdentifierMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the String->Object (identifiers->identified objects) Map.
createIndex(AssociationColumn, String, String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create a Index object for a foreign key fk_oto does not have index fk_mto has index fk_mtm has index
CreateInterfaceFile - Class in org.biomage.tools.generate_classes
Description: Class that is responsible for generating a java file for the interface represented by the association end node passed into the constructor.
CreateInterfaceFile(String, Element, Map, Map) - Constructor for class org.biomage.tools.generate_classes.CreateInterfaceFile
Description: Constructor for the interface file generator.
createInterfaceFiles(Map, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: For each interface name, create a CreateInterfaceFile object.
CreateJavaClasses - Class in org.biomage.tools.generate_java
 
CreateJavaClasses() - Constructor for class org.biomage.tools.generate_java.CreateJavaClasses
Description: Constructor for the CreateJavaClasses object.
CreateJavaClassFile - Class in org.biomage.tools.generate_java
Description: Base Class for other classes to generate Java class files.
CreateJavaClassFile(CreateFile) - Constructor for class org.biomage.tools.generate_java.CreateJavaClassFile
 
CreateJavaClassFile.WriteDataAttrInformation - Class in org.biomage.tools.generate_java
Description: Inner class to write attribute information.
CreateJavaClassFile.WriteDataAttrInformation() - Constructor for class org.biomage.tools.generate_java.CreateJavaClassFile.WriteDataAttrInformation
Description: C'tor for class.
CreateJavaFile - Class in org.biomage.tools.generate_java
Description: Base Class for other classes to generate Java class files.
CreateJavaFile(CreateFile) - Constructor for class org.biomage.tools.generate_java.CreateJavaFile
 
CreateJavaFile.rankComparator - Class in org.biomage.tools.generate_java
Description: An inner class which implements the Comparator Interface.
CreateJavaFile.rankComparator() - Constructor for class org.biomage.tools.generate_java.CreateJavaFile.rankComparator
 
CreateJavaFile.WriteAssociationAttrInformation - Class in org.biomage.tools.generate_java
Description: Inner class to hold association attribute information.
CreateJavaFile.WriteAssociationAttrInformation() - Constructor for class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: C'tor for class.
CreateJavaFile.WriteAttrInformation - Class in org.biomage.tools.generate_java
Description: Inner class to write attribute information.
CreateJavaFile.WriteAttrInformation() - Constructor for class org.biomage.tools.generate_java.CreateJavaFile.WriteAttrInformation
Description: C'tor for class.
CreateJavaFile.WriteRoleInformation - Class in org.biomage.tools.generate_java
 
CreateJavaFile.WriteRoleInformation(CreateFile.RoleInformation) - Constructor for class org.biomage.tools.generate_java.CreateJavaFile.WriteRoleInformation
 
CreateJavaMAGEFile - Class in org.biomage.tools.generate_java
Description:
CreateJavaMAGEFile(CreateFile, Vector) - Constructor for class org.biomage.tools.generate_java.CreateJavaMAGEFile
 
CreateJavaPackageFile - Class in org.biomage.tools.generate_java
Description: Base Class for other classes to generate Java class files.
CreateJavaPackageFile(CreateFile) - Constructor for class org.biomage.tools.generate_java.CreateJavaPackageFile
 
createLinkColumn(String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create a column for a linking table
createLinkingKey(AssociationColumn, AssociationColumn) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create a linkingKey object and set into the table
createLinkingTable(CreateFile, String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create a linking table
createMage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
CreateMageClasses - Class in org.biomage.tools.generate_classes
 
CreateMageClasses(String[]) - Constructor for class org.biomage.tools.generate_classes.CreateMageClasses
Description: Constructor for the CreateMageJavaClasses object.
CreateMageClasses.CreateClassTransformer - Interface in org.biomage.tools.generate_classes
Description: An interface implemented by classes that take a class list and transform the members by either changing the relationships or adding or subtracting classes.
CreateMageClassFileList - Class in org.biomage.tools.generate_classes
 
CreateMageClassFileList() - Constructor for class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Constructor for the CreateMageJavaClasses object.
CreateMageClassFileList.AssociationInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold the association and which association end is the "owner".
CreateMageClassFileList.ExtendedAssociation - Class in org.biomage.tools.generate_classes
Description: Allows a chain of associations to be built.
CreateMageClassFileList.ExtendedAssociation() - Constructor for class org.biomage.tools.generate_classes.CreateMageClassFileList.ExtendedAssociation
 
CreateMageClassFileList.ExtensionMechanisms - Class in org.biomage.tools.generate_classes
Description: Inner class to hold the extension information from the xml.
CreateMageClassFileList.PackageInformation - Class in org.biomage.tools.generate_classes
Description: Inner class to hold the package information from the xml.
CreateMageDTDClasses - Class in org.biomage.tools.generate_classes
 
CreateMageDTDClasses(String[]) - Constructor for class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Constructor for the CreateMageDTDClasses object.
CreateMageER - Class in org.biomage.tools.generate_er
 
CreateMageER() - Constructor for class org.biomage.tools.generate_er.CreateMageER
Description: Constructor for the CreateMageER object.
CreateMAGEFile - Class in org.biomage.tools.generate_classes
Description: Class that is resposible for generating a java file for the class represented by the class node passed into the constructor.
CreateMAGEFile(Vector, Element) - Constructor for class org.biomage.tools.generate_classes.CreateMAGEFile
Description: Constructor for the MAGE file generator.
createMAGEJava() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the MAGEJava object.
createMAGEJava() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the MAGEJava object.
createMAGEObject(String, Attributes) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
createMAGEObject(String, Attributes) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
createMethodsMap() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the String->Method MultiMap.
createMethodsMap() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the String->Method MultiMap.
createMGEDMeasurementRestriction(String, OntologyEntry, OntologyEntry) - Static method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
CreateObjectException - Exception in gov.nih.nci.caarray.services.exception
 
CreateObjectException() - Constructor for exception gov.nih.nci.caarray.services.exception.CreateObjectException
 
CreateObjectException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateObjectException
 
CreateObjectException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateObjectException
 
CreateObjectException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateObjectException
 
createObjectStack() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Factory method to instantiate the created Objects Stack.
createObjectStack() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the created Objects Stack.
createPackageClassFiles(Element, Map, Map, Vector, Map) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: For each class in the XMI, will create a CreateClassFile object and place it on the return Vector.
createPackageDir(String, String) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Creates the directory for the package.
CreatePackageFile - Class in org.biomage.tools.generate_classes
Description: Class that is resposible for generating a java file for the class represented by the class node passed into the constructor.
CreatePackageFile(Element, Element, Map, Map) - Constructor for class org.biomage.tools.generate_classes.CreatePackageFile
Description: Constructor for the package file generator.
createParameterValues(ProtocolApplicationForm, ProtocolData) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
createParameterValues(ProtocolApplicationForm, ProtocolData) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
createProtectionElem(String, String, String, String, String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Create a protection element.
createProtectionElem_Refactored(String, String, String, String, String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Create a protection element.
createProtectionGroupData(String[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
createQueueObjectMessage(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
createQueueObjectMessage(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
createReference(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: If not owned, creates the *_ref element and attlist then creates the element and attlist declarations for the class.
createRoleDeclarations(StringBuffer) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the element and attlist declarations for the role names of the class.
createSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
creates a secured element
createSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
creates a secured element
createSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
creates a secured element
createSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
creates a secured element
CreateSecuredElement - Class in gov.nih.nci.caarray.services.security.test.usecases
 
CreateSecuredElement() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.CreateSecuredElement
 
CreateSecuredElementException - Exception in gov.nih.nci.caarray.services.exception
 
CreateSecuredElementException() - Constructor for exception gov.nih.nci.caarray.services.exception.CreateSecuredElementException
 
CreateSecuredElementException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateSecuredElementException
 
CreateSecuredElementException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateSecuredElementException
 
CreateSecuredElementException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.CreateSecuredElementException
 
createTopicObjectMessage(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
createTopicObjectMessage(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
CreateTransformedClassFile - Class in org.biomage.tools.generate_java
 
CreateTransformedClassFile(String, String, String, int) - Constructor for class org.biomage.tools.generate_java.CreateTransformedClassFile
Creates a new instance of CreateTransformedClassFile
CreateTransformedInterfaceFile - Class in org.biomage.tools.generate_java
 
CreateTransformedInterfaceFile(String, String[]) - Constructor for class org.biomage.tools.generate_java.CreateTransformedInterfaceFile
Creates a new instance of CreateTransformedInterfaceFile
createUnique(Vector) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create a Unique object which takes a vector of columns
createUnitData() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestUtils
 
createUnresolvedRefList() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Factory method to instantiate the UnresolvedRefs Stack.
createValuesSet() - Method in class org.biomage.tools.xmlutils.MultiHashMap
Factory method for instantiating objects of type Set for use as the containers of multiple values mapped to a single key.
createValuesSet() - Method in class org.biomage.tools.xmlutils.MultiHashtable
Factory method for instantiating objects of type Set for use as the containers of multiple values mapped to a single key.
createVocabData(long, String, String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
createVocabData() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
CreateWriteFiles(Vector) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: Create the write classes for each of the class files.
createXMLStrings() - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Creates the different entities, elements and attlists for the class.
createXMLStrings() - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
Description: Creates the different entities, elements and attlists for the class.
createXMLStrings() - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
Description: Creates the element declaration for the top-level model.
createXMLStrings() - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
Description: Creates the element declaration for the package.
createZip(String, String[], boolean) - Static method in class gov.nih.nci.caarray.services.util.file.FileZipper
Creates a zip file and adds the specified fileNames to it.
creatingSoftware - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
creatingSoftwareVersion - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
creation - Variable in class org.biomage.AuditAndSecurity.Audit.Action
 
CubeCreator - Class in gov.nih.nci.caarray.services.fileparse
 
CubeCreator(ParsingQuantitationType[], ParsingDesignElement[], int) - Constructor for class gov.nih.nci.caarray.services.fileparse.CubeCreator
Constructor to initialize the cube to it's needed values
CULTIVAR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
CURATOR_EMAIL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
CURATOR_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
Roles defined.
CustomCommonsFormFile - Class in gov.nih.nci.caarray.ui.core
This class implements the Struts FormFile interface by wrapping the Commons FileUpload FileItem interface.
CustomCommonsFormFile(FileItem) - Constructor for class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Constructs an instance of this class which wraps the supplied file item.
CustomDataCubeIOHelpers - Class in gov.nih.nci.caarray.services.mageloader
Description: Class that provides static helper metheds for writing and reading external cube data to/from a file.
CustomDataCubeIOHelpers() - Constructor for class gov.nih.nci.caarray.services.mageloader.CustomDataCubeIOHelpers
 
CustomFormFile - Interface in gov.nih.nci.caarray.ui.core
 
customizeQuery(Object, PersistenceBroker, CollectionDescriptor, QueryByCriteria) - Method in class gov.nih.nci.caarray.services.util.ojb.QueryCustomizerExcludingObjectsMarkedAsDeleted
 
CustomMAGEContentHandler - Class in gov.nih.nci.caarray.services.util.mage
Description: Content handler for MAGE.
CustomMAGEContentHandler() - Constructor for class gov.nih.nci.caarray.services.util.mage.CustomMAGEContentHandler
 
CustomMultipartRequestHandler - Class in gov.nih.nci.caarray.ui.core
Extending to override functionality
CustomMultipartRequestHandler() - Constructor for class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
 

D

dAgg(CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
DATA - Static variable in class org.biomage.tools.generate_er.CreateMageER
table type is data
DATA_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
dataAttributeInformation(Element, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Puts together the information on the simple datatypes.
dataAttrInfo - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on the simple datatypes attributes for this class.
Database - Class in org.biomage.Description
An address to a repository.
Database() - Constructor for class org.biomage.Description.Database
Default constructor.
Database(Attributes) - Constructor for class org.biomage.Description.Database
Attribute constructor.
database - Variable in class org.biomage.Description.DatabaseEntry
Reference to the database where the DataEntry instance can be found.
database_ - Variable in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
database_list - Variable in class org.biomage.Description.Description_package
An address to a repository.
DatabaseComparator - Class in gov.nih.nci.caarray.ui.core
 
DatabaseComparator() - Constructor for class gov.nih.nci.caarray.ui.core.DatabaseComparator
 
DatabaseData - Class in gov.nih.nci.caarray.common.data.vocab
 
DatabaseData() - Constructor for class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
DatabaseEntry - Class in org.biomage.Description
A reference to a record in a database.
DatabaseEntry() - Constructor for class org.biomage.Description.DatabaseEntry
Default constructor.
DatabaseEntry(Attributes) - Constructor for class org.biomage.Description.DatabaseEntry
Attribute constructor.
databaseId - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
DatabaseImportMAGEContentHandler - Class in gov.nih.nci.caarray.services.mageloader
Description: Content handler for MAGE.
DatabaseImportMAGEContentHandler(String, ProtectionGroupData[]) - Constructor for class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
DatabaseImportMAGEReader - Class in gov.nih.nci.caarray.services.mageloader
 
DatabaseImportMAGEReader(String, boolean, String, ProtectionGroupData[]) - Constructor for class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEReader
 
DatabaseImportMAGEReader(String, String[]) - Constructor for class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEReader
 
DatabaseImportMAGEReader(String, String[], String, ProtectionGroupData[]) - Constructor for class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEReader
 
databaseName - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
databaseReferences - Variable in class org.biomage.Description.Description
References to entries in databases.
databases - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
databaseVersion - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
DataColumn - Class in org.biomage.tools.generate_er
 
DataColumn() - Constructor for class org.biomage.tools.generate_er.DataColumn
Description: Constructor for the DataColumn object.
DataColumnDescriptor - Enum in gov.nih.nci.caarray.services.bioassaydata.descriptor
Represents a column in a data table in the database used to hold bio assay data.
DataConverter - Class in gov.nih.nci.caarray.services.util.dataconverter
 
DataDescInterface - Interface in gov.nih.nci.caarray.common.data.util
 
DataExternal - Class in org.biomage.BioAssayData
Transformed class to associate external data to the BioAssayDataCube
DataExternal() - Constructor for class org.biomage.BioAssayData.DataExternal
Default constructor.
DataExternal(Attributes) - Constructor for class org.biomage.BioAssayData.DataExternal
Attribute constructor.
DataFileAssessment - Class in gov.nih.nci.caarray.services.hybridization.ejb
Contains information about the current state of a given data file.
DataFileAssessment(File) - Constructor for class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
DataFileLoaderClient - Class in gov.nih.nci.caarray.loader
Reloads the existing array designs.
DataFileLoaderClient() - Constructor for class gov.nih.nci.caarray.loader.DataFileLoaderClient
 
DataFileParseException - Exception in gov.nih.nci.caarray.services.bioassaydata.reader
 
DataFileParseException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.bioassaydata.reader.DataFileParseException
 
DataFileProcessor - Interface in gov.nih.nci.caarray.services.fileparse
 
DataFileProcessorFactory - Class in gov.nih.nci.caarray.services.fileparse
 
DataFileProcessorFactory() - Constructor for class gov.nih.nci.caarray.services.fileparse.DataFileProcessorFactory
 
DataFileReloadConfiguration - Class in gov.nih.nci.caarray.services.hybridization.ejb
Contains the configurable options settings for a data file reload job.
DataFileReloadConfiguration() - Constructor for class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
DataFileReloadResults - Class in gov.nih.nci.caarray.services.hybridization.ejb
Contains the results of a data file reload job.
DataFileReloadResults(File, boolean, String) - Constructor for class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadResults
 
DataFileRepairResults - Class in gov.nih.nci.caarray.services.hybridization.ejb
Results from a repair operation.
DataFileRepairResults() - Constructor for class gov.nih.nci.caarray.services.hybridization.ejb.DataFileRepairResults
 
DataHandlerDataSourceException - Exception in gov.nih.nci.caarray.services.bioassaydata
Indicates a system exception during data retrieval.
DataHandlerDataSourceException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceException
 
DataHeaderMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
This class represents the mappings of a data file's header names to their values.
DataHeaderMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
DataInternal - Class in org.biomage.BioAssayData
Transformed class to associate whitespaced delimited data to the BioAssayDataCube
DataInternal() - Constructor for class org.biomage.BioAssayData.DataInternal
Default constructor.
DataInternal(Attributes) - Constructor for class org.biomage.BioAssayData.DataInternal
Attribute constructor.
DataJobHandlerImpl - Class in gov.nih.nci.caarray.services.fileupload2
 
DataJobHandlerImpl() - Constructor for class gov.nih.nci.caarray.services.fileupload2.DataJobHandlerImpl
 
DataLoader - Interface in org.biomage.tools.apps.annot.data
 
DataMatrix - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
The data matrix implementation
DataMatrix() - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.DataMatrix
 
DataRow - Interface in gov.nih.nci.caarray.services.fileparse
 
DataSet - Class in gov.nih.nci.caarray.services.fileparse2.parsers
This class represents all the data that is structured according to the DataHeaderMap and DataTableMap.
DataSet() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataSet
 
dataSet_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
DataSetMapper - Class in gov.nih.nci.caarray.services.fileparse2.parsers
This class glues the mappings of headers and data table for a data file structured as a simple list of header records and data rows to the file's and file header's parsers.
DataSetMapper() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
dataSetMapper_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
dataSetMapper_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
DataSetMapperMap - Class in gov.nih.nci.caarray.services.fileparse2.util
 
DataSetMapperMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.util.DataSetMapperMap
 
DataTable - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
DataTable(String[]) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
 
DataTable(String[], String[]) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
 
DataTableDescriptor - Enum in gov.nih.nci.caarray.services.bioassaydata.descriptor
Represents a database table used to store bio assay data.
DataTableMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
DataTableMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DataTableMap
 
dataType - Variable in class org.biomage.HigherLevelAnalysis.NodeValue
The data type of the any element.
dataType - Variable in class org.biomage.Protocol.Parameter
The type of data generated by the parameter i.e.
dataType - Variable in class org.biomage.QuantitationType.QuantitationType
The specific type for the quantitations.
DataTypeEnum - Enum in gov.nih.nci.caarray.services.bioassaydata.descriptor
Data types used in QuantitationTypeDescriptors.
dataTypeInformation(Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains the data type and puts it on a map keyed by the model element id.
Date2NameValueTypeFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
Date2NameValueTypeFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Date2NameValueTypeFieldMapper
 
Date2StringFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
Date2StringFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Date2StringFieldMapper
 
Datum - Class in org.biomage.BioAssayData
Transformed container to hold a value.
Datum() - Constructor for class org.biomage.BioAssayData.Datum
Default constructor.
Datum(Attributes) - Constructor for class org.biomage.BioAssayData.Datum
Attribute constructor.
days - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
DbArrayDesignDataSource - Class in gov.nih.nci.caarray.services.arraydesign
 
DbArrayDesignDataSource(ArrayDesignSecurityHelper) - Constructor for class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
DbConnectionBroker - Class in org.biomage.tools.helpers
DbConnectionBroker A servlet-based broker for database connections.
DbConnectionBroker(String, String, String, String, int, int, String, double) - Constructor for class org.biomage.tools.helpers.DbConnectionBroker
Creates a new Connection Broker
dbDriver: JDBC driver.
DbConnectionBroker(String, String, String, String, int, int, String, double, boolean) - Constructor for class org.biomage.tools.helpers.DbConnectionBroker
 
DbConnectionBroker(String, String, String, String, int, int, String, double, boolean, int, int) - Constructor for class org.biomage.tools.helpers.DbConnectionBroker
 
DBException - Exception in gov.nih.nci.caarray.services.exception
This exception is used when a generic problem accessing the database in encountered.
DBException() - Constructor for exception gov.nih.nci.caarray.services.exception.DBException
DBException constructor comment.
DBException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.DBException
Constructs a new DBException with the specified detail message.
DBException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.DBException
 
DBException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.DBException
DBException constructor comment.
DbFileUploadEntrySaver - Class in gov.nih.nci.caarray.services.hybridization
Stores HybridizationFileUploadEntry to the caArray database instance.
DbFileUploadEntrySaver() - Constructor for class gov.nih.nci.caarray.services.hybridization.DbFileUploadEntrySaver
 
DBQ - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
DBUtils - Class in gov.nih.nci.caarray.services.util
 
deassignElementToRole(long, String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Deprecated. Not used, marked for removal
deassignProtectionElementOwner(String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Unset a Protected Element Owner as the data is public
deassignSecuredElementOwner(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Deassign Secured Element Owner
deassignSecuredElementOwner(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Deassign Secured Element Owner
deassignSecuredElementOwner(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Deassign Secured Element Owner
deassignSecuredElementOwner(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Deassign Secured Element Owner
DEFAULT_BATCH_SIZE - Static variable in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
DEFAULT_FLUSH_INTERVAL - Static variable in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
DEFAULT_MAX_ATTEMPTS - Static variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
The number of times an unsuccessful message may be put back into the queue.
DEFAULT_PATH - Static variable in class org.biomage.tools.generate_classes.CreateMageClasses
Description: The default namespace.
DEFAULT_PATH - Static variable in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: The default namespace.
DEFAULT_QUEUE_CONN_FACT - Static variable in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
DEFAULT_REGION - Static variable in class gov.nih.nci.caarray.services.util.cache.EHCacheHelper
The used default region name.
DEFAULT_REGION - Static variable in class gov.nih.nci.caarray.services.util.cache.JCSHelper
 
DEFAULT_SIZE_MAX - Static variable in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
The default value for the maximum allowable size, in bytes, of an uploaded file.
DEFAULT_SIZE_THRESHOLD - Static variable in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
The default value for the threshold which determines whether an uploaded file will be written to disk or cached in memory.
DEFAULT_TOPIC_CONN_FACT - Static variable in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
DEFAULT_UPDATER - Static variable in class gov.nih.nci.caarray.services.security.mageom.SecuredElementIdUpdaterFactory
 
DEFAULT_WAIT_TIME - Static variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
The base time a message will wait before being re-queued.
DefaultAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
This class is the default assembler that relies solely on the mapper for each of the source objects to the target object to perform the conversion.
DefaultAssembler(Class) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.DefaultAssembler
 
defaultHandler() - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementOrphanHandlerFactory
 
DefaultJMSMessageCollection - Class in gov.nih.nci.caarray.services.util.jms
 
DefaultJMSMessageCollection() - Constructor for class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageCollection
 
DefaultJMSMessageCollection(int) - Constructor for class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageCollection
 
DefaultJMSMessageCollection(Collection) - Constructor for class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageCollection
 
DefaultJMSMessageHandler - Class in gov.nih.nci.caarray.services.util.jms
 
DefaultSecuredElementIdUpdater - Class in gov.nih.nci.caarray.services.security.mageom
 
DefaultSecuredElementIdUpdater() - Constructor for class gov.nih.nci.caarray.services.security.mageom.DefaultSecuredElementIdUpdater
 
defaultSecureElementIdUpdater() - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementIdUpdaterFactory
 
defaultValue - Variable in class org.biomage.Protocol.Parameter
Allows the optional specification of a default values and the unit for the Parameter
defaultValue - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation.ParamInfo
 
DefaultZoneMatcher - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers
The default implementation of ZoneMatcher to allow looking up a Zone such that Zone.name is used as the identifier of a Zone and the parsed feature's zoneIdentifier is to be matched to it to retrieve the Zone for it.
DefaultZoneMatcher() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.DefaultZoneMatcher
 
defectType - Variable in class org.biomage.Array.FeatureDefect
Indicates the type of defect (e.g.
defectType - Variable in class org.biomage.Array.ZoneDefect
Indicates the type of defect (e.g.
degrees_C - Variable in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
degrees_F - Variable in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailAction
 
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailAction
 
deleteAdditionalDataProcessing(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteAdditionalDataProcessingFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteAdditionalDataProcessingFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteAdditionalQualifier(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteAdditionalQualifierFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteAdditionalQualifierFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteAdditionalUploadedFile(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteAdditionalUploadedFileFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteAdditionalUploadedFileFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteAnnotationFromHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
deleteAnnotationFromHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
deleteAnnotationFromHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
deleteArray(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailAction
 
deleteArrayDesign(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
deleteArrayDesign(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Attempts to physically delete the specified ArrayDesign if it contains no Features, Reporters and CompositeSequences.
deleteArrayDesign(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
deleteArrayDesign(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
deleteArrayDesignFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
deleteArrayDesignFileUploadGroupByArrayDesign(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Delete the fileUploadGroup that maintains the uploaded files for the specified ArrayDesign.
deleteArrayGroup(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
deleteArrayGroup(long) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
Remove the specified ArrayGroup from the persistence store.
deleteArrayGroup(long) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
Retrieve a particular Array based on the id.
deleteBibliographicReferenceFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteBioAssayFromExperiment(BioAssay, Experiment) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteBioSample(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
deleteBioSample(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
deleteBioSample(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Deletes a BioSample
deleteBioSource(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
deleteBioSource(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
deleteBioSource(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Deletes a BioSource
deleteByQuery(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Delegates to OJB's deleteByQuery which executes a DELETE query.
deleteByQuery(Query) - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
deleteCompositeGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Remove the specified CompositeGroup from the persistence store.
deleteCompound(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
deleteCompound(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
 
deleted - Variable in class org.biomage.ArrayDesign.ArrayDesign
 
deleted - Variable in class org.biomage.BioAssay.BioAssay
caARRAY-specific marker for a DELETED BioAssay.
deleted - Variable in class org.biomage.Experiment.Experiment
caARRAY-specific marker if this Experiment is deleted.
deleteDirectory(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
deleteDirectory(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
deleteExperiment(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteExperiment(ExperimentData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteExperiment(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteExperiment(ExperimentData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deletes an experiment and associated files from the system.
deleteExperiment(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteExperimentalFactorFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteExperimentalFactorFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteExperimentalFactorFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteFactorValueFromExperimentalFactor(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteFactorValueFromExperimentalFactor(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteFactorValueFromExperimentalFactor(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteFeatureGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Remove the specified FeatureGroup from the persistence store.
deleteHardware(long) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
deleteHardware(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
deleteHardware(long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Remove the specified hardware from the persistence store.
deleteHardware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
deleteHardwareAssociation(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
deleteHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
deleteHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
deleteHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
deleteHybridizationFileUploadEntryFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteHybridizationFileUploadFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteHybridizationFileUploadFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. - No longer applicable
deleteHybridizationFileUploadFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteHybridizationFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
deleteHybridizations(HybridizationDeletionConfiguration) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteHybridizations(HybridizationDeletionConfiguration) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deletes an experiment and associated files from the system.
deleteLabeledExtract(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
deleteLabeledExtract(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
deleteLabeledExtract(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Deletes a LabeledExtract
deleteMeasurement(long) - Method in class gov.nih.nci.caarray.services.protocol.MeasurementManagerDB
 
deleteMessages(String, MessageData[]) - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
deleteMtoNRelation(Object, Object, String) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Deletes a many-to-many association between two objects.
deleteMultipleHybridizationFiles(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
deleteObject(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Deletes an object.
deleteObject(Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Deletes an object.
deleteObject(Class, Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Deletes the object given its class type and ID.
deleteObjectByQuery(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Deletes an object by query.
deleteOntology(long) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
deleteOrganization(long) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
deleteOrganization(long) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
deleteOrganization(long) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
deleteParameter(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
deleteParameter(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
deleteParameter(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
deleteParameterFromHardware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
deleteParameterFromHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
deleteParameterFromHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Remove the specified parameter from the specified hardware and also delete the parameter from the persistence store.
deleteParameterFromProtocol(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
deleteParameterFromProtocol(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
deleteParameterFromProtocol(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Removes the specified Parameter from the specified Protocol and delete it from the persistence store.
deleteParameterFromSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
deleteParameterFromSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
deleteParameterFromSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Remove the parameter from the software and also delete the parameter from the persistence store.
deletePerson(long) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
deletePerson(long) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
deletePerson(long) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
deletePotocolApplicationFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
deletePotocolApplicationFromArrayGroup(long, long) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
deleteProtectionElem(long) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Delete a protection element.
deleteProtocol(long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
deleteProtocol(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
deleteProtocol(long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Removes the specified Protocol from the persistence store.
deleteProtocolApplicationFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
deleteProtocolApplicationFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
deleteProtocolApplicationFromArrayGroup(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
deleteProtocolApplicationFromArrayGroup(long, long) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
deletePublicationFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deletePublicationFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteQualityControlFromExperiment(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
deleteQualityControlFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
deleteQualityControlFromExperiment(long, long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
deleteReporterGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Remove the specified ReporterGroup from the persistence store.
deleteSoftware(long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
deleteSoftware(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
deleteSoftware(long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Deletes the specified software from the persistence store.
deleteSoftware(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
deleteSoftwareAssociation(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
deleteSoftwareAssociation(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
deleteTreatment(SampleDetailForm, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
deleteTreatmentFromBioMaterial(long, long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
deleteTreatmentFromBioMaterial(long, long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
deleteTreatmentFromBioMaterial(long, long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Deletes a treatment from a biomaterial
DeleteTreatmentFromBioMaterial - Class in gov.nih.nci.caarray.services.biomaterial.test
 
DeleteTreatmentFromBioMaterial(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.DeleteTreatmentFromBioMaterial
 
deleteUploadedFile(String, String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
deleteUserAdminRole(Long, Long) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
deleteVocabulary(long) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
deleteVocabulary(long) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
DELETION_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
DELETION_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
DELETION_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
DELETION_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
DELETION_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
DELETION_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
DELETION_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
DELETION_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
DelimitedExporter - Class in gov.nih.nci.caarray.services.util.parse
 
DelimitedExporter() - Constructor for class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
 
DelimitedFileReader - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
DelimitedFileReader(BufferedReader, String[], String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileReader
 
DelimitedFileReader(BufferedReader, BasicDynaClass, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileReader
 
DelimitedFileReader(BufferedReader, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileReader
 
DelimitedFileWriter - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
DelimitedFileWriter(String, String[]) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileWriter
 
DelimitedFileWriter(String, String[], String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileWriter
 
DelimitedImportDefaultListener - Class in gov.nih.nci.caarray.services.util.parse
 
DelimitedImportDefaultListener() - Constructor for class gov.nih.nci.caarray.services.util.parse.DelimitedImportDefaultListener
 
DelimitedImportListener - Interface in gov.nih.nci.caarray.services.util.parse
 
DelimitedImportParser - Class in gov.nih.nci.caarray.services.util.parse
 
DelimitedImportParser() - Constructor for class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
DerivedBioAssay - Class in org.biomage.BioAssay
A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
DerivedBioAssay() - Constructor for class org.biomage.BioAssay.DerivedBioAssay
Default constructor.
DerivedBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.DerivedBioAssay
Attribute constructor.
derivedBioAssayData - Variable in class org.biomage.BioAssay.DerivedBioAssay
The data associated with the DerivedBioAssay.
DerivedBioAssayData - Class in org.biomage.BioAssayData
The output of a transformation event.
DerivedBioAssayData() - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData
Default constructor.
DerivedBioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.DerivedBioAssayData
Attribute constructor.
derivedBioAssayDataTarget - Variable in class org.biomage.BioAssayData.Transformation
The association between the DerivedBioAssayData and the Transformation event that produced it.
derivedBioAssayMap - Variable in class org.biomage.BioAssay.DerivedBioAssay
The DerivedBioAssay that is produced by the sources of the BioAssayMap.
DerivedSignal - Class in org.biomage.QuantitationType
A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements.
DerivedSignal() - Constructor for class org.biomage.QuantitationType.DerivedSignal
Default constructor.
DerivedSignal(Attributes) - Constructor for class org.biomage.QuantitationType.DerivedSignal
Attribute constructor.
desc_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
desc_ - Variable in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
Describable - Class in org.biomage.Common
Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions.
Describable() - Constructor for class org.biomage.Common.Describable
Default constructor.
Describable(Attributes) - Constructor for class org.biomage.Common.Describable
Attribute constructor.
description - Variable in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
description - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
Description - Class in org.biomage.Description
A free text description of an object.
Description() - Constructor for class org.biomage.Description.Description
Default constructor.
Description(Attributes) - Constructor for class org.biomage.Description.Description
Attribute constructor.
description_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
description_ - Variable in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
description_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
description_package - Variable in class org.biomage.Common.MAGEJava
The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.
Description_package - Class in org.biomage.Description
The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.
Description_package() - Constructor for class org.biomage.Description.Description_package
Default constructor.
Description_package(Attributes) - Constructor for class org.biomage.Description.Description_package
Attribute constructor.
Description_package.Database_list - Class in org.biomage.Description
Inner list class for holding multiple entries for attribute database.
Description_package.Database_list() - Constructor for class org.biomage.Description.Description_package.Database_list
 
DescriptionFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
DescriptionFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.DescriptionFieldMapper
 
designElement - Variable in class org.biomage.BioAssayData.DesignElementTuple
The DesignElement associated with the value of the BioAssayDatum.
DesignElement - Class in org.biomage.DesignElement
An element of an array.
DesignElement() - Constructor for class org.biomage.DesignElement.DesignElement
Default constructor.
DesignElement(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement
Attribute constructor.
designElement_package - Variable in class org.biomage.Common.MAGEJava
The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array.
DesignElement_package - Class in org.biomage.DesignElement
The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array.
DesignElement_package() - Constructor for class org.biomage.DesignElement.DesignElement_package
Default constructor.
DesignElement_package(Attributes) - Constructor for class org.biomage.DesignElement.DesignElement_package
Attribute constructor.
DesignElement_package.CompositeCompositeMap_list - Class in org.biomage.DesignElement
Inner list class for holding multiple entries for attribute compositeCompositeMap.
DesignElement_package.CompositeCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list
 
DesignElement_package.CompositeSequence_list - Class in org.biomage.DesignElement
Inner list class for holding multiple entries for attribute compositeSequence.
DesignElement_package.CompositeSequence_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list
 
DesignElement_package.FeatureReporterMap_list - Class in org.biomage.DesignElement
Inner list class for holding multiple entries for attribute featureReporterMap.
DesignElement_package.FeatureReporterMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list
 
DesignElement_package.Reporter_list - Class in org.biomage.DesignElement
Inner list class for holding multiple entries for attribute reporter.
DesignElement_package.Reporter_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.Reporter_list
 
DesignElement_package.ReporterCompositeMap_list - Class in org.biomage.DesignElement
Inner list class for holding multiple entries for attribute reporterCompositeMap.
DesignElement_package.ReporterCompositeMap_list() - Constructor for class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list
 
DesignElementColumnsMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
DesignElementColumnsMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
designElementDimension - Variable in class org.biomage.BioAssayData.BioAssayData
The DesignElements of the BioAssayData.
DesignElementDimension - Class in org.biomage.BioAssayData
An ordered list of designElements.
DesignElementDimension() - Constructor for class org.biomage.BioAssayData.DesignElementDimension
Default constructor.
DesignElementDimension(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementDimension
Attribute constructor.
designElementDimension - Variable in class org.biomage.HigherLevelAnalysis.NodeContents
The relevant DesignElements for this NodeContents from the BioAssayData.
designElementDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
An ordered list of designElements.
DesignElementDimensionCreator - Class in gov.nih.nci.caarray.services.bioassaydata
 
DesignElementDimensionCreator() - Constructor for class gov.nih.nci.caarray.services.bioassaydata.DesignElementDimensionCreator
 
DesignElementFinder - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
 
DesignElementFinder() - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.DesignElementFinder
 
DesignElementGroup - Class in org.biomage.ArrayDesign
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
DesignElementGroup() - Constructor for class org.biomage.ArrayDesign.DesignElementGroup
Default constructor.
DesignElementGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.DesignElementGroup
Attribute constructor.
DesignElementManagerDB - Class in gov.nih.nci.caarray.services.fileparse2
 
DesignElementManagerDB() - Constructor for class gov.nih.nci.caarray.services.fileparse2.DesignElementManagerDB
Default Constructor
DesignElementMap - Class in org.biomage.BioAssayData
A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
DesignElementMap() - Constructor for class org.biomage.BioAssayData.DesignElementMap
Default constructor.
DesignElementMap(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMap
Attribute constructor.
DesignElementMapping - Class in org.biomage.BioAssayData
Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
DesignElementMapping() - Constructor for class org.biomage.BioAssayData.DesignElementMapping
Default constructor.
DesignElementMapping(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementMapping
Attribute constructor.
designElementMapping - Variable in class org.biomage.BioAssayData.Transformation
The collection of mappings for the DesignElements.
designElementMaps - Variable in class org.biomage.BioAssayData.DesignElementMapping
The maps for the DesignElements.
DesignElementRetrievalSettings - Class in gov.nih.nci.caarray.services.arraydesign
 
DesignElementRetrievalSettings() - Constructor for class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings
 
DesignElementRetrievalSettings.AttributeInfo - Class in gov.nih.nci.caarray.services.arraydesign
 
DesignElementService - Interface in gov.nih.nci.caarray.services.fileparse
 
DesignElementServiceFactory - Class in gov.nih.nci.caarray.services.fileparse
 
DesignElementServiceFactory() - Constructor for class gov.nih.nci.caarray.services.fileparse.DesignElementServiceFactory
 
DesignElementTuple - Class in org.biomage.BioAssayData
Transformed container to specify a DesignElement and QuantitationTypes for that Element.
DesignElementTuple() - Constructor for class org.biomage.BioAssayData.DesignElementTuple
Default constructor.
DesignElementTuple(Attributes) - Constructor for class org.biomage.BioAssayData.DesignElementTuple
Attribute constructor.
DesignProviderRole - Class in org.biomage.ArrayDesign
 
DesignProviderRole() - Constructor for class org.biomage.ArrayDesign.DesignProviderRole
 
DesignProviderRoleData - Class in gov.nih.nci.caarray.common.data.arraydesign
 
DesignProviderRoleData() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData
 
designProviderRoles - Variable in class org.biomage.ArrayDesign.ArrayDesign
The providers of the ArrayDesign that have a role which describes how he/she contributes the ArrayDesign, e.g.
destroy() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Destroy all content for this form file.
destroy() - Method in class gov.nih.nci.caarray.ui.core.SecurityContextFilter
Destroys the filter.
destroy(int) - Method in class org.biomage.tools.helpers.DbConnectionBroker
Multi-phase shutdown.
destroy() - Method in class org.biomage.tools.helpers.DbConnectionBroker
Less safe shutdown.
determineCurrentVisibilitys(SecuredElementData) - Static method in class gov.nih.nci.caarray.ui.protocol.ProtocolUIUtils
 
DEVELOPER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
DEVELOPMENTAL_STAGE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
developmentalStage_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
developmentalStageId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
developmentalStages_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
DEVELSTAGE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
disableAndRememberPreviousValueForCollectionDescriptorCascadeRetrieve(ClassDescriptor, Map, String) - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
disableAndRememberPreviousValueForObjectDescriptorCascadeRetrieve(ClassDescriptor, Map, String) - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
disableConstraintsAndIndexes() - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
disableConstraintsAndIndexes() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Disables array design indexes and constraints to enable fast loading of array designs.
disableConstraintsAndIndexes() - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Disables array design indexes and constraints to enable fast loading of array designs.
disableIndexesAndConstraints() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Disables constraints and drops indexes in order to faster load array design data.
disableIndexesAndConstraints() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
disableIndexesAndConstraints() - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
disableUpload() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
 
DISEASE_LOCATION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
DISEASE_STAGE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
DISEASE_STAGE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
DISEASE_STATE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
DISEASE_STATE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
diseaseLocation_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseLocationId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseLocations_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseStage_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseStageId - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseStages_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseState - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseStateId - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
diseaseStates - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
DISPLAY_TAG_PAGE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
DISPLAY_TAG_SIZE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
displayInstruction() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.HelpFrame
 
displayPreviousList(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
displayProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentDataProcessingAction
 
displayResults(Object[], Object[], String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.ResultFrame
 
displaySelectedProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
displaySelectedProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
displayUploadedFilesSummary(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
displayUseCases() - Method in class gov.nih.nci.caarray.services.fileparse.test.Tester
Disply available use cases.
displayUseCases() - Method in class gov.nih.nci.caarray.services.security.test.Tester
Disply available use cases.
displayUseCases() - Method in class gov.nih.nci.caarray.services.test.Tester
Disply available use cases.
displayUseCases() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
Disply available use cases.
dispose() - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
 
distance - Variable in class org.biomage.Measurement.Measurement.KindCV
 
DISTANCE_UNIT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
distanceUnit - Variable in class org.biomage.Array.ArrayGroup
The unit of the measurement attributes.
distanceUnit - Variable in class org.biomage.Array.Fiducial
The units the fiducial is measured in.
distanceUnit - Variable in class org.biomage.Array.PositionDelta
The unit for the attributes.
distanceUnit - Variable in class org.biomage.ArrayDesign.FeatureGroup
The unit for the feature measures.
distanceUnit - Variable in class org.biomage.ArrayDesign.Zone
Unit for the Zone attributes.
distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneGroup
Unit for the ZoneGroup attributes.
distanceUnit - Variable in class org.biomage.ArrayDesign.ZoneLayout
Unit of the ZoneLayout attributes.
distanceUnit - Variable in class org.biomage.DesignElement.Position
The units of the x, y positions.
DistanceUnit - Class in org.biomage.Measurement
Distance
DistanceUnit() - Constructor for class org.biomage.Measurement.DistanceUnit
Default constructor.
DistanceUnit(Attributes) - Constructor for class org.biomage.Measurement.DistanceUnit
Attribute constructor.
DistanceUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
dl - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorBodyWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.IncludeWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.RemoveFromWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
doAssocations() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.TemplateWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ClassDeclWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
doAttrs() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
doBase() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
doBase() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
doBase() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
doBase() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
docInformation(Element) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains all the extension mechanism information and puts it on a map keyed by the model element id.
doesBioMaterialHaveTreatment(long, long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class gov.nih.nci.caarray.ui.core.SecurityContextFilter
Performs a temporary JAAS login for the duration of the request.
doGet(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.DownloadFile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessBatchFileDownload
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFileUpload
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailAction
 
done(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
doneFormatting_ - Variable in class gov.nih.nci.caarray.services.util.mage.MAGEWriter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.DownloadFile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessBatchFileDownload
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFileUpload
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
doReset(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
downloadArrayDesignFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
downloadBatchFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
downloadDataProcessFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
DownloadFile - Class in gov.nih.nci.caarray.services.util.file
 
DownloadFile() - Constructor for class gov.nih.nci.caarray.services.util.file.DownloadFile
 
downloadFiles(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBatchDownloadAction
 
downloadFiles(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationDetailDoneAction
 
downloadGal(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
downloadHybridizationFiles(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
downloadMage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
downloadMAGEML(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
downloadUploadedFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
DQB - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
duplicateArrayGroup(long, String) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
duplicateArrayGroup(long, String) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
duplicateArrayGroup(long, String) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
Makes a duplicate of the specified ArrayGroup.
duplicateBioMaterial(long, Class, String) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
duplicateBioSample(long, String) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Makes a copy of the given biomaterial.
duplicateBioSource(long, String) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
duplicateBioSource(long, String) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Applies the specified treatment to produce the specified output Makes a copy of the given biomaterial.
DuplicateBioSourceTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
DuplicateBioSourceTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.DuplicateBioSourceTest
 
duplicateLabeledExtract(long, String) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Makes a copy of the given biomaterial.
duplicateLabelExtract(long, String) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 

E

E - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
ECOTYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
editable - Variable in class org.biomage.Common.Extendable
 
EHCacheHelper - Class in gov.nih.nci.caarray.services.util.cache
 
EHCacheHelper() - Constructor for class gov.nih.nci.caarray.services.util.cache.EHCacheHelper
 
EJB_CREATE_EXCEPTION - Static variable in class gov.nih.nci.caarray.common.exception.UIMessageConstants
 
EJB_CREATE_EXCEPTION - Static variable in class gov.nih.nci.caarray.services.exception.ServerMessageConstants
 
EJB_REMOTE_EXCEPTION - Static variable in class gov.nih.nci.caarray.common.exception.UIMessageConstants
 
EJB_REMOTE_EXCEPTION - Static variable in class gov.nih.nci.caarray.services.exception.ServerMessageConstants
 
EJB_REMOVE_EXCEPTION - Static variable in class gov.nih.nci.caarray.common.exception.UIMessageConstants
 
EJB_REMOVE_EXCEPTION - Static variable in class gov.nih.nci.caarray.services.exception.ServerMessageConstants
 
ejbActivate() - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
ejbCreate() - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
ejbPassivate() - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
called when remove method is called.
ejbRemove() - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
ejbRemove() - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
called when remove method is called.
EJBUtils - Class in gov.nih.nci.caarray.services.util
 
EJBUtils() - Constructor for class gov.nih.nci.caarray.services.util.EJBUtils
 
ELEMENT_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
emailParsingNotification(HybridizationFileUploadGroup, String) - Static method in class gov.nih.nci.caarray.services.fileparse2.HybridizationFileParsingService
Sends an email message to the owner of the experiment for which the specified fileUploadGroup is, curator and caarray_admin to notify about the result of the parsing of the specified HybridizationFileUploadGroup.
EMPTY - Static variable in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
 
emptyMAGEobject() - Method in class org.biomage.Array.Array
 
emptyMAGEobject() - Method in class org.biomage.Array.Array_package
 
emptyMAGEobject() - Method in class org.biomage.Array.ArrayGroup
 
emptyMAGEobject() - Method in class org.biomage.Array.ArrayManufacture
 
emptyMAGEobject() - Method in class org.biomage.Array.ArrayManufactureDeviation
 
emptyMAGEobject() - Method in class org.biomage.Array.FeatureDefect
 
emptyMAGEobject() - Method in class org.biomage.Array.Fiducial
 
emptyMAGEobject() - Method in class org.biomage.Array.ManufactureLIMS
 
emptyMAGEobject() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
 
emptyMAGEobject() - Method in class org.biomage.Array.PositionDelta
 
emptyMAGEobject() - Method in class org.biomage.Array.ZoneDefect
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.CompositeGroup
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.FeatureGroup
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.ReporterGroup
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.Zone
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.ZoneGroup
 
emptyMAGEobject() - Method in class org.biomage.ArrayDesign.ZoneLayout
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.Audit
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.Organization
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.Person
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.Security
 
emptyMAGEobject() - Method in class org.biomage.AuditAndSecurity.SecurityGroup
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.BioAssay_package
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.BioAssayCreation
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.BioAssayTreatment
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.Channel
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.DerivedBioAssay
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.FeatureExtraction
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.Hybridization
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.Image
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.ImageAcquisition
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.MeasuredBioAssay
 
emptyMAGEobject() - Method in class org.biomage.BioAssay.PhysicalBioAssay
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioAssayData_package
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioAssayDimension
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioAssayMap
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioAssayMapping
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioAssayTuple
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioDataCube
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.BioDataTuples
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.DataExternal
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.DataInternal
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.Datum
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.DerivedBioAssayData
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.DesignElementMapping
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.DesignElementTuple
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.FeatureDimension
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.ReporterDimension
 
emptyMAGEobject() - Method in class org.biomage.BioAssayData.Transformation
 
emptyMAGEobject() - Method in class org.biomage.BioEvent.BioEvent_package
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.BioMaterial_package
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.BioSample
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.BioSource
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.Compound
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.CompoundMeasurement
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.LabeledExtract
 
emptyMAGEobject() - Method in class org.biomage.BioMaterial.Treatment
 
emptyMAGEobject() - Method in class org.biomage.BioSequence.BioSequence
 
emptyMAGEobject() - Method in class org.biomage.BioSequence.BioSequence_package
 
emptyMAGEobject() - Method in class org.biomage.BioSequence.SeqFeature
 
emptyMAGEobject() - Method in class org.biomage.BioSequence.SeqFeatureLocation
 
emptyMAGEobject() - Method in class org.biomage.BioSequence.SequencePosition
 
emptyMAGEobject() - Method in class org.biomage.BQS.BibliographicReference
 
emptyMAGEobject() - Method in class org.biomage.BQS.BQS_package
 
emptyMAGEobject() - Method in class org.biomage.Common.NameValueType
 
emptyMAGEobject() - Method in class org.biomage.Description.Database
 
emptyMAGEobject() - Method in class org.biomage.Description.DatabaseEntry
 
emptyMAGEobject() - Method in class org.biomage.Description.Description
 
emptyMAGEobject() - Method in class org.biomage.Description.Description_package
 
emptyMAGEobject() - Method in class org.biomage.Description.ExternalReference
 
emptyMAGEobject() - Method in class org.biomage.Description.OntologyEntry
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.CompositeCompositeMap
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.CompositePosition
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.CompositeSequence
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.DesignElement_package
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.Feature
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.FeatureInformation
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.FeatureLocation
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.FeatureReporterMap
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.MismatchInformation
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.Position
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.Reporter
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.ReporterCompositeMap
 
emptyMAGEobject() - Method in class org.biomage.DesignElement.ReporterPosition
 
emptyMAGEobject() - Method in class org.biomage.Experiment.Experiment
 
emptyMAGEobject() - Method in class org.biomage.Experiment.Experiment_package
 
emptyMAGEobject() - Method in class org.biomage.Experiment.ExperimentalFactor
 
emptyMAGEobject() - Method in class org.biomage.Experiment.ExperimentDesign
 
emptyMAGEobject() - Method in class org.biomage.Experiment.FactorValue
 
emptyMAGEobject() - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
 
emptyMAGEobject() - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
 
emptyMAGEobject() - Method in class org.biomage.HigherLevelAnalysis.Node
 
emptyMAGEobject() - Method in class org.biomage.HigherLevelAnalysis.NodeContents
 
emptyMAGEobject() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
 
emptyMAGEobject() - Method in class org.biomage.Measurement.ConcentrationUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.DistanceUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.MassUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.Measurement
 
emptyMAGEobject() - Method in class org.biomage.Measurement.Measurement_package
 
emptyMAGEobject() - Method in class org.biomage.Measurement.QuantityUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.TemperatureUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.TimeUnit
 
emptyMAGEobject() - Method in class org.biomage.Measurement.VolumeUnit
 
emptyMAGEobject() - Method in class org.biomage.Protocol.Hardware
 
emptyMAGEobject() - Method in class org.biomage.Protocol.HardwareApplication
 
emptyMAGEobject() - Method in class org.biomage.Protocol.Parameter
 
emptyMAGEobject() - Method in class org.biomage.Protocol.ParameterValue
 
emptyMAGEobject() - Method in class org.biomage.Protocol.Protocol
 
emptyMAGEobject() - Method in class org.biomage.Protocol.Protocol_package
 
emptyMAGEobject() - Method in class org.biomage.Protocol.ProtocolApplication
 
emptyMAGEobject() - Method in class org.biomage.Protocol.Software
 
emptyMAGEobject() - Method in class org.biomage.Protocol.SoftwareApplication
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.DerivedSignal
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.Error
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.ExpectedValue
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.Failed
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.MeasuredSignal
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.PresentAbsent
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.PValue
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.QuantitationType_package
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.Ratio
 
emptyMAGEobject() - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
 
enableConstraintsAndIndexes() - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
enableConstraintsAndIndexes() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Re-enables array design indexes and constraints disabled in disableConstraintsAndIndexes.
enableConstraintsAndIndexes() - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Re-enables array design indexes and constraints disabled in disableConstraintsAndIndexes.
enableIndexesAndConstraints() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Re-enables constraints and adds indexes after array design loading.
enableIndexesAndConstraints() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
enableIndexesAndConstraints() - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
endDocument() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
endDocument() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
endElement(String, String, String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
endElement(String, String, String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
endPrefixMapping(String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
endPrefixMapping(String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
endQueueSession(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
endQueueSession(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
endTopicSession(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
endTopicSession(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
entityPrefix - Variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: String to use as prefix for the entities for this class.
EntrySaveException - Exception in gov.nih.nci.caarray.services.hybridization
Indicates that the system was unable to update a file upload entry.
enumerateIdentifiable(Vector, Map) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: This is a recursive function to determine abolutely whether or not an Object is identifiable.
ENVIRONMENTAL_HISTORY_DESIGN_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
environmentalHistoryDesign_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
equals(Object) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
equals(Object) - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings.AttributeInfo
 
equals(Object) - Method in class gov.nih.nci.caarray.services.security.CaArrayPrincipal
Compare this CaArrayPrincipal's name against another Principal
equals(Object) - Method in class org.biomage.ArrayDesign.DesignProviderRole
Compare this DesignProviderRole with the specified one if they're equal.
equals(Object) - Method in class org.biomage.Common.Extendable
Tests if this Extendable is the same reference as the specified object or it has the same ID.
equals(Object) - Method in class org.biomage.Experiment.ExperimentProviderRole
Compare this ExperimentProviderRole with the specified one if they're equal.
equals(Object) - Method in class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
error - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
Error - Class in org.biomage.QuantitationType
Error measurement of a quantitation.
Error() - Constructor for class org.biomage.QuantitationType.Error
Default constructor.
Error(Attributes) - Constructor for class org.biomage.QuantitationType.Error
Attribute constructor.
error_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
error_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
error_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
errorColor - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
errorLed - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
escapeXMLSensitiveCharacters(String) - Static method in class org.biomage.tools.helpers.StringManipHelpers
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.core.BaseAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.core.BaseDispatchAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserManagementAction
 
executeUpdate(ClassDescriptor, Object) - Method in class gov.nih.nci.caarray.services.util.ojb.JdbcAccessImpl
 
executeUpdateSQL(String, ClassDescriptor, ValueContainer[], ValueContainer[]) - Method in class gov.nih.nci.caarray.services.util.ojb.JdbcAccessImpl
performs a SQL UPDTE, INSERT or DELETE statement against RDBMS.
exists(Class, Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Check if the specified object that matches the specified ID and is of the specified Class type exists.
EXP_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
EXP_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
ExpectedValue - Class in org.biomage.QuantitationType
Indication of what value is expected of the associated standard quantitation type.
ExpectedValue() - Constructor for class org.biomage.QuantitationType.ExpectedValue
Default constructor.
ExpectedValue(Attributes) - Constructor for class org.biomage.QuantitationType.ExpectedValue
Attribute constructor.
EXPERIMENT - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
EXPERIMENT - Static variable in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
EXPERIMENT - Static variable in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
Experiment - Class in org.biomage.Experiment
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
Experiment() - Constructor for class org.biomage.Experiment.Experiment
Default constructor.
Experiment(Attributes) - Constructor for class org.biomage.Experiment.Experiment
Attribute constructor.
EXPERIMENT_DESIGN_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
EXPERIMENT_FTP_DIR - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
experiment_list - Variable in class org.biomage.Experiment.Experiment_package
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
experiment_package - Variable in class org.biomage.Common.MAGEJava
Represents the container for a hierarchical grouping of BioAssays.
Experiment_package - Class in org.biomage.Experiment
Represents the container for a hierarchical grouping of BioAssays.
Experiment_package() - Constructor for class org.biomage.Experiment.Experiment_package
Default constructor.
Experiment_package(Attributes) - Constructor for class org.biomage.Experiment.Experiment_package
Attribute constructor.
Experiment_package.Experiment_list - Class in org.biomage.Experiment
Inner list class for holding multiple entries for attribute experiment.
Experiment_package.Experiment_list() - Constructor for class org.biomage.Experiment.Experiment_package.Experiment_list
 
ExperimentAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentAction
 
ExperimentAddAdditionalHybPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentAddAdditionalHybPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentAddAdditionalHybPageAction
 
ExperimentAddHybPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentAddHybPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentAddHybPageAction
 
ExperimentAdditionalQualifierAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentAdditionalQualifierAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalQualifierAction
 
experimentAdditionalUploadedFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ExperimentAdditionalUploadFilePageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentAdditionalUploadFilePageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalUploadFilePageAction
 
experimental - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
EXPERIMENTAL_FACTOR_CATEGORY - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ExperimentalFactor - Class in org.biomage.Experiment
ExperimentFactors are the dependent variables of an experiment (e.g.
ExperimentalFactor() - Constructor for class org.biomage.Experiment.ExperimentalFactor
Default constructor.
ExperimentalFactor(Attributes) - Constructor for class org.biomage.Experiment.ExperimentalFactor
Attribute constructor.
experimentalFactor - Variable in class org.biomage.Experiment.FactorValue
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
ExperimentalFactorData - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentalFactorData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
experimentalFactors - Variable in class org.biomage.Experiment.ExperimentDesign
The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.
ExperimentAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
ExperimentAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.ExperimentAssembler
 
ExperimentBaseForm - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentBaseForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
experimentBasicInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method retrieves array design information and hibridization file types, and presents them to the users to make a proper selection.
ExperimentBatchDownloadAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentBatchDownloadAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentBatchDownloadAction
 
experimentBatchDownloadPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ExperimentCleanerClient - Class in gov.nih.nci.caarray.loader
Client used to delete obsolete experiments and hybridizations from caArray.
ExperimentCleanerClient() - Constructor for class gov.nih.nci.caarray.loader.ExperimentCleanerClient
 
ExperimentCleaningConfiguration - Class in gov.nih.nci.caarray.services.experiment.ejb
Complete configuration information for experiment deletion and cleaning jobs, loaded from a file named "experiment_cleaner.properties" on the classpath.
ExperimentCleaningConfiguration() - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
ExperimentContactPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentContactPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentContactPageAction
 
ExperimentData - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
experimentDataProcessingPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ExperimentDataProcessingPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentDataProcessingPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentDataProcessingPageAction
 
ExperimentDeletionResult - Class in gov.nih.nci.caarray.services.experiment.ejb
Summarizes information from an experiment deletion.
ExperimentDeletionResult() - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.ExperimentDeletionResult
 
ExperimentDesc - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentDesc() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
ExperimentDesign - Class in org.biomage.Experiment
The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
ExperimentDesign() - Constructor for class org.biomage.Experiment.ExperimentDesign
Default constructor.
ExperimentDesign(Attributes) - Constructor for class org.biomage.Experiment.ExperimentDesign
Attribute constructor.
experimentDesigns - Variable in class org.biomage.Experiment.Experiment
The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
ExperimentDetailForm - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentDetailForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
ExperimentDetailPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentDetailPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentDetailPageAction
 
experimentFactorPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ExperimentFileDownloadServlet - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentFileDownloadServlet() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentFileDownloadServlet
 
ExperimentFileTypeConstants - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentFileTypeConstants() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
ExperimentFtpData - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentFtpData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
ExperimentHybridizationAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentHybridizationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAction
 
ExperimentHybridizationAnnotationAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentHybridizationAnnotationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
ExperimentHybridizationDetailDoneAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentHybridizationDetailDoneAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationDetailDoneAction
 
ExperimentImportMageMLAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentImportMageMLAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentImportMageMLAction
 
ExperimentManagementTest - Class in gov.nih.nci.caarray.services.experiment.test
 
ExperimentManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
ExperimentManagerDB - Class in gov.nih.nci.caarray.services.experiment
 
ExperimentManagerDB() - Constructor for class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
ExperimentManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
ExperimentManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
ExperimentManagerEJB - Class in gov.nih.nci.caarray.services.experiment.ejb
ExperimentManagerEJB
ExperimentManagerEJB() - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
ExperimentNewAdditionalQualifierAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentNewAdditionalQualifierAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentNewAdditionalQualifierAction
 
ExperimentNewDataObject - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentNewDataObject() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
experimentNewHybridizationPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ExperimentNewPageAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentNewPageAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageAction
 
ExperimentNewPageContinueAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentNewPageContinueAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageContinueAction
 
ExperimentProviderRole - Class in org.biomage.Experiment
 
ExperimentProviderRole() - Constructor for class org.biomage.Experiment.ExperimentProviderRole
 
ExperimentProviderRoleData - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentProviderRoleData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData
 
ExperimentSearchAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentSearchAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentSearchAction
 
ExperimentSearchCriteria - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
ExperimentSearchForm - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentSearchForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
ExperimentSearchTest - Class in gov.nih.nci.caarray.ui.test
 
ExperimentSearchTest(String) - Constructor for class gov.nih.nci.caarray.ui.test.ExperimentSearchTest
 
ExperimentShortDesc - Class in gov.nih.nci.caarray.common.data.experiment
 
ExperimentShortDesc() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentShortDesc
 
ExperimentTypeFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
ExperimentTypeFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ExperimentTypeFieldMapper
 
ExperimentUIConstants - Class in gov.nih.nci.caarray.ui.experiment.data
 
ExperimentUIConstants() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
ExperimentUploadAction - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentUploadAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentUploadAction
 
ExperimentUtils - Class in gov.nih.nci.caarray.services.experiment
 
ExperimentUtils - Class in gov.nih.nci.caarray.ui.experiment
 
ExperimentUtils() - Constructor for class gov.nih.nci.caarray.ui.experiment.ExperimentUtils
 
ExperimentValidationUtil - Class in gov.nih.nci.caarray.ui.experiment.data
 
ExperimentValidationUtil() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.ExperimentValidationUtil
 
ExperimentView - Class in gov.nih.nci.caarray.common.data.experiment
This class is intended for carrying data for display purposes only.
ExperimentView() - Constructor for class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
exportArrayDesign(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
Generates MAGEML for the specified ArrayDesign and zips it up in a file having the specified path.
exportArrayDesign(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLExportManagerDB
 
exportArrayDesign(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
exportExperiment(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
Generates MAGEML for the specified experiment and zips it up in a file having the specified path.
exportExperiment(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLExportManagerDB
 
exportExperiment(long, String, boolean) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
exportMAGEML(Class, Object, String) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
For testing only
ExportMAGEML - Class in gov.nih.nci.caarray.services.test.usecases
 
ExportMAGEML() - Constructor for class gov.nih.nci.caarray.services.test.usecases.ExportMAGEML
 
Extendable - Class in org.biomage.Common
Abstract class that specifies for subclasses an association to NameValueTypes.
Extendable() - Constructor for class org.biomage.Common.Extendable
Default constructor.
Extendable(Attributes) - Constructor for class org.biomage.Common.Extendable
Attribute constructor.
ExternalDataCubeIOHelpers - Class in org.biomage.tools.helpers
Description: Class that provides static helper metheds for writing and reading external cube data to/from a file.
ExternalDataCubeIOHelpers() - Constructor for class org.biomage.tools.helpers.ExternalDataCubeIOHelpers
 
externalLIMS - Variable in class org.biomage.BioMaterial.Compound
Reference to an entry in an external LIMS data source.
externalReference - Variable in class org.biomage.Description.Description
Specifies where the described instance was originally obtained from.
ExternalReference - Class in org.biomage.Description
A reference to the originating source for the object.
ExternalReference() - Constructor for class org.biomage.Description.ExternalReference
Default constructor.
ExternalReference(Attributes) - Constructor for class org.biomage.Description.ExternalReference
Attribute constructor.
ExtractData - Class in gov.nih.nci.caarray.ui.experiment.data
 
ExtractData() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.ExtractData
 
ExtractDropDownData - Class in gov.nih.nci.caarray.ui.experiment.data
 
ExtractDropDownData() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
extractHeaderSection(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 

F

facePanel - Variable in class org.biomage.tools.apps.annot.PagePanel
 
FACTOR_VALUE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
FactorDropDownData - Class in gov.nih.nci.caarray.ui.experiment.data
 
FactorDropDownData() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
factorsave(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.AddExperimentFactorAction
 
FactorValue - Class in org.biomage.Experiment
The value for a ExperimentalFactor
FactorValue() - Constructor for class org.biomage.Experiment.FactorValue
Default constructor.
FactorValue(Attributes) - Constructor for class org.biomage.Experiment.FactorValue
Attribute constructor.
FactorValueData - Class in gov.nih.nci.caarray.common.data.experiment
 
FactorValueData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
factorValues - Variable in class org.biomage.Experiment.ExperimentalFactor
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.
Failed - Class in org.biomage.QuantitationType
Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay.
Failed() - Constructor for class org.biomage.QuantitationType.Failed
Default constructor.
Failed(Attributes) - Constructor for class org.biomage.QuantitationType.Failed
Attribute constructor.
FAILURE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
FALSE - Static variable in class org.biomage.tools.generate_er.CreateMageER
the foreign key does not cause a cascade action
FAMILY_HISTORY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
familyHistory_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
fax_ - Variable in class gov.nih.nci.caarray.common.data.contact.ContactData
 
feature - Variable in class org.biomage.Array.FeatureDefect
The feature that was manufactured defectively.
feature - Variable in class org.biomage.Array.ManufactureLIMS
The feature whose LIMS information is being described.
Feature - Class in org.biomage.DesignElement
An intended position on an array.
Feature() - Constructor for class org.biomage.DesignElement.Feature
Default constructor.
Feature(Attributes) - Constructor for class org.biomage.DesignElement.Feature
Attribute constructor.
feature - Variable in class org.biomage.DesignElement.FeatureInformation
The feature the FeatureInformation is supplying information for.
FeatureDefect - Class in org.biomage.Array
Stores the defect information for a feature.
FeatureDefect() - Constructor for class org.biomage.Array.FeatureDefect
Default constructor.
FeatureDefect(Attributes) - Constructor for class org.biomage.Array.FeatureDefect
Attribute constructor.
featureDefects - Variable in class org.biomage.Array.ArrayManufactureDeviation
Description on features who are manufactured in a different location than specified in the ArrayDesign.
FeatureDimension - Class in org.biomage.BioAssayData
Specialized DesignElementDimension to hold Features.
FeatureDimension() - Constructor for class org.biomage.BioAssayData.FeatureDimension
Default constructor.
FeatureDimension(Attributes) - Constructor for class org.biomage.BioAssayData.FeatureDimension
Attribute constructor.
FeatureExtraction - Class in org.biomage.BioAssay
The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
FeatureExtraction() - Constructor for class org.biomage.BioAssay.FeatureExtraction
Default constructor.
FeatureExtraction(Attributes) - Constructor for class org.biomage.BioAssay.FeatureExtraction
Attribute constructor.
featureExtraction - Variable in class org.biomage.BioAssay.MeasuredBioAssay
The association between the MeasuredBioAssay and the FeatureExtraction Event.
FeatureGroup - Class in org.biomage.ArrayDesign
A collection of like features.
FeatureGroup() - Constructor for class org.biomage.ArrayDesign.FeatureGroup
Default constructor.
FeatureGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.FeatureGroup
Attribute constructor.
featureGroup - Variable in class org.biomage.DesignElement.Feature
The features that belong to this group.
FeatureGroupData - Class in gov.nih.nci.caarray.common.data.arraydesign
 
FeatureGroupData() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupData
 
FeatureGroupDesc - Class in gov.nih.nci.caarray.common.data.arraydesign
 
FeatureGroupDesc() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
FeatureGroupManagerDB - Class in gov.nih.nci.caarray.services.arraydesign
 
FeatureGroupManagerDB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
 
featureGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
The grouping of like Features together.
FeatureGroupSearchCriteria - Class in gov.nih.nci.caarray.common.data.arraydesign
 
FeatureGroupSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
FeatureInformation - Class in org.biomage.DesignElement
As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter.
FeatureInformation() - Constructor for class org.biomage.DesignElement.FeatureInformation
Default constructor.
FeatureInformation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureInformation
Attribute constructor.
featureInformationSources - Variable in class org.biomage.DesignElement.FeatureReporterMap
Typically, the features on an array that are manufactured with this reporter's BioSequence.
featureLIMSs - Variable in class org.biomage.Array.ArrayManufacture
Information on the manufacture of the features.
featureLocation - Variable in class org.biomage.DesignElement.Feature
Location of this feature relative to a grid.
FeatureLocation - Class in org.biomage.DesignElement
Specifies where a feature is located relative to a grid.
FeatureLocation() - Constructor for class org.biomage.DesignElement.FeatureLocation
Default constructor.
FeatureLocation(Attributes) - Constructor for class org.biomage.DesignElement.FeatureLocation
Attribute constructor.
featureProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method is the combined form of getFeatureProtocolData method and saveFeatureProtocolInfo method due to the change in the jsp page where a single method parameter is used for submitting the form data.
FeatureReporterMap - Class in org.biomage.DesignElement
A FeatureReporterMap is the description of how source features are transformed into a target reporter.
FeatureReporterMap() - Constructor for class org.biomage.DesignElement.FeatureReporterMap
Default constructor.
FeatureReporterMap(Attributes) - Constructor for class org.biomage.DesignElement.FeatureReporterMap
Attribute constructor.
featureReporterMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
A FeatureReporterMap is the description of how source features are transformed into a target reporter.
featureReporterMaps - Variable in class org.biomage.DesignElement.Reporter
Associates features with their reporter.
features - Variable in class org.biomage.ArrayDesign.FeatureGroup
The features that belong to this group.
featureShape - Variable in class org.biomage.ArrayDesign.FeatureGroup
The expected shape of the feature on the array: circular, oval, square, etc.
FetchFileList(String, String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpTunnelingFetchFileList
 
FetchFileListTest - Class in gov.nih.nci.caarray.services.test
 
FetchFileListTest() - Constructor for class gov.nih.nci.caarray.services.test.FetchFileListTest
 
fg - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
Fiducial - Class in org.biomage.Array
A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.
Fiducial() - Constructor for class org.biomage.Array.Fiducial
Default constructor.
Fiducial(Attributes) - Constructor for class org.biomage.Array.Fiducial
Attribute constructor.
fiducials - Variable in class org.biomage.Array.ArrayGroup
Association to the marks on the Array for alignment for the scanner.
fiducialType - Variable in class org.biomage.Array.Fiducial
A descriptive string that indicates the type of a fiducial (e.g.
FieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
This class describes how an attribute of a class is mapped to a attribute of another class.
FieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
fileCategory - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
FileData - Class in gov.nih.nci.caarray.common.data.util
This class contains information about the a file for download by the web client.
FileData() - Constructor for class gov.nih.nci.caarray.common.data.util.FileData
 
FileDataObject - Class in gov.nih.nci.caarray.services.util.fileuploadapplet
 
FileDataObject() - Constructor for class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
fileExtension - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
fileGAL_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
Full path to Definition File
FileLocatorUtils - Class in gov.nih.nci.caarray.services.util.file
Looks up file locations
FileLocatorUtils() - Constructor for class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
fileMAGE_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
Full path to Annotation File
FileMessageInterface - Interface in gov.nih.nci.caarray.services.fileparse
 
FileMessageTypes - Class in gov.nih.nci.caarray.services.fileparse
 
FileMessageTypes() - Constructor for class gov.nih.nci.caarray.services.fileparse.FileMessageTypes
 
FilePacker - Class in gov.nih.nci.caarray.services.util.file
 
FilePacker() - Constructor for class gov.nih.nci.caarray.services.util.file.FilePacker
 
FileParseManagerDB - Class in gov.nih.nci.caarray.services.fileparse
 
FileParseManagerDB() - Constructor for class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
FileParserDelegate - Class in gov.nih.nci.caarray.services.fileparse2.mdb
This class represents a JMS client that publishes a request for asynchronously parsing files of a hybridization or array design.
FileParserDelegate() - Constructor for class gov.nih.nci.caarray.services.fileparse2.mdb.FileParserDelegate
 
FileParsingDelegate - Class in gov.nih.nci.caarray.services.fileparse
Then it sends a JMS message on
FileParsingDelegate() - Constructor for class gov.nih.nci.caarray.services.fileparse.FileParsingDelegate
 
FileParsingEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
FileParsingEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
FileParsingEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
FileParsingEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
FileParsingService - Class in gov.nih.nci.caarray.services.fileparse
The service to call when you need files parsed
FileParsingService(Long, Long, UploadFile[], UploadFileTypes.MICROARRAY_FILE_TYPE) - Constructor for class gov.nih.nci.caarray.services.fileparse.FileParsingService
Constructor intializes with the required elements
filePath_ - Variable in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
FileType - Class in gov.nih.nci.caarray.common.data.fileupload2
This class represents an upload file type for array design and hybridization.
FileType() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
FileTypeFactory - Class in gov.nih.nci.caarray.services.fileparse2.util
 
FileTypeFactory() - Constructor for class gov.nih.nci.caarray.services.fileparse2.util.FileTypeFactory
 
FileTypeGroupMap - Class in gov.nih.nci.caarray.services.fileparse2.util
 
FileTypeGroupMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
FileTypeManager - Class in gov.nih.nci.caarray.services.fileupload
A simple helper class that organizes the files by file type
FileTypeManager() - Constructor for class gov.nih.nci.caarray.services.fileupload.FileTypeManager
 
FileTypeMap - Class in gov.nih.nci.caarray.common.data.fileupload2
This class provides the mappings for fileTypeId to the FileType object which contains further information about the file type.
FileTypeMap() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap
 
FileUploadDelegate - Class in gov.nih.nci.caarray.services.fileupload
 
FileUploadDelegate() - Constructor for class gov.nih.nci.caarray.services.fileupload.FileUploadDelegate
 
FileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
FileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
FileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
FileUploadEntryData(String, FileType, String, String) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
FileUploadEntryLookupException - Exception in gov.nih.nci.caarray.services.hybridization.ejb
 
FileUploadEntryLookupException() - Constructor for exception gov.nih.nci.caarray.services.hybridization.ejb.FileUploadEntryLookupException
 
FileUploadEntryLookupException(String) - Constructor for exception gov.nih.nci.caarray.services.hybridization.ejb.FileUploadEntryLookupException
 
FileUploadEntryLookupException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.hybridization.ejb.FileUploadEntryLookupException
 
FileUploadEntryLookupException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.hybridization.ejb.FileUploadEntryLookupException
 
FileUploadEntrySaver - Interface in gov.nih.nci.caarray.services.hybridization
Manages storage of HybridizationFileUploadEntries.
FileUploadGroup - Class in gov.nih.nci.caarray.services.fileupload2
 
FileUploadGroup() - Constructor for class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
FileUploadGroupData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
FileUploadGroupData(FileType[]) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
Constructs an instance of this class with an array of FileTypes which can be accepted for the files to be uploaded.
FileUploadHandlerMDB - Class in gov.nih.nci.caarray.services.fileupload2.mdb
Receives and handles queued requests to parse arrayd esign hybridization data files.
FileUploadHandlerMDB() - Constructor for class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
FileUploadHistory - Class in gov.nih.nci.caarray.services.fileupload2
Uploaded file history bean Title: caArray Description: MicroArray data repository and application Copyright: (c) 2005 NCICB.
FileUploadHistory() - Constructor for class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Default Constructor
FileUploadHistoryData - Class in gov.nih.nci.caarray.common.data.fileupload2
Uploaded file history data bean using CRC32s Title: caArray Description: MicroArray data repository and application Copyright: (c) 2005 NCICB.
FileUploadHistoryData(FileUploadEntryData, String, Date, String) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Default Constructor
FileUploadHistorySearchCriteria - Class in gov.nih.nci.caarray.common.data.fileupload2
 
FileUploadHistorySearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistorySearchCriteria
 
FileUploadManagerDB - Class in gov.nih.nci.caarray.services.fileupload2
 
FileUploadManagerDB() - Constructor for class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Default Constructor
FileUploadManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
FileUploadManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
FileUploadManagerEJB - Class in gov.nih.nci.caarray.services.fileupload2.ejb
 
FileUploadManagerEJB() - Constructor for class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
FileUploadManagerMDB - Class in gov.nih.nci.caarray.services.fileparse.mdb
 
FileUploadManagerMDB() - Constructor for class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB
 
FileUploadUtils - Class in gov.nih.nci.caarray.services.fileupload2
 
FileUtility - Class in gov.nih.nci.caarray.services.util.file
Provides utility functions to assist in local file system management.
FileValidator - Class in gov.nih.nci.caarray.services.util.file
File validator for testing integrity of files using CRC32s Title: caArray Description: MicroArray data repository and application Copyright: (c) 2005 NCICB.
FileValidator() - Constructor for class gov.nih.nci.caarray.services.util.file.FileValidator
Default Constructor
fileZipExtension - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
FileZipper - Class in gov.nih.nci.caarray.services.util.file
This object creates a zip file containing the set of files within a SelectedFiles object.
FileZipper() - Constructor for class gov.nih.nci.caarray.services.util.file.FileZipper
 
finalize() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
finalize() - Method in class org.biomage.tools.helpers.JDBCConnectionImpl2
 
findArrayDesignId(Long) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignFinder
 
findFileTypeOther() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
Finds fileType that has category=CATEGORY_OTHER.
finish() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Cleans up at the end of a request.
finishPageTwo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
FIRSTLINE - Static variable in class org.biomage.tools.generate_er.CreateMageER
first line in the MAGE_ER.xml file
fixDataType(CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
fl - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
FloatValidator - Class in org.biomage.tools.apps.annot.validator
 
FloatValidator() - Constructor for class org.biomage.tools.apps.annot.validator.FloatValidator
 
flush() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
flushAllQueues() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
flushAllTopics() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
flushQueue(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
fM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
fmol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
FOREIGNKEY - Static variable in class org.biomage.tools.generate_er.CreateMageER
indicate the column is a one_to_one foreign key.
ForeignKey - Class in org.biomage.tools.generate_er
 
ForeignKey() - Constructor for class org.biomage.tools.generate_er.ForeignKey
Description: Constructor for the ForeignKey object.
ForeignKey(String, String, String, String, String) - Constructor for class org.biomage.tools.generate_er.ForeignKey
Description: Constructor for the ForeignKey object.
ForeignKey(ForeignKey) - Constructor for class org.biomage.tools.generate_er.ForeignKey
Description: Constructor for the ForeignKey object.
format - Variable in class org.biomage.BioAssay.Image
The file format of the image typically a TIF or a JPEG.
formatForView(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Sets root physical bio assay and expected protocols prior to handing this object off for copying into a data or view object for display.
formatTextAreaString(String) - Static method in class gov.nih.nci.caarray.ui.StringFormatter
 
FormUtils - Class in gov.nih.nci.caarray.ui.core
 
FormUtils() - Constructor for class gov.nih.nci.caarray.ui.core.FormUtils
 
FORWARD_CANCEL - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
FORWARD_SUCCESS - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
freeConnection(Connection) - Method in class org.biomage.tools.helpers.DbConnectionBroker
Frees a connection.
FTP_ACTION_COMMAND - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_APPLET_JAR - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_DESTINATION - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_ENDJMPTO_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_PASSWORD - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_SERVER_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
FTP_USERNAME - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 

G

g - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
g_per_L - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
GalBlockData - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalBlockData() - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
GalFeatureData - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalFeatureData() - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
GalFileParseHandler - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalFileParseHandler(String) - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
Constructor with file to be parsed
GalHeaderListener - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalHeaderListener() - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
 
GalHeaderParser - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalHeaderParser(File) - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
Constructor with neccessary items
GalIdGenerator - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalIdGenerator() - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalIdGenerator
 
GalImportService - Class in gov.nih.nci.caarray.services.fileparse.gal
 
GalImportService(ArrayDesignDesc, String) - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.GalImportService
Constructor with required items
GalToMageMapping - Class in gov.nih.nci.caarray.services.fileparse.gal.magemapping
 
GalToMageMapping() - Constructor for class gov.nih.nci.caarray.services.fileparse.gal.magemapping.GalToMageMapping
 
GENEPIX_GAL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
GENEPIX_GAL_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
GENEPIX_GAL_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
GENEPIX_GPR_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
GENEPIX_GPR_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
GENEPIX_GPR_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
GENEPIX_GPS_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
GENEPIX_GPS_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
GENEPIX_SPOT_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
GENEPIX_SPOT_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
GENEPIX_SPOT_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
GenePixDataMatrix - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GenePixDataMatrix() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDataMatrix
 
GenePixDesignElement - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GenePixDesignElement() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
GenePixDesignElementService - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GenePixDesignElementService() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElementService
 
GenepixGalArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.genepix
Loads array design annotation from a GenePix GAL file.
GenePixGALFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
GenePixGALFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.GenePixGALFileHeaderParser
 
GenePixGALFileHeaderParser(DataSetMapper, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.GenePixGALFileHeaderParser
 
GenepixGalFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.genepix
Indicates a badly formatted GAL file.
GenePixGALZoneMatcher - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers
This ZoneMatcher is to look up Zone for a GAL file.
GenePixGALZoneMatcher() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.GenePixGALZoneMatcher
 
GenepixGprArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.genepix
Loads array design annotation from a GenePix GPR file (used as a last resort if data files are not associated with a complete array design).
GenepixGprFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.genepix
Indicates a badly formatted GAL file.
GenepixGprReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Provides functionality to read GenePix GPR files.
GenePixQuantificationService - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GenePixQuantificationService() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantificationService
 
GenePixQuantitationType - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GenePixQuantitationType() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantitationType
 
GENERAL_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
GeneralException - Exception in gov.nih.nci.caarray.common.exception
This exception is used when a generic problem is encountered.
GeneralException(String) - Constructor for exception gov.nih.nci.caarray.common.exception.GeneralException
Creates a new instance of GeneralException with a reason.
GeneralException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.common.exception.GeneralException
 
GeneralException(Throwable) - Constructor for exception gov.nih.nci.caarray.common.exception.GeneralException
 
GeneralSecuredElementUpdateTester - Class in gov.nih.nci.caarray.services.security.test
 
GeneralSecuredElementUpdateTester() - Constructor for class gov.nih.nci.caarray.services.security.test.GeneralSecuredElementUpdateTester
 
GENERATED_ARRAY_NAME - Static variable in class gov.nih.nci.caarray.common.data.array.ArrayConstants
 
generateMage(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
generateMage(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Generates a MAGE-ML file for the array design given.
generateMAGEML(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
generation_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
GENERATION_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
GENETIC_MODIFICATION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
geneticModificationDescription_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
geneticModificationId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
geneticModificationName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
geneticModifications_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
genotype_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
GENOTYPE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
GEOGRAPHIC_LOCATION_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
geographicLocation_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
get(SourceType, String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
get(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
get(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
get(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
get(Object) - Method in class gov.nih.nci.caarray.services.util.cache.CaArrayCache
 
get(Object) - Method in class gov.nih.nci.caarray.services.util.cache.CaArrayCache2
 
get(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl
 
get(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanWrapper
 
getAbsoluteFilePath() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
getAcceptableFileTypes() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
Gets the file types with which this instance is constructed.
getAccession() - Method in class org.biomage.Description.DatabaseEntry
Get method for accession
getAccessionNumber() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getAccessionNumber() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getAccessionNumber() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getAccessions() - Method in class org.biomage.BQS.BibliographicReference
Get method for accessions
getAccessions() - Method in interface org.biomage.Interface.HasAccessions
Get method for accessions
getAccessionVersion() - Method in class org.biomage.Description.DatabaseEntry
Get method for accessionVersion
getAction() - Method in class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData
 
getAction() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm
 
getAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getAction() - Method in class org.biomage.AuditAndSecurity.Audit
Get method for action
getAction() - Method in class org.biomage.BioMaterial.ActionProtocolTypeMap
 
getAction() - Method in class org.biomage.BioMaterial.Treatment
Get method for action
getAction() - Method in interface org.biomage.Interface.HasAction
Get method for action
getActionCommand() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getActionMeasurement() - Method in class org.biomage.BioMaterial.Treatment
Get method for actionMeasurement
getActionMeasurement() - Method in interface org.biomage.Interface.HasActionMeasurement
Get method for actionMeasurement
getActionProtocolTypeMap() - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getActionProtocolTypeMap() - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
Retrieves all available ActionProtocolTypeMapData's.
getActionProtocolTypeMaps() - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Retrieves all available ActionProtocolTypeMap's.
getActivityDate() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getActivityDate() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getActivityDate() - Method in class org.biomage.Protocol.ProtocolApplication
Get method for activityDate
getActivityDateAsString() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getActivityDateString() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getActualUserName(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getAdditionalDataApplyProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalDataProcessData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalDataProcessDownloadPath() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalDataProcessing(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getAdditionalDataProcessing(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves the AdditionalDataProcessingData object from the persistence store.
getAdditionalDataProcessing(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getAdditionalDataProcessingFile() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalDataProcessings() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getAdditionalDataProcessings(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves the AdditionalDataProcessingData object from the persistence store.
getAdditionalDataProcessings(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getAdditionalFeatureColumns() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
getAdditionalFileUploadCancel() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalQualifier(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getAdditionalQualifierData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalQualifierDataID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalQualifierName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalQualifiers() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getAdditionalQualifierSource() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalQualifierValue() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalReporterFileLocation() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getAdditionalReporterFileLocation() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getAdditionalReporterFileLocation() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getAdditionalUploadedFile(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getAdditionalUploadedFile(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves a AdditionalDataProcessingData object from the persistence store.
getAdditionalUploadedFile(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getAdditionalUploadedFileData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalUploadedFiles() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getAdditionalUploadedFiles(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves the AdditionalDataProcessingData object from the persistence store.
getAdditionalUploadedFiles(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getAdditionalUploadFile() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAdditionalUploadFileDesc() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getAddress() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
getAddress() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getAddress() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getAddress() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getAddress() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getAddress() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for address
getAddress1() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getAddress2() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getAdjustments() - Method in class org.biomage.Array.ArrayManufactureDeviation
Get method for adjustments
getAdjustments() - Method in interface org.biomage.Interface.HasAdjustments
Get method for adjustments
getAffiliation() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getAffiliation() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getAffiliation() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getAffiliation() - Method in class org.biomage.AuditAndSecurity.Person
Get method for affiliation
getAffiliation() - Method in interface org.biomage.Interface.HasAffiliation
Get method for affiliation
getAffiliationId() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getAffiliationName() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getAffiliations() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getAffyLibraryDirectory() - Static method in class gov.nih.nci.caarray.services.arraydesign.AffymetrixCdfLocatorUtil
 
getAffyLibraryDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getAge() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getAge() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAge(Connection) - Method in class org.biomage.tools.helpers.DbConnectionBroker
Returns the age of a connection -- the time since it was handed out to an application.
getAgeMax() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeMaxUnitId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeMaxUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeMin() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeMinUnitId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeMinUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeOrRange() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getAgeTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeUnitId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAgeValue() - Method in class org.biomage.Description.Ontology.Age
 
getAllArrayDesigns() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns all array designs in the system
getAllArrayDesigns() - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getAllCharacteristics() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getAllColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Returns all column names that appear in the data file's data table.
getAllColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileReader
 
getAllele() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAllElements() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns a hash table containing both text and file request parameters.
getAllFileTypes() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap
 
getAllGroups() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getAllGroupsSelection() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getAllHardware() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getAllHardware() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getAllHybridizationFileUploadEntries() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getAllProperties() - Static method in class gov.nih.nci.caarray.services.util.properties.QuantitationNamesProperties
 
getAllSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getAllSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getAllSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getAllValues() - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
getAllValues() - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
getAmount() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getAmountUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getAnalysisResults() - Method in class org.biomage.Experiment.Experiment
Get method for analysisResults
getAnalysisResults() - Method in interface org.biomage.Interface.HasAnalysisResults
Get method for analysisResults
getAndWriteDesignElementsToFile(long, String, DesignElementColumnsMap) - Method in class gov.nih.nci.caarray.services.fileparse2.DesignElementManagerDB
 
getAnnotationId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getAnnotations() - Method in class org.biomage.Description.Description
Get method for annotations
getAnnotations() - Method in class org.biomage.Experiment.ExperimentalFactor
Get method for annotations
getAnnotations() - Method in interface org.biomage.Interface.HasAnnotations
Get method for annotations
getApplicationId() - Method in class gov.nih.nci.caarray.common.data.security.Role
Return the applicationId
getApplicationId() - Static method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getApplyMode() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getApplyProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getApplyProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArchive_value() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getArchiveValue() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getArchiveValue() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getArgumentToken(String[], String) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Common code to obtain the argument associated with the option from the command line.
getArray() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getArray() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getArray(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
This method returns a Array that has the specified ID by delegating the call to the same method in ArrayManagerDB.
getArray() - Method in class org.biomage.BioAssay.BioAssayCreation
Get method for array
getArray() - Method in interface org.biomage.Interface.HasArray
Get method for array
getArray_list() - Method in class org.biomage.Array.Array_package
Get method for array_list
getArray_package() - Method in class org.biomage.Common.MAGEJava
Get method for array_package
getArrayBatch() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayBatch() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayBatchName() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getArrayBatchName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getArrayBatchName() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getArrayDesign() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getArrayDesign() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getArrayDesign() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
 
getArrayDesign(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getArrayDesign(String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns the existing array design matching the given identifier or null if none exists yet.
getArrayDesign(long) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns the array design requested.
getArrayDesign(String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Returns the requested array design.
getArrayDesign(long) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Returns the array design matching the given id.
getArrayDesign(String) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
getArrayDesign(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
getArrayDesign(String) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getArrayDesign(long) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getArrayDesign(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtArrayDesignLoader
Creates and returns the array design object from the .TXT file.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGalArrayDesignLoader
Creates and returns the array design object from the .CDF file.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGprArrayDesignLoader
Creates and returns the array design object from the .CDF file.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtArrayDesignLoader
Creates and returns the array design object from the .TXT file.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGalArrayDesignLoader
Creates and returns the array design object from the .CDF file.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprArrayDesignLoader
Creates and returns the array design object from the .CDF file.
getArrayDesign(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
This method returns a PhysicalArrayDesign that has the specified ID by delegating the call to the same method in ArrayDesignManagerDB.
getArrayDesign() - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
 
getArrayDesign() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getArrayDesign() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayDesign() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayDesign() - Method in class org.biomage.Array.Array
Get method for arrayDesign
getArrayDesign() - Method in interface org.biomage.Interface.HasArrayDesign
Get method for arrayDesign
getArrayDesign_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Get method for arrayDesign_list
getArrayDesign_package() - Method in class org.biomage.Common.MAGEJava
Get method for arrayDesign_package
getArrayDesignDataFileInputDirectory(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
This method is for release 1.3 to get the temporary directory to store the files to be parsed into ArrayDesign.
getArrayDesignDesc() - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
getArrayDesignFile() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getArrayDesignFileDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the final directory for placing the arrayDesign's uploaded files including MAGE-ML and GAL.
getArrayDesignFileHandler() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileHandlerFactory
 
getArrayDesignFileInputDirectory(Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
This method is for release 1.3.1.
getArrayDesignFileToken() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getArrayDesignFileTypeGroupMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
getArrayDesignFileTypes(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getArrayDesignFileTypes(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
getArrayDesignFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getArrayDesignFileUploadEntry(PhysicalArrayDesign) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns the upload entry associated with the array design, or null if there is none.
getArrayDesignFileUploadEntry(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
getArrayDesignFileUploadEntry(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getArrayDesignFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getArrayDesignFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getArrayDesignFileUploadEntryByArrayDesignId(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getArrayDesignFileUploadEntryByArrayDesignId(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getArrayDesignFileUploadEntryByArrayDesignId(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getArrayDesignFileUploadEntryData() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getArrayDesignFileUploadGroup(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getArrayDesignFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getArrayDesignFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getArrayDesignFileUploadGroupByArrayDesign(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getArrayDesignId() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getArrayDesignID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayDesignID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getArrayDesignID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayDesignMAGEMLFileDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the arrayDesign files, if not there it makes it.
getArrayDesignManager() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerFactory
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getArrayDesignName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayDesigns(ArrayDesignSearchCriteria) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Get an array of ArrayDesign that match the specified Criteria and that the array design is NOT marked as deleted.
getArrayDesigns() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getArrayDesignsToReload() - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getArrayDesignsToReload() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Returns a list of array designs (top-level object only) that require reloading.
getArrayDesignsToReload() - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Returns array designs that should be reloaded.
getArrayDesignUploadedFileData(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getArrayDesignUploadedFileData(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
getArrayDesignUploadedFileData(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Gets the information about the uploaded arraydesign files for the specified ArrayDesign.
getArrayDesignView(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getArrayDesignView(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
getArrayGroup() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getArrayGroup() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getArrayGroup(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
getArrayGroup(long) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
getArrayGroup(long) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
Retrieves a particular Array given its ID.
getArrayGroup(long, String[], ArrayManagerDB) - Static method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
getArrayGroup() - Method in class org.biomage.Array.Array
Get method for arrayGroup
getArrayGroup() - Method in interface org.biomage.Interface.HasArrayGroup
Get method for arrayGroup
getArrayGroup_list() - Method in class org.biomage.Array.Array_package
Get method for arrayGroup_list
getArrayGroupBarCode() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayGroupDescription() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayGroups(ArraySearchCriteria) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
Get an array of Array that match the specified Criteria and that the array is NOT marked as deleted.
getArrayGroupsByArrayDesign(long) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
Get an array of ArrayGroup whose array is associated with the specified ArrayDesign.
getArrayGroupSpacingX() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayGroupSpacingY() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayGroupTemplateName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getArrayIdentifier() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getArrayIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getArrayIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getArrayIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getArrayIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayIdentifier() - Method in class org.biomage.Array.Array
Get method for arrayIdentifier
getArrayIdentifier() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getArrayIdentifierId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getArrayIdentifiers() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getArrayIdentifiers() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getArrayIdentifiers() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getArrayLength() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayManufacture_list() - Method in class org.biomage.Array.Array_package
Get method for arrayManufacture_list
getArrayManufactureDeviations() - Method in class org.biomage.Array.Array
Get method for arrayManufactureDeviations
getArrayManufactureDeviations() - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Get method for arrayManufactureDeviations
getArrayManufacturer() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getArrayManufacturers() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getArrayManufacturers() - Method in class org.biomage.Array.ArrayManufacture
Get method for arrayManufacturers
getArrayManufacturers() - Method in interface org.biomage.Interface.HasArrayManufacturers
Get method for arrayManufacturers
getArrayName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getArrayNameArrayDesignName() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getArrayOrientationMark() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayOrientationMarkPosition() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrays() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrays() - Method in class org.biomage.Array.ArrayGroup
Get method for arrays
getArrays() - Method in class org.biomage.Array.ArrayManufacture
Get method for arrays
getArrays() - Method in interface org.biomage.Interface.HasArrays
Get method for arrays
getArraySearchPage(HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
getArraySpacingX() - Method in class org.biomage.Array.ArrayGroup
Get method for arraySpacingX
getArraySpacingY() - Method in class org.biomage.Array.ArrayGroup
Get method for arraySpacingY
getArrayWidth() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getArrayXOrigin() - Method in class org.biomage.Array.Array
Get method for arrayXOrigin
getArrayYOrigin() - Method in class org.biomage.Array.Array
Get method for arrayYOrigin
getAsDouble(String) - Method in interface gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBean
 
getAsDouble(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
getAsDouble(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
getAsDouble(String) - Method in interface gov.nih.nci.caarray.services.util.parse.LocalDynaBean
 
getAsDouble(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl
 
getAsDouble(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanWrapper
 
getAsInteger(String) - Method in interface gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBean
 
getAsInteger(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
getAsInteger(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
getAsLong(String) - Method in interface gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBean
 
getAsLong(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
getAsLong(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
getAssembler(Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
getAssignableValues() - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
getAssignedGroups() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getAssociatedHardware() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getAssociatedSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getAssociatedSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getAssociationEndClassifier(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the classifier of the association end element.
getAssociationEndMultiplicityRangeLower(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the multiplicity range lower of the association end element.
getAssociationEndMultiplicityRangeUpper(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the multiplicity range upper of the association end element.
getAssociationInfo() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the Vector of association information.
getAssociations() - Method in class org.biomage.Description.Ontology.Age
 
getAssociations() - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Get method for associations
getAssociations() - Method in class org.biomage.Description.Ontology.Biometrics
 
getAssociations() - Method in class org.biomage.Description.Ontology.ChromosomalAberration
 
getAssociations() - Method in class org.biomage.Description.OntologyEntry
Get method for associations
getAssociations() - Method in interface org.biomage.Interface.HasAssociations
Get method for associations
getAssoColumnVector() - Method in class org.biomage.tools.generate_er.Table
Description: get the vector for all association columns
getAsString(String) - Method in interface gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBean
 
getAsString(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
getAsString(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
getAsString(String) - Method in interface gov.nih.nci.caarray.services.util.parse.LocalDynaBean
 
getAsString(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl
 
getAsString(String) - Method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanWrapper
 
getAtmosphere() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getAttachmentType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getAttachmentType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getAttachmentTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getAttachmentTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getAttachmentTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getAttempts() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
getAttribute() - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings.AttributeInfo
 
getAttributeClassifier(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the classifier of the association end element.
getAttributeHash() - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getAttributeInfos() - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings
 
getAttributeMultiplicityRangeLower(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the multiplicity range lower of the association end element.
getAttributes(Class) - Static method in class gov.nih.nci.caarray.services.util.properties.CompoundAttrsProperties
 
getAttributes(Class) - Static method in class gov.nih.nci.caarray.services.util.properties.OntologyEntryAttrsProperties
 
getAttributes() - Method in class org.biomage.tools.apps.annot.data.PageRecord
 
getAttrInfo() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the Vector of attribute information.
getAttrVarName(CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Pass through to return the variable name to write out.
getAttrVarName(CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaPackageFile
Description: Pass through to return the variable name to write out.
getAuditAndSecurity_package() - Method in class org.biomage.Common.MAGEJava
Get method for auditAndSecurity_package
getAuditTrail() - Method in class org.biomage.Common.Describable
Get method for auditTrail
getAuditTrail() - Method in interface org.biomage.Interface.HasAuditTrail
Get method for auditTrail
getAuthConf() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getAuthConf() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getAuthenticationDAObj() - Method in class gov.nih.nci.caarray.services.security.SecurityObjFactory
Return a authentication data service object specified in the configuration file
getAuthorizationDAObj() - Method in class gov.nih.nci.caarray.services.security.SecurityObjFactory
Return a authorization data service object specified in the configuration file.
getAuthors() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getAuthors() - Method in class org.biomage.BQS.BibliographicReference
Get method for authors
getAvailableArrays(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
getAvailableArrays(long) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
getBack() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getBack() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getBarcode() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getBarcode() - Method in class org.biomage.Array.ArrayGroup
Get method for barcode
getBarrierFacility() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBaseClass() - Method in class org.biomage.tools.generate_er.Table
Description: get teh base class name of the table
getBaseClassCreateFile() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the base class createFile.
getBaseClassFileName() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the base class name.
getBaseClassID() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the base class name.
getBaseFileName(String) - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the base file name from the supplied file path.
getBasis() - Method in class org.biomage.BioSequence.SeqFeature
Get method for basis
getBatch() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getBatchFileName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getBatchFileResults() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getBatchSize() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
getBean(String) - Method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getBeans() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportDefaultListener
 
getBeans() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
A convienience method to get DynaBeans using the default listener
getBedding() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBibliographicReference(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getBibliographicReferences() - Method in class org.biomage.Description.Description
Get method for bibliographicReferences
getBibliographicReferences() - Method in interface org.biomage.Interface.HasBibliographicReferences
Get method for bibliographicReferences
getBioAssay() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getBioAssay() - Method in class org.biomage.BioAssayData.BioAssayTuple
Get method for bioAssay
getBioAssay() - Method in interface org.biomage.Interface.HasBioAssay
Get method for bioAssay
getBioAssay_list() - Method in class org.biomage.BioAssay.BioAssay_package
Get method for bioAssay_list
getBioAssay_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioAssay_package
getBioAssayCreation() - Method in class org.biomage.BioAssay.PhysicalBioAssay
Get method for bioAssayCreation
getBioAssayCreation() - Method in interface org.biomage.Interface.HasBioAssayCreation
Get method for bioAssayCreation
getBioAssayData() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getBioAssayData() - Method in class org.biomage.Experiment.Experiment
Get method for bioAssayData
getBioAssayData() - Method in interface org.biomage.Interface.HasBioAssayData
Get method for bioAssayData
getBioAssayData_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for bioAssayData_list
getBioAssayData_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioAssayData_package
getBioAssayDataCluster_list() - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Get method for bioAssayDataCluster_list
getBioAssayDataLoader() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataLoaderFactory
 
getBioAssayDataSources() - Method in class org.biomage.BioAssayData.Transformation
Get method for bioAssayDataSources
getBioAssayDataSources() - Method in interface org.biomage.Interface.HasBioAssayDataSources
Get method for bioAssayDataSources
getBioAssayDatum(BioAssay, QuantitationType, DesignElement) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
 
getBioAssayDimension() - Method in class org.biomage.BioAssayData.BioAssayData
Get method for bioAssayDimension
getBioAssayDimension() - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Get method for bioAssayDimension
getBioAssayDimension() - Method in interface org.biomage.Interface.HasBioAssayDimension
Get method for bioAssayDimension
getBioAssayDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for bioAssayDimension_list
getBioAssayFactorValues() - Method in class org.biomage.BioAssay.BioAssay
Get method for bioAssayFactorValues
getBioAssayFactorValues() - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Get method for bioAssayFactorValues
getBioAssayFiles() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getBioAssayId() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
getBioAssayId() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
getBioAssayMap_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for bioAssayMap_list
getBioAssayMapping() - Method in class org.biomage.BioAssayData.Transformation
Get method for bioAssayMapping
getBioAssayMapping() - Method in interface org.biomage.Interface.HasBioAssayMapping
Get method for bioAssayMapping
getBioAssayMaps() - Method in class org.biomage.BioAssayData.BioAssayMapping
Get method for bioAssayMaps
getBioAssayMaps() - Method in interface org.biomage.Interface.HasBioAssayMaps
Get method for bioAssayMaps
getBioAssayMapTarget() - Method in class org.biomage.BioAssayData.BioAssayMap
Get method for bioAssayMapTarget
getBioAssayMapTarget() - Method in interface org.biomage.Interface.HasBioAssayMapTarget
Get method for bioAssayMapTarget
getBioAssays() - Method in class org.biomage.BioAssayData.BioAssayDimension
Get method for bioAssays
getBioAssays() - Method in class org.biomage.Experiment.Experiment
Get method for bioAssays
getBioAssays() - Method in interface org.biomage.Interface.HasBioAssays
Get method for bioAssays
getBioAssayTreatments() - Method in class org.biomage.BioAssay.PhysicalBioAssay
Get method for bioAssayTreatments
getBioAssayTreatments() - Method in interface org.biomage.Interface.HasBioAssayTreatments
Get method for bioAssayTreatments
getBioAssayTuples() - Method in class org.biomage.BioAssayData.BioDataTuples
Get method for bioAssayTuples
getBioAssayTuples() - Method in interface org.biomage.Interface.HasBioAssayTupleData
Get method for bioAssayTuples
getBioDataValues() - Method in class org.biomage.BioAssayData.BioAssayData
Get method for bioDataValues
getBioDataValues() - Method in interface org.biomage.Interface.HasBioDataValues
Get method for bioDataValues
getBioEvent_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioEvent_package
getBiologicalCharacteristics() - Method in class org.biomage.DesignElement.CompositeSequence
Get method for biologicalCharacteristics
getBiologicalCharacteristics() - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Get method for biologicalCharacteristics
getBioMaterial(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getBioMaterial(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieve a BioMaterial
getBioMaterial(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieve BioMaterial
getBioMaterial() - Method in class org.biomage.Array.ManufactureLIMS
Get method for bioMaterial
getBioMaterial() - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
Get method for bioMaterial
getBioMaterial() - Method in interface org.biomage.Interface.HasBioMaterial
Get method for bioMaterial
getBioMaterial_list() - Method in class org.biomage.BioMaterial.BioMaterial_package
Get method for bioMaterial_list
getBioMaterial_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioMaterial_package
getBiomaterialCharacteristics() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiomaterialCharacteristics() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getBiomaterialCharacteristics() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getBiomaterialId() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getBioMaterialName() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getBioMaterialPlateCol() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateCol
getBioMaterialPlateIdentifier() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateIdentifier
getBioMaterialPlateRow() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Get method for bioMaterialPlateRow
getBioMaterials(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getBioMaterials(BioMaterialSearchCriteria, Class) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Get available BioMaterials.
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getBiometricHeight() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricHeightUnitId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricHeightUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricHeightUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricWeight() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricWeightUnitId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricWeightUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBiometricWeightUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getBioSample(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getBioSample(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieve a BioSample
getBioSample(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the BioSampleData object from the persistence store.
getBioSampleByTreatment(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieve the BioSample which has a Treatment that matches the specified treatmentId.
getBiosampleId() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getBioSamples(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getBiosamples() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getBioSampleType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleDesc
 
getBioSampleView(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getBioSampleView(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the BioSampleData object from the persistence store.
getBioSequence_list() - Method in class org.biomage.BioSequence.BioSequence_package
Get method for bioSequence_list
getBioSequence_package() - Method in class org.biomage.Common.MAGEJava
Get method for bioSequence_package
getBioSource(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getBioSource(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieve a BioSource
getBioSource(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the BioSourceData object from the persistence store.
getBiosourceDeleteLink() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return biosource description after formatting.
getBiosourceDescription() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return biosource description after formatting.
getBiosourceId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getBiosourceName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getBioSources(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getBiosources() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getBiosourceType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getBioSourceType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceDesc
 
getBiosourceType() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getBiosourceTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getBiosourceTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getBioSourceView(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getBioSourceView(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the BioSourceView object from the persistence store.
getBlock() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getBlockInt() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getBlockNumber() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
getBlockNumber() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
getBlocks() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
 
getBQS_package() - Method in class org.biomage.Common.MAGEJava
Get method for bQS_package
getBroker() - Static method in class org.biomage.tools.helpers.JDBCConnection2
 
getButton() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getButtonName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getByIdentifier(Class, String, boolean) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Get object by identifier, if not there it makes it when insertIfNotFound is true.
getBytesCompressed() - Method in class gov.nih.nci.caarray.services.util.file.FileZipper
return the number of bytes of source dtata files that have been sent to the zip compression function.
getBytesCompressed() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
return the number of bytes of source dtata files that have been sent to the zip compression function.
getBytesSent() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Simply return the current bytsSent value used as part of upload summary.
getBytesSent() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getCaArrayDesignFileEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
getCaArrayDesignFileEntryData() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getCache(Identity, Object, int) - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCachePerClassImpl
 
getCaFileEntry() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignFileParsingJob
 
getCaFileEntryData() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
getCaFileUploadHistory() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
getCaFileUploadHistoryData() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getCallBack() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
getCaMagemlFileEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
getCaMagemlFileEntryData() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getCanBeNull() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get if this column can have null as a value
getCancel() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getCancelURI() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getCanReload() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getCanRepair() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getCard() - Method in class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
getCascade() - Method in class org.biomage.tools.generate_er.ForeignKey
Description: get if the foreign table owns this table
getCascadingStore(ClassDescriptor, String) - Static method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
getCaseSensitivityUserName(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
retrieve the case-sensitive username Used as a workaround to cope with LDAP authentication accepting a case-insensitive login/user name.
getCaseSensitivityUserName(String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
 
getCategories() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
getCategory() - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
getCategory() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getCategory() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getCategory() - Method in class org.biomage.Description.Database
 
getCategory() - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Get method for category
getCategory() - Method in class org.biomage.Description.OntologyEntry
Get method for category
getCategory() - Method in class org.biomage.Experiment.ExperimentalFactor
Get method for category
getCategory() - Method in interface org.biomage.Interface.HasCategory
Get method for category
getCdfFile(String) - Static method in class gov.nih.nci.caarray.services.arraydesign.AffymetrixCdfLocatorUtil
 
getCel_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getCELFeatureIterator(Long) - Method in class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
getCelFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getCelFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getCelFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getCellLine() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCellLineId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCellLines() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCellType() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCellTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCellTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getChannel() - Method in interface org.biomage.Interface.HasChannel
Get method for channel
getChannel() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for channel
getChannel_list() - Method in class org.biomage.BioAssay.BioAssay_package
Get method for channel_list
getChannelId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getChannelOne() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getChannelOneExtract() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelOneExtract() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelOneExtract() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannelOneFactorValues() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelOneFactorValues() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelOneFactorValues() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannelOneSpike() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getChannelOneSpikedControl() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelOneSpikedControl() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelOneSpikedControl() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannels() - Method in class org.biomage.BioAssay.BioAssay
Get method for channels
getChannels() - Method in class org.biomage.BioAssay.Image
Get method for channels
getChannels() - Method in interface org.biomage.Interface.HasChannels
Get method for channels
getChannelTwo() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getChannelTwoExtract() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getChannelTwoExtract() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelTwoExtract() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelTwoExtract() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannelTwoExtract() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getChannelTwoFactorValues() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getChannelTwoFactorValues() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelTwoFactorValues() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelTwoFactorValues() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannelTwoFactorValues() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getChannelTwoSpike() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getChannelTwoSpikedControl() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getChannelTwoSpikedControl() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getChannelTwoSpikedControl() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getChannelTwoSpikedControl() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getChannelTwoSpikedControl() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getCharacteristics() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
getCharacteristics() - Method in class org.biomage.BioMaterial.BioMaterial
Get method for characteristics
getCharacteristics() - Method in interface org.biomage.Interface.HasCharacteristics
Get method for characteristics
getCharacteristicsFromSourceBioSourcesOf(long, Class) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieves a list of distinct characteristics of the source BioSource's that are used to produce the specified product BioSample or LabeledExtract.
getCharList() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getChildVocabularies(long) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getChildVocabularies(long) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
getChp_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getChpFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getChpFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getChpFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getChromosomalAberrationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getChromosomalAberrations() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getChromosomalAberrationTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getChromosomalAberrationTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getCity() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getCity() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getCity() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getClassDoc() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the documentation for the class.
getClassFileName() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns Class name.
getClassMapper(Class, Class) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository
 
getClassMapper() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getClassMappers(Class) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository
 
getClassName() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
getClassName() - Method in class gov.nih.nci.caarray.services.security.mageom.PathElement
 
getClassName() - Method in class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
getClassName() - Method in class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
getClassName() - Method in class org.biomage.tools.generate_classes.CreatePackageFile
Description: Returns the class name of the class.
getClassWithModelName(String) - Method in class org.biomage.Common.MAGEJava
getClassWithModelName(String modelName) This method returns a MAGE class given it's common Model name.
getClinicalHistory() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getClinicalTest() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getClinicalTreatment() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getClusterBioAssayData() - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Get method for clusterBioAssayData
getClusterBioAssayData() - Method in interface org.biomage.Interface.HasClusterBioAssayData
Get method for clusterBioAssayData
getCode(String) - Method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypes
 
getCol() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
getColumn() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
getColumn() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
getColumn() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
getColumn() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getColumn() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
getColumn() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getColumn() - Method in class org.biomage.ArrayDesign.Zone
Get method for column
getColumn() - Method in class org.biomage.DesignElement.FeatureLocation
Get method for column
getColumnDelimiter() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTableMap
 
getColumnId() - Method in class org.biomage.tools.generate_er.ForeignKey
Description: get the column id of the foreign key
getColumnId() - Method in class org.biomage.tools.generate_er.Index
Description: get the column id of the column that is indexed
getColumnID() - Method in class org.biomage.tools.generate_er.PrimaryKey
Description: get id of the primery key column
getColumnInt() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getColumnName() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataColumnDescriptor
 
getColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
getColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Returns the column names that are to be read.
getColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTableMap
 
getColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
getColumnNumber() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
getComment() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the comment.
getComment() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for comment.
getComment() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get the comment of the column
getComment() - Method in class org.biomage.tools.generate_er.Table
Description: get teh comment of the table
getCompleteDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getCompletionDate() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getCompletionDateFormatted() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getCompletionPercent() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getComponentCompounds() - Method in class org.biomage.BioMaterial.Compound
Get method for componentCompounds
getComponentCompounds() - Method in interface org.biomage.Interface.HasComponentCompounds
Get method for componentCompounds
getComposite() - Method in class org.biomage.DesignElement.CompositePosition
Get method for composite
getComposite() - Method in interface org.biomage.Interface.HasComposite
Get method for composite
getCompositeCompositeMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
Get method for compositeCompositeMap_list
getCompositeCompositeMaps() - Method in class org.biomage.DesignElement.CompositeSequence
Get method for compositeCompositeMaps
getCompositeCompositeMaps() - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Get method for compositeCompositeMaps
getCompositeGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Retrieve the CompositeGroup that has the specified ID.
getCompositeGroup_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Get method for compositeGroup_list
getCompositeGroupId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
getCompositeGroups(CompositeGroupSearchCriteria) - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Searches compositeGroups.
getCompositeGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for compositeGroups
getCompositeGroups() - Method in interface org.biomage.Interface.HasCompositeGroups
Get method for compositeGroups
getCompositeIterator(Long) - Method in class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
getCompositePositionSources() - Method in class org.biomage.DesignElement.CompositeCompositeMap
Get method for compositePositionSources
getCompositePositionSources() - Method in interface org.biomage.Interface.HasCompositePositionSources
Get method for compositePositionSources
getCompositeSequence() - Method in class org.biomage.DesignElement.CompositeCompositeMap
Get method for compositeSequence
getCompositeSequence() - Method in class org.biomage.DesignElement.ReporterCompositeMap
Get method for compositeSequence
getCompositeSequence() - Method in interface org.biomage.Interface.HasCompositeSequence
Get method for compositeSequence
getCompositeSequence_list() - Method in class org.biomage.DesignElement.DesignElement_package
Get method for compositeSequence_list
getCompositeSequences() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
getCompositeSequences() - Method in class org.biomage.ArrayDesign.CompositeGroup
Get method for compositeSequences
getCompositeSequences() - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Get method for compositeSequences
getCompositeSequences() - Method in interface org.biomage.Interface.HasCompositeSequences
Get method for compositeSequences
getCompound() - Method in class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData
 
getCompound() - Method in class org.biomage.BioMaterial.CompoundMeasurement
Get method for compound
getCompound() - Method in interface org.biomage.Interface.HasCompound
Get method for compound
getCompound_list() - Method in class org.biomage.BioMaterial.BioMaterial_package
Get method for compound_list
getCompoundData() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundID() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundIndices() - Method in class org.biomage.BioMaterial.Compound
Get method for compoundIndices
getCompoundIndices() - Method in interface org.biomage.Interface.HasCompoundIndices
Get method for compoundIndices
getCompoundMData() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getCompoundMData() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getCompoundMeasurements() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getCompoundMeasurements() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundMeasurements() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundMeasurements() - Method in class org.biomage.BioMaterial.Treatment
Get method for compoundMeasurements
getCompoundMeasurements() - Method in interface org.biomage.Interface.HasCompoundMeasurements
Get method for compoundMeasurements
getCompoundmeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundmeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundmeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundmeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundmeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundmeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundmeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundmeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundmeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundModifyUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompoundOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompoundOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getCompounds() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCompounds() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getConcreteSubClassNames() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: A vector of the instantiable subclass class names.
getConfidenceIndicators() - Method in interface org.biomage.Interface.HasConfidenceIndicators
Get method for confidenceIndicators
getConfidenceIndicators() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for confidenceIndicators
getConfirmPassword() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getConnection() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
getConnection() - Method in class org.biomage.tools.helpers.DbConnectionBroker
 
getConnection() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
getConstrainedElements(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns a NodeList of constrained elements.
getConstraintString(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the string representing the constraint.
getContact() - Method in class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData
 
getContact() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData
 
getContact() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getContact() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getContact() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getContact() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getContact() - Method in class org.biomage.ArrayDesign.DesignProviderRole
 
getContact() - Method in class org.biomage.Experiment.ExperimentProviderRole
 
getContact_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Get method for contact_list
getContactId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getContactId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getContactID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getContactor() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getContactor() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getContacts() - Method in class org.biomage.Description.Database
Get method for contacts
getContacts() - Method in interface org.biomage.Interface.HasContacts
Get method for contacts
getContainedFeatures() - Method in class org.biomage.BioAssayData.FeatureDimension
Get method for containedFeatures
getContainedFeatures() - Method in interface org.biomage.Interface.HasContainedFeatures
Get method for containedFeatures
getContent() - Method in interface org.biomage.tools.xmlutils.PCData
 
getContent() - Method in class org.biomage.tools.xmlutils.PCDataImpl
 
getContentType() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getContentType() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getContentType() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getContentType() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getContentType() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getContentType() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the content type for this file.
getControlFeatures() - Method in class org.biomage.DesignElement.Feature
Get method for controlFeatures
getControlFeatures() - Method in interface org.biomage.Interface.HasControlFeatures
Get method for controlFeatures
getControlledFeatures() - Method in class org.biomage.DesignElement.Feature
Get method for controlledFeatures
getControlledFeatures() - Method in interface org.biomage.Interface.HasControlledFeatures
Get method for controlledFeatures
getControlType() - Method in class org.biomage.DesignElement.DesignElement
Get method for controlType
getControlType() - Method in interface org.biomage.Interface.HasControlType
Get method for controlType
getConvertFields() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.TargetClass
 
getCoordinate() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for coordinate
getCoordinate() - Method in interface org.biomage.Interface.HasCoordinate
Get method for coordinate
getCopied() - Method in class org.biomage.BioMaterial.BioMaterial
 
getCopyLabelExtract() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getCopyLabelExtractChannel2() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getCopySpikeControl() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getCopySpikeControlChannel2() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getCountry() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getCountry() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getCountry() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getCrc32() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
getCreateFile() - Method in class org.biomage.tools.generate_classes.CreateFile.IdentifierAttrInformation
Description: Method to return the underlying CreateFile the association is based on.
getCreatingSoftware() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getCreatingSoftware() - Method in enum org.biomage.BioAssayData.SourceType
 
getCreatingSoftwareVersion() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getCreationDate() - Method in class gov.nih.nci.caarray.common.data.util.FileData
 
getCreationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getCreationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getCreationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getCreationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getCreationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getCube() - Method in class gov.nih.nci.caarray.services.fileparse.CubeCreator
 
getCube() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.BioDataCubeCreator
 
getCubeStringBDQ(BioAssay) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
Get the cube in the order people like to see it
getCubeStringBQD(BioAssay) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
Get the cube in the caArray natural order
getCultivarOrEcotype() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm
 
getCuratorMessage() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getCurrentDate() - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getCurrentFileName() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
This method is called by the thread to pass the current uploading file name to the applet for display, so the user knows what file is being uploaded.
getCurrentFileName() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getCurrentSelection() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
getDarrayDesignID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getData(String) - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
getData() - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
getDataAccessMode() - Static method in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
getDataAccessMode() - Static method in class gov.nih.nci.caarray.services.security.test.Tester
 
getDataAccessMode() - Static method in class gov.nih.nci.caarray.services.test.Tester
 
getDataAccessMode() - Static method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
getDatabase() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
getDatabase() - Method in class org.biomage.Description.DatabaseEntry
Get method for database
getDatabase() - Method in interface org.biomage.Interface.HasDatabase
Get method for database
getDatabase_list() - Method in class org.biomage.Description.Description_package
Get method for database_list
getDatabaseId() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getDatabaseName() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getDatabaseReference() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getDatabaseReference() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getDatabaseReferences() - Method in class org.biomage.Description.Description
Get method for databaseReferences
getDatabaseReferences() - Method in interface org.biomage.Interface.HasDatabaseReferences
Get method for databaseReferences
getDatabases() - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getDatabases(String) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getDatabases() - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
getDatabases(String) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
Retrieves a list of public databases that are applicable for the specified controlled vocabulary's category.
getDatabases(String, Boolean) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getDatabases() - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getDatabases() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getDatabaseVersion() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getDataColumn() - Method in class org.biomage.tools.generate_er.PrimaryKey
Description: get primary key column
getDataColumnDescriptor() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getDataColumnVector() - Method in class org.biomage.tools.generate_er.Table
Description: get the vector for all simple data columns
getDataExternal() - Method in class org.biomage.BioAssayData.BioDataCube
Get method for dataExternal
getDataExternalFiles() - Method in class gov.nih.nci.caarray.services.util.mage.MAGEWriter
Gets the DataExternal files created for the dependent BioAssay's if the generated object is an Experiment.
getDataFile() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getDataFile() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getDataFileProcessorService(UploadFileTypes.MICROARRAY_FILE_TYPE) - Static method in class gov.nih.nci.caarray.services.fileparse.DataFileProcessorFactory
 
getDataFilesDirectory(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getDataFilesDirectory(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Gets the directory for storing additional uploaded files and and additional data processing files that are associated with an experiment.
getDataFormat() - Method in class org.biomage.BioAssayData.DataExternal
Get method for dataFormat
getDataFormatInfoURI() - Method in class org.biomage.BioAssayData.DataExternal
Get method for dataFormatInfoURI
getDataFromForm(ArrayDesignBaseForm, ArrayDesignData) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
getDataHeader() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSet
 
getDataHeaderMap() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
getDataInternal() - Method in class org.biomage.BioAssayData.BioDataCube
Get method for dataInternal
getDataMatrix(String, String) - Method in interface gov.nih.nci.caarray.services.fileparse.DataFileProcessor
 
getDataMatrix(String, String) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprParsingService
 
getDataProcessHardwareParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessHardwareSerialNumber() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessProtocolDescription() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessProtocolParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessProtocolPerformers() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessSoftwareParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessSoftwareReleaseDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessSoftwareVersion() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataProcessURI() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDataSet() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
getDataSetMapper(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getDataSetMapper() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
getDataSetMapper() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
getDataSetMapper(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.DataSetMapperMap
 
getDataSetMapperMap() - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getDataSetMapperMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.util.DataSetMapperMap
 
getDataSource() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getDataTable() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSet
 
getDataTableMap() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
getDataType() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
getDataType() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getDataType() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getDataType() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Get method for dataType
getDataType() - Method in interface org.biomage.Interface.HasDataType
Get method for dataType
getDataType() - Method in class org.biomage.Protocol.Parameter
Get method for dataType
getDataType() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for dataType
getDatatype() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for datatype.
getDatatype(CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: Pass through get method for datatype.
getDatatype(CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAttrInformation
Description: Pass through get method for datatype.
getDataTypeId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getDataTypes() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getDataZipFile(String, long) - Static method in class gov.nih.nci.caarray.ui.experiment.ExperimentFileDownloadServlet
 
getDate() - Method in class org.biomage.AuditAndSecurity.Audit
Get method for date
getDateFromString(String) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getDateFromString() - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getDateString(Date, String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getDatum() - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
Get method for datum
getDbName() - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
getDefaultDateString(Date) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getDefaultURL() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getDefaultURL() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getDefaultURL() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getDefaultURLWithSid() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
This method will return a defaultURL string with a session id (jsessionid) appended at the end for session identification by the server.
getDefaultValue() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
getDefaultValue() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getDefaultValue() - Method in interface org.biomage.Interface.HasDefaultValue
Get method for defaultValue
getDefaultValue() - Method in class org.biomage.Protocol.Parameter
Get method for defaultValue
getDefectType() - Method in class org.biomage.Array.FeatureDefect
Get method for defectType
getDefectType() - Method in class org.biomage.Array.ZoneDefect
Get method for defectType
getDefectType() - Method in interface org.biomage.Interface.HasDefectType
Get method for defectType
getDeleteAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getDeleteLabel() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getDeltaX() - Method in class org.biomage.Array.PositionDelta
Get method for deltaX
getDeltaY() - Method in class org.biomage.Array.PositionDelta
Get method for deltaY
getDepartment() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getDepartment() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getDepartment() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getDept() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getDerivedBioAssay() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getDerivedBioAssay() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getDerivedBioAssayData() - Method in class org.biomage.BioAssay.DerivedBioAssay
Get method for derivedBioAssayData
getDerivedBioAssayData() - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Get method for derivedBioAssayData
getDerivedBioAssayDataTarget() - Method in class org.biomage.BioAssayData.Transformation
Get method for derivedBioAssayDataTarget
getDerivedBioAssayDataTarget() - Method in interface org.biomage.Interface.HasDerivedBioAssayDataTarget
Get method for derivedBioAssayDataTarget
getDerivedBioAssayMap() - Method in class org.biomage.BioAssay.DerivedBioAssay
Get method for derivedBioAssayMap
getDerivedBioAssayMap() - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Get method for derivedBioAssayMap
getDesc() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getDesc() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Returns the description of the specific status change for the uploaded file (can be null)
getDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Returns the description of the specific status change for the uploaded file (can be null)
getDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getDescription() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
getDescription() - Method in class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.fileparse.test.usecases.CanParseFiles
Get descriptive information on use case
getDescription() - Method in interface gov.nih.nci.caarray.services.fileparse.test.usecases.UseCase
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Returns the description of the specific status change for the uploaded file (can be null)
getDescription() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getDescription() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Returns the description of the specific status change for the uploaded file (can be null)
getDescription() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElement
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItf
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CanUserAccessElementItfPG
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.CreateSecuredElement
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetElementProtectionGroups
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetProtectionGroups
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.GetUserRole
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.IsUsrElementOwner
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.RemoveSecuredElement
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementOwner
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementProtectionGroups
Get descriptive information on use case
getDescription() - Method in interface gov.nih.nci.caarray.services.security.test.usecases.UseCase
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.test.usecases.ExportMAGEML
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistArrayDesign
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistExperiment
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.test.usecases.PersistProtocol
Get descriptive information on use case
getDescription() - Method in interface gov.nih.nci.caarray.services.test.usecases.UseCase
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetBioAssayDatum
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.CanGetByQuantitationType
Get descriptive information on use case
getDescription() - Method in interface gov.nih.nci.caarray.services.util.netcdf.test.usecases.UseCase
Get descriptive information on use case
getDescription() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getDescription() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getDescription() - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Get method for description
getDescription() - Method in class org.biomage.Description.OntologyEntry
Get method for description
getDescription() - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
getDescription_() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getDescription_package() - Method in class org.biomage.Common.MAGEJava
Get method for description_package
getDescriptions() - Method in class org.biomage.Common.Describable
Get method for descriptions
getDescriptions() - Method in interface org.biomage.Interface.HasDescriptions
Get method for descriptions
getDesignElement() - Method in class org.biomage.BioAssayData.DesignElementTuple
Get method for designElement
getDesignElement() - Method in interface org.biomage.Interface.HasDesignElement
Get method for designElement
getDesignElement_package() - Method in class org.biomage.Common.MAGEJava
Get method for designElement_package
getDesignElementColumn2PropertyMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
getDesignElementColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
getDesignElementColumnsMap() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
getDesignElementDimension() - Method in class org.biomage.BioAssayData.BioAssayData
Get method for designElementDimension
getDesignElementDimension() - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Get method for designElementDimension
getDesignElementDimension() - Method in interface org.biomage.Interface.HasDesignElementDimension
Get method for designElementDimension
getDesignElementDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for designElementDimension_list
getDesignElementGroupShortClassName(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.DesignElementManagerDB
 
getDesignElementId() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
getDesignElementId() - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingDesignElement
 
getDesignElementList(Long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElementService
 
getDesignElementMapping() - Method in class org.biomage.BioAssayData.Transformation
Get method for designElementMapping
getDesignElementMapping() - Method in interface org.biomage.Interface.HasDesignElementMapping
Get method for designElementMapping
getDesignElementMaps() - Method in class org.biomage.BioAssayData.DesignElementMapping
Get method for designElementMaps
getDesignElementMaps() - Method in interface org.biomage.Interface.HasDesignElementMaps
Get method for designElementMaps
getDesignElementProperties() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
getDesignElements(long, HybridizationFileType) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.DesignElementFinder
 
getDesignElementService(UploadFileTypes.MICROARRAY_FILE_TYPE) - Static method in class gov.nih.nci.caarray.services.fileparse.DesignElementServiceFactory
 
getDesignElementsFileLocation(Long, UploadFileTypes.MICROARRAY_FILE_TYPE) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getDesignElementsFileLocation(long, HybridizationFileType) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Get the cache file for DesignElements based on the specified UploadFileType provided by the new hybridization parsing service.
getDesignElementsFromFile(String, DesignElementColumnsMap) - Method in class gov.nih.nci.caarray.services.fileparse2.DesignElementManagerDB
 
getDesignElementTuples() - Method in class org.biomage.BioAssayData.BioAssayTuple
Get method for designElementTuples
getDesignElementTuples() - Method in interface org.biomage.Interface.HasDesignElementTuples
Get method for designElementTuples
getDesignProviderRoles() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
getDesignProviderRoles() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getDesignProviders() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for designProviders
getDesignProviders() - Method in interface org.biomage.Interface.HasDesignProviders
Get method for designProviders
getDestination() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getDetails(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
Performs a new specific search using the OntologyEntry id value as provided from the intial search results and passed in the request by user selection.
getDevelopmentalStage() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDevelopmentalStageId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDevelopmentalStages() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDfactorNameID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDfactorValueID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getDirectory() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
getDiseaseLocation() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseLocationId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseLocations() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseStage() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseStageId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseStages() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseState() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseStateId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDiseaseStates() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getDisplayName() - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
getDistanceUnit() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getDistanceUnit() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getDistanceUnit() - Method in class org.biomage.Array.ArrayGroup
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.Array.Fiducial
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.Array.PositionDelta
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.ArrayDesign.Zone
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.ArrayDesign.ZoneLayout
Get method for distanceUnit
getDistanceUnit() - Method in class org.biomage.DesignElement.Position
Get method for distanceUnit
getDistanceUnit() - Method in interface org.biomage.Interface.HasDistanceUnit
Get method for distanceUnit
getDocumentation(Map, String) - Static method in class org.biomage.tools.generate_classes.CreateFile
Description: Obtains the documentation for the given id.
getDOMFromFile(String) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Reads the file and creates the DOM structure.
getDurationString() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Calculate the day, hour, minute and second used for uploading this batch of files, and compose a StringBuffer to be used by the applet as part of the summary content.
getDurationString() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getEditable() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
getEditable() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getEditable() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getEditor() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getEditor() - Method in class org.biomage.BQS.BibliographicReference
Get method for editor
getElementGroups(String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Returns an array of ProtectionGroups with which the protectionElement is associated
getElementID(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the ID of the element.
getElementIDRef(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the IDRef of the element.
getElementName(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the name of the element.
getElementProtectionGroups(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets Protection Groups associated with a Object
getElementProtectionGroups(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets Protection Groups associated with a Object
getElementProtectionGroups(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets Protection Groups associated with a Object
getElementProtectionGroups(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets Protection Groups associated with a Object
GetElementProtectionGroups - Class in gov.nih.nci.caarray.services.security.test.usecases
 
GetElementProtectionGroups() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.GetElementProtectionGroups
 
getElementText(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the text of the element.
getElementTypes() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.CollectionField
 
getElementValue(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the value of the element.
getEmail() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
getEmail() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
getEmail() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getEmail(String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthenticationDAItf
The email address associated with the login name.
getEmail(String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecurityServiceItf
The email address associated with the login name.
getEmail(String) - Method in class gov.nih.nci.caarray.services.security.LdapAuthenticationDAObj
The email address associated with the login name.
getEmail(String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthenticationDAObj
The email address associated with the login name.
getEmail(String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
The email address associated with the login name.
getEmail(String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
The email address associated with the owner of an object.
getEmail() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getEmail() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getEmail() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getEmail() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getEmail() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for email
getEmailAddress() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getEmailAddress() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getEmailAddress() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getEmailAddress() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getEmailAddress() - Method in class org.biomage.AuditAndSecurity.User
 
getEmailSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getEnd() - Method in class org.biomage.BioSequence.SequencePosition
Get method for end
getEndAtLine() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Returns the endAtLine.
getEndDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getEndDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getEndDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getEndDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getEndJumptoUrl() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getEndManufactureDate() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getEnumValues() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for whether the datatype is an enumeration.
getEnumValues(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getEnumVector() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get all enumeration values
getEnvironmentalHistoryDesign() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getError() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getError() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getError() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getError() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getError() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getError() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getErrorCode() - Method in exception gov.nih.nci.caarray.common.exception.GeneralException
 
getErrors() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
 
getErrors() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getEventOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getEventOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getExp_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperiment() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
getExperiment() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
getExperiment() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getExperiment() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getExperiment() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getExperiment(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getExperiment() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getExperiment(Long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getExperiment(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves the Experiment object from the persistence store.
getExperiment(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getExperiment() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getExperiment() - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
getExperiment() - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
getExperiment() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getExperiment_list() - Method in class org.biomage.Experiment.Experiment_package
Get method for experiment_list
getExperiment_package() - Method in class org.biomage.Common.MAGEJava
Get method for experiment_package
getExperimentalFactor(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getExperimentalFactor() - Method in class org.biomage.Experiment.FactorValue
Get method for experimentalFactor
getExperimentalFactor() - Method in interface org.biomage.Interface.HasExperimentalFactor
Get method for experimentalFactor
getExperimentalFactors() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getExperimentalFactors(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
getExperimentalFactors(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getExperimentalFactors() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for experimentalFactors
getExperimentalFactors() - Method in interface org.biomage.Interface.HasExperimentalFactors
Get method for experimentalFactors
getExperimentCompleteDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentCompleteDate() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentCompleteDate_() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentData() - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
getExperimentDataFilesDirectory(Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the experimentData files, if not there it makes it.
getExperimentDataFilesDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getExperimentDate(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
Workaround for efficiency to get the date for experiment fast.
getExperimentDesc() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getExperimentDesigns() - Method in class org.biomage.Experiment.Experiment
Get method for experimentDesigns
getExperimentDesigns() - Method in interface org.biomage.Interface.HasExperimentDesigns
Get method for experimentDesigns
getExperimentFactorData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentFactorScaleID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentFactorTypeID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentId() - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
getExperimentId() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getExperimentIds() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getExperimentIdsToDelete() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getExperimentInputFileDirectory(Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the input files, if the directory doesn't exist, it is created.
getExperimentInputFileDirectory(long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the input files, if the directory doesn't exist, it is created.
getExperimentInputFileDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Input directory for Experiment MAGEML upload
getExperimentMAGEMLData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentMAGEMLFileDirectory() - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the experimentMAGEML files, if the directory doesn't exists, creates it.
getExperimentMAGEMLFileDirectory(Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Finds the logical directory for the generated experiment MAGEML files, if the directory doesn't exists, creates it.
getExperimentMAGEMLFileDirectory(Long, boolean) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getExperimentName() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getExperimentName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getExperimentProviderRoles() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getExperiments() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getExperiments(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
Gets Experiments.
getExperimentSearchTypeID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getExperimentsReferencingArrayGroup(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getExperimentTitle() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentTitle() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getExperimentTitle() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentTitle_() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentType() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getExperimentType() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getExperimentType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExperimentType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getExperimentType() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentType_() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExperimentTypeID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getExperimentTypes() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getExperimentView(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getExperimentView(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Retrieves the Experiment object from the persistence store.
getExperimentVisibilities() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getExpFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getExpFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getExpFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getExpId() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
getExpId() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
 
getExpId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getExpId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getExportedFromDB() - Method in class org.biomage.Description.ExternalReference
Get method for exportedFromDB
getExportedFromServer() - Method in class org.biomage.Description.ExternalReference
Get method for exportedFromServer
getExportID() - Method in class org.biomage.Description.ExternalReference
Get method for exportID
getExportName() - Method in class org.biomage.Description.ExternalReference
Get method for exportName
getExtension(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileUtility
Returns the extension part of the file's name.
getExtension(File) - Static method in class gov.nih.nci.caarray.services.util.file.FileUtility
Returns the extension part of the file's name.
getExtension() - Method in enum org.biomage.BioAssayData.SourceType
 
getExternalLIMS() - Method in class org.biomage.BioMaterial.Compound
Get method for externalLIMS
getExternalLIMS() - Method in interface org.biomage.Interface.HasExternalLIMS
Get method for externalLIMS
getExternalReference() - Method in class org.biomage.Description.Description
Get method for externalReference
getExternalReference() - Method in interface org.biomage.Interface.HasExternalReference
Get method for externalReference
getExtract() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getExtract() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getExtract() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExtract() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getExtractCh2() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getExtractID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getExtractID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getExtractIDCh2() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFactorForChannelOne() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFactorForChannelOne() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getFactorForChannelTwo() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFactorForChannelTwo() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getFactorID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorLevel() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getFactorLevelCh2() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getFactorLevelChOne() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFactorLevelChTwo() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFactorLevels() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getFactorName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFactorDataObject
 
getFactorNames() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorNames() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getFactorTypes() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorValue() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorValue() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFactorDataObject
 
getFactorValueID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactorValues() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
getFactorValues() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getFactorValues(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getFactorValues(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
getFactorValues(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getFactorValues() - Method in class org.biomage.Experiment.ExperimentalFactor
Get method for factorValues
getFactorValues() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getFactorValues() - Method in interface org.biomage.Interface.HasFactorValues
Get method for factorValues
getFactTypes() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFactTypes() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getFailFiles() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
returns all failed files to applet so applet can display them as part of the summary popup window.
getFailFiles() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getFailTypes() - Method in class org.biomage.DesignElement.Reporter
Get method for failTypes
getFailTypes() - Method in interface org.biomage.Interface.HasFailTypes
Get method for failTypes
getFailureDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
getFailureDescription() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getFailureDescription() - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
getFailureMessage() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Returns error message derived from the Exception thrown during the uploading process at the time of this method is called.
getFailureMessage() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getFamilyHistory() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getFax() - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
getFax() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for fax
getFaxNumber() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getFaxNumber() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getFaxNumber() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getFeature() - Method in class org.biomage.Array.FeatureDefect
Get method for feature
getFeature() - Method in class org.biomage.Array.ManufactureLIMS
Get method for feature
getFeature() - Method in class org.biomage.DesignElement.FeatureInformation
Get method for feature
getFeature() - Method in interface org.biomage.Interface.HasFeature
Get method for feature
getFeatureActivateDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureActivateDate() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getFeatureData() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
 
getFeatureDefects() - Method in class org.biomage.Array.ArrayManufactureDeviation
Get method for featureDefects
getFeatureDefects() - Method in interface org.biomage.Interface.HasFeatureDefects
Get method for featureDefects
getFeatureDiameter() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getFeatureExtraction() - Method in class org.biomage.BioAssay.MeasuredBioAssay
Get method for featureExtraction
getFeatureExtraction() - Method in interface org.biomage.Interface.HasFeatureExtraction
Get method for featureExtraction
getFeatureExtractionProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getFeatureExtractionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getFeatureExtractionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getFeatureExtractionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getFeatureGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Retrieve the FeatureGroup that has the specified ID.
getFeatureGroup() - Method in class org.biomage.DesignElement.Feature
Get method for featureGroup
getFeatureGroup() - Method in interface org.biomage.Interface.HasFeatureGroup
Get method for featureGroup
getFeatureGroupId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getFeatureGroups(FeatureGroupSearchCriteria) - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Searches featureGroups.
getFeatureGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for featureGroups
getFeatureGroups() - Method in interface org.biomage.Interface.HasFeatureGroups
Get method for featureGroups
getFeatureHeight() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getFeatureHeight() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getFeatureHeight() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for featureHeight
getFeatureInformationSources() - Method in class org.biomage.DesignElement.FeatureReporterMap
Get method for featureInformationSources
getFeatureInformationSources() - Method in interface org.biomage.Interface.HasFeatureInformationSources
Get method for featureInformationSources
getFeatureIterator(Long) - Method in class gov.nih.nci.caarray.services.fileparse.FileParseManagerDB
 
getFeatureLength() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getFeatureLength() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getFeatureLength() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for featureLength
getFeatureLIMSs() - Method in class org.biomage.Array.ArrayManufacture
Get method for featureLIMSs
getFeatureLIMSs() - Method in interface org.biomage.Interface.HasFeatureLIMSs
Get method for featureLIMSs
getFeatureLocation() - Method in class org.biomage.DesignElement.Feature
Get method for featureLocation
getFeatureLocation() - Method in interface org.biomage.Interface.HasFeatureLocation
Get method for featureLocation
getFeatureNum() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
getFeatureParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureParameters() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getFeaturePerformerID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getFeatureProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getFeatureProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFeatureProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFeatureProtocolData(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
getFeatureProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getFeatureProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFeatureProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFeatureProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getFeatureProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFeatureProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFeatureProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFeatureReporterMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
Get method for featureReporterMap_list
getFeatureReporterMaps() - Method in class org.biomage.DesignElement.Reporter
Get method for featureReporterMaps
getFeatureReporterMaps() - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Get method for featureReporterMaps
getFeatures() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for features
getFeatures() - Method in interface org.biomage.Interface.HasFeatures
Get method for features
getFeatureShape() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getFeatureShape() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getFeatureShape() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for featureShape
getFeatureShape() - Method in interface org.biomage.Interface.HasFeatureShape
Get method for featureShape
getFeatureWidth() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getFeatureWidth() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getFeatureWidth() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for featureWidth
getFiducials() - Method in class org.biomage.Array.ArrayGroup
Get method for fiducials
getFiducials() - Method in interface org.biomage.Interface.HasFiducials
Get method for fiducials
getFiducialType() - Method in class org.biomage.Array.Fiducial
Get method for fiducialType
getFiducialType() - Method in interface org.biomage.Interface.HasFiducialType
Get method for fiducialType
getFieldMapperInfo() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getFieldMappers() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
getFileAdditional() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getFileArrayDesignData() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
getFileCategory() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getFileData() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the data for this file as a byte array.
getFileData() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
getFileData() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
getFileElements() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns a hash table containing the file (that is, non-text) request parameters.
getFileEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
getFileEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
getFileEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
 
getFileEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getFileEntryId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
getFileEntryId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
 
getFileEntryId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getFileExtension() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getFileExtension() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getFileExtension() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getFileGAL() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getFileGroupId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
getFileGroupId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
getFileGroupId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
getFileGroupId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFileGroupId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getFileHeaderParser(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getFileHeaderParser() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
Returns the optionally configured parser for parsing a file's header.
getFileHistoryEntries(FileUploadHistorySearchCriteria) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Gets MAGEMLFileUploadEntries.
getFileId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getFileId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getFileList() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getFileList() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
getFileList() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
getFileList() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFileListForArrayDesign(String) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
getFileListForExperiment(long) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
getFileListForMageOM(String) - Method in class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
getFileListSize() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
To return the size of the fileList.
getFileListSize() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
To return the size of the fileList.
getFileMAGE() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getFileMAGEML() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFileMappingType() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
getFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getFileName() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
getFileName() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
getFileName() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
getFileName(File) - Method in class gov.nih.nci.caarray.services.util.file.ReadZipFileContent
 
getFilename(File, int) - Static method in class gov.nih.nci.caarray.services.util.file.ZipUtil
Returns the file name (with no path) for the Zip entry at the index given.
getFileName() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
To retrieve the file name from file's absolute path.
getFileName() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the (client-side) file name for this file.
getFileName() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getFileName() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getFileName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getFileNameMap() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
get a Map of the selected files (the key is the file name, the data is the file type)
getFilenames() - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
getFileNamesFromFileUploadEntries() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
 
getFilenameURI() - Method in class org.biomage.BioAssayData.DataExternal
Get method for filenameURI
getFileNameWithoutParent(String) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
Returns only the file if the specified fileName is a full path.
getFileNameWithoutParentAndExtension(String) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
Returns only the file if the specified fileName is a full path and has extension.
getFileNameWithoutParentAndExtension(FileUploadEntryData) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
getFileNameWithoutParentAndExtension(String, FileType) - Static method in class gov.nih.nci.caarray.services.fileupload2.FileUploadUtils
 
getFileParser(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getFileParser() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
getFileParsingEntry() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadEntryData
 
getFileParsingEntry() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getFileParsingEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
 
getFileParsingEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
getFileParsingEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getFileParsingEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
getFileParsingEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
getFileParsingEntryId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getFileParsingEntryId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
getFileParsingEntryId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getFilePath() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
getFilePath() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getFilePath() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getFiles() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getFiles() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
getFileSize() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the size, in bytes, of this file.
getFileType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap
 
getFileType() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the fileType of this upload file.
getFileType() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getFileType(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeFactory
 
getFileType() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
getFileType() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the fileType of this upload file.
getFileType() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
getFileType() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
getFileType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFileType() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFileType() - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Returns what kind of model element this class is based on.
getFileType() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns what kind of model element this class is based on.
getFileType() - Method in class org.biomage.tools.generate_classes.CreateInterfaceFile
Description: Returns what kind of model element this class is based on.
getFileType() - Method in class org.biomage.tools.generate_classes.CreateMAGEFile
Description: Returns what kind of model element this class is based on.
getFileType() - Method in class org.biomage.tools.generate_classes.CreatePackageFile
Description: Returns what kind of model element this class is based on.
getFileType() - Method in class org.biomage.tools.generate_java.CreateTransformedInterfaceFile
 
getFileTypeByGuessing(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getFileTypeById(String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getFileTypeById(String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getFileTypeById(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getFileTypeId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the fileType of this upload file.
getFileTypeId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getFileTypeId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the fileType of this upload file.
getFileTypeMappings() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap
 
getFileTypeName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getFileTypes() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getFileUploadAction() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return sample fileUploadAction after formatting.
getFileUploadEntries() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
 
getFileUploadEntries(FileType) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getFileUploadEntries() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getFileUploadEntries() - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
getFileUploadEntries() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
getFileUploadEntries() - Method in class gov.nih.nci.caarray.services.hybridization.HybridizationDataJob
 
getFileUploadEntry() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Returns the id for the FileUploadEntry record associated with this history record, foreign key.
getFileUploadEntry() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistorySearchCriteria
 
getFileUploadEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
Returns the FileUploadEntry record associated with this ArrayDesignUploadFile record, foreign key.
getFileUploadEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Returns the id for the FileUploadEntry record associated with this history record, foreign key.
getFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getFileUploadEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
Returns the FileUploadEntry record associated with this HybridizationUploadFile record, foreign key.
getFileUploadEntry() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
Returns the FileUploadEntry record associated with this MAGEMLUploadFile record, foreign key.
getFileZipExtension() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getFirstElementByTagName(Element, String) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the first descendant Element with a given tag name, in the order in which they are encountered in a preorder traversal of this Element tree.
getFirstElementByTagNameArray(Element, String[]) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the first descendant Element with a given tag name, in the order in which they are encountered in a preorder traversal of this Element tree.
getFirstName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
getFirstName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
getFirstName() - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
getFirstName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getFirstName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getFirstName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getFirstName() - Method in class org.biomage.AuditAndSecurity.Person
Get method for firstName
getFirstName() - Method in class org.biomage.AuditAndSecurity.User
 
getFirstNameSearch() - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
getFirstNameSearch() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getFirstNameSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getFor(String, String) - Static method in enum org.biomage.BioAssayData.SourceType
 
getFor021() - Method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
orginal first dimension in the first dimension orginal third dimension in the second dimension orginal second dimension in the third dimension
getFor102() - Method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
orginal second dimension in the first dimension orginal first dimension in the second dimension orginal third dimension in the third dimension
getFor120() - Method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
orginal second dimension in the first dimension orginal third dimension in the second dimension orginal first dimension in the third dimension
getFor201() - Method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
orginal third dimension in the first dimension orginal first dimension in the second dimension orginal second dimension in the third dimension
getFor210() - Method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
orginal third dimension in the first dimension orginal second dimension in the second dimension orginal first dimension in the third dimension
getForeignKey() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the foreign key object of this table
getForeignKeyType() - Method in class org.biomage.tools.generate_er.ForeignKey
Description: get the type of the foreign key
getForeignTable() - Method in class org.biomage.tools.generate_er.ForeignKey
Description: get the name of the foreign table
getForeignTablePrimaryKey() - Method in class org.biomage.tools.generate_er.ForeignKey
Description: get the name of the foreign table primary key
getFormat() - Method in class org.biomage.BioAssay.Image
Get method for format
getFormat() - Method in interface org.biomage.Interface.HasFormat
Get method for format
getFormattedDate(Long) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getFormattedDate() - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getFormattedDate(Date) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
getFreeText() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
getFrom() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getFromAccessions(int) - Method in class org.biomage.BQS.BibliographicReference
Method to get DatabaseEntry from Accessions_list
getFromAccessions(int) - Method in interface org.biomage.Interface.HasAccessions
Method to get DatabaseEntry from Accessions_list
getFromAdjustments(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to get ZoneDefect from Adjustments_list
getFromAdjustments(int) - Method in interface org.biomage.Interface.HasAdjustments
Method to get ZoneDefect from Adjustments_list
getFromAnalysisResults(int) - Method in class org.biomage.Experiment.Experiment
Method to get BioAssayDataCluster from AnalysisResults_list
getFromAnalysisResults(int) - Method in interface org.biomage.Interface.HasAnalysisResults
Method to get BioAssayDataCluster from AnalysisResults_list
getFromAnnotations(int) - Method in class org.biomage.Description.Description
Method to get OntologyEntry from Annotations_list
getFromAnnotations(int) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to get OntologyEntry from Annotations_list
getFromAnnotations(int) - Method in interface org.biomage.Interface.HasAnnotations
Method to get OntologyEntry from Annotations_list
getFromArray_list(int) - Method in class org.biomage.Array.Array_package
Method to get Array from Array_list
getFromArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to get ArrayDesign from ArrayDesign_list
getFromArrayGroup_list(int) - Method in class org.biomage.Array.Array_package
Method to get ArrayGroup from ArrayGroup_list
getFromArrayManufacture_list(int) - Method in class org.biomage.Array.Array_package
Method to get ArrayManufacture from ArrayManufacture_list
getFromArrayManufactureDeviations(int) - Method in class org.biomage.Array.Array
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list
getFromArrayManufactureDeviations(int) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list
getFromArrayManufacturers(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get Contact from ArrayManufacturers_list
getFromArrayManufacturers(int) - Method in interface org.biomage.Interface.HasArrayManufacturers
Method to get Contact from ArrayManufacturers_list
getFromArrays(int) - Method in class org.biomage.Array.ArrayGroup
Method to get Array from Arrays_list
getFromArrays(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get Array from Arrays_list
getFromArrays(int) - Method in interface org.biomage.Interface.HasArrays
Method to get Array from Arrays_list
getFromAssociations(int) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Method to get OntologyEntry from Associations_list
getFromAssociations(int) - Method in class org.biomage.Description.OntologyEntry
Method to get OntologyEntry from Associations_list
getFromAssociations(int) - Method in interface org.biomage.Interface.HasAssociations
Method to get OntologyEntry from Associations_list
getFromAuditTrail(int) - Method in class org.biomage.Common.Describable
Method to get Audit from AuditTrail_list
getFromAuditTrail(int) - Method in interface org.biomage.Interface.HasAuditTrail
Method to get Audit from AuditTrail_list
getFromBibliographicReferences(int) - Method in class org.biomage.Description.Description
Method to get BibliographicReference from BibliographicReferences_list
getFromBibliographicReferences(int) - Method in interface org.biomage.Interface.HasBibliographicReferences
Method to get BibliographicReference from BibliographicReferences_list
getFromBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
Method to get BioAssay from BioAssay_list
getFromBioAssayData(int) - Method in class org.biomage.Experiment.Experiment
Method to get BioAssayData from BioAssayData_list
getFromBioAssayData(int) - Method in interface org.biomage.Interface.HasBioAssayData
Method to get BioAssayData from BioAssayData_list
getFromBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get BioAssayData from BioAssayData_list
getFromBioAssayDataCluster_list(int) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Method to get BioAssayDataCluster from BioAssayDataCluster_list
getFromBioAssayDataSources(int) - Method in class org.biomage.BioAssayData.Transformation
Method to get BioAssayData from BioAssayDataSources_list
getFromBioAssayDataSources(int) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Method to get BioAssayData from BioAssayDataSources_list
getFromBioAssayDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get BioAssayDimension from BioAssayDimension_list
getFromBioAssayFactorValues(int) - Method in class org.biomage.BioAssay.BioAssay
Method to get FactorValue from BioAssayFactorValues_list
getFromBioAssayFactorValues(int) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Method to get FactorValue from BioAssayFactorValues_list
getFromBioAssayMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get BioAssayMap from BioAssayMap_list
getFromBioAssayMaps(int) - Method in class org.biomage.BioAssayData.BioAssayMapping
Method to get BioAssayMap from BioAssayMaps_list
getFromBioAssayMaps(int) - Method in interface org.biomage.Interface.HasBioAssayMaps
Method to get BioAssayMap from BioAssayMaps_list
getFromBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayDimension
Method to get BioAssay from BioAssays_list
getFromBioAssays(int) - Method in class org.biomage.Experiment.Experiment
Method to get BioAssay from BioAssays_list
getFromBioAssays(int) - Method in interface org.biomage.Interface.HasBioAssays
Method to get BioAssay from BioAssays_list
getFromBioAssayTreatments(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to get BioAssayTreatment from BioAssayTreatments_list
getFromBioAssayTreatments(int) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Method to get BioAssayTreatment from BioAssayTreatments_list
getFromBioAssayTuples(int) - Method in class org.biomage.BioAssayData.BioDataTuples
Method to get BioAssayTuple from BioAssayTuples_list
getFromBioAssayTuples(int) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Method to get BioAssayTuple from BioAssayTuples_list
getFromBiologicalCharacteristics(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to get BioSequence from BiologicalCharacteristics_list
getFromBiologicalCharacteristics(int) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Method to get BioSequence from BiologicalCharacteristics_list
getFromBioMaterial_list(int) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to get BioMaterial from BioMaterial_list
getFromBioSequence_list(int) - Method in class org.biomage.BioSequence.BioSequence_package
Method to get BioSequence from BioSequence_list
getFromChannel_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
Method to get Channel from Channel_list
getFromChannels(int) - Method in class org.biomage.BioAssay.BioAssay
Method to get Channel from Channels_list
getFromChannels(int) - Method in class org.biomage.BioAssay.Image
Method to get Channel from Channels_list
getFromChannels(int) - Method in interface org.biomage.Interface.HasChannels
Method to get Channel from Channels_list
getFromCharacteristics(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to get OntologyEntry from Characteristics_list
getFromCharacteristics(int) - Method in interface org.biomage.Interface.HasCharacteristics
Method to get OntologyEntry from Characteristics_list
getFromComponentCompounds(int) - Method in class org.biomage.BioMaterial.Compound
Method to get CompoundMeasurement from ComponentCompounds_list
getFromComponentCompounds(int) - Method in interface org.biomage.Interface.HasComponentCompounds
Method to get CompoundMeasurement from ComponentCompounds_list
getFromCompositeCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to get CompositeCompositeMap from CompositeCompositeMap_list
getFromCompositeCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to get CompositeCompositeMap from CompositeCompositeMaps_list
getFromCompositeCompositeMaps(int) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Method to get CompositeCompositeMap from CompositeCompositeMaps_list
getFromCompositeGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to get CompositeGroup from CompositeGroup_list
getFromCompositeGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to get CompositeGroup from CompositeGroups_list
getFromCompositeGroups(int) - Method in interface org.biomage.Interface.HasCompositeGroups
Method to get CompositeGroup from CompositeGroups_list
getFromCompositePositionSources(int) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Method to get CompositePosition from CompositePositionSources_list
getFromCompositePositionSources(int) - Method in interface org.biomage.Interface.HasCompositePositionSources
Method to get CompositePosition from CompositePositionSources_list
getFromCompositeSequence_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to get CompositeSequence from CompositeSequence_list
getFromCompositeSequences(int) - Method in class org.biomage.ArrayDesign.CompositeGroup
Method to get CompositeSequence from CompositeSequences_list
getFromCompositeSequences(int) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Method to get CompositeSequence from CompositeSequences_list
getFromCompositeSequences(int) - Method in interface org.biomage.Interface.HasCompositeSequences
Method to get CompositeSequence from CompositeSequences_list
getFromCompound_list(int) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to get Compound from Compound_list
getFromCompoundIndices(int) - Method in class org.biomage.BioMaterial.Compound
Method to get OntologyEntry from CompoundIndices_list
getFromCompoundIndices(int) - Method in interface org.biomage.Interface.HasCompoundIndices
Method to get OntologyEntry from CompoundIndices_list
getFromCompoundMeasurements(int) - Method in class org.biomage.BioMaterial.Treatment
Method to get CompoundMeasurement from CompoundMeasurements_list
getFromCompoundMeasurements(int) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Method to get CompoundMeasurement from CompoundMeasurements_list
getFromConfidenceIndicators(int) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Method to get ConfidenceIndicator from ConfidenceIndicators_list
getFromConfidenceIndicators(int) - Method in class org.biomage.QuantitationType.QuantitationType
Method to get ConfidenceIndicator from ConfidenceIndicators_list
getFromContact_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to get Contact from Contact_list
getFromContacts(int) - Method in class org.biomage.Description.Database
Method to get Contact from Contacts_list
getFromContacts(int) - Method in interface org.biomage.Interface.HasContacts
Method to get Contact from Contacts_list
getFromContainedFeatures(int) - Method in class org.biomage.BioAssayData.FeatureDimension
Method to get Feature from ContainedFeatures_list
getFromContainedFeatures(int) - Method in interface org.biomage.Interface.HasContainedFeatures
Method to get Feature from ContainedFeatures_list
getFromControlFeatures(int) - Method in class org.biomage.DesignElement.Feature
Method to get Feature from ControlFeatures_list
getFromControlFeatures(int) - Method in interface org.biomage.Interface.HasControlFeatures
Method to get Feature from ControlFeatures_list
getFromControlledFeatures(int) - Method in class org.biomage.DesignElement.Feature
Method to get Feature from ControlledFeatures_list
getFromControlledFeatures(int) - Method in interface org.biomage.Interface.HasControlledFeatures
Method to get Feature from ControlledFeatures_list
getFromDatabase_list(int) - Method in class org.biomage.Description.Description_package
Method to get Database from Database_list
getFromDatabaseReferences(int) - Method in class org.biomage.Description.Description
Method to get DatabaseEntry from DatabaseReferences_list
getFromDatabaseReferences(int) - Method in interface org.biomage.Interface.HasDatabaseReferences
Method to get DatabaseEntry from DatabaseReferences_list
getFromDerivedBioAssayData(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to get DerivedBioAssayData from DerivedBioAssayData_list
getFromDerivedBioAssayData(int) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Method to get DerivedBioAssayData from DerivedBioAssayData_list
getFromDerivedBioAssayMap(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to get BioAssayMap from DerivedBioAssayMap_list
getFromDerivedBioAssayMap(int) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Method to get BioAssayMap from DerivedBioAssayMap_list
getFromDescriptions(int) - Method in class org.biomage.Common.Describable
Method to get Description from Descriptions_list
getFromDescriptions(int) - Method in interface org.biomage.Interface.HasDescriptions
Method to get Description from Descriptions_list
getFromDesignElementDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get DesignElementDimension from DesignElementDimension_list
getFromDesignElementMaps(int) - Method in class org.biomage.BioAssayData.DesignElementMapping
Method to get DesignElementMap from DesignElementMaps_list
getFromDesignElementMaps(int) - Method in interface org.biomage.Interface.HasDesignElementMaps
Method to get DesignElementMap from DesignElementMaps_list
getFromDesignElementTuples(int) - Method in class org.biomage.BioAssayData.BioAssayTuple
Method to get DesignElementTuple from DesignElementTuples_list
getFromDesignElementTuples(int) - Method in interface org.biomage.Interface.HasDesignElementTuples
Method to get DesignElementTuple from DesignElementTuples_list
getFromDesignProviderRoles(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getFromDesignProviders(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to get Contact from DesignProviders_list
getFromDesignProviders(int) - Method in interface org.biomage.Interface.HasDesignProviders
Method to get Contact from DesignProviders_list
getFromExperiment_list(int) - Method in class org.biomage.Experiment.Experiment_package
Method to get Experiment from Experiment_list
getFromExperimentalFactors(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to get ExperimentalFactor from ExperimentalFactors_list
getFromExperimentalFactors(int) - Method in interface org.biomage.Interface.HasExperimentalFactors
Method to get ExperimentalFactor from ExperimentalFactors_list
getFromExperimentDesigns(int) - Method in class org.biomage.Experiment.Experiment
Method to get ExperimentDesign from ExperimentDesigns_list
getFromExperimentDesigns(int) - Method in interface org.biomage.Interface.HasExperimentDesigns
Method to get ExperimentDesign from ExperimentDesigns_list
getFromFactorValues(int) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to get FactorValue from FactorValues_list
getFromFactorValues(int) - Method in interface org.biomage.Interface.HasFactorValues
Method to get FactorValue from FactorValues_list
getFromFailTypes(int) - Method in class org.biomage.DesignElement.Reporter
Method to get OntologyEntry from FailTypes_list
getFromFailTypes(int) - Method in interface org.biomage.Interface.HasFailTypes
Method to get OntologyEntry from FailTypes_list
getFromFeatureDefects(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to get FeatureDefect from FeatureDefects_list
getFromFeatureDefects(int) - Method in interface org.biomage.Interface.HasFeatureDefects
Method to get FeatureDefect from FeatureDefects_list
getFromFeatureGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to get FeatureGroup from FeatureGroups_list
getFromFeatureGroups(int) - Method in interface org.biomage.Interface.HasFeatureGroups
Method to get FeatureGroup from FeatureGroups_list
getFromFeatureInformationSources(int) - Method in class org.biomage.DesignElement.FeatureReporterMap
Method to get FeatureInformation from FeatureInformationSources_list
getFromFeatureInformationSources(int) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Method to get FeatureInformation from FeatureInformationSources_list
getFromFeatureLIMSs(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get ManufactureLIMS from FeatureLIMSs_list
getFromFeatureLIMSs(int) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Method to get ManufactureLIMS from FeatureLIMSs_list
getFromFeatureReporterMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to get FeatureReporterMap from FeatureReporterMap_list
getFromFeatureReporterMaps(int) - Method in class org.biomage.DesignElement.Reporter
Method to get FeatureReporterMap from FeatureReporterMaps_list
getFromFeatureReporterMaps(int) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Method to get FeatureReporterMap from FeatureReporterMaps_list
getFromFeatures(int) - Method in class org.biomage.ArrayDesign.FeatureGroup
Method to get Feature from Features_list
getFromFeatures(int) - Method in interface org.biomage.Interface.HasFeatures
Method to get Feature from Features_list
getFromFiducials(int) - Method in class org.biomage.Array.ArrayGroup
Method to get Fiducial from Fiducials_list
getFromFiducials(int) - Method in interface org.biomage.Interface.HasFiducials
Method to get Fiducial from Fiducials_list
getFromHardware_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to get Hardware from Hardware_list
getFromHardwareApplications(int) - Method in interface org.biomage.Interface.HasHardwareApplications
Method to get HardwareApplication from HardwareApplications_list
getFromHardwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to get HardwareApplication from HardwareApplications_list
getFromHardwareManufacturers(int) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Method to get Contact from HardwareManufacturers_list
getFromHardwareManufacturers(int) - Method in class org.biomage.Protocol.Hardware
Method to get Contact from HardwareManufacturers_list
getFromHardwares(int) - Method in interface org.biomage.Interface.HasHardwares
Method to get Hardware from Hardwares_list
getFromHardwares(int) - Method in class org.biomage.Protocol.Protocol
Method to get Hardware from Hardwares_list
getFromImages(int) - Method in class org.biomage.BioAssay.ImageAcquisition
Method to get Image from Images_list
getFromImages(int) - Method in interface org.biomage.Interface.HasImages
Method to get Image from Images_list
getFromImmobilizedCharacteristics(int) - Method in class org.biomage.DesignElement.Reporter
Method to get BioSequence from ImmobilizedCharacteristics_list
getFromImmobilizedCharacteristics(int) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Method to get BioSequence from ImmobilizedCharacteristics_list
getFromLabels(int) - Method in class org.biomage.BioAssay.Channel
Method to get Compound from Labels_list
getFromLabels(int) - Method in class org.biomage.BioMaterial.LabeledExtract
Method to get Compound from Labels_list
getFromLabels(int) - Method in interface org.biomage.Interface.HasLabels
Method to get Compound from Labels_list
getFromMeasuredBioAssayData(int) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
getFromMeasuredBioAssayData(int) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
getFromMembers(int) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Method to get Contact from Members_list
getFromMembers(int) - Method in interface org.biomage.Interface.HasMembers
Method to get Contact from Members_list
getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.CompositePosition
Method to get MismatchInformation from MismatchInformation_list
getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.FeatureInformation
Method to get MismatchInformation from MismatchInformation_list
getFromMismatchInformation(int) - Method in class org.biomage.DesignElement.ReporterPosition
Method to get MismatchInformation from MismatchInformation_list
getFromMismatchInformation(int) - Method in interface org.biomage.Interface.HasMismatchInformation
Method to get MismatchInformation from MismatchInformation_list
getFromNodeContents(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to get NodeContents from NodeContents_list
getFromNodeContents(int) - Method in interface org.biomage.Interface.HasNodeContents
Method to get NodeContents from NodeContents_list
getFromNodes(int) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Method to get Node from Nodes_list
getFromNodes(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to get Node from Nodes_list
getFromNodes(int) - Method in interface org.biomage.Interface.HasNodes
Method to get Node from Nodes_list
getFromNodeValue(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to get NodeValue from NodeValue_list
getFromNodeValue(int) - Method in interface org.biomage.Interface.HasNodeValue
Method to get NodeValue from NodeValue_list
getFromOntologyEntries(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get OntologyEntry from OntologyEntries_list
getFromOntologyEntries(int) - Method in interface org.biomage.Interface.HasOntologyEntries
Method to get OntologyEntry from OntologyEntries_list
getFromOwner(int) - Method in class org.biomage.AuditAndSecurity.Security
Method to get Contact from Owner_list
getFromOwner(int) - Method in interface org.biomage.Interface.HasOwner
Method to get Contact from Owner_list
getFromParameters(int) - Method in class org.biomage.BQS.BibliographicReference
Method to get OntologyEntry from Parameters_list
getFromParameters(int) - Method in interface org.biomage.Interface.HasParameters
Method to get OntologyEntry from Parameters_list
getFromParameterTypes(int) - Method in interface org.biomage.Interface.HasParameterTypes
Method to get Parameter from ParameterTypes_list
getFromParameterTypes(int) - Method in class org.biomage.Protocol.Parameterizable
Method to get Parameter from ParameterTypes_list
getFromParameterValues(int) - Method in interface org.biomage.Interface.HasParameterValues
Method to get ParameterValue from ParameterValues_list
getFromParameterValues(int) - Method in class org.biomage.Protocol.ParameterizableApplication
Method to get ParameterValue from ParameterValues_list
getFromPerformers(int) - Method in interface org.biomage.Interface.HasPerformers
Method to get Person from Performers_list
getFromPerformers(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to get Person from Performers_list
getFromPhysicalBioAssayData(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to get Image from PhysicalBioAssayData_list
getFromPhysicalBioAssayData(int) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Method to get Image from PhysicalBioAssayData_list
getFromPropertySets(int) - Method in class org.biomage.Common.Extendable
Method to get NameValueType from PropertySets_list
getFromPropertySets(int) - Method in class org.biomage.Common.NameValueType
Method to get NameValueType from PropertySets_list
getFromPropertySets(int) - Method in interface org.biomage.Interface.HasPropertySets
Method to get NameValueType from PropertySets_list
getFromProtocol_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to get Protocol from Protocol_list
getFromProtocolApplications(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get ProtocolApplication from ProtocolApplications_list
getFromProtocolApplications(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to get ProtocolApplication from ProtocolApplications_list
getFromProtocolApplications(int) - Method in class org.biomage.BioEvent.BioEvent
Method to get ProtocolApplication from ProtocolApplications_list
getFromProtocolApplications(int) - Method in interface org.biomage.Interface.HasProtocolApplications
Method to get ProtocolApplication from ProtocolApplications_list
getFromProviderRoles(int) - Method in class org.biomage.Experiment.Experiment
 
getFromProviders(int) - Method in class org.biomage.Experiment.Experiment
Method to get Contact from Providers_list
getFromProviders(int) - Method in interface org.biomage.Interface.HasProviders
Method to get Contact from Providers_list
getFromQualityControlStatistics(int) - Method in class org.biomage.Array.ArrayManufacture
Method to get NameValueType from QualityControlStatistics_list
getFromQualityControlStatistics(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to get NameValueType from QualityControlStatistics_list
getFromQualityControlStatistics(int) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Method to get NameValueType from QualityControlStatistics_list
getFromQuantitationType_list(int) - Method in class org.biomage.QuantitationType.QuantitationType_package
Method to get QuantitationType from QuantitationType_list
getFromQuantitationTypeDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get QuantitationTypeDimension from QuantitationTypeDimension_list
getFromQuantitationTypeMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to get QuantitationTypeMap from QuantitationTypeMap_list
getFromQuantitationTypeMaps(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Method to get QuantitationTypeMap from QuantitationTypeMaps_list
getFromQuantitationTypeMaps(int) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Method to get QuantitationTypeMap from QuantitationTypeMaps_list
getFromQuantitationTypeMaps(int) - Method in class org.biomage.QuantitationType.QuantitationType
Method to get QuantitationTypeMap from QuantitationTypeMaps_list
getFromQuantitationTypes(int) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Method to get QuantitationType from QuantitationTypes_list
getFromQuantitationTypes(int) - Method in interface org.biomage.Interface.HasQuantitationTypes
Method to get QuantitationType from QuantitationTypes_list
getFromQuantitationTypeTuples(int) - Method in class org.biomage.BioAssayData.DesignElementTuple
Method to get QuantitationTypeTuple from QuantitationTypeTuples_list
getFromQuantitationTypeTuples(int) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Method to get QuantitationTypeTuple from QuantitationTypeTuples_list
getFromRegions(int) - Method in class org.biomage.BioSequence.SeqFeature
Method to get SeqFeatureLocation from Regions_list
getFromRegions(int) - Method in interface org.biomage.Interface.HasRegions
Method to get SeqFeatureLocation from Regions_list
getFromReporter_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to get Reporter from Reporter_list
getFromReporterCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to get ReporterCompositeMap from ReporterCompositeMap_list
getFromReporterCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to get ReporterCompositeMap from ReporterCompositeMaps_list
getFromReporterCompositeMaps(int) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Method to get ReporterCompositeMap from ReporterCompositeMaps_list
getFromReporterGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to get ReporterGroup from ReporterGroup_list
getFromReporterGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to get ReporterGroup from ReporterGroups_list
getFromReporterGroups(int) - Method in interface org.biomage.Interface.HasReporterGroups
Method to get ReporterGroup from ReporterGroups_list
getFromReporterPositionSources(int) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Method to get ReporterPosition from ReporterPositionSources_list
getFromReporterPositionSources(int) - Method in interface org.biomage.Interface.HasReporterPositionSources
Method to get ReporterPosition from ReporterPositionSources_list
getFromReporters(int) - Method in class org.biomage.ArrayDesign.ReporterGroup
Method to get Reporter from Reporters_list
getFromReporters(int) - Method in class org.biomage.BioAssayData.ReporterDimension
Method to get Reporter from Reporters_list
getFromReporters(int) - Method in interface org.biomage.Interface.HasReporters
Method to get Reporter from Reporters_list
getFromRoles(int) - Method in class org.biomage.AuditAndSecurity.Contact
Method to get OntologyEntry from Roles_list
getFromRoles(int) - Method in interface org.biomage.Interface.HasRoles
Method to get OntologyEntry from Roles_list
getFromSecurity_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to get Security from Security_list
getFromSecurityGroup_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to get SecurityGroup from SecurityGroup_list
getFromSecurityGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
Method to get SecurityGroup from SecurityGroups_list
getFromSecurityGroups(int) - Method in interface org.biomage.Interface.HasSecurityGroups
Method to get SecurityGroup from SecurityGroups_list
getFromSeqFeatures(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get SeqFeature from SeqFeatures_list
getFromSeqFeatures(int) - Method in interface org.biomage.Interface.HasSeqFeatures
Method to get SeqFeature from SeqFeatures_list
getFromSequenceDatabases(int) - Method in class org.biomage.BioSequence.BioSequence
Method to get DatabaseEntry from SequenceDatabases_list
getFromSequenceDatabases(int) - Method in interface org.biomage.Interface.HasSequenceDatabases
Method to get DatabaseEntry from SequenceDatabases_list
getFromSoftware_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to get Software from Software_list
getFromSoftwareApplications(int) - Method in interface org.biomage.Interface.HasSoftwareApplications
Method to get SoftwareApplication from SoftwareApplications_list
getFromSoftwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to get SoftwareApplication from SoftwareApplications_list
getFromSoftwareManufacturers(int) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Method to get Contact from SoftwareManufacturers_list
getFromSoftwareManufacturers(int) - Method in class org.biomage.Protocol.Software
Method to get Contact from SoftwareManufacturers_list
getFromSoftwares(int) - Method in interface org.biomage.Interface.HasSoftwares
Method to get Software from Softwares_list
getFromSoftwares(int) - Method in class org.biomage.Protocol.Hardware
Method to get Software from Softwares_list
getFromSoftwares(int) - Method in class org.biomage.Protocol.Protocol
Method to get Software from Softwares_list
getFromSoftwares(int) - Method in class org.biomage.Protocol.Software
Method to get Software from Softwares_list
getFromSourceBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayMap
Method to get BioAssay from SourceBioAssays_list
getFromSourceBioAssays(int) - Method in interface org.biomage.Interface.HasSourceBioAssays
Method to get BioAssay from SourceBioAssays_list
getFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioAssay.BioAssayCreation
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
getFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioMaterial.Treatment
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
getFromSourceBioMaterialMeasurements(int) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
getFromSourceContact(int) - Method in class org.biomage.BioMaterial.BioSource
Method to get Contact from SourceContact_list
getFromSourceContact(int) - Method in interface org.biomage.Interface.HasSourceContact
Method to get Contact from SourceContact_list
getFromSourcesQuantitationType(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Method to get QuantitationType from SourcesQuantitationType_list
getFromSourcesQuantitationType(int) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Method to get QuantitationType from SourcesQuantitationType_list
getFromSubregions(int) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to get SeqFeatureLocation from Subregions_list
getFromSubregions(int) - Method in interface org.biomage.Interface.HasSubregions
Method to get SeqFeatureLocation from Subregions_list
getFromSummaryStatistics(int) - Method in class org.biomage.BioAssayData.BioAssayData
Method to get NameValueType from SummaryStatistics_list
getFromSummaryStatistics(int) - Method in interface org.biomage.Interface.HasSummaryStatistics
Method to get NameValueType from SummaryStatistics_list
getFromTopLevelBioAssays(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to get BioAssay from TopLevelBioAssays_list
getFromTopLevelBioAssays(int) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Method to get BioAssay from TopLevelBioAssays_list
getFromTopLevelBioMaterials(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to get Treatment from Treatments_list
getFromTopLevelBioMaterials(int) - Method in interface org.biomage.Interface.HasTopBioMaterial
Method to get BioMaterial from TopLevelBioMaterials_list
getFromTreatments(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to get Treatment from Treatments_list
getFromTreatments(int) - Method in interface org.biomage.Interface.HasTreatments
Method to get Treatment from Treatments_list
getFromTypes(int) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Method to get OntologyEntry from Types_list
getFromTypes(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to get OntologyEntry from Types_list
getFromTypes(int) - Method in interface org.biomage.Interface.HasTypes
Method to get OntologyEntry from Types_list
getFromZoneGroups(int) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Method to get ZoneGroup from ZoneGroups_list
getFromZoneGroups(int) - Method in interface org.biomage.Interface.HasZoneGroups
Method to get ZoneGroup from ZoneGroups_list
getFromZoneLocations(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
Method to get Zone from ZoneLocations_list
getFromZoneLocations(int) - Method in interface org.biomage.Interface.HasZoneLocations
Method to get Zone from ZoneLocations_list
getFullName() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
getFullName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getFullName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getFullName(String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: change the first letter to be capitalized and insert a space between words dataType to Data Type
getFullName() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get the full name of the column
getFullNameLastFirstMiddle() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getFullNameWithEmptyForNull() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getGalBlocks() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
 
getGALFile(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getGALFile(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Gets the information about the gal files for the specified ArrayDesign.
getGALFileFinalDestination(Long) - Static method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignUploadDelegate
 
getGalFileInputLocation(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getGalFileLocation() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getGalToMageMapping(ArrayDesignDesc, GalBlockData[], GalFeatureData[]) - Method in class gov.nih.nci.caarray.services.fileparse.gal.magemapping.GalToMageMapping
 
getGeneIdentifier() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getGeneration() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGeneticModificationDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGeneticModificationId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGeneticModificationName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGeneticModifications() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGenotype() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGeographicLocation() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getGpr_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getGprFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getGprFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getGprFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getGprFromSpotFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getGprFromSpotFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getGprFromSpotFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getGprInfo() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprFileParseHandler
 
getGprInfo() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
 
getGps_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getGpsFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getGpsFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getGpsFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getGroup() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getGroup(long) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
getGroup(long) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getGroup(long) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Gets a GroupData object that matches the given Id.
getGroupAssignmentStatus() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
 
getGroupId() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractIlluminaCsvReader
 
getGroupName() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getGroupName() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getGroupName() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getGroupName() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupSearchCriteria
 
getGroupName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
getGroupName() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getGroupName() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getGroupName() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getGroupNameSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm
 
getGroups() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getGroups() - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getGroups(GroupSearchCriteria) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getGroups() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getGroups() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getHardware() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData
 
getHardware() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getHardware(long) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
getHardware(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
Get a Hardware that has the specified ID.
getHardware(long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Retrieve the Hardware that has the specified ID.
getHardware() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getHardware() - Method in interface org.biomage.Interface.HasHardware
Get method for hardware
getHardware() - Method in class org.biomage.Protocol.HardwareApplication
Get method for hardware
getHardware() - Method in class org.biomage.Protocol.Software
Get method for hardware
getHardware_list() - Method in class org.biomage.Protocol.Protocol_package
Get method for hardware_list
getHardwareApplications() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getHardwareApplications() - Method in interface org.biomage.Interface.HasHardwareApplications
Get method for hardwareApplications
getHardwareApplications() - Method in class org.biomage.Protocol.ProtocolApplication
Get method for hardwareApplications
getHardwareId() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getHardwareId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareID() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getHardwareMake() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareManagerDB() - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
getHardwareManufacturerId() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getHardwareManufacturerId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareManufacturerName() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareManufacturers() - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
getHardwareManufacturers() - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
getHardwareManufacturers() - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Retrieves all the Organization's that are currently associated with one or more hardware as manufacturers.
getHardwareManufacturers() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareManufacturers() - Method in interface org.biomage.Interface.HasHardwareManufacturers
Get method for hardwareManufacturers
getHardwareManufacturers() - Method in class org.biomage.Protocol.Hardware
Get method for hardwareManufacturers
getHardwareModel() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareName() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwares() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getHardwares(HardwareSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Get available hardwares.
getHardwares() - Method in interface org.biomage.Interface.HasHardwares
Get method for hardwares
getHardwares() - Method in class org.biomage.Protocol.Protocol
Get method for hardwares
getHardwareTypeId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHardwareTypes() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getHeader() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
getHeaderNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
getHeaderNameValueDelimiter() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
getHeaderRecordDelimiter() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
getHeight() - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
getHeight() - Method in class org.biomage.Description.Ontology.Biometrics
 
getHeightMeasurement() - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
getHeightMeasurement() - Method in class org.biomage.Description.Ontology.Biometrics
 
getHigherLevelAnalysis_package() - Method in class org.biomage.Common.MAGEJava
Get method for higherLevelAnalysis_package
getHistology() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getHost() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getHostIP() - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
getHostname() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getHostname() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getHostName() - Static method in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
getHttpTunnelingURL() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getHumidity() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getHybridization() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizationActivityDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationData() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationDataObj
 
getHybridizationData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationDeletionConfigurations() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getHybridizationFactors() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationFactorValues() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationFileHandler() - Method in class gov.nih.nci.caarray.services.hybridization.HybridizationFileHandlerFactory
 
getHybridizationFileParsingEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getHybridizationFileType(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeFactory
 
getHybridizationFileTypeGroupMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
getHybridizationFileTypes(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getHybridizationFileTypes(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
getHybridizationFileUpload(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getHybridizationFileUpload(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadEntry
getHybridizationFileUpload(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getHybridizationFileUploadEntries(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getHybridizationFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getHybridizationFileUploadEntrySummaries(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getHybridizationFileUploadEntrySummaries(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getHybridizationFileUploadGroup(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getHybridizationFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getHybridizationFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getHybridizationFileUploads() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getHybridizationFileUploads(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getHybridizationFileUploads(long[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getHybridizationFileUploads(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This method is replaced by FileUploadManagerEJB.getHybridizationFileUploadEntries
getHybridizationFileUploads(long[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
getHybridizationFileUploads(long[]) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getHybridizationFileUploads(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getHybridizationGroupName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationGroupName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getHybridizationId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getHybridizationMappingType() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getHybridizationParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationParameters() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getHybridizationPerformerID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getHybridizationProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getHybridizationProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getHybridizationProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method transfers array batch, array identifier, labeled extracts and factors information user just selected into a container object HybridizationFileUploadData, and then retrieves and presents all available hybridization protocols to the users to make a selection.
getHybridizationProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizationProtocolActiveDate() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getHybridizationProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getHybridizationProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getHybridizationProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getHybridizationProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizationProtocolDesc(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
getHybridizationProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getHybridizationProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizationProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getHybridizationProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getHybridizationProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizationProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizationProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getHybridizations() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getHybridizations() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getHybridizationSoftwareNames() - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getHybridizationSoftwareNames() - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getHybridizationSoftwareNames() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Retrieves the distinct list of creating software names from all FileTypes.
getId() - Method in class gov.nih.nci.caarray.common.data.array.ArrayData
 
getId() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getId() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getId() - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
getId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
 
getId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Gets the unique identifier that identifies this file type.
getId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
 
getId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getId() - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getId() - Method in class gov.nih.nci.caarray.common.data.security.RoleData
 
getId() - Method in class gov.nih.nci.caarray.common.data.security.VisibilityData
 
getId() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
getId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getId() - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
getId() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getId() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
getId() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
getID() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getId() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantitationType
 
getId() - Method in class gov.nih.nci.caarray.services.fileparse.ParsingBioAssay
 
getId() - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingQuantitationType
 
getId() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
getId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
getId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
 
getId() - Method in class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean
 
getId() - Method in class gov.nih.nci.caarray.services.security.db.ProtectionAppGroupElement
 
getId() - Method in class gov.nih.nci.caarray.services.security.db.ProtectionElement
 
getId() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
getId() - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
getId() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getId() - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
getId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ReporterTypeData
 
getId() - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
getId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getId() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getId() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getId() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractData
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getId() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.OptionData
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getId() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getId() - Method in class org.biomage.Common.Extendable
 
getId() - Method in class org.biomage.Common.NameValueType
 
getId() - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
getId() - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
getId() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getID() - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Obtains the XMI id.
getIdasLong() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
This method returns a long type as an id from a string id which has a format of 123456789990_1 generated by the server as a key to store hybridization annotation data.
getIdentifiable(Class, String) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
getIdentifier() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
getIdentifier() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getIdentifier() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getIdentifier() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getIdentifier() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getIdentifier() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getIdentifier() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getIdentifier() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getIdentifier() - Method in class org.biomage.Common.Identifiable
Get method for identifier
getIdentifier() - Method in class org.biomage.Common.MAGEJava
 
getIdentifierLIMS() - Method in class org.biomage.Array.ManufactureLIMS
Get method for identifierLIMS
getIdentifierLIMS() - Method in interface org.biomage.Interface.HasIdentifierLIMS
Get method for identifierLIMS
getIdentifierObjects() - Method in class gov.nih.nci.caarray.services.util.mage.CustomMAGEContentHandler
 
getIdentity() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
 
getIdentityAsLong(Identity) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
 
getIdVector() - Method in class org.biomage.tools.generate_er.Unique
Description: get the vector holding all column_ids for Unique
getImageAcquisitionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getImageAcquisitionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
getImageAcquisitionProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getImageActivateDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageActivateDate() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getImageParameters() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageParameters() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getImagePerformerID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getImageProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getImageProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getImageProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageProtocolData() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getImageProtocolData(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
getImageProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getImageProtocolID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getImageProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getImageProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getImageProtocolName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getImageProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getImageProtocols() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getImages() - Method in class org.biomage.BioAssay.ImageAcquisition
Get method for images
getImages() - Method in interface org.biomage.Interface.HasImages
Get method for images
getImmobilizedCharacteristics() - Method in class org.biomage.DesignElement.Reporter
Get method for immobilizedCharacteristics
getImmobilizedCharacteristics() - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Get method for immobilizedCharacteristics
getImplementation() - Method in class gov.nih.nci.caarray.services.util.db.ODMGImplementationManager
 
getImported() - Method in class org.biomage.BioMaterial.BioMaterial
Method to return if this BioMaterial is imported from MAGEML.
getImports() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns Set of packageImports.
getIncludeAllSubCategories() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getIndex() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getIndex() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getIndexColumn() - Method in class org.biomage.tools.generate_er.Index
Description: get the column the is indexed
getIndexOfIndexedProperty(String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getIndexVector() - Method in class org.biomage.tools.generate_er.Table
Description: get the vector containing all indexes
getIndividual() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getIndividualTreatmentId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getInformation() - Method in class org.biomage.Array.Array
Get method for information
getInformation() - Method in interface org.biomage.Interface.HasInformation
Get method for information
getInitialTimePoint() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getInitialTimePoint() - Method in class org.biomage.Description.Ontology.Age
 
getInitialTimePointId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getInitialTimePointName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getInitialTimePoints() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getInitialValue() - Method in class org.biomage.tools.generate_classes.CreateClassFile.DataTypeAttrInformation
Description: Get method for the initialValue.
getInitialValue(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the classifier of the association end element.
getInputFilesDirectory() - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getInputFilesDirectory(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
Use to get directory for download files.
getInputFilesDirectory() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Gets the directory for uploading Experiment MAGEML's to.
getInputFilesDirectory(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. need to sraigten backend. Move files from ftp area to common area and download from there
getInputStream() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
getInputStream() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
This method gets an InputStream for reading the zip file.
getInputStream() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Get an InputStream that represents this file.
getInstance() - Static method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerFactory
 
getInstance() - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileHandlerFactory
 
getInstance() - Static method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataLoaderFactory
 
getInstance() - Static method in class gov.nih.nci.caarray.services.hybridization.HybridizationFileHandlerFactory
 
getInstance() - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getInstance() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository
 
getInstance() - Static method in class gov.nih.nci.caarray.services.util.db.ODMGImplementationManager
 
getInstance() - Static method in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
getInstance() - Static method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
getInstance() - Static method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getInstanceIndex() - Method in class org.biomage.tools.helpers.OntologyHelper
 
getInstances() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getInstances(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getInstancesNames() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getInstitutionName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getInstitutionName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getInstitutionName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getInstitutionName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getInstitutionName() - Method in class org.biomage.AuditAndSecurity.User
 
getInstitutionSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getInteger(Object) - Method in interface gov.nih.nci.caarray.services.security.db.SecurityDSConnectionUtil.CustomRowMap
 
getInterfaceInfo() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns interfaceInfo.
getInterfaceName(String) - Static method in class org.biomage.tools.generate_classes.CreateInterfaceFile
Description: Converts a role name to an interface name.
getInternalId() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getInternalId() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getInvestigator() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getInvestigatorID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getInvestigators() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getIsAbstract() - Method in class org.biomage.tools.generate_er.Table
Description: get if the class is abstract
getIsActiveUser() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getIsActiveUser(String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
 
getIsActiveUser(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getIsAdminUser() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getIsAdminUser() - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
getIsAdminUser() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getIsAdminUser() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getIsApproximateLength() - Method in class org.biomage.BioSequence.BioSequence
Get method for isApproximateLength
getIsBackground() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for isBackground
getIsCancel() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getIsCancel() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getIsCircular() - Method in class org.biomage.BioSequence.BioSequence
Get method for isCircular
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getIsEditable() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
getIsEditable() - Method in interface gov.nih.nci.caarray.services.security.intf.SecuredElementItf
 
getIsEditable() - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getIsEditable() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getIsEditable() - Method in class org.biomage.Common.Extendable
 
getIsExperimentOwnedByCurrentUser() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getIsFactorEmpty() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getIsLDAPAuthorization() - Static method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getIsLoggedInUserAnAdmin(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getIsNew() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getIsOrdered() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for isOrdered.
getIsSolvent() - Method in class org.biomage.BioMaterial.Compound
Get method for isSolvent
getIsStopped() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
getIsStopped() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
getIssue() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getIssue() - Method in class org.biomage.BQS.BibliographicReference
Get method for issue
getJavaDateFromString(String) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
getJavaPropertyName(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
Translates a given quantTypeName to its DynaBean's attribute name as defined in quantitationNames.properties.
getJavaPropertyName(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
getKindCV() - Method in class org.biomage.Measurement.Measurement
Get method for kindCV
getLabel() - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData
 
getLabel() - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
getLabel() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getLabeledExtract(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getLabeledExtract(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Retrieve a LabeledExtract Object
getLabeledExtract(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
getLabeledExtractID() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getLabeledExtractName() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getLabeledExtracts(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getLabeledExtractSelection(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method gives user choices of a physical array batch information, a physical array identifier, labeled extracts for the hybridization, and factors that affect the experiment outcomes.
getLabeledExtractView(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getLabeledExtractView(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the LabeledExtractView object from the persistence store.
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getLabelId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getLabelName() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getLabels() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getLabels() - Method in class org.biomage.BioAssay.Channel
Get method for labels
getLabels() - Method in class org.biomage.BioMaterial.LabeledExtract
Get method for labels
getLabels() - Method in interface org.biomage.Interface.HasLabels
Get method for labels
getLableledExtractDescription() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return labeled extract description after formatting.
getLargeElementCountFlag() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getLargeElementCountFlag() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getLargeElementCountFlag() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getLastDocument() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
getLastDocument() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
getLastName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
getLastName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
getLastName() - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
getLastName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getLastName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getLastName() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getLastName() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getLastName() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getLastName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getLastName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getLastName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getLastName() - Method in class org.biomage.AuditAndSecurity.Person
Get method for lastName
getLastName() - Method in class org.biomage.AuditAndSecurity.User
 
getLastNameSearch() - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
getLastNameSearch() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getLastNameSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getLatestMAGEML(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
getLatestMAGEML(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Gets the information about the latest caARRAY-generated MAGEML for the specified experiment.
getLatestModifiedFile(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getLatestModifiedFile(String, String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Retrieves the latest created file in the specified directory.
getLdapAuthorizationBeingPerformed() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getLength() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getLength() - Method in class org.biomage.Array.ArrayGroup
Get method for length
getLength() - Method in class org.biomage.BioSequence.BioSequence
Get method for length
getLevels() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getLight() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getLineCount() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
 
getLineCount() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
 
getLinkingKey() - Method in class org.biomage.tools.generate_er.Table
Description: get the linking key for the table
getLinkOne() - Method in class org.biomage.tools.generate_er.LinkingKey
Description: get the column of link1 linking key
getLinkOneId() - Method in class org.biomage.tools.generate_er.LinkingKey
Description: get the column id of link1 linking key
getLinkTwo() - Method in class org.biomage.tools.generate_er.LinkingKey
Description: get the column of link2 linking key
getLinkTwoId() - Method in class org.biomage.tools.generate_er.LinkingKey
Description: get the column id of link2 linking key
getListener() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
 
getListener() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
 
getListener() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Returns the listener.
getLocalHome(String) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
Retrieve a LocalHome object for an EJB.
getLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
getLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
getLocation() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getLocation() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getLocation() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getLocation() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getLocation() - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
getLocation() - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
getLoginName() - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
getLoginName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getLoginName() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getLoginName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getLoginName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getLoginName() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
getLoginName() - Method in class org.biomage.AuditAndSecurity.User
 
getLoginNameSearch() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getLong(Object) - Method in interface gov.nih.nci.caarray.services.security.db.SecurityDSConnectionUtil.CustomRowMap
 
getLowerRightX() - Method in class org.biomage.ArrayDesign.Zone
Get method for lowerRightX
getLowerRightY() - Method in class org.biomage.ArrayDesign.Zone
Get method for lowerRightY
getMageFileLocation() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getMageIdentifier() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getMAGEJava() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Get the finished MAGE top-level object
getMAGEJava() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Get the finished MAGE top-level object
getMagellFileGroupId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getMagellFileGroupId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getMAGEML(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
getMAGEML(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Gets the information about the MAGEML for the specified ArrayDesign.
getMAGEMLFileEntries(MAGEMLFileUploadSearchCriteria) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Gets MAGEMLFileUploadEntries.
getMAGEMLFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
getMAGEMLFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
getMAGEMLFileUploadEntry(long) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
getMAGEobj() - Method in class gov.nih.nci.caarray.services.util.mage.MAGEReader
Deprecated.  
getMAGEobj() - Method in class org.biomage.tools.xmlutils.MAGEReader
 
getMageTypesForBioAssays(ParsingBioAssay[]) - Static method in class gov.nih.nci.caarray.services.fileparse.CaArrayToMageConversion
 
getMageTypesForDesignElements(ParsingDesignElement[], UploadFileTypes.MICROARRAY_FILE_TYPE) - Static method in class gov.nih.nci.caarray.services.fileparse.CaArrayToMageConversion
 
getMageTypesForParsingTypes(ParsingQuantitationType[]) - Static method in class gov.nih.nci.caarray.services.fileparse.CaArrayToMageConversion
 
getMake() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getMake() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getMake() - Method in class org.biomage.Protocol.Hardware
Get method for make
getManufacture() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getManufacture() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getManufactureDate() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getManufactureDate() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getManufactureDateEnd() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
getManufactureDateStart() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
getManufactureDateString() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getManufactureID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getManufactureID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getManufacturer() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getManufacturer() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getManufacturer() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getManufacturer() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getManufacturerId() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getManufacturerId() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getManufacturerId() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getManufacturerId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
getManufacturerName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
getManufacturerName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getManufacturers() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getManufacturersFromForm(ArrayBaseForm, ArrayGroupDesc) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
getManufacturingDate() - Method in class org.biomage.Array.ArrayManufacture
Get method for manufacturingDate
getManufacturingProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.array.ArrayData
 
getManufacturingProtocolId() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getMapperClassName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getMapping() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Retrieves the action mapping with which this handler is associated.
getMatch() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
getMatchedObject(List, Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
getMatchingEntries(DataFileReloadConfiguration) - Method in class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
getMatchingEntries(DataFileReloadConfiguration) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
getMaterialType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getMaterialType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getMaterialType() - Method in class org.biomage.BioMaterial.BioMaterial
Get method for materialType
getMaterialType() - Method in interface org.biomage.Interface.HasMaterialType
Get method for materialType
getMaterialTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMaterialTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getMaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getMaterialTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMaterialTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getMaterialTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getMaterialTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMaterialTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMatrix() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprFileParseHandler
 
getMax() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getMaxCard() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for maxCard.
getMaxCard() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the maximum cardinality of the assocaition class.
getMaxFilesToProcess() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getMaxMeasurement() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getMaxMeasurement() - Method in class org.biomage.Description.Ontology.Age
 
getMaxRowSpan() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
getMaxValue() - Method in class org.biomage.Description.Ontology.Age
 
getMeasuredBioAssay() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
getMeasuredBioAssay() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getMeasuredBioAssayData() - Method in class org.biomage.BioAssay.MeasuredBioAssay
Get method for measuredBioAssayData
getMeasuredBioAssayData() - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Get method for measuredBioAssayData
getMeasuredBioAssayTarget() - Method in class org.biomage.BioAssay.FeatureExtraction
Get method for measuredBioAssayTarget
getMeasuredBioAssayTarget() - Method in interface org.biomage.Interface.HasMeasuredBioAssayTarget
Get method for measuredBioAssayTarget
getMeasurement() - Method in class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData
 
getMeasurement() - Method in class gov.nih.nci.caarray.common.data.biomaterial.SplitBioSampleData
 
getMeasurement() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getMeasurement() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getMeasurement(long) - Method in class gov.nih.nci.caarray.services.protocol.MeasurementManagerDB
 
getMeasurement() - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
Get method for measurement
getMeasurement() - Method in class org.biomage.BioMaterial.CompoundMeasurement
Get method for measurement
getMeasurement() - Method in class org.biomage.Description.Ontology.Age
 
getMeasurement() - Method in class org.biomage.Experiment.FactorValue
Get method for measurement
getMeasurement() - Method in interface org.biomage.Interface.HasMeasurement
Get method for measurement
getMeasurement_package() - Method in class org.biomage.Common.MAGEJava
Get method for measurement_package
getMeasurementType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getMeasurementTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getMeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getMeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
Returns the selected measurement unit
getMeasurementUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMeasurementUnit1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnit2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnitName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getMeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getMeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMeasurementUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMeasurementUnits1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnits2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMeasurementUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMeasurementUnitType1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnitType2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMeasurementUnitTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMeasurementValue1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMeasurementValue2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMedia() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMediaId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMediaTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMembers() - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Get method for members
getMembers() - Method in interface org.biomage.Interface.HasMembers
Get method for members
getMessage() - Method in class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
 
getMessages(String) - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
getMessageType() - Method in interface gov.nih.nci.caarray.services.fileparse.FileMessageInterface
 
getMessageType() - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
return the type of message
getMessageType() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
return the type of message
getMetaColumn() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
getMetaRow() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
GetMeth(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
getMethod() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getMethod() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getMethod() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
getMethod() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getMethod() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getMethodInfo() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the Vector of method information.
getMiddleInitial() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getMiddleInitial() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getMiddleInitials() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getMiddleInitials() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getMidInitials() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
getMidInitials() - Method in class org.biomage.AuditAndSecurity.Person
Get method for midInitials
getMin() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getMinCard() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for minCard.
getMinCard() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the minimum cardinality of the assocaition class.
getMinMeasurement() - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
getMinMeasurement() - Method in class org.biomage.Description.Ontology.Age
 
getMinutesToRun() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getMinValue() - Method in class org.biomage.Description.Ontology.Age
 
getMismatchInformation() - Method in class org.biomage.DesignElement.CompositePosition
Get method for mismatchInformation
getMismatchInformation() - Method in class org.biomage.DesignElement.FeatureInformation
Get method for mismatchInformation
getMismatchInformation() - Method in class org.biomage.DesignElement.ReporterPosition
Get method for mismatchInformation
getMismatchInformation() - Method in interface org.biomage.Interface.HasMismatchInformation
Get method for mismatchInformation
getMode() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getMode() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getMode() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getMode_() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getModel() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getModel() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getModel() - Method in class org.biomage.Protocol.Hardware
Get method for model
getModelClassName() - Method in class org.biomage.Array.Array
 
getModelClassName() - Method in class org.biomage.Array.Array_package
 
getModelClassName() - Method in class org.biomage.Array.ArrayGroup
 
getModelClassName() - Method in class org.biomage.Array.ArrayManufacture
 
getModelClassName() - Method in class org.biomage.Array.ArrayManufactureDeviation
 
getModelClassName() - Method in class org.biomage.Array.FeatureDefect
 
getModelClassName() - Method in class org.biomage.Array.Fiducial
 
getModelClassName() - Method in class org.biomage.Array.ManufactureLIMS
 
getModelClassName() - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
 
getModelClassName() - Method in class org.biomage.Array.PositionDelta
 
getModelClassName() - Method in class org.biomage.Array.ZoneDefect
 
getModelClassName() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getModelClassName() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
 
getModelClassName() - Method in class org.biomage.ArrayDesign.CompositeGroup
 
getModelClassName() - Method in class org.biomage.ArrayDesign.DesignElementGroup
 
getModelClassName() - Method in class org.biomage.ArrayDesign.FeatureGroup
 
getModelClassName() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
 
getModelClassName() - Method in class org.biomage.ArrayDesign.ReporterGroup
 
getModelClassName() - Method in class org.biomage.ArrayDesign.Zone
 
getModelClassName() - Method in class org.biomage.ArrayDesign.ZoneGroup
 
getModelClassName() - Method in class org.biomage.ArrayDesign.ZoneLayout
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.Audit
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.Contact
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.Organization
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.Person
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.Security
 
getModelClassName() - Method in class org.biomage.AuditAndSecurity.SecurityGroup
 
getModelClassName() - Method in class org.biomage.BioAssay.BioAssay
 
getModelClassName() - Method in class org.biomage.BioAssay.BioAssay_package
 
getModelClassName() - Method in class org.biomage.BioAssay.BioAssayCreation
 
getModelClassName() - Method in class org.biomage.BioAssay.BioAssayTreatment
 
getModelClassName() - Method in class org.biomage.BioAssay.Channel
 
getModelClassName() - Method in class org.biomage.BioAssay.DerivedBioAssay
 
getModelClassName() - Method in class org.biomage.BioAssay.FeatureExtraction
 
getModelClassName() - Method in class org.biomage.BioAssay.Hybridization
 
getModelClassName() - Method in class org.biomage.BioAssay.Image
 
getModelClassName() - Method in class org.biomage.BioAssay.ImageAcquisition
 
getModelClassName() - Method in class org.biomage.BioAssay.MeasuredBioAssay
 
getModelClassName() - Method in class org.biomage.BioAssay.PhysicalBioAssay
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayData
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayData_package
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayMap
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayMapping
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioAssayTuple
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioDataCube
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioDataTuples
 
getModelClassName() - Method in class org.biomage.BioAssayData.BioDataValues
 
getModelClassName() - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.DataExternal
 
getModelClassName() - Method in class org.biomage.BioAssayData.DataInternal
 
getModelClassName() - Method in class org.biomage.BioAssayData.Datum
 
getModelClassName() - Method in class org.biomage.BioAssayData.DerivedBioAssayData
 
getModelClassName() - Method in class org.biomage.BioAssayData.DesignElementDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.DesignElementMap
 
getModelClassName() - Method in class org.biomage.BioAssayData.DesignElementMapping
 
getModelClassName() - Method in class org.biomage.BioAssayData.DesignElementTuple
 
getModelClassName() - Method in class org.biomage.BioAssayData.FeatureDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
 
getModelClassName() - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
 
getModelClassName() - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
 
getModelClassName() - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
 
getModelClassName() - Method in class org.biomage.BioAssayData.ReporterDimension
 
getModelClassName() - Method in class org.biomage.BioAssayData.Transformation
 
getModelClassName() - Method in class org.biomage.BioEvent.BioEvent
 
getModelClassName() - Method in class org.biomage.BioEvent.BioEvent_package
 
getModelClassName() - Method in class org.biomage.BioEvent.Map
 
getModelClassName() - Method in class org.biomage.BioMaterial.BioMaterial
 
getModelClassName() - Method in class org.biomage.BioMaterial.BioMaterial_package
 
getModelClassName() - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
 
getModelClassName() - Method in class org.biomage.BioMaterial.BioSample
 
getModelClassName() - Method in class org.biomage.BioMaterial.BioSource
 
getModelClassName() - Method in class org.biomage.BioMaterial.Compound
 
getModelClassName() - Method in class org.biomage.BioMaterial.CompoundMeasurement
 
getModelClassName() - Method in class org.biomage.BioMaterial.LabeledExtract
 
getModelClassName() - Method in class org.biomage.BioMaterial.Treatment
 
getModelClassName() - Method in class org.biomage.BioSequence.BioSequence
 
getModelClassName() - Method in class org.biomage.BioSequence.BioSequence_package
 
getModelClassName() - Method in class org.biomage.BioSequence.SeqFeature
 
getModelClassName() - Method in class org.biomage.BioSequence.SeqFeatureLocation
 
getModelClassName() - Method in class org.biomage.BioSequence.SequencePosition
 
getModelClassName() - Method in class org.biomage.BQS.BibliographicReference
 
getModelClassName() - Method in class org.biomage.BQS.BQS_package
 
getModelClassName() - Method in class org.biomage.Common.Describable
 
getModelClassName() - Method in class org.biomage.Common.Extendable
 
getModelClassName() - Method in class org.biomage.Common.Identifiable
 
getModelClassName() - Method in class org.biomage.Common.MAGEJava
 
getModelClassName() - Method in class org.biomage.Common.NameValueType
 
getModelClassName() - Method in class org.biomage.Description.Database
 
getModelClassName() - Method in class org.biomage.Description.DatabaseEntry
 
getModelClassName() - Method in class org.biomage.Description.Description
 
getModelClassName() - Method in class org.biomage.Description.Description_package
 
getModelClassName() - Method in class org.biomage.Description.ExternalReference
 
getModelClassName() - Method in class org.biomage.Description.OntologyEntry
 
getModelClassName() - Method in class org.biomage.DesignElement.CompositeCompositeMap
 
getModelClassName() - Method in class org.biomage.DesignElement.CompositePosition
 
getModelClassName() - Method in class org.biomage.DesignElement.CompositeSequence
 
getModelClassName() - Method in class org.biomage.DesignElement.DesignElement
 
getModelClassName() - Method in class org.biomage.DesignElement.DesignElement_package
 
getModelClassName() - Method in class org.biomage.DesignElement.Feature
 
getModelClassName() - Method in class org.biomage.DesignElement.FeatureInformation
 
getModelClassName() - Method in class org.biomage.DesignElement.FeatureLocation
 
getModelClassName() - Method in class org.biomage.DesignElement.FeatureReporterMap
 
getModelClassName() - Method in class org.biomage.DesignElement.MismatchInformation
 
getModelClassName() - Method in class org.biomage.DesignElement.Position
 
getModelClassName() - Method in class org.biomage.DesignElement.Reporter
 
getModelClassName() - Method in class org.biomage.DesignElement.ReporterCompositeMap
 
getModelClassName() - Method in class org.biomage.DesignElement.ReporterPosition
 
getModelClassName() - Method in class org.biomage.Experiment.Experiment
 
getModelClassName() - Method in class org.biomage.Experiment.Experiment_package
 
getModelClassName() - Method in class org.biomage.Experiment.ExperimentalFactor
 
getModelClassName() - Method in class org.biomage.Experiment.ExperimentDesign
 
getModelClassName() - Method in class org.biomage.Experiment.FactorValue
 
getModelClassName() - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
 
getModelClassName() - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
 
getModelClassName() - Method in class org.biomage.HigherLevelAnalysis.Node
 
getModelClassName() - Method in class org.biomage.HigherLevelAnalysis.NodeContents
 
getModelClassName() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
 
getModelClassName() - Method in class org.biomage.Measurement.ConcentrationUnit
 
getModelClassName() - Method in class org.biomage.Measurement.DistanceUnit
 
getModelClassName() - Method in class org.biomage.Measurement.MassUnit
 
getModelClassName() - Method in class org.biomage.Measurement.Measurement
 
getModelClassName() - Method in class org.biomage.Measurement.Measurement_package
 
getModelClassName() - Method in class org.biomage.Measurement.QuantityUnit
 
getModelClassName() - Method in class org.biomage.Measurement.TemperatureUnit
 
getModelClassName() - Method in class org.biomage.Measurement.TimeUnit
 
getModelClassName() - Method in class org.biomage.Measurement.Unit
 
getModelClassName() - Method in class org.biomage.Measurement.VolumeUnit
 
getModelClassName() - Method in class org.biomage.Protocol.Hardware
 
getModelClassName() - Method in class org.biomage.Protocol.HardwareApplication
 
getModelClassName() - Method in class org.biomage.Protocol.Parameter
 
getModelClassName() - Method in class org.biomage.Protocol.Parameterizable
 
getModelClassName() - Method in class org.biomage.Protocol.ParameterizableApplication
 
getModelClassName() - Method in class org.biomage.Protocol.ParameterValue
 
getModelClassName() - Method in class org.biomage.Protocol.Protocol
 
getModelClassName() - Method in class org.biomage.Protocol.Protocol_package
 
getModelClassName() - Method in class org.biomage.Protocol.ProtocolApplication
 
getModelClassName() - Method in class org.biomage.Protocol.Software
 
getModelClassName() - Method in class org.biomage.Protocol.SoftwareApplication
 
getModelClassName() - Method in class org.biomage.QuantitationType.ConfidenceIndicator
 
getModelClassName() - Method in class org.biomage.QuantitationType.DerivedSignal
 
getModelClassName() - Method in class org.biomage.QuantitationType.Error
 
getModelClassName() - Method in class org.biomage.QuantitationType.ExpectedValue
 
getModelClassName() - Method in class org.biomage.QuantitationType.Failed
 
getModelClassName() - Method in class org.biomage.QuantitationType.MeasuredSignal
 
getModelClassName() - Method in class org.biomage.QuantitationType.PresentAbsent
 
getModelClassName() - Method in class org.biomage.QuantitationType.PValue
 
getModelClassName() - Method in class org.biomage.QuantitationType.QuantitationType
 
getModelClassName() - Method in class org.biomage.QuantitationType.QuantitationType_package
 
getModelClassName() - Method in class org.biomage.QuantitationType.Ratio
 
getModelClassName() - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
 
getModelClassName() - Method in class org.biomage.QuantitationType.StandardQuantitationType
 
getModifyUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getModifyUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getModifyUnitValue() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getModule() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getModule() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getModule() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getMsgToCurator() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getMsgToCurator() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getMsgToCurator() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getMsgToCurator() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getMsgToCurator() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getMultipleIdItem() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return fileUoloadId
getMultipleIds() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
getName() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
getName() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
getName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.measurement.UnitData
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
getName() - Method in class gov.nih.nci.caarray.common.data.security.RoleData
 
getName() - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
getName() - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
getName() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getName() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getName() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
getName() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getName() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantitationType
 
getName() - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingQuantitationType
 
getName() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
getName() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getName() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getName() - Method in class gov.nih.nci.caarray.services.security.CaArrayPrincipal
Return the Sample username for this CaArrayPrincipal.
getName() - Method in class gov.nih.nci.caarray.services.security.mageom.PathElement
 
getName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
getName() - Method in class gov.nih.nci.caarray.services.util.file.FileZipper
Method to get the name of the zip file.
getName() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
Method to get the name of the zip file.
getName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ReporterTypeData
 
getName() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getName() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getName() - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractData
 
getName() - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
getName() - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
getName() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getName() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getName() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getName() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getName() - Method in class gov.nih.nci.caarray.ui.useradmin.OptionData
 
getName() - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
getName() - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
getName() - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
getName() - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
getName() - Method in class org.biomage.Common.Identifiable
Get method for name
getName() - Method in class org.biomage.Common.MAGEJava
 
getName() - Method in class org.biomage.Common.NameValueType
Get method for name
getName() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Get method for name
getName() - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.Measurement.KindCV
 
getName() - Method in class org.biomage.Measurement.Measurement.Type
 
getName() - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
getName() - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
getName() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the name.
getName() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for name.
getName() - Static method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
 
getName() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get teh name of the column
getName() - Method in class org.biomage.tools.generate_er.Index
Description: get the name of the index
getName() - Method in class org.biomage.tools.generate_er.Table
Description: get teh name of the table
getName() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getNameAction() - Method in class org.biomage.AuditAndSecurity.Audit
Return the current name of the Enumeration type of Action.
getNameAndDatabase() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getNameBasis() - Method in class org.biomage.BioSequence.SeqFeature
Return the current name of the Enumeration type of Basis.
getNameByValue(int) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
getNameByValue(int) - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
getNameByValue(int) - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
getNameByValue(int) - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
getNameByValue(int) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.Measurement.KindCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.Measurement.Type
 
getNameByValue(int) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
getNameByValue(int) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
getNameByValueAction(int) - Method in class org.biomage.AuditAndSecurity.Audit
For Action get the Name of the Enumeration type by passing a Value to it.
getNameByValueBasis(int) - Method in class org.biomage.BioSequence.SeqFeature
For Basis get the Name of the Enumeration type by passing a Value to it.
getNameByValueKindCV(int) - Method in class org.biomage.Measurement.Measurement
For KindCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueOrder(int) - Method in class org.biomage.BioAssayData.BioDataCube
For Order get the Name of the Enumeration type by passing a Value to it.
getNameByValueOrientationMarkPosition(int) - Method in class org.biomage.Array.ArrayGroup
For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it.
getNameByValueType(int) - Method in class org.biomage.Measurement.Measurement
For Type get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.ConcentrationUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.DistanceUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.MassUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.QuantityUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TemperatureUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TimeUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.VolumeUnit
For UnitNameCV get the Name of the Enumeration type by passing a Value to it.
getNameKindCV() - Method in class org.biomage.Measurement.Measurement
Return the current name of the Enumeration type of KindCV.
getNameOrder() - Method in class org.biomage.BioAssayData.BioDataCube
Return the current name of the Enumeration type of Order.
getNameOrientationMarkPosition() - Method in class org.biomage.Array.ArrayGroup
Return the current name of the Enumeration type of OrientationMarkPosition.
getNameSearch() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
getNameType() - Method in class org.biomage.Measurement.Measurement
Return the current name of the Enumeration type of Type.
getNameUnitNameCV() - Method in class org.biomage.Measurement.ConcentrationUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.DistanceUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.MassUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.QuantityUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.TemperatureUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.TimeUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameUnitNameCV() - Method in class org.biomage.Measurement.VolumeUnit
Return the current name of the Enumeration type of UnitNameCV.
getNameValueTypes(long) - Method in class gov.nih.nci.caarray.services.util.mage.MAGEManagerDB
 
getNeedsRepair() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getNestedProperty(Object, String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getNestedPropertyParentType(Object, String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getNETCDFFileLocation(Long, Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Locates the file path name for the .nc (NETCDF) file that stores the the parsed quantification data or BioDataCube for the specified BioAssay contained in the specified Experiment.
getNETCDFFileLocation(String, Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
Locates the file path name for the .nc (NETCDF) file that stores the the parsed quantification data or BioDataCube for the specified BioAssay.
getNETCDFOutputFileDirectory(Long) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getNewBioAssay() - Static method in class gov.nih.nci.caarray.services.fileparse.BioAssayService
 
getNewHardwareId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getNewLabel() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getNewMaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getNewMaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getNewSequence() - Method in class org.biomage.DesignElement.MismatchInformation
Get method for newSequence
getNewSoftwareId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getNewSoftwareId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getNewTaxonTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getNewTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getNewTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
getNewTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getNewTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
getNextId() - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalIdGenerator
 
getNextId() - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.InternalFeatureIdGenerator
 
getNodeContents() - Method in class org.biomage.HigherLevelAnalysis.Node
Get method for nodeContents
getNodeContents() - Method in interface org.biomage.Interface.HasNodeContents
Get method for nodeContents
getNodes() - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Get method for nodes
getNodes() - Method in class org.biomage.HigherLevelAnalysis.Node
Get method for nodes
getNodes() - Method in interface org.biomage.Interface.HasNodes
Get method for nodes
getNodeValue() - Method in class org.biomage.HigherLevelAnalysis.Node
Get method for nodeValue
getNodeValue() - Method in interface org.biomage.Interface.HasNodeValue
Get method for nodeValue
getNonBioAssayFiles() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getNonNullDataId(VocabData) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getNonNullDataName(VocabData) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getNonNumericMap() - Method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
getNonNumericQuantitationType(Long) - Static method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
getNonParseableFiles() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
getNormalizationDescription() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for normalizationDescription
getNormalizationDescription() - Method in interface org.biomage.Interface.HasNormalizationDescription
Get method for normalizationDescription
getNotify() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
 
getNotify() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
 
getNotifyReply() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Simply returns a string value received from server as part of response.
getNotifyReply() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getNotifyURL() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getNotifyURL() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getNotifyURL() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getNotifyURLWithSid() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
This method will return a notifyURL string with a session id (jsessionid) appended at the end for session identification by the server.
getNumArrays() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getNumArrays() - Method in class org.biomage.Array.ArrayGroup
Get method for numArrays
getNumberChanels() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getNumberCopies() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
getNumberHybridization() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
getNumberOfChannels() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getNumberOfChannels() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getNumberOfChannels() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getNumberOfChannels() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getNumberOfChannels() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getNumberOfFactor() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getNumberOfFactorValues() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getNumberOfFeatures() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getNumberOfFeatures() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getNumberOfFeatures() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for numberOfFeatures
getNumberOfHybridization() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getNumberOfHybridization() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getNumberOfHybridizations() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getNumberOfXFeatures() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getNumberOfYFeatures() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getNumberSamples() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getNumChannels() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getNumFactors() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getNumFeaturesPerCol() - Method in class org.biomage.ArrayDesign.ZoneLayout
Get method for numFeaturesPerCol
getNumFeaturesPerRow() - Method in class org.biomage.ArrayDesign.ZoneLayout
Get method for numFeaturesPerRow
getNumHybridizations() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getNutrients() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getObject(Query) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
This method will return a single object that matches the specified query.
getObject(List, long) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestUtils
 
getObject(Object[], long) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestUtils
 
getObject(Query, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
This method will return a single object that matches the specified query.
getObject(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
This method will return a single object that matches the specified query.
getObject(Class, Class, Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Gets an object of the specified class that matches the specified ID.
getObject(Class, Class, Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Gets an object of the specified class that matches the specified ID.
getObject(Class, Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Gets an object of the specified class that matches the specified ID.
getObject(Class, Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Gets an object of the specified class that matches the specified ID.
getObject() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getObject() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getObjectId() - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
getObjectId() - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
getObjectId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getObjectIterator(Query, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
This method will return a lazy loading Iterator that materializes the object that meet the specification of the specified query each time the next() method is invoked.
getObjectIterator(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
getObjects(Query) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
This method will return a collection of objects that meets the specified query.
getObjects(Query) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
This method will return a collection of objects that meets the specified query.
getObjects(Query, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
This method will return a collection of objects that meets the specified query.
getObjects(Class) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Retrieve an array of objects of the specified class type.
getObjects(Object, Hashtable) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportDefaultListener
 
getObjects(Object, Hashtable) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
A convienience method to get Objects using the default listener
getObjectType() - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
getOjbClass() - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings.AttributeInfo
 
getOkFiles() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Returns all uploaded files to applet so applet can display them as part of the summary popup window.
getOkFiles() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getOntologies(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getOntologies(long) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getOntology(long) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getOntology(String, String) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
getOntologyEntries() - Method in class org.biomage.BioSequence.BioSequence
Get method for ontologyEntries
getOntologyEntries() - Method in interface org.biomage.Interface.HasOntologyEntries
Get method for ontologyEntries
getOntologyEntry(String, String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns the entry corresponding to the data given or null if not found.
getOntologyEntry(String, String) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getOntologyEntry(Object, String, List) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.VocabDataFieldMapper
 
getOntologyEntryByCategory(String, List) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.VocabDataFieldMapper
Get from the specified list of OntologyEntrys the element whose category matches the specified category.
getOntologyEntryOrNull(String, String) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Returns the requested OntologyEntry or null if not found.
getOntologyEntryValue() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataTypeEnum
 
getOntologyEntryValue() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.ScaleEnum
 
getOntologyReference() - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Get method for ontologyReference
getOntologyReference() - Method in class org.biomage.Description.OntologyEntry
Get method for ontologyReference
getOntologyReference() - Method in interface org.biomage.Interface.HasOntologyReference
Get method for ontologyReference
getOntologyReference(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getOperationElements(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns a NodeList of operation elements.
getOperationSpecification(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the specification(semantics) of an operation.
getOrder() - Method in class org.biomage.BioAssayData.BioDataCube
Get method for order
getOrder() - Method in class org.biomage.BioMaterial.Treatment
Get method for order
getOrgAddress() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getOrganismPart() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganismPartId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganismParts() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganismStatus() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganismStatuses() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganismStatusId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getOrganization() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getOrganization() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getOrganization(long) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
getOrganization(OrganizationDescriptor) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Returns the Organization corresponding to the descriptor given, creating if necessary.
getOrganization(OrganizationDescriptor) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
getOrganization(long) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getOrganization(long) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
getOrganizationData() - Method in enum gov.nih.nci.caarray.services.contact.OrganizationDescriptor
 
getOrganizationName() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationSearchCriteria
 
getOrganizationName() - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
getOrganizations() - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
getOrganizations() - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getOrganizations(OrganizationSearchCriteria) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getOrganizations() - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
getOrientationMark() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getOrientationMark() - Method in class org.biomage.Array.ArrayGroup
Get method for orientationMark
getOrientationMarkPosition() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getOrientationMarkPosition() - Method in class org.biomage.Array.ArrayGroup
Get method for orientationMarkPosition
getOrientationMarkPositionName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getOrientationMarkPositions() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getOriginalFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the original file name of uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the original file name of uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
Returns the original file name for uplaoded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getOriginalFileName() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the original file name of uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the original file name of uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
Returns the original file name for the uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
Returns the original file name for the uploaded file
getOriginalFileName() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getOriginalName() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
getOriginalProtocolId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getOriginalProtocolsApp() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getOriginalType() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for originalType.
getOriginalValue(DesignElementRetrievalSettings.AttributeInfo) - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings
 
getOriginRelativeTo() - Method in class org.biomage.Array.Array
Get method for originRelativeTo
getOther_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getOtherCompoundModifyUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOtherCompoundModifyUnitTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOtherCompoundUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherCompoundUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOtherCompoundUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherCompoundUnitTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherCompoundUnitTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOtherExperimentType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getOtherExperimentType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getOtherKind() - Method in class org.biomage.Measurement.Measurement
Get method for otherKind
getOtherNav() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for otherNav.
getOtherNav() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the maximum cardinality of this class for the association relationship
getOtherProperties() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getOtherProperties() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
Returns other properties which would be stored as MAGE Reporter.propertySets.
getOtherPropertyNames(DynaBean, String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
Returns other property names in the specified bean that are not in the specified array of property names.
getOtherUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherUnit() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOtherUnitType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherUnitTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getOtherUnitTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getOutputDesc() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getOutputDesc1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getOutputDesc2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getOutputName() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getOutputName1() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getOutputName2() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getOwner() - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
getOwner() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getOwner() - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
getOwner() - Method in class org.biomage.AuditAndSecurity.Security
Get method for owner
getOwner() - Method in interface org.biomage.Interface.HasOwner
Get method for owner
getOwner() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return if this association is the owner of the relationship.
getOwnerClass() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
getOwnerEmail(String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns email address of the owner of a given object.
getOwnerEmail(String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns email address of the owner of a given object.
getOwnersEmail(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets email information for the owner of an object.
getOwnersEmail(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets email information for the owner of an object.
getOwnersEmail(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets email information for the specified object.
getOwnersEmail(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets email information for the specified object.
getOwnerUserName() - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
getPackageID(Element) - Static method in class org.biomage.tools.generate_classes.CreateFile
Description: Obtains the ID of a package from a class node.
getPackageName() - Method in class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
getPackageName() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns Class name.
getPackageNodeFromCfg() - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Reads the file and creates the DOM structure and gets the XMI element.
getPages() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getPages() - Method in class org.biomage.BQS.BibliographicReference
Get method for pages
getParameter() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
getParameterElements(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns a NodeList of parameter elements.
getParameterFromForm(ParameterAddForm) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getParameterId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getParameterKind(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the kind of the parameter ("return", "inout", etc.).
getParameters() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
getParameters() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getParameters() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getParameters() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getParameters() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getParameters() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getParameters() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getParameters() - Method in class org.biomage.BQS.BibliographicReference
Get method for parameters
getParameters() - Method in interface org.biomage.Interface.HasParameters
Get method for parameters
getParameterType() - Method in interface org.biomage.Interface.HasParameterType
Get method for parameterType
getParameterType() - Method in class org.biomage.Protocol.ParameterValue
Get method for parameterType
getParameterTypeID(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the id of the parameter element's data type.
getParameterTypeOfPropertySetter(Object, String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getParameterTypes() - Method in interface org.biomage.Interface.HasParameterTypes
Get method for parameterTypes
getParameterTypes() - Method in class org.biomage.Protocol.Parameterizable
Get method for parameterTypes
getParameterValues() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData
 
getParameterValues() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getParameterValues() - Method in interface org.biomage.Interface.HasParameterValues
Get method for parameterValues
getParameterValues() - Method in class org.biomage.Protocol.ParameterizableApplication
Get method for parameterValues
getParamInfos() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the parameters.
getParent() - Method in class org.biomage.AuditAndSecurity.Organization
Get method for parent
getParent() - Method in interface org.biomage.Interface.HasParent
Get method for parent
getParentBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getParentBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getParentBioSampleId() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getParentBioSourceId() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getParentNames() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getParents() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getParents() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getParents() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getParseable() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getParsedFeatureColumn2PropertyMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
getParsedFeatureProperty2ColumnMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
getParsingDesignElements(Long) - Method in interface gov.nih.nci.caarray.services.fileparse.DesignElementService
 
getParsingDesignElements(Long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElementService
 
getParsingEndDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
getParsingEndDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
getParsingEndDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getParsingEndDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
getParsingEndDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
getParsingQuatitationTypes(UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantificationService
Gets the quatitations based on a type
getParsingQuatitationTypes(UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in interface gov.nih.nci.caarray.services.fileparse.QuantitationTypeService
 
getParsingResult() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return sample parsingResult after formatting.
getParsingStartDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
getParsingStartDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
getParsingStartDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getParsingStartDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
getParsingStartDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
getParsingSucceeded() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
Returns the status of the parsing
getParsingSucceeded() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
Returns the status of the parsing
getParsingSucceeded() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
Returns the status of the parsing
getParsingSucceeded() - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
Returns the status of the parsing
getParsingSucceeded() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
Returns the status of the parsing
getPassword() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getPassword() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getPassword() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getPassword() - Method in class gov.nih.nci.caarray.services.util.UserInfo
 
getPassword() - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
getPassword() - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
getPassword() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getPathElements() - Method in class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
getPathExpressionsForPrimary(String) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getPathInfoForPrimary(String) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getPathInfos() - Method in class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
getPathName() - Method in class gov.nih.nci.caarray.common.data.util.FileData
 
getPathName() - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
getPathogenTest() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPcData() - Method in class org.biomage.BioAssayData.DataInternal
Get method for pcData
getPercentage() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
To calculate the percentage of upload that is completed.
getPerformer() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getPerformer() - Method in class org.biomage.AuditAndSecurity.Audit
Get method for performer
getPerformer() - Method in interface org.biomage.Interface.HasPerformer
Get method for performer
getPerformerID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPerformerId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getPerformers() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPerformers() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getPerformers() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getPerformers() - Method in interface org.biomage.Interface.HasPerformers
Get method for performers
getPerformers() - Method in class org.biomage.Protocol.ProtocolApplication
Get method for performers
getPermissibleFileExtension() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getPermissibleFileExtension() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getPermissibleFileExtension() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getPermission(String, String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns an array of Roles which has the permission to access the protection element defined by its application name, object ID and attribute.
getPermission(String, String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns an array of Roles which has the permission to access the protection element defined by its application name, object ID and attribute.
getPermittedObjects(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
 
getPersistenceBroker() - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
getPersistenceBroker() - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Gets a PersistenceBroker from the pool for the default profile.
getPersistenceBroker(String) - Method in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
getPersistenceBroker() - Method in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
getPersistenceBrokerFactory() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
Looks up the PBF implementation.
getPerson(long) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
getPerson(long) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getPerson(long) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
 
getPersons() - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
getPersons() - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getPersons(PersonSearchCriteria) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
getPersons() - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Gets a list of all contact users in and returns a PersonData object for each.
getPhenotype() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPhone() - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
getPhone() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getPhone() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for phone
getPhoneNumber() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getPhoneNumber() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getPhysicalBioAssay() - Method in class org.biomage.BioAssay.BioAssayTreatment
Get method for physicalBioAssay
getPhysicalBioAssay() - Method in interface org.biomage.Interface.HasPhysicalBioAssay
Get method for physicalBioAssay
getPhysicalBioAssayData() - Method in class org.biomage.BioAssay.PhysicalBioAssay
Get method for physicalBioAssayData
getPhysicalBioAssayData() - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Get method for physicalBioAssayData
getPhysicalBioAssaySource() - Method in class org.biomage.BioAssay.FeatureExtraction
Get method for physicalBioAssaySource
getPhysicalBioAssaySource() - Method in interface org.biomage.Interface.HasPhysicalBioAssaySource
Get method for physicalBioAssaySource
getPhysicalBioAssayTarget() - Method in class org.biomage.BioAssay.BioAssayCreation
Get method for physicalBioAssayTarget
getPhysicalBioAssayTarget() - Method in interface org.biomage.Interface.HasPhysicalBioAssayTarget
Get method for physicalBioAssayTarget
getPK() - Method in class org.biomage.tools.generate_er.Table
Description: get primary key of the table
getPloidy() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPloidyId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPloidys() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPolymerType() - Method in class org.biomage.BioSequence.BioSequence
Get method for polymerType
getPolymerType() - Method in interface org.biomage.Interface.HasPolymerType
Get method for polymerType
getPopulationDensity() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getPort() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getPort() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getPosition() - Method in class org.biomage.Array.Fiducial
Get method for position
getPosition() - Method in class org.biomage.DesignElement.Feature
Get method for position
getPosition() - Method in interface org.biomage.Interface.HasPosition
Get method for position
getPositionDelta() - Method in class org.biomage.Array.FeatureDefect
Get method for positionDelta
getPositionDelta() - Method in class org.biomage.Array.ZoneDefect
Get method for positionDelta
getPositionDelta() - Method in interface org.biomage.Interface.HasPositionDelta
Get method for positionDelta
getPossibleNames(Extendable, String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getPossibleNames(OntologyHelper.ClassInformation, String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getPostconditions() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the postconditions.
getPrecedence() - Method in class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
getPreconditions() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the preconditions.
getPrevious() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPrimaryClassName() - Method in class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
getPrimaryInfo(String) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getPrincipalInvestigator() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
Return the PI for the Experiment
getPrincipalInvestigator() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getProblems() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getProducerTransformation() - Method in class org.biomage.BioAssayData.DerivedBioAssayData
Get method for producerTransformation
getProducerTransformation() - Method in interface org.biomage.Interface.HasProducerTransformation
Get method for producerTransformation
getProperties() - Method in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
getProperties() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getPropertiesInfo(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getProperty(Object, String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getProperty(String) - Static method in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
getProperty(String) - Static method in class gov.nih.nci.caarray.services.util.properties.ParsingProperties
 
getProperty(String) - Method in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
getProperty(String) - Static method in class gov.nih.nci.caarray.services.util.properties.QuantitationNamesProperties
 
getProperty(String) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getPropertySets() - Method in class org.biomage.Common.Extendable
Get method for propertySets
getPropertySets() - Method in class org.biomage.Common.NameValueType
Get method for propertySets
getPropertySets() - Method in interface org.biomage.Interface.HasPropertySets
Get method for propertySets
getProtectionElementId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getProtectionElementID(String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Returns protection elementID based on object ID and the application name
getProtectionGroupId() - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
getProtectionGroupId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.security.RoleAssignmentData
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets all the protection Groups in the system
getProtectionGroups() - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets all the protection Groups in the system
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets all the protection Groups in the system
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets all the protection Groups in the system
getProtectionGroups() - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Returns an array of ProtectionGroups which are present in the application.
GetProtectionGroups - Class in gov.nih.nci.caarray.services.security.test.usecases
 
GetProtectionGroups() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.GetProtectionGroups
 
getProtectionGroupsFromObject(SecuredElementItf) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
getProtectionGroupTypeId() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getProtectionGroupTypeId() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getProtectionGroupTypeId() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getProtectionTypeId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getProtocol() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getProtocol(long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
getProtocol(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
This method returns a Protocol that has the specified ID by delegating the call to the same method in ProtocolManagerDB.
getProtocol(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
Get a Protocol that has the specified ID.
getProtocol(long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Searches for the Protocol that match the specified ID.
getProtocol() - Method in interface org.biomage.Interface.HasProtocol
Get method for protocol
getProtocol() - Method in class org.biomage.Protocol.ProtocolApplication
Get method for protocol
getProtocol_list() - Method in class org.biomage.Protocol.Protocol_package
Get method for protocol_list
getProtocol_package() - Method in class org.biomage.Common.MAGEJava
Get method for protocol_package
getProtocolActivityDate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getProtocolApp(int) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
getProtocolApplication(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProtocolApplication(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getProtocolApplication() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getProtocolApplication() - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
getProtocolApplicationId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
getProtocolApplications(long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Gets an array of ProtocolApplication that use the specified Protocol.
getProtocolApplications() - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getProtocolApplications() - Method in class org.biomage.Array.ArrayManufacture
Get method for protocolApplications
getProtocolApplications() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for protocolApplications
getProtocolApplications() - Method in class org.biomage.BioEvent.BioEvent
Get method for protocolApplications
getProtocolApplications() - Method in interface org.biomage.Interface.HasProtocolApplications
Get method for protocolApplications
getProtocolDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getProtocolId() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getProtocolId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getProtocolPerformerID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getProtocols(ProtocolSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Gets an array of Protocol's that match the specified criteria.
getProtocols() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getProtocols() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getProtocols() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getProtocolsApp() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getProtocolsList(String, ProtocolManagerDelegate) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
getProtocolsList(String, ProtocolManagerDelegate) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
getProtocolType() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getProtocolTypeId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getProtocolTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getProtocolTypes() - Method in class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData
 
getProtocolTypes(long) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getProtocolTypes() - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Get available protocol types.
getProtocolTypes(long) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
Retrieves an array of controlled vocabularies representing protocol types given the ID of a controlled vocabulary representing a treatment action.
getProtocolTypes(long) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Retrieves the list of protocol types that are mapped to the specified action.
getProtocolTypes() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getProtocolTypes() - Method in class org.biomage.BioMaterial.ActionProtocolTypeMap
 
getProtocolVisibility() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getProtocolVisibility() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getProvidedByAffymetrix() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProvider() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getProvider() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData
 
getProvider() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
getProvider() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getProviderDescriptor() - Method in enum gov.nih.nci.caarray.services.arraydesign.ArrayDesignType
 
getProviderId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getProviderId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getProviderId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProviderId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getProviderName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getProviderRoles() - Method in class org.biomage.Experiment.Experiment
 
getProviders() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getProviders() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getProviders() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getProviders() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getProviders() - Method in class org.biomage.Experiment.Experiment
Get method for providers
getProviders() - Method in interface org.biomage.Interface.HasProviders
Get method for providers
getProvidersOrgs() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getProvidersOrgs() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getProviderType() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getPublication() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getPublication() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublication() - Method in class org.biomage.BQS.BibliographicReference
Get method for publication
getPublicationAuthor() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationCancel() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationData() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationDataID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationEditor() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationIssue() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationMedID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationPage() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublications() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getPublicationTitle() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationURI() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublicationVolume() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublisher() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getPublisher() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPublisher() - Method in class org.biomage.BQS.BibliographicReference
Get method for publisher
getPublishYear() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPubMedId() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getPubMedLink() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getPubMedLink_() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getPwd() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getQuality() - Method in class org.biomage.Array.ManufactureLIMS
Get method for quality
getQualityControl() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
getQualityControl() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getQualityControlDescription(long) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
getQualityControlDescription() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getQualityControlDescription() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for qualityControlDescription
getQualityControlDescription() - Method in interface org.biomage.Interface.HasQualityControlDescription
Get method for qualityControlDescription
getQualityControlStatistics() - Method in class org.biomage.Array.ArrayManufacture
Get method for qualityControlStatistics
getQualityControlStatistics() - Method in class org.biomage.BioMaterial.BioMaterial
Get method for qualityControlStatistics
getQualityControlStatistics() - Method in interface org.biomage.Interface.HasQualityControlStatistics
Get method for qualityControlStatistics
getQualityControlType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getQuantitation(String) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
getQuantitationArray(BioAssay, QuantitationType) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
 
getQuantitationDimension() - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Get method for quantitationDimension
getQuantitationDimension() - Method in interface org.biomage.Interface.HasQuantitationDimension
Get method for quantitationDimension
getQuantitations(BioAssay) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
Gets an entire quantitation type for an assay
getQuantitationType() - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
Get method for quantitationType
getQuantitationType() - Method in interface org.biomage.Interface.HasQuantitationType
Get method for quantitationType
getQuantitationType_list() - Method in class org.biomage.QuantitationType.QuantitationType_package
Get method for quantitationType_list
getQuantitationType_package() - Method in class org.biomage.Common.MAGEJava
Get method for quantitationType_package
getQuantitationTypeColumn2SimpleQuantitationTypeMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.QuantitationTypeColumnsMap
 
getQuantitationTypeColumnNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.QuantitationTypeColumnsMap
Gets the names of the quantitation type columns from the quantitationTypeColumn2SimpleQuantitationTypeMappings.
getQuantitationTypeColumnsMap(String) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.QuantitationTypeFinder
 
getQuantitationTypeColumnsMap() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
getQuantitationTypeDescriptors() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
 
getQuantitationTypeDimension() - Method in class org.biomage.BioAssayData.BioAssayData
Get method for quantitationTypeDimension
getQuantitationTypeDimension() - Method in interface org.biomage.Interface.HasQuantitationTypeDimension
Get method for quantitationTypeDimension
getQuantitationTypeDimension_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for quantitationTypeDimension_list
getQuantitationTypeMap_list() - Method in class org.biomage.BioAssayData.BioAssayData_package
Get method for quantitationTypeMap_list
getQuantitationTypeMapping() - Method in class org.biomage.BioAssayData.Transformation
Get method for quantitationTypeMapping
getQuantitationTypeMapping() - Method in interface org.biomage.Interface.HasQuantitationTypeMapping
Get method for quantitationTypeMapping
getQuantitationTypeMaps() - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Get method for quantitationTypeMaps
getQuantitationTypeMaps() - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Get method for quantitationTypeMaps
getQuantitationTypeMaps() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for quantitationTypeMaps
getQuantitationTypeName() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getQuantitationTypeName(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
Translates a given javaPropertyName to its original quantification name as defined in quantitationNames.properties.
getQuantitationTypeName(String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
getQuantitationTypeName2JavaPropertyNameMap() - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
getQuantitationTypeName2JavaPropertyNameMappings() - Method in class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
getQuantitationTypeProperties() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
getQuantitationTypes() - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Get method for quantitationTypes
getQuantitationTypes() - Method in interface org.biomage.Interface.HasQuantitationTypes
Get method for quantitationTypes
getQuantitationTypeService(UploadFileTypes.MICROARRAY_FILE_TYPE) - Static method in class gov.nih.nci.caarray.services.fileparse.QuantitationTypeServiceFactory
 
getQuantitationTypesFileLocation(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
getQuantitationTypesFromFile(String) - Method in class gov.nih.nci.caarray.services.fileparse2.QuantitationTypeManagerDB
 
getQuantitationTypeTuples() - Method in class org.biomage.BioAssayData.DesignElementTuple
Get method for quantitationTypeTuples
getQuantitationTypeTuples() - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Get method for quantitationTypeTuples
getQueue(String) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getQueueConnectionFactory() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getQueueConnectionFactory(String) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getQueueName() - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
getQueueSessionNames() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
getQueueSessionNames() - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
getRank() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get rank of this assocaition to the others.
getReader() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
getReason() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getReason() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
getRecord() - Method in class org.biomage.tools.apps.annot.data.PageRecord
 
getRegionName() - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
 
getRegions() - Method in class org.biomage.BioSequence.SeqFeature
Get method for regions
getRegions() - Method in interface org.biomage.Interface.HasRegions
Get method for regions
getReleaseDate() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
getReleaseDate() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getReleaseDate() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getReleaseDate() - Method in class org.biomage.Protocol.SoftwareApplication
Get method for releaseDate
getReleaseDateAsString() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
getReload() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getRemoteHome(String, Class) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
Retrieve the EJBHome object given an EJB Home and its corresponding JNDI name.
getRepair() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getReplacedLength() - Method in class org.biomage.DesignElement.MismatchInformation
Get method for replacedLength
getReplicateDescription() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for replicateDescription
getReplicateDescription() - Method in interface org.biomage.Interface.HasReplicateDescription
Get method for replicateDescription
getReporter() - Method in class org.biomage.DesignElement.FeatureReporterMap
Get method for reporter
getReporter() - Method in class org.biomage.DesignElement.ReporterPosition
Get method for reporter
getReporter() - Method in interface org.biomage.Interface.HasReporter
Get method for reporter
getReporter_list() - Method in class org.biomage.DesignElement.DesignElement_package
Get method for reporter_list
getReporterCompositeMap_list() - Method in class org.biomage.DesignElement.DesignElement_package
Get method for reporterCompositeMap_list
getReporterCompositeMaps() - Method in class org.biomage.DesignElement.CompositeSequence
Get method for reporterCompositeMaps
getReporterCompositeMaps() - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Get method for reporterCompositeMaps
getReporterFileLocation() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getReporterFileLocation() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getReporterFileLocation() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getReporterFileType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getReporterFileType() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
getReporterGroup(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Retrieve the ReporterGroup that has the specified ID.
getReporterGroup_list() - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Get method for reporterGroup_list
getReporterGroupId() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
getReporterGroups(ReporterGroupSearchCriteria) - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Searches reporterGroups.
getReporterGroups() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for reporterGroups
getReporterGroups() - Method in interface org.biomage.Interface.HasReporterGroups
Get method for reporterGroups
getReporterPositionSources() - Method in class org.biomage.DesignElement.ReporterCompositeMap
Get method for reporterPositionSources
getReporterPositionSources() - Method in interface org.biomage.Interface.HasReporterPositionSources
Get method for reporterPositionSources
getReporters() - Method in class org.biomage.ArrayDesign.ReporterGroup
Get method for reporters
getReporters() - Method in class org.biomage.BioAssayData.ReporterDimension
Get method for reporters
getReporters() - Method in interface org.biomage.Interface.HasReporters
Get method for reporters
getReporterTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getReporterTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getReporterTypeID() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getReporterTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getReporterTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getReporterTypes() - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
getReporterTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getRepository() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
getRepository() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
getRepositoryPath(ModuleConfig) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns the path to the temporary directory to be used for uploaded files which are written to disk.
getRequestAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getRequired() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
getResultingBiomaterialType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getResultingBiomaterialType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getResultingBiomaterialType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getResultingBiomaterialTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getResultingBiomaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getResultingBiomaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getResultingBiomaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getResultingBiomaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getResultingBiomaterialTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getResultingDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getResultingDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getResultingDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getResultingDescription() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getResultingName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getResultingName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getResultingName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getResultingName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getResultingName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getResults() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
getResults() - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
getResults() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm
 
getResults() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getReturnFwd() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
getReturnType() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the returnType.
getRole() - Method in class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData
 
getRole() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData
 
getRole() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getRole() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getRole() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
getRole(String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthenticationDAItf
Returns an array of Role objects associated with the login name.
getRole(String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecurityServiceItf
Returns an array of Role objects associated with the loginName/passwd.
getRole(String) - Method in class gov.nih.nci.caarray.services.security.LdapAuthenticationDAObj
Returns an array of Role objects associated with the login name.
getRole(String, String) - Method in class gov.nih.nci.caarray.services.security.LdapAuthenticationDAObj
Returns an array of Role objects associated with the login name and application.
getRole(String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthenticationDAObj
Returns an array of Role objects associated with the login name.
getRole(String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthenticationDAObj
Returns an array of Role objects associated with the login name and application.
getRole(String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns an array of Role objects associated with the loginName/passwd.
getRole() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getRole() - Method in class org.biomage.ArrayDesign.DesignProviderRole
 
getRole() - Method in class org.biomage.Experiment.ExperimentProviderRole
 
getRoleDesc() - Method in class gov.nih.nci.caarray.common.data.security.Role
Return the roleDesc
getRoleId() - Method in class gov.nih.nci.caarray.common.data.security.Role
Return the roleId
getRoleId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getRoleId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getRoleName() - Method in class gov.nih.nci.caarray.common.data.security.Role
Return the roleName
getRoleNames() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether the role names for this class.
getRoles() - Method in class gov.nih.nci.caarray.common.data.security.UserRoleData
 
getRoles() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getRoles() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for roles
getRoles() - Method in interface org.biomage.Interface.HasRoles
Get method for roles
getRolesArray() - Method in class gov.nih.nci.caarray.common.data.security.UserRoleData
 
getRoleSelection() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getRoleSets() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
 
getRow() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
getRow() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.GenepixGprReader
 
getRow() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
getRow() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
getRow() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getRow() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
getRow() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getRow() - Method in class org.biomage.ArrayDesign.Zone
Get method for row
getRow() - Method in class org.biomage.DesignElement.FeatureLocation
Get method for row
getRowInt() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
getRowNumber() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
getRows() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Method getRows.
getRowsAsList() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
For efficiency, return a List of LocalDynaBean's each of which represents a data row.
getRs() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
getSampleDescription() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return sample description after formatting.
getSampleId() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
getSampleName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
getSampleName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getSampleName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getSampleType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getSampleType() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
getSampleType() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getSampleTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getSampleTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
getSampleTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getScale() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
getScale() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getScale() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Get method for scale
getScale() - Method in interface org.biomage.Interface.HasScale
Get method for scale
getScale() - Method in class org.biomage.QuantitationType.QuantitationType
Get method for scale
getScales() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getScaleType() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
getScaleTypes() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getScanningProtocol() - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
getSchemaName() - Static method in class org.biomage.tools.helpers.JDBCConnection2
 
getScope() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for scope.
getSearchResults() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
getSearchResults() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
getSecondaryInfo(String) - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getSecondaryInfos() - Method in class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
getSecondaryInfos() - Method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getSecuredElement() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getSecuredElementClassName() - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
getSecuredElementId() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getSecuredElementId() - Method in interface gov.nih.nci.caarray.services.security.intf.SecuredElementItf
 
getSecuredElementId() - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
getSecuredElementId() - Method in class org.biomage.Common.Extendable
 
getSecurity() - Method in class org.biomage.Common.Describable
Get method for security
getSecurity() - Method in interface org.biomage.Interface.HasSecurity
Get method for security
getSecurity_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Get method for security_list
getSecurityDataSource() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getSecurityGroup_list() - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Get method for securityGroup_list
getSecurityGroups() - Method in class org.biomage.AuditAndSecurity.Security
Get method for securityGroups
getSecurityGroups() - Method in interface org.biomage.Interface.HasSecurityGroups
Get method for securityGroups
getSelectedBiomaterial() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getSelectedBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getSelectedBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
getSelectedCharacteristics() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getSelectedManufacturers() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getSelectedQualityControlTypeID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getSelectedVisibilities() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getSelectedVisibilities() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getSelectedVisibilityIds() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getSelectedVisibilityNames() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
getSelectedVisibilityNames() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getSelectedVisibilitys(ProtectionGroupData[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getSelectedVisibilitys(ProtectionGroupData[], String[], String[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getSelectedVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
getSemantics() - Method in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
Description: Get method for the semantics.
getSeqFeatures() - Method in class org.biomage.BioSequence.BioSequence
Get method for seqFeatures
getSeqFeatures() - Method in interface org.biomage.Interface.HasSeqFeatures
Get method for seqFeatures
getSequence(PersistenceBroker, FieldDescriptor, String) - Method in class gov.nih.nci.caarray.services.util.ojb.CaArraySequenceManagerHighLowImpl
 
getSequence() - Method in class org.biomage.BioSequence.BioSequence
Get method for sequence
getSequenceDatabases() - Method in class org.biomage.BioSequence.BioSequence
Get method for sequenceDatabases
getSequenceDatabases() - Method in interface org.biomage.Interface.HasSequenceDatabases
Get method for sequenceDatabases
getSequencesById(int, Class) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
 
getSerialNumber() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData
 
getSerialNumber() - Method in class org.biomage.Protocol.HardwareApplication
Get method for serialNumber
getServerURL() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getServlet() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Retrieves the servlet with which this handler is associated.
getSex() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getSexId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getSexTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getShouldBeAdminUser() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getSid() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getSid() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getSid() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getSimpleQuantitationTypes() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.QuantitationTypeColumnsMap
 
getSimpleQuatitationTypes(String) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.QuantitationTypeFinder
Gets the quatitations based on a type
getSize() - Method in class gov.nih.nci.caarray.common.data.util.FileData
Gets the file size.
getSize() - Method in class org.biomage.tools.helpers.DbConnectionBroker
Returns the number of connections in the dynamic pool.
getSizeMax(ModuleConfig) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns the maximum allowable size, in bytes, of an uploaded file.
getSizeThreshold(ModuleConfig) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns the size threshold which determines whether an uploaded file will be written to disk or cached in memory.
getSobject() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getSoftware() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
getSoftware(long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
getSoftware(long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
Get a Software that has the specified ID.
getSoftware(long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Retrieve the Software that has the specified ID.
getSoftware() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getSoftware() - Method in interface org.biomage.Interface.HasSoftware
Get method for software
getSoftware() - Method in class org.biomage.Protocol.SoftwareApplication
Get method for software
getSoftware_list() - Method in class org.biomage.Protocol.Protocol_package
Get method for software_list
getSoftwareApplications() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
getSoftwareApplications() - Method in interface org.biomage.Interface.HasSoftwareApplications
Get method for softwareApplications
getSoftwareApplications() - Method in class org.biomage.Protocol.ProtocolApplication
Get method for softwareApplications
getSoftwareId() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getSoftwareId() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareManagerDB() - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
 
getSoftwareManufacturerId() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getSoftwareManufacturerId() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareManufacturerName() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareManufacturers() - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
getSoftwareManufacturers() - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
getSoftwareManufacturers() - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
 
getSoftwareManufacturers() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareManufacturers() - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Get method for softwareManufacturers
getSoftwareManufacturers() - Method in class org.biomage.Protocol.Software
Get method for softwareManufacturers
getSoftwareName() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MICROARRAY_FILE_TYPE
 
getSoftwares() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
getSoftwares() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getSoftwares() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getSoftwares(SoftwareSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Get available softwares.
getSoftwares() - Method in interface org.biomage.Interface.HasSoftwares
Get method for softwares
getSoftwares() - Method in class org.biomage.Protocol.Hardware
Get method for softwares
getSoftwares() - Method in class org.biomage.Protocol.Protocol
Get method for softwares
getSoftwares() - Method in class org.biomage.Protocol.Software
Get method for softwares
getSoftwareTypeId() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareTypeName() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSoftwareTypes() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
getSokey() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
getSource() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
getSourceBioAssays() - Method in class org.biomage.BioAssayData.BioAssayMap
Get method for sourceBioAssays
getSourceBioAssays() - Method in interface org.biomage.Interface.HasSourceBioAssays
Get method for sourceBioAssays
getSourceBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getSourceBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getSourceBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getSourceBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getSourceBiomaterialId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getSourceBioMaterialMeasurements() - Method in class org.biomage.BioAssay.BioAssayCreation
Get method for sourceBioMaterialMeasurements
getSourceBioMaterialMeasurements() - Method in class org.biomage.BioMaterial.Treatment
Get method for sourceBioMaterialMeasurements
getSourceBioMaterialMeasurements() - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Get method for sourceBioMaterialMeasurements
getSourceBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getSourceBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getSourceBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getSourceBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getSourceBiomaterialName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getSourceBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
getSourceBiomaterials() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getSourceClass() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
getSourceClassName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.DTOClass
 
getSourceContact() - Method in class org.biomage.BioMaterial.BioSource
Get method for sourceContact
getSourceContact() - Method in interface org.biomage.Interface.HasSourceContact
Get method for sourceContact
getSourceElementTypeNames() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getSourceException() - Method in exception gov.nih.nci.caarray.services.exception.DBException
Gets the sourceException.
getSourceException() - Method in exception gov.nih.nci.caarray.services.exception.ParseException
Gets the sourceException.
getSourceField() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getSourceFieldClassName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getSourceFieldName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getSourcesQuantitationType() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Get method for sourcesQuantitationType
getSourcesQuantitationType() - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Get method for sourcesQuantitationType
getSourceType() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getSourceType() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getSourceType() - Method in class org.biomage.BioAssayData.BioDataCube
 
getSpacingBetweenCols() - Method in class org.biomage.ArrayDesign.ZoneLayout
Get method for spacingBetweenCols
getSpacingBetweenRows() - Method in class org.biomage.ArrayDesign.ZoneLayout
Get method for spacingBetweenRows
getSpacingsBetweenZonesX() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for spacingsBetweenZonesX
getSpacingsBetweenZonesY() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for spacingsBetweenZonesY
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getSpecies() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getSpecies() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getSpecies() - Method in class org.biomage.ArrayDesign.DesignElementGroup
Get method for species
getSpecies() - Method in class org.biomage.BioSequence.BioSequence
Get method for species
getSpecies() - Method in interface org.biomage.Interface.HasSpecies
Get method for species
getSpeciesLists() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getSpeciesType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getSpeciesTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSpeciesTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getSpeciesTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSpeciesTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSpeciesTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getSpikedControl() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getSpikedControl() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getSpikedControl() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getSpikedControlCh2() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getSpikedControlID() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getSpikedControlID() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getSpikedControlIDCh2() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
getSpikedControls() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getSplitAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
getSqlInLimit() - Static method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
getStart() - Method in class org.biomage.BioSequence.SequencePosition
Get method for start
getStartAtLine() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Returns the startAtLine.
getStartCoord() - Method in class org.biomage.DesignElement.MismatchInformation
Get method for startCoord
getStartDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getStartDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getStartDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getStartDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getStartManufactureDate() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getState() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getState() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getState() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getStatus() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the status of the uploaded file
getStatus() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Returns the status of the uploaded file for which this history record pertains.
getStatus() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the status of the uploaded file
getStatus() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Returns the status of the uploaded file for which this history record pertains.
getStatus() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getStatus() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getStatus() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the status of the uploaded file
getStatus() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Returns the status of the uploaded file for which this history record pertains.
getStatus() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the status of the uploaded file
getStatus() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Returns the status of the uploaded file for which this history record pertains.
getStatus() - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
getStatus() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getStatus() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the date the status of the uploaded file was set
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Returns the date the status of the uploaded file history was set
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the data the status of the uploaded file was set
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Returns the date the status of the uploaded file history was set
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
getStatusDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getStatusDate() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the date the status of the uploaded file was set
getStatusDate() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Returns the date the status of the uploaded file history was set
getStatusDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the date the status of the uploaded file was set
getStatusDate() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Returns the date the status of the uploaded file history was set
getStatusDate() - Method in class gov.nih.nci.caarray.ui.CaarrayDecorator
Return sample uploadTime after formatting.
getStatuses() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getStatusSelection() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
getStatusString() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getStrainOrLine() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getStrainOrLineId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getStrainOrLines() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getStrandType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getStrandType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getStrandType() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for strandType
getStrandTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getStrandTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getStrandTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getString(Object) - Method in interface gov.nih.nci.caarray.services.security.db.SecurityDSConnectionUtil.CustomRowMap
 
getSubCategories(String) - Static method in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
Gets the sub-categories for the specified categories as defined in ontologyCategories.properties.
getSubCategories(String) - Static method in class gov.nih.nci.caarray.services.util.properties.OntologyCategoriesProperties
 
getSubClasses() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
getSubClassNames(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
getSubject() - Method in class gov.nih.nci.caarray.services.util.UserInfo
 
getSubject() - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
getSubmitted() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getSubregions() - Method in class org.biomage.BioSequence.SeqFeatureLocation
Get method for subregions
getSubregions() - Method in interface org.biomage.Interface.HasSubregions
Get method for subregions
getSubSoftwareID() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getSubstrateType() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getSubstrateType() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getSubstrateType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getSubstrateType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getSubstrateType() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getSubstrateType() - Method in class org.biomage.Array.ArrayGroup
Get method for substrateType
getSubstrateType() - Method in interface org.biomage.Interface.HasSubstrateType
Get method for substrateType
getSubstrateTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSubstrateTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
getSubstrateTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSubstrateTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
getSubstrateTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getSubstrateTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSummaryStatistics() - Method in class org.biomage.BioAssayData.BioAssayData
Get method for summaryStatistics
getSummaryStatistics() - Method in interface org.biomage.Interface.HasSummaryStatistics
Get method for summaryStatistics
getSurfaceType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getSurfaceType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getSurfaceType() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Get method for surfaceType
getSurfaceType() - Method in interface org.biomage.Interface.HasSurfaceType
Get method for surfaceType
getSurfaceTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSurfaceTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSurfaceTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getSystemUsers() - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets all the active Users of the system.
getSystemUsers() - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets all the active Users of the system.
getTableDescriptor() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataColumnDescriptor
 
getTarget() - Method in class org.biomage.BioAssay.BioAssayTreatment
Get method for target
getTarget() - Method in interface org.biomage.Interface.HasTarget
Get method for target
getTargetClass() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
getTargetClass() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.DTOClass
 
getTargetClassName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.TargetClass
 
getTargetDesignElementClassName() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
getTargetDesignElementPropertyNames() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
getTargetedCellType() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTargetedCellTypeId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTargetedCellTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTargetElementTypeNames() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getTargetField() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
getTargetFieldClassName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getTargetFieldName() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
getTargetId() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractIlluminaCsvReader
 
getTargetQuantitationType() - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Get method for targetQuantitationType
getTargetQuantitationType() - Method in interface org.biomage.Interface.HasTargetQuantitationType
Get method for targetQuantitationType
getTargetQuantitationType() - Method in class org.biomage.QuantitationType.ConfidenceIndicator
Get method for targetQuantitationType
getTargetSimpleDesignElementClass() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
getTaxonName() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getTaxonType() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTaxonTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTechnologyType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getTechnologyType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getTechnologyType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getTechnologyType() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getTechnologyType() - Method in class org.biomage.ArrayDesign.FeatureGroup
Get method for technologyType
getTechnologyType() - Method in interface org.biomage.Interface.HasTechnologyType
Get method for technologyType
getTechnologyTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getTechnologyTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getTechnologyTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getTempDirectory() - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
getTemperature() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getText() - Method in class org.biomage.Description.Description
Get method for text
getText() - Method in class org.biomage.Protocol.Protocol
Get method for text
getTextElements() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Returns a hash table containing the text (that is, non-file) request parameters.
getTheColumnOrder() - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method getTheColumnOrder.
getTheDelimiter() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Returns the theDelimiter.
getTheDelimiter() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Returns the theDelimiter.
getTheFileName() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Returns the fileName.
getTheFileName() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Returns the theFileName.
getTheRows() - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method getTheRows.
getTheTable() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Returns the theTable.
getThisMaxCard() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for thisMaxCard.
getThisMaxCard() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the minimum cardinality of this class for the association relationship
getThisMinCard() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for thisMinCard.
getThisMinCard() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the maximum cardinality of this class for the association relationship
getThisNav() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for thisNav.
getThisNav() - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: return the maximum cardinality of this class for the association relationship
getTimeBytes() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
getTimeStamp() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
getTitle() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getTitle() - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
getTitle() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getTitle() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getTitle() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getTitle() - Method in class org.biomage.BQS.BibliographicReference
Get method for title
getTitle() - Method in class org.biomage.Protocol.Protocol
Get method for title
getTokenValue(Document, String) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns the text of the element with name of token.
getTolerance() - Method in class org.biomage.Array.ArrayManufacture
Get method for tolerance
getTollFreePhone() - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
getTollFreePhone() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for tollFreePhone
getTopic(String) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getTopicConnectionFactory() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
 
getTopicConnectionFactory(String) - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
Obtain the TopicConnectionFactory for sending/receiving JMS messages
getTopicSessionNames() - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
getTopicSessionNames() - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
getTopLevelBioAssays() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for topLevelBioAssays
getTopLevelBioAssays() - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Get method for topLevelBioAssays
getTopLevelBioMaterials() - Method in class org.biomage.BioMaterial.BioMaterial
Get method for treatments
getTopLevelBioMaterials() - Method in interface org.biomage.Interface.HasTopBioMaterial
Get method for topLevelBioMaterials
getTopMostSourceBioMaterials(BioMaterial) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Gets the parents of the specified bio material, which are in most cases bio sources.
getTransactionConnection() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
getTransactionTimeoutMinutes() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getTreatment(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getTreatment(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getTreatment(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Retrieves the TreatmentData object from the persistence store.
getTreatmentAction() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getTreatmentAction(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentAction(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentAction() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentAction(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentEvent(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
This function allows the passing of the TreatmentEvents from the request to the form.
getTreatmentEvent(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentEvent(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentEventId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getTreatmentEvents() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getTreatmentEvents() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getTreatmentEvents() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentEvents() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentEvents() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTreatmentEventss(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
This function allows the passing of the TreatmentEvents from the request to the form.
getTreatmentId() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTreatmentNumber() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentOrder() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTreatments() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
getTreatments(long) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
getTreatments(long) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
getTreatments(long) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
 
getTreatments() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getTreatments() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatments() - Method in class org.biomage.BioMaterial.BioMaterial
Get method for treatments
getTreatments() - Method in interface org.biomage.Interface.HasTreatments
Get method for treatments
GetTreatmentTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
GetTreatmentTest() - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.GetTreatmentTest
 
getTreatmentType() - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
getTreatmentType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getTreatmentType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatmentType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentType() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTreatmentTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
getTreatmentTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatmentTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
getTreatmentTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentTypeName() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTreatmentTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
getTreatmentTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
getTreatmentTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
getTreatmentTypes() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
getTumorGrading() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTumorGradingId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTumorGradings() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getTunnelURL() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getTunnelURL() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getTxt_file_exist() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getTxtFile() - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
getTxtFileLocation() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getTxtFileLocation() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getType() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
getType() - Method in class gov.nih.nci.caarray.common.data.measurement.UnitData
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getType() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getType() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
getType() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getType() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getType() - Method in class org.biomage.BioAssay.DerivedBioAssay
Get method for type
getType() - Method in class org.biomage.BioMaterial.BioSample
Get method for type
getType() - Method in class org.biomage.BioSequence.BioSequence
Get method for type
getType() - Method in class org.biomage.Common.NameValueType
Get method for type
getType() - Method in class org.biomage.Description.DatabaseEntry
Get method for type
getType() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Get method for type
getType() - Method in interface org.biomage.Interface.HasType
Get method for type
getType() - Method in class org.biomage.Measurement.Measurement
Get method for type
getType() - Method in class org.biomage.Protocol.Hardware
Get method for type
getType() - Method in class org.biomage.Protocol.Protocol
Get method for type
getType() - Method in class org.biomage.Protocol.Software
Get method for type
getType() - Method in class org.biomage.tools.generate_er.DataColumn
Description: get the type of the column
getType() - Method in class org.biomage.tools.generate_er.Table
Description: get teh type of the table
getTypeAggregated() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Get method for type of aggregated.
getTypeName() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
getTypeRole() - Method in class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
getTypes() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
getTypes() - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
getTypes() - Method in class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData
 
getTypes() - Method in class org.biomage.ArrayDesign.DesignElementGroup
Get method for types
getTypes() - Method in class org.biomage.Description.Ontology.ChromosomalAberration
 
getTypes() - Method in class org.biomage.Experiment.ExperimentDesign
Get method for types
getTypes() - Method in interface org.biomage.Interface.HasTypes
Get method for types
getUnique() - Method in class org.biomage.tools.generate_er.Table
Description: get the Unique column for the table
getUniqueKey() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
Creates a unique key to represent this hybridization row using DesignElement attributes.
getUniqueKey() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleDesignElement
Returns the unique key representing this DesignElement from the keyProperty attribute.
getUniqueKeyFromNonKeyProperties() - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleDesignElement
Creates a unique key to represent this DesignElement using the properties other than the attribute Id.
getUniqueVector() - Method in class org.biomage.tools.generate_er.Unique
Description: get the vector holding all columns for Unique
getUnit() - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
getUnit() - Method in interface org.biomage.Interface.HasUnit
Get method for unit
getUnit() - Method in class org.biomage.Measurement.Measurement
Get method for unit
getUnitName() - Method in class org.biomage.Measurement.Unit
Get method for unitName
getUnitNameCV() - Method in class org.biomage.Measurement.ConcentrationUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.DistanceUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.MassUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.QuantityUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.TemperatureUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.TimeUnit
Get method for unitNameCV
getUnitNameCV() - Method in class org.biomage.Measurement.VolumeUnit
Get method for unitNameCV
getUnitNameId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnitNameOther() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnitNames() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnitOtherId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnits() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
getUnits(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
This method is used to get the correct units for the type of measurement specified by this measurement type id
getUnitTypeId() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnitTypeOther() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUnitTypes() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
getUpdateDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getUpdateDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getUpdateDate() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getUpdateDate() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
getUpdateDate() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
getUpdateDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getUpdateDate() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getUploadDate() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
getUploadedFileData() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
getUploadedFileName(FormFile) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getUploadedFileValidatorCode(FormFile) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getUploadFileValue() - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
getUploadGroupName() - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
getUploadGroupName() - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
getUploadTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getUploadTypeId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getUploadTypeName() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getUploadTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getUploadTypes() - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
getUploadTypes() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
getUploadURL() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
getUploadURL() - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
getUploadURL() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
getUploadURLWithSid() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
This method will return a uploadURL string with a session id (jsessionid) appended at the end for session identification by the server.
getUpperLeftX() - Method in class org.biomage.ArrayDesign.Zone
Get method for upperLeftX
getUpperLeftY() - Method in class org.biomage.ArrayDesign.Zone
Get method for upperLeftY
getUpperX() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getUpperY() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
getURI() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
getURI() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
getURI() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
getURI() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
getURI() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getURI() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
getURI() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
getURI() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getURI() - Method in class org.biomage.AuditAndSecurity.Contact
Get method for URI
getURI() - Method in class org.biomage.BioAssay.Image
Get method for URI
getURI() - Method in class org.biomage.BQS.BibliographicReference
Get method for URI
getURI() - Method in class org.biomage.Description.Database
Get method for URI
getURI() - Method in class org.biomage.Description.DatabaseEntry
Get method for URI
getURI() - Method in class org.biomage.Description.Description
Get method for URI
getURI() - Method in class org.biomage.Protocol.Parameterizable
Get method for URI
getUrl() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getUrl() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
getUrl() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getUseCount() - Method in class org.biomage.tools.helpers.DbConnectionBroker
Returns the number of connections in use.
getUser() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getUser(long) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
getUser(long) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getUser(long) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Gets a UserData object that matches the given Id.
getUserAdminRoleId() - Static method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getUserDefined() - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
getUserDefined() - Method in class org.biomage.Description.Database
 
getUserEmail() - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets email information for the current user.
getUserEmail(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets email information for the specified user.
getUserEmail() - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets email information for the current user.
getUserEmail(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets email information for the specified user.
getUserEmail() - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets email information for the current user.
getUserEmail(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets email information for the specified user.
getUserEmail() - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets email information for the current user.
getUserEmail(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets email information for the specified user.
getUserGroupData() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getUserGroupInfo(long) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
getUserGroupInfo(long) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getUserGroupInfo(long) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Gets a Vector that has a list of all the Groups with appropriate information.
getUserId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the submitters name for the uploaded file
getUserId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the submitters name for the uploaded file
getUserId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getUserId() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getUserId() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
getUserId() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the submitters name for the uploaded file
getUserId() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the submitters name for the uploaded file
getUserId() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
getUserId() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
getUserName() - Method in class gov.nih.nci.caarray.common.data.security.UserRoleData
 
getUserName() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getUsername() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignFileParsingJob
 
getUsername() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
getUsername() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
getUsername() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
getUsername() - Method in class gov.nih.nci.caarray.services.hybridization.HybridizationDataJob
 
getUserName(SessionContext) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
getUserName() - Method in class gov.nih.nci.caarray.services.util.UserInfo
 
getUserName() - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
getUserName() - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
getUserNamePrincipal() - Method in class gov.nih.nci.caarray.services.util.UserInfo
 
getUserNamePrincipal() - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
GetUserRole - Class in gov.nih.nci.caarray.services.security.test.usecases
 
GetUserRole() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.GetUserRole
 
getUserRoleCollection() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getUserRoleData(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getUserRoleData(String, String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets role information for the specified user.
getUserRoleData(String, String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets role information for the specified user.
getUserRoleData(String, String) - Static method in class gov.nih.nci.caarray.services.security.CaSecurityManagerHelper
 
getUserRoleData(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Gets role information for the specified user.
getUserRoleData(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Gets role information for the specified user.
getUserRoles() - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
getUserRoles() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
getUserRoles() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
getUserRoleSelection() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getUsers() - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
getUsers() - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Gets role information for the specified user.
getUsers() - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Gets role information for the specified user.
getUsers() - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Returns an array of ProtectionGroups which are present in the application.
getUsers() - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getUsers(UserSearchCriteria) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
getUserStatusCollection() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getUserStatusSelection() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
getUserTransaction() - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
getUserTransaction() - Method in class gov.nih.nci.caarray.services.util.ServiceLocator
Looks up UserTransaction.
getValidate() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getValidate() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
getValidatorCode() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Returns the validatorCode for the uploaded file
getValidatorCode() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the validatorCode for the uploaded file
getValidatorCode() - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
getValidatorCode() - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Returns the validatorCode for the uploaded file
getValidatorCode() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the validatorCode for the uploaded file
getValidatorCode(File) - Static method in class gov.nih.nci.caarray.services.util.file.FileValidator
Retrieves the CRC32 as vaidatorCode for the submitted file
getValidatorCode(File) - Static method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.AppletValidatorCodeGenerator
Retrieves the CRC32 as vaidatorCode for the submitted file
getValidatorCode() - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
Returns the CRC32 validatorCode for the uploaded file
getValidatorCode() - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
Returns the CRC32 validatorCode for the uploaded file
getValue() - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
getValue() - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
getValue() - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
getValue() - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
getValue(QuantitationTypeDescriptor) - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
 
getValue(ParsingQuantitationType) - Method in interface gov.nih.nci.caarray.services.fileparse.DataRow
 
getValue(ParsingDesignElement, ParsingQuantitationType) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDataMatrix
Gets a value
getValue(ParsingQuantitationType) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
Gets the value for a given quantitation type
getValue(ParsingDesignElement, ParsingQuantitationType) - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingDataMatrix
 
getValue() - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.test.IAccess
 
getValue(SimpleDesignElement, SimpleQuantitationType) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.DataMatrix
 
getValue(String) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
getValue(SimpleQuantitationType) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
getValue(Integer) - Method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypes
 
getValue(Object) - Static method in class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
 
getValue() - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
getValue() - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
getValue() - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
getValue() - Method in class org.biomage.BioAssayData.Datum
Get method for value
getValue() - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
getValue() - Method in class org.biomage.Common.NameValueType
Get method for value
getValue() - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Get method for value
getValue() - Method in class org.biomage.Description.OntologyEntry
Get method for value
getValue() - Method in class org.biomage.Experiment.FactorValue
Get method for value
getValue() - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Get method for value
getValue() - Method in interface org.biomage.Interface.HasValue
Get method for value
getValue() - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.Measurement
Get method for value
getValue() - Method in class org.biomage.Measurement.Measurement.KindCV
 
getValue() - Method in class org.biomage.Measurement.Measurement.Type
 
getValue() - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
getValue() - Method in class org.biomage.Protocol.ParameterValue
Get method for value
getValue1() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.HolderBean
 
getValue2() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.HolderBean
 
getValueAction() - Method in class org.biomage.AuditAndSecurity.Audit
Return the currrent value of the Enumeration type of Action.
getValueAsFloat(String, String) - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
 
getValueAsInteger(String, String) - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
getValueAsString(String, String) - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
getValueBasis() - Method in class org.biomage.BioSequence.SeqFeature
Return the currrent value of the Enumeration type of Basis.
getValueByName(String) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
getValueByName(String) - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
getValueByName(String) - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
getValueByName(String) - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
getValueByName(String) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.Measurement.KindCV
 
getValueByName(String) - Method in class org.biomage.Measurement.Measurement.Type
 
getValueByName(String) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
getValueByName(String) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
getValueByNameAction(String) - Method in class org.biomage.AuditAndSecurity.Audit
For Action get the Value of the Enumeration type by passing a Name to it.
getValueByNameBasis(String) - Method in class org.biomage.BioSequence.SeqFeature
For Basis get the Value of the Enumeration type by passing a Name to it.
getValueByNameKindCV(String) - Method in class org.biomage.Measurement.Measurement
For KindCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameOrder(String) - Method in class org.biomage.BioAssayData.BioDataCube
For Order get the Value of the Enumeration type by passing a Name to it.
getValueByNameOrientationMarkPosition(String) - Method in class org.biomage.Array.ArrayGroup
For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it.
getValueByNameType(String) - Method in class org.biomage.Measurement.Measurement
For Type get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.ConcentrationUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.DistanceUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.MassUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.QuantityUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TemperatureUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TimeUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.VolumeUnit
For UnitNameCV get the Value of the Enumeration type by passing a Name to it.
getValueId() - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
getValueId() - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
getValueKindCV() - Method in class org.biomage.Measurement.Measurement
Return the currrent value of the Enumeration type of KindCV.
getValueName() - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
getValueOrder() - Method in class org.biomage.BioAssayData.BioDataCube
Return the currrent value of the Enumeration type of Order.
getValueOrientationMarkPosition() - Method in class org.biomage.Array.ArrayGroup
Return the currrent value of the Enumeration type of OrientationMarkPosition.
getValueType() - Method in class org.biomage.Measurement.Measurement
Return the currrent value of the Enumeration type of Type.
getValueUnitNameCV() - Method in class org.biomage.Measurement.ConcentrationUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.DistanceUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.MassUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.QuantityUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.TemperatureUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.TimeUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getValueUnitNameCV() - Method in class org.biomage.Measurement.VolumeUnit
Return the currrent value of the Enumeration type of UnitNameCV.
getVersion() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
getVersion() - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
getVersion() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
getVersion() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
getVersion() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
getVersion() - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
getVersion() - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
getVersion() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
getVersion() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getVersion() - Method in class org.biomage.ArrayDesign.ArrayDesign
Get method for version
getVersion() - Method in class org.biomage.Description.Database
Get method for version
getVersion() - Method in class org.biomage.Protocol.SoftwareApplication
Get method for version
getVersion() - Static method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
 
getVisibilities() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
getVisibility() - Method in class gov.nih.nci.caarray.common.data.security.VisibilityData
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
getVisibility() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
getVisibility() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns the visibility.
getVisibilityDropdown() - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
getVisibilityDropdown() - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
getVisibilityDropdown() - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getVisibilityFromForm(ArrayDesignBaseForm, ArrayDesignDesc) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
getVisibilityFromForm(ArrayBaseForm, ArrayGroupDesc) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
getVisibilityId() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
getVisibilityName() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
getVisibilityName() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
getVisibilityName() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
getVisibilitys() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
getVisibleEntries(SessionContext, OntologyEntry[]) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
 
getVocabDropdown(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getVocabDropdown(String, boolean) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
getVocabId() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
getVocabulary(long) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
getVocabulary(long) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
getVolume() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getVolume() - Method in class org.biomage.BQS.BibliographicReference
Get method for volume
getWaitTime() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
getWaitTime() - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
getWarnings() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
getWarningType() - Method in class org.biomage.DesignElement.Reporter
Get method for warningType
getWarningType() - Method in interface org.biomage.Interface.HasWarningType
Get method for warningType
getWater() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
getWeight() - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
getWeight() - Method in class org.biomage.Description.Ontology.Biometrics
 
getWeightMeasurement() - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
getWeightMeasurement() - Method in class org.biomage.Description.Ontology.Biometrics
 
getWidth() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
getWidth() - Method in class org.biomage.Array.ArrayGroup
Get method for width
getX() - Method in class org.biomage.DesignElement.Position
Get method for x
getXMINodeFromFile(String) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Reads the file and creates the DOM structure and gets the XMI element.
getXSpacing() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getY() - Method in class org.biomage.DesignElement.Position
Get method for y
getYear() - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
getYear() - Method in class org.biomage.BQS.BibliographicReference
Get method for year
getYSpacing() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getZip() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
getZip() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
getZip() - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
getZipFileName() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
Generate a zip file name for this selected file.
getZipFileName(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
Generate a zip file name for this selected file based on the file name passed in.
getZipFilePath() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
getZipFileSize() - Method in class gov.nih.nci.caarray.services.util.file.FileZipper
Get the size of the zip file created by this class
getZipFileSize() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
Get the size of the zip file created by this class
getZone() - Method in class org.biomage.Array.ZoneDefect
Get method for zone
getZone() - Method in class org.biomage.DesignElement.Feature
Get method for zone
getZone() - Method in interface org.biomage.Interface.HasZone
Get method for zone
getZoneColumn() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getZoneGroup() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
getZoneGroup() - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
getZoneGroup() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
getZoneGroups() - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Get method for zoneGroups
getZoneGroups() - Method in interface org.biomage.Interface.HasZoneGroups
Get method for zoneGroups
getZoneIdentifier() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getZoneLayout() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for zoneLayout
getZoneLayout() - Method in interface org.biomage.Interface.HasZoneLayout
Get method for zoneLayout
getZoneLocations() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for zoneLocations
getZoneLocations() - Method in interface org.biomage.Interface.HasZoneLocations
Get method for zoneLocations
getZoneMatcher() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataSetMapper
 
getZoneNumber() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
getZoneNumber() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
getZoneNumber() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
getZoneRow() - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
getZonesPerX() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for zonesPerX
getZonesPerY() - Method in class org.biomage.ArrayDesign.ZoneGroup
Get method for zonesPerY
goToBiomaterial(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
gov.nih.nci.caarray.common.data.array - package gov.nih.nci.caarray.common.data.array
 
gov.nih.nci.caarray.common.data.arraydesign - package gov.nih.nci.caarray.common.data.arraydesign
 
gov.nih.nci.caarray.common.data.biomaterial - package gov.nih.nci.caarray.common.data.biomaterial
 
gov.nih.nci.caarray.common.data.contact - package gov.nih.nci.caarray.common.data.contact
 
gov.nih.nci.caarray.common.data.designelement - package gov.nih.nci.caarray.common.data.designelement
 
gov.nih.nci.caarray.common.data.experiment - package gov.nih.nci.caarray.common.data.experiment
 
gov.nih.nci.caarray.common.data.fileupload2 - package gov.nih.nci.caarray.common.data.fileupload2
 
gov.nih.nci.caarray.common.data.measurement - package gov.nih.nci.caarray.common.data.measurement
 
gov.nih.nci.caarray.common.data.protocol - package gov.nih.nci.caarray.common.data.protocol
 
gov.nih.nci.caarray.common.data.security - package gov.nih.nci.caarray.common.data.security
 
gov.nih.nci.caarray.common.data.useradmin - package gov.nih.nci.caarray.common.data.useradmin
 
gov.nih.nci.caarray.common.data.util - package gov.nih.nci.caarray.common.data.util
 
gov.nih.nci.caarray.common.data.vocab - package gov.nih.nci.caarray.common.data.vocab
 
gov.nih.nci.caarray.common.delegate - package gov.nih.nci.caarray.common.delegate
 
gov.nih.nci.caarray.common.exception - package gov.nih.nci.caarray.common.exception
 
gov.nih.nci.caarray.common.util - package gov.nih.nci.caarray.common.util
 
gov.nih.nci.caarray.loader - package gov.nih.nci.caarray.loader
 
gov.nih.nci.caarray.services.array - package gov.nih.nci.caarray.services.array
 
gov.nih.nci.caarray.services.array.ejb - package gov.nih.nci.caarray.services.array.ejb
 
gov.nih.nci.caarray.services.array.test - package gov.nih.nci.caarray.services.array.test
 
gov.nih.nci.caarray.services.arraydesign - package gov.nih.nci.caarray.services.arraydesign
 
gov.nih.nci.caarray.services.arraydesign.ejb - package gov.nih.nci.caarray.services.arraydesign.ejb
 
gov.nih.nci.caarray.services.arraydesign.loader - package gov.nih.nci.caarray.services.arraydesign.loader
 
gov.nih.nci.caarray.services.arraydesign.loader.affymetrix - package gov.nih.nci.caarray.services.arraydesign.loader.affymetrix
 
gov.nih.nci.caarray.services.arraydesign.loader.agilent - package gov.nih.nci.caarray.services.arraydesign.loader.agilent
 
gov.nih.nci.caarray.services.arraydesign.loader.genepix - package gov.nih.nci.caarray.services.arraydesign.loader.genepix
 
gov.nih.nci.caarray.services.arraydesign.loader.handler - package gov.nih.nci.caarray.services.arraydesign.loader.handler
 
gov.nih.nci.caarray.services.arraydesign.loader.illumina - package gov.nih.nci.caarray.services.arraydesign.loader.illumina
 
gov.nih.nci.caarray.services.arraydesign.loader.imagene - package gov.nih.nci.caarray.services.arraydesign.loader.imagene
 
gov.nih.nci.caarray.services.arraydesign.loader.ucsf - package gov.nih.nci.caarray.services.arraydesign.loader.ucsf
 
gov.nih.nci.caarray.services.arraydesign.test - package gov.nih.nci.caarray.services.arraydesign.test
 
gov.nih.nci.caarray.services.bioassaydata - package gov.nih.nci.caarray.services.bioassaydata
 
gov.nih.nci.caarray.services.bioassaydata.descriptor - package gov.nih.nci.caarray.services.bioassaydata.descriptor
 
gov.nih.nci.caarray.services.bioassaydata.reader - package gov.nih.nci.caarray.services.bioassaydata.reader
 
gov.nih.nci.caarray.services.biomaterial - package gov.nih.nci.caarray.services.biomaterial
 
gov.nih.nci.caarray.services.biomaterial.ejb - package gov.nih.nci.caarray.services.biomaterial.ejb
 
gov.nih.nci.caarray.services.biomaterial.test - package gov.nih.nci.caarray.services.biomaterial.test
 
gov.nih.nci.caarray.services.contact - package gov.nih.nci.caarray.services.contact
 
gov.nih.nci.caarray.services.contact.ejb - package gov.nih.nci.caarray.services.contact.ejb
 
gov.nih.nci.caarray.services.contact.test - package gov.nih.nci.caarray.services.contact.test
 
gov.nih.nci.caarray.services.exception - package gov.nih.nci.caarray.services.exception
 
gov.nih.nci.caarray.services.experiment - package gov.nih.nci.caarray.services.experiment
 
gov.nih.nci.caarray.services.experiment.ejb - package gov.nih.nci.caarray.services.experiment.ejb
 
gov.nih.nci.caarray.services.experiment.test - package gov.nih.nci.caarray.services.experiment.test
 
gov.nih.nci.caarray.services.fileparse - package gov.nih.nci.caarray.services.fileparse
 
gov.nih.nci.caarray.services.fileparse.gal - package gov.nih.nci.caarray.services.fileparse.gal
 
gov.nih.nci.caarray.services.fileparse.gal.magemapping - package gov.nih.nci.caarray.services.fileparse.gal.magemapping
 
gov.nih.nci.caarray.services.fileparse.gpr - package gov.nih.nci.caarray.services.fileparse.gpr
 
gov.nih.nci.caarray.services.fileparse.mdb - package gov.nih.nci.caarray.services.fileparse.mdb
 
gov.nih.nci.caarray.services.fileparse.test - package gov.nih.nci.caarray.services.fileparse.test
 
gov.nih.nci.caarray.services.fileparse.test.usecases - package gov.nih.nci.caarray.services.fileparse.test.usecases
 
gov.nih.nci.caarray.services.fileparse2 - package gov.nih.nci.caarray.services.fileparse2
 
gov.nih.nci.caarray.services.fileparse2.arraydesign - package gov.nih.nci.caarray.services.fileparse2.arraydesign
 
gov.nih.nci.caarray.services.fileparse2.arraydesign.test - package gov.nih.nci.caarray.services.fileparse2.arraydesign.test
 
gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers - package gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers
 
gov.nih.nci.caarray.services.fileparse2.hybridization - package gov.nih.nci.caarray.services.fileparse2.hybridization
 
gov.nih.nci.caarray.services.fileparse2.mdb - package gov.nih.nci.caarray.services.fileparse2.mdb
 
gov.nih.nci.caarray.services.fileparse2.parsers - package gov.nih.nci.caarray.services.fileparse2.parsers
 
gov.nih.nci.caarray.services.fileparse2.parsers.test - package gov.nih.nci.caarray.services.fileparse2.parsers.test
 
gov.nih.nci.caarray.services.fileparse2.util - package gov.nih.nci.caarray.services.fileparse2.util
 
gov.nih.nci.caarray.services.fileupload - package gov.nih.nci.caarray.services.fileupload
 
gov.nih.nci.caarray.services.fileupload2 - package gov.nih.nci.caarray.services.fileupload2
This package provides supporting persistable beans for managing hybridization and array design file upload and parsing processes...
gov.nih.nci.caarray.services.fileupload2.ejb - package gov.nih.nci.caarray.services.fileupload2.ejb
 
gov.nih.nci.caarray.services.fileupload2.mdb - package gov.nih.nci.caarray.services.fileupload2.mdb
 
gov.nih.nci.caarray.services.hybridization - package gov.nih.nci.caarray.services.hybridization
 
gov.nih.nci.caarray.services.hybridization.ejb - package gov.nih.nci.caarray.services.hybridization.ejb
 
gov.nih.nci.caarray.services.mageloader - package gov.nih.nci.caarray.services.mageloader
 
gov.nih.nci.caarray.services.mageloader.test - package gov.nih.nci.caarray.services.mageloader.test
 
gov.nih.nci.caarray.services.mageml - package gov.nih.nci.caarray.services.mageml
 
gov.nih.nci.caarray.services.mageml.ejb - package gov.nih.nci.caarray.services.mageml.ejb
 
gov.nih.nci.caarray.services.mageml.mdb - package gov.nih.nci.caarray.services.mageml.mdb
 
gov.nih.nci.caarray.services.protocol - package gov.nih.nci.caarray.services.protocol
 
gov.nih.nci.caarray.services.protocol.ejb - package gov.nih.nci.caarray.services.protocol.ejb
 
gov.nih.nci.caarray.services.protocol.test - package gov.nih.nci.caarray.services.protocol.test
 
gov.nih.nci.caarray.services.security - package gov.nih.nci.caarray.services.security
 
gov.nih.nci.caarray.services.security.db - package gov.nih.nci.caarray.services.security.db
 
gov.nih.nci.caarray.services.security.ejb - package gov.nih.nci.caarray.services.security.ejb
 
gov.nih.nci.caarray.services.security.intf - package gov.nih.nci.caarray.services.security.intf
 
gov.nih.nci.caarray.services.security.mageom - package gov.nih.nci.caarray.services.security.mageom
 
gov.nih.nci.caarray.services.security.mageom.mdb - package gov.nih.nci.caarray.services.security.mageom.mdb
 
gov.nih.nci.caarray.services.security.test - package gov.nih.nci.caarray.services.security.test
 
gov.nih.nci.caarray.services.security.test.usecases - package gov.nih.nci.caarray.services.security.test.usecases
 
gov.nih.nci.caarray.services.test - package gov.nih.nci.caarray.services.test
 
gov.nih.nci.caarray.services.test.ejb - package gov.nih.nci.caarray.services.test.ejb
 
gov.nih.nci.caarray.services.test.usecases - package gov.nih.nci.caarray.services.test.usecases
 
gov.nih.nci.caarray.services.useradmin - package gov.nih.nci.caarray.services.useradmin
 
gov.nih.nci.caarray.services.useradmin.ejb - package gov.nih.nci.caarray.services.useradmin.ejb
 
gov.nih.nci.caarray.services.useradmin.test - package gov.nih.nci.caarray.services.useradmin.test
 
gov.nih.nci.caarray.services.util - package gov.nih.nci.caarray.services.util
 
gov.nih.nci.caarray.services.util.cache - package gov.nih.nci.caarray.services.util.cache
 
gov.nih.nci.caarray.services.util.dataconverter - package gov.nih.nci.caarray.services.util.dataconverter
 
gov.nih.nci.caarray.services.util.dataconverter.assembler - package gov.nih.nci.caarray.services.util.dataconverter.assembler
 
gov.nih.nci.caarray.services.util.dataconverter.mapper - package gov.nih.nci.caarray.services.util.dataconverter.mapper
 
gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers - package gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
gov.nih.nci.caarray.services.util.dataconverter.test - package gov.nih.nci.caarray.services.util.dataconverter.test
 
gov.nih.nci.caarray.services.util.db - package gov.nih.nci.caarray.services.util.db
 
gov.nih.nci.caarray.services.util.file - package gov.nih.nci.caarray.services.util.file
 
gov.nih.nci.caarray.services.util.fileuploadapplet - package gov.nih.nci.caarray.services.util.fileuploadapplet
 
gov.nih.nci.caarray.services.util.httpfileuploadapplet - package gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
gov.nih.nci.caarray.services.util.jms - package gov.nih.nci.caarray.services.util.jms
 
gov.nih.nci.caarray.services.util.mage - package gov.nih.nci.caarray.services.util.mage
 
gov.nih.nci.caarray.services.util.netcdf - package gov.nih.nci.caarray.services.util.netcdf
 
gov.nih.nci.caarray.services.util.netcdf.test - package gov.nih.nci.caarray.services.util.netcdf.test
 
gov.nih.nci.caarray.services.util.netcdf.test.usecases - package gov.nih.nci.caarray.services.util.netcdf.test.usecases
 
gov.nih.nci.caarray.services.util.ojb - package gov.nih.nci.caarray.services.util.ojb
 
gov.nih.nci.caarray.services.util.ojb.conversions - package gov.nih.nci.caarray.services.util.ojb.conversions
 
gov.nih.nci.caarray.services.util.parse - package gov.nih.nci.caarray.services.util.parse
 
gov.nih.nci.caarray.services.util.properties - package gov.nih.nci.caarray.services.util.properties
 
gov.nih.nci.caarray.services.util.transaction - package gov.nih.nci.caarray.services.util.transaction
 
gov.nih.nci.caarray.services.vocab - package gov.nih.nci.caarray.services.vocab
 
gov.nih.nci.caarray.services.vocab.ejb - package gov.nih.nci.caarray.services.vocab.ejb
 
gov.nih.nci.caarray.services.vocab.test - package gov.nih.nci.caarray.services.vocab.test
 
gov.nih.nci.caarray.ui - package gov.nih.nci.caarray.ui
 
gov.nih.nci.caarray.ui.arraydesign - package gov.nih.nci.caarray.ui.arraydesign
 
gov.nih.nci.caarray.ui.biomaterial - package gov.nih.nci.caarray.ui.biomaterial
 
gov.nih.nci.caarray.ui.contact - package gov.nih.nci.caarray.ui.contact
 
gov.nih.nci.caarray.ui.core - package gov.nih.nci.caarray.ui.core
 
gov.nih.nci.caarray.ui.experiment - package gov.nih.nci.caarray.ui.experiment
 
gov.nih.nci.caarray.ui.experiment.data - package gov.nih.nci.caarray.ui.experiment.data
 
gov.nih.nci.caarray.ui.login - package gov.nih.nci.caarray.ui.login
 
gov.nih.nci.caarray.ui.ontology - package gov.nih.nci.caarray.ui.ontology
 
gov.nih.nci.caarray.ui.protocol - package gov.nih.nci.caarray.ui.protocol
 
gov.nih.nci.caarray.ui.test - package gov.nih.nci.caarray.ui.test
 
gov.nih.nci.caarray.ui.useradmin - package gov.nih.nci.caarray.ui.useradmin
 
GPR_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
GprDataRow - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GprDataRow(LocalDynaBean) - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
GprFileParseHandler - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GprFileParseHandler(String) - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GprFileParseHandler
Constructor with filename
GprHeaderListener - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GprHeaderListener() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
 
GprHeaderParser - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GprHeaderParser(File) - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
Constructor with file to parse
GprParsingService - Class in gov.nih.nci.caarray.services.fileparse.gpr
 
GprParsingService() - Constructor for class gov.nih.nci.caarray.services.fileparse.gpr.GprParsingService
 
GPS_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
gram_percent - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
GROUP_CURATOR - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
GROUP_MEMBER - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
GROUP_NAME - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
JAAS Group containing subject roles
GroupAddUpdateAction - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
GroupAddUpdateForm - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
GroupData - Class in gov.nih.nci.caarray.common.data.useradmin
 
GroupData() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
GroupDetailAction - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupDetailAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupDetailAction
 
GroupDetailForm - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupDetailForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
GroupSearchAction - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupSearchAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
GroupSearchCriteria - Class in gov.nih.nci.caarray.common.data.useradmin
 
GroupSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.GroupSearchCriteria
 
GroupSearchForm - Class in gov.nih.nci.caarray.ui.useradmin
 
GroupSearchForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm
 
guessFileType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
GuiSet - Class in org.biomage.tools.apps.annot
 
GuiSet() - Constructor for class org.biomage.tools.apps.annot.GuiSet
 
guiSet - Variable in class org.biomage.tools.apps.annot.PagePanel
 

H

H - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
HALF_INDENT - Static variable in class org.biomage.tools.generate_er.CreateMageER
one indent: a tab key
handle(ArrayDesignFileParsingJob) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileParsingJobHandlerImpl
 
handle(HybridizationDataJob) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationDataJobHandlerImpl
 
handle(Callback[]) - Method in class gov.nih.nci.caarray.services.security.CaarrayCallBackHandler
 
handle(String) - Method in class gov.nih.nci.caarray.services.security.mageom.LoggingSecuredElementOrphanHandler
 
handle(String) - Method in interface gov.nih.nci.caarray.services.security.mageom.SecuredElementOrphanHandler
 
handle(Callback[]) - Method in class gov.nih.nci.caarray.services.util.TestCallbackHandler
 
handleArrayDesignFile(ArrayDesignFileParsingJob) - Method in interface gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileHandler
Loads the given array design from the file provided.
handleCancel(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
handleEnd(boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
handleEnd(boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
handleFile(HybridizationFileUploadEntry, String) - Method in interface gov.nih.nci.caarray.services.hybridization.HybridizationFileHandler
 
handleFileUploads(ArrayDesignValues) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignUploadDelegate
This class performs the buisness logic as far as selecting the correct service to perform parsing of array design files.
handleFileUploads(UploadFileValues) - Method in class gov.nih.nci.caarray.services.fileupload.FileUploadDelegate
 
handleJob(HybridizationDataJob) - Method in class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
handleJob(HybridizationDataJob) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
handleManufacturerBug(OrganizationDesc) - Static method in class gov.nih.nci.caarray.ui.protocol.ProtocolUIUtils
 
handleRequest(HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Parses the input stream and partitions the parsed items into a set of form fields and a set of file items.
Hardware - Class in org.biomage.Protocol
Hardware represents the hardware used.
Hardware() - Constructor for class org.biomage.Protocol.Hardware
Default constructor.
Hardware(Attributes) - Constructor for class org.biomage.Protocol.Hardware
Attribute constructor.
hardware - Variable in class org.biomage.Protocol.HardwareApplication
The underlying hardware.
hardware - Variable in class org.biomage.Protocol.Software
Associates Hardware and Software together.
hardware_list - Variable in class org.biomage.Protocol.Protocol_package
Hardware represents the hardware used.
HARDWARE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
HardwareAddUpdateAction - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
HardwareAddUpdateForm - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
HardwareApplication - Class in org.biomage.Protocol
The use of a piece of hardware with the requisite Parameters and ParameterValues.
HardwareApplication() - Constructor for class org.biomage.Protocol.HardwareApplication
Default constructor.
HardwareApplication(Attributes) - Constructor for class org.biomage.Protocol.HardwareApplication
Attribute constructor.
HardwareApplicationData - Class in gov.nih.nci.caarray.common.data.protocol
 
HardwareApplicationData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData
 
hardwareApplications - Variable in class org.biomage.Protocol.ProtocolApplication
The use of hardware for the application of the protocol.
HardwareBaseForm - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareBaseForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
HardwareData - Class in gov.nih.nci.caarray.common.data.protocol
 
HardwareData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
HardwareDesc - Class in gov.nih.nci.caarray.common.data.protocol
 
HardwareDesc() - Constructor for class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
HardwareDetailAction - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareDetailAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
HardwareDetailForm - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareDetailForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
hardwareId_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareMake_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
HardwareManagerDB - Class in gov.nih.nci.caarray.services.protocol
 
HardwareManagerDB() - Constructor for class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Default Constructor
HardwareManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
HardwareManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
HardwareManagerEJB - Class in gov.nih.nci.caarray.services.protocol.ejb
HardwareManagerEJB
HardwareManagerEJB() - Constructor for class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
hardwareManufacturerId_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareManufacturerName_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareManufacturers - Variable in class org.biomage.Protocol.Hardware
Contact for information on the Hardware.
hardwareManufacturers_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareModel_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareName_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwares - Variable in class org.biomage.Protocol.Protocol
Hardware used by this protocol.
HardwareSearchAction - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareSearchAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
HardwareSearchCriteria - Class in gov.nih.nci.caarray.common.data.protocol
 
HardwareSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
HardwareSearchForm - Class in gov.nih.nci.caarray.ui.protocol
 
HardwareSearchForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
HardwaresSoftwaresParameterTypesFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
HardwaresSoftwaresParameterTypesFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.HardwaresSoftwaresParameterTypesFieldMapper
 
hardwareTypeId_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareTypeName_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
hardwareTypes_ - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
HasAccessions - Interface in org.biomage.Interface
 
HasAccessions.Accessions_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute accessions.
HasAccessions.Accessions_list() - Constructor for class org.biomage.Interface.HasAccessions.Accessions_list
 
HasAction - Interface in org.biomage.Interface
 
HasActionMeasurement - Interface in org.biomage.Interface
 
HasAdjustments - Interface in org.biomage.Interface
 
HasAdjustments.Adjustments_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute adjustments.
HasAdjustments.Adjustments_list() - Constructor for class org.biomage.Interface.HasAdjustments.Adjustments_list
 
HasAffiliation - Interface in org.biomage.Interface
 
HasAnalysisResults - Interface in org.biomage.Interface
 
HasAnalysisResults.AnalysisResults_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute analysisResults.
HasAnalysisResults.AnalysisResults_list() - Constructor for class org.biomage.Interface.HasAnalysisResults.AnalysisResults_list
 
HasAnnotations - Interface in org.biomage.Interface
 
HasAnnotations.Annotations_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute annotations.
HasAnnotations.Annotations_list() - Constructor for class org.biomage.Interface.HasAnnotations.Annotations_list
 
HasArray - Interface in org.biomage.Interface
 
HasArrayDesign - Interface in org.biomage.Interface
 
HasArrayGroup - Interface in org.biomage.Interface
 
HasArrayManufactureDeviations - Interface in org.biomage.Interface
 
HasArrayManufactureDeviations.ArrayManufactureDeviations_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute arrayManufactureDeviations.
HasArrayManufactureDeviations.ArrayManufactureDeviations_list() - Constructor for class org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list
 
HasArrayManufacturers - Interface in org.biomage.Interface
 
HasArrayManufacturers.ArrayManufacturers_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute arrayManufacturers.
HasArrayManufacturers.ArrayManufacturers_list() - Constructor for class org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list
 
HasArrays - Interface in org.biomage.Interface
 
HasArrays.Arrays_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute arrays.
HasArrays.Arrays_list() - Constructor for class org.biomage.Interface.HasArrays.Arrays_list
 
HasAssociations - Interface in org.biomage.Interface
 
HasAssociations.Associations_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute associations.
HasAssociations.Associations_list() - Constructor for class org.biomage.Interface.HasAssociations.Associations_list
 
HasAuditTrail - Interface in org.biomage.Interface
 
HasAuditTrail.AuditTrail_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute auditTrail.
HasAuditTrail.AuditTrail_list() - Constructor for class org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
HasBibliographicReferences - Interface in org.biomage.Interface
 
HasBibliographicReferences.BibliographicReferences_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bibliographicReferences.
HasBibliographicReferences.BibliographicReferences_list() - Constructor for class org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list
 
HasBioAssay - Interface in org.biomage.Interface
 
HasBioAssayCreation - Interface in org.biomage.Interface
 
HasBioAssayData - Interface in org.biomage.Interface
 
HasBioAssayData.BioAssayData_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayData.
HasBioAssayData.BioAssayData_list() - Constructor for class org.biomage.Interface.HasBioAssayData.BioAssayData_list
 
HasBioAssayDataSources - Interface in org.biomage.Interface
 
HasBioAssayDataSources.BioAssayDataSources_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayDataSources.
HasBioAssayDataSources.BioAssayDataSources_list() - Constructor for class org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list
 
HasBioAssayDimension - Interface in org.biomage.Interface
 
HasBioAssayFactorValues - Interface in org.biomage.Interface
 
HasBioAssayFactorValues.BioAssayFactorValues_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayFactorValues.
HasBioAssayFactorValues.BioAssayFactorValues_list() - Constructor for class org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list
 
HasBioAssayMapping - Interface in org.biomage.Interface
 
HasBioAssayMaps - Interface in org.biomage.Interface
 
HasBioAssayMaps.BioAssayMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayMaps.
HasBioAssayMaps.BioAssayMaps_list() - Constructor for class org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list
 
HasBioAssayMapTarget - Interface in org.biomage.Interface
 
HasBioAssays - Interface in org.biomage.Interface
 
HasBioAssays.BioAssays_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssays.
HasBioAssays.BioAssays_list() - Constructor for class org.biomage.Interface.HasBioAssays.BioAssays_list
 
HasBioAssayTreatments - Interface in org.biomage.Interface
 
HasBioAssayTreatments.BioAssayTreatments_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayTreatments.
HasBioAssayTreatments.BioAssayTreatments_list() - Constructor for class org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list
 
HasBioAssayTupleData - Interface in org.biomage.Interface
 
HasBioAssayTupleData.BioAssayTuples_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute bioAssayTuples.
HasBioAssayTupleData.BioAssayTuples_list() - Constructor for class org.biomage.Interface.HasBioAssayTupleData.BioAssayTuples_list
 
HasBioDataValues - Interface in org.biomage.Interface
 
HasBiologicalCharacteristics - Interface in org.biomage.Interface
 
HasBiologicalCharacteristics.BiologicalCharacteristics_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute biologicalCharacteristics.
HasBiologicalCharacteristics.BiologicalCharacteristics_list() - Constructor for class org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list
 
HasBioMaterial - Interface in org.biomage.Interface
 
HasCategory - Interface in org.biomage.Interface
 
HasChannel - Interface in org.biomage.Interface
 
HasChannels - Interface in org.biomage.Interface
 
HasChannels.Channels_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute channels.
HasChannels.Channels_list() - Constructor for class org.biomage.Interface.HasChannels.Channels_list
 
HasCharacteristics - Interface in org.biomage.Interface
 
HasCharacteristics.Characteristics_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute characteristics.
HasCharacteristics.Characteristics_list() - Constructor for class org.biomage.Interface.HasCharacteristics.Characteristics_list
 
HasClusterBioAssayData - Interface in org.biomage.Interface
 
HasComponentCompounds - Interface in org.biomage.Interface
 
HasComponentCompounds.ComponentCompounds_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute componentCompounds.
HasComponentCompounds.ComponentCompounds_list() - Constructor for class org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list
 
HasComposite - Interface in org.biomage.Interface
 
HasCompositeCompositeMaps - Interface in org.biomage.Interface
 
HasCompositeCompositeMaps.CompositeCompositeMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compositeCompositeMaps.
HasCompositeCompositeMaps.CompositeCompositeMaps_list() - Constructor for class org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list
 
HasCompositeGroups - Interface in org.biomage.Interface
 
HasCompositeGroups.CompositeGroups_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compositeGroups.
HasCompositeGroups.CompositeGroups_list() - Constructor for class org.biomage.Interface.HasCompositeGroups.CompositeGroups_list
 
HasCompositePositionSources - Interface in org.biomage.Interface
 
HasCompositePositionSources.CompositePositionSources_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compositePositionSources.
HasCompositePositionSources.CompositePositionSources_list() - Constructor for class org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list
 
HasCompositeSequence - Interface in org.biomage.Interface
 
HasCompositeSequences - Interface in org.biomage.Interface
 
HasCompositeSequences.CompositeSequences_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compositeSequences.
HasCompositeSequences.CompositeSequences_list() - Constructor for class org.biomage.Interface.HasCompositeSequences.CompositeSequences_list
 
HasCompound - Interface in org.biomage.Interface
 
HasCompoundIndices - Interface in org.biomage.Interface
 
HasCompoundIndices.CompoundIndices_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compoundIndices.
HasCompoundIndices.CompoundIndices_list() - Constructor for class org.biomage.Interface.HasCompoundIndices.CompoundIndices_list
 
HasCompoundMeasurements - Interface in org.biomage.Interface
 
HasCompoundMeasurements.CompoundMeasurements_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute compoundMeasurements.
HasCompoundMeasurements.CompoundMeasurements_list() - Constructor for class org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list
 
HasConfidenceIndicators - Interface in org.biomage.Interface
 
HasConfidenceIndicators.ConfidenceIndicators_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute confidenceIndicators.
HasConfidenceIndicators.ConfidenceIndicators_list() - Constructor for class org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list
 
HasContacts - Interface in org.biomage.Interface
 
HasContacts.Contacts_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute contacts.
HasContacts.Contacts_list() - Constructor for class org.biomage.Interface.HasContacts.Contacts_list
 
HasContainedFeatures - Interface in org.biomage.Interface
 
HasContainedFeatures.ContainedFeatures_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute containedFeatures.
HasContainedFeatures.ContainedFeatures_list() - Constructor for class org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list
 
HasControlFeatures - Interface in org.biomage.Interface
 
HasControlFeatures.ControlFeatures_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute controlFeatures.
HasControlFeatures.ControlFeatures_list() - Constructor for class org.biomage.Interface.HasControlFeatures.ControlFeatures_list
 
HasControlledFeatures - Interface in org.biomage.Interface
 
HasControlledFeatures.ControlledFeatures_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute controlledFeatures.
HasControlledFeatures.ControlledFeatures_list() - Constructor for class org.biomage.Interface.HasControlledFeatures.ControlledFeatures_list
 
HasControlType - Interface in org.biomage.Interface
 
HasCoordinate - Interface in org.biomage.Interface
 
HasDatabase - Interface in org.biomage.Interface
 
HasDatabaseReferences - Interface in org.biomage.Interface
 
HasDatabaseReferences.DatabaseReferences_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute databaseReferences.
HasDatabaseReferences.DatabaseReferences_list() - Constructor for class org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list
 
HasDataType - Interface in org.biomage.Interface
 
HasDefaultValue - Interface in org.biomage.Interface
 
HasDefectType - Interface in org.biomage.Interface
 
HasDerivedBioAssayData - Interface in org.biomage.Interface
 
HasDerivedBioAssayData.DerivedBioAssayData_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute derivedBioAssayData.
HasDerivedBioAssayData.DerivedBioAssayData_list() - Constructor for class org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list
 
HasDerivedBioAssayDataTarget - Interface in org.biomage.Interface
 
HasDerivedBioAssayMap - Interface in org.biomage.Interface
 
HasDerivedBioAssayMap.DerivedBioAssayMap_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute derivedBioAssayMap.
HasDerivedBioAssayMap.DerivedBioAssayMap_list() - Constructor for class org.biomage.Interface.HasDerivedBioAssayMap.DerivedBioAssayMap_list
 
HasDescriptions - Interface in org.biomage.Interface
 
HasDescriptions.Descriptions_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute descriptions.
HasDescriptions.Descriptions_list() - Constructor for class org.biomage.Interface.HasDescriptions.Descriptions_list
 
HasDesignElement - Interface in org.biomage.Interface
 
HasDesignElementDimension - Interface in org.biomage.Interface
 
HasDesignElementMapping - Interface in org.biomage.Interface
 
HasDesignElementMaps - Interface in org.biomage.Interface
 
HasDesignElementMaps.DesignElementMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute designElementMaps.
HasDesignElementMaps.DesignElementMaps_list() - Constructor for class org.biomage.Interface.HasDesignElementMaps.DesignElementMaps_list
 
HasDesignElementTuples - Interface in org.biomage.Interface
 
HasDesignElementTuples.DesignElementTuples_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute designElementTuples.
HasDesignElementTuples.DesignElementTuples_list() - Constructor for class org.biomage.Interface.HasDesignElementTuples.DesignElementTuples_list
 
HasDesignProviders - Interface in org.biomage.Interface
 
HasDesignProviders.DesignProviders_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute designProviders.
HasDesignProviders.DesignProviders_list() - Constructor for class org.biomage.Interface.HasDesignProviders.DesignProviders_list
 
HasDistanceUnit - Interface in org.biomage.Interface
 
HasExperimentalFactor - Interface in org.biomage.Interface
 
HasExperimentalFactors - Interface in org.biomage.Interface
 
HasExperimentalFactors.ExperimentalFactors_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute experimentalFactors.
HasExperimentalFactors.ExperimentalFactors_list() - Constructor for class org.biomage.Interface.HasExperimentalFactors.ExperimentalFactors_list
 
HasExperimentDesigns - Interface in org.biomage.Interface
 
HasExperimentDesigns.ExperimentDesigns_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute experimentDesigns.
HasExperimentDesigns.ExperimentDesigns_list() - Constructor for class org.biomage.Interface.HasExperimentDesigns.ExperimentDesigns_list
 
HasExternalLIMS - Interface in org.biomage.Interface
 
HasExternalReference - Interface in org.biomage.Interface
 
HasFactorValues - Interface in org.biomage.Interface
 
HasFactorValues.FactorValues_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute factorValues.
HasFactorValues.FactorValues_list() - Constructor for class org.biomage.Interface.HasFactorValues.FactorValues_list
 
HasFailTypes - Interface in org.biomage.Interface
 
HasFailTypes.FailTypes_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute failTypes.
HasFailTypes.FailTypes_list() - Constructor for class org.biomage.Interface.HasFailTypes.FailTypes_list
 
HasFeature - Interface in org.biomage.Interface
 
HasFeatureDefects - Interface in org.biomage.Interface
 
HasFeatureDefects.FeatureDefects_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute featureDefects.
HasFeatureDefects.FeatureDefects_list() - Constructor for class org.biomage.Interface.HasFeatureDefects.FeatureDefects_list
 
HasFeatureExtraction - Interface in org.biomage.Interface
 
HasFeatureGroup - Interface in org.biomage.Interface
 
HasFeatureGroups - Interface in org.biomage.Interface
 
HasFeatureGroups.FeatureGroups_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute featureGroups.
HasFeatureGroups.FeatureGroups_list() - Constructor for class org.biomage.Interface.HasFeatureGroups.FeatureGroups_list
 
HasFeatureInformationSources - Interface in org.biomage.Interface
 
HasFeatureInformationSources.FeatureInformationSources_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute featureInformationSources.
HasFeatureInformationSources.FeatureInformationSources_list() - Constructor for class org.biomage.Interface.HasFeatureInformationSources.FeatureInformationSources_list
 
HasFeatureLIMSs - Interface in org.biomage.Interface
 
HasFeatureLIMSs.FeatureLIMSs_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute featureLIMSs.
HasFeatureLIMSs.FeatureLIMSs_list() - Constructor for class org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list
 
HasFeatureLocation - Interface in org.biomage.Interface
 
HasFeatureReporterMaps - Interface in org.biomage.Interface
 
HasFeatureReporterMaps.FeatureReporterMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute featureReporterMaps.
HasFeatureReporterMaps.FeatureReporterMaps_list() - Constructor for class org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list
 
HasFeatures - Interface in org.biomage.Interface
 
HasFeatures.Features_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute features.
HasFeatures.Features_list() - Constructor for class org.biomage.Interface.HasFeatures.Features_list
 
HasFeatureShape - Interface in org.biomage.Interface
 
HasFiducials - Interface in org.biomage.Interface
 
HasFiducials.Fiducials_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute fiducials.
HasFiducials.Fiducials_list() - Constructor for class org.biomage.Interface.HasFiducials.Fiducials_list
 
HasFiducialType - Interface in org.biomage.Interface
 
HasFormat - Interface in org.biomage.Interface
 
HasHardware - Interface in org.biomage.Interface
 
HasHardwareApplications - Interface in org.biomage.Interface
 
HasHardwareApplications.HardwareApplications_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute hardwareApplications.
HasHardwareApplications.HardwareApplications_list() - Constructor for class org.biomage.Interface.HasHardwareApplications.HardwareApplications_list
 
HasHardwareManufacturers - Interface in org.biomage.Interface
 
HasHardwareManufacturers.HardwareManufacturers_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute hardwareManufacturers.
HasHardwareManufacturers.HardwareManufacturers_list() - Constructor for class org.biomage.Interface.HasHardwareManufacturers.HardwareManufacturers_list
 
HasHardwares - Interface in org.biomage.Interface
 
HasHardwares.Hardwares_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute hardwares.
HasHardwares.Hardwares_list() - Constructor for class org.biomage.Interface.HasHardwares.Hardwares_list
 
hashCode() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
hashCode() - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings.AttributeInfo
 
hashCode() - Method in class gov.nih.nci.caarray.services.security.CaArrayPrincipal
 
HasIdentifierLIMS - Interface in org.biomage.Interface
 
HasImages - Interface in org.biomage.Interface
 
HasImages.Images_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute images.
HasImages.Images_list() - Constructor for class org.biomage.Interface.HasImages.Images_list
 
HasImmobilizedCharacteristics - Interface in org.biomage.Interface
 
HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute immobilizedCharacteristics.
HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list() - Constructor for class org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list
 
HasInformation - Interface in org.biomage.Interface
 
hasInstances() - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
HasLabels - Interface in org.biomage.Interface
 
HasLabels.Labels_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute labels.
HasLabels.Labels_list() - Constructor for class org.biomage.Interface.HasLabels.Labels_list
 
HasMaterialType - Interface in org.biomage.Interface
 
HasMeasuredBioAssayData - Interface in org.biomage.Interface
 
HasMeasuredBioAssayData.MeasuredBioAssayData_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute measuredBioAssayData.
HasMeasuredBioAssayData.MeasuredBioAssayData_list() - Constructor for class org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list
 
HasMeasuredBioAssayTarget - Interface in org.biomage.Interface
 
HasMeasurement - Interface in org.biomage.Interface
 
HasMembers - Interface in org.biomage.Interface
 
HasMembers.Members_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute members.
HasMembers.Members_list() - Constructor for class org.biomage.Interface.HasMembers.Members_list
 
HasMismatchInformation - Interface in org.biomage.Interface
 
HasMismatchInformation.MismatchInformation_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute mismatchInformation.
HasMismatchInformation.MismatchInformation_list() - Constructor for class org.biomage.Interface.HasMismatchInformation.MismatchInformation_list
 
HasNodeContents - Interface in org.biomage.Interface
 
HasNodeContents.NodeContents_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute nodeContents.
HasNodeContents.NodeContents_list() - Constructor for class org.biomage.Interface.HasNodeContents.NodeContents_list
 
HasNodes - Interface in org.biomage.Interface
 
HasNodes.Nodes_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute nodes.
HasNodes.Nodes_list() - Constructor for class org.biomage.Interface.HasNodes.Nodes_list
 
HasNodeValue - Interface in org.biomage.Interface
 
HasNodeValue.NodeValue_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute nodeValue.
HasNodeValue.NodeValue_list() - Constructor for class org.biomage.Interface.HasNodeValue.NodeValue_list
 
HasNormalizationDescription - Interface in org.biomage.Interface
 
HasOntologyEntries - Interface in org.biomage.Interface
 
HasOntologyEntries.OntologyEntries_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute ontologyEntries.
HasOntologyEntries.OntologyEntries_list() - Constructor for class org.biomage.Interface.HasOntologyEntries.OntologyEntries_list
 
HasOntologyReference - Interface in org.biomage.Interface
 
HasOwner - Interface in org.biomage.Interface
 
HasOwner.Owner_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute owner.
HasOwner.Owner_list() - Constructor for class org.biomage.Interface.HasOwner.Owner_list
 
HasParameters - Interface in org.biomage.Interface
 
HasParameters.Parameters_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute parameters.
HasParameters.Parameters_list() - Constructor for class org.biomage.Interface.HasParameters.Parameters_list
 
HasParameterType - Interface in org.biomage.Interface
 
HasParameterTypes - Interface in org.biomage.Interface
 
HasParameterTypes.ParameterTypes_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute parameterTypes.
HasParameterTypes.ParameterTypes_list() - Constructor for class org.biomage.Interface.HasParameterTypes.ParameterTypes_list
 
HasParameterValues - Interface in org.biomage.Interface
 
HasParameterValues.ParameterValues_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute parameterValues.
HasParameterValues.ParameterValues_list() - Constructor for class org.biomage.Interface.HasParameterValues.ParameterValues_list
 
HasParent - Interface in org.biomage.Interface
 
HasPerformer - Interface in org.biomage.Interface
 
HasPerformers - Interface in org.biomage.Interface
 
HasPerformers.Performers_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute performers.
HasPerformers.Performers_list() - Constructor for class org.biomage.Interface.HasPerformers.Performers_list
 
hasPermission(String, String, String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given role's access permission to a protection element defined by its application name, object ID and attribute.
hasPermission(String, String[], String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given role's access permission to a protection element defined by its application name, object ID and attribute.
hasPermission(String, String, String, String[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given user/role's access permission to a collection of protection elements defined by its application name, object ID and attribute.
hasPermission(String, String[], String, String[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given user/roles' access permission to a collection of protection elements defined by its application name, object ID and attribute.
hasPermission(String, String, String, String[], long[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given user/role's access permission to a collection of protection elements defined by its application name, object ID and attribute.
hasPermission(String, String[], String, String[], long[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns the given user/role's access permission to a collection of protection elements defined by its application name, object ID and attribute.
hasPermission(String, String, String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns the given role's access permission to a protection element defined by its application name, object ID and attribute.
hasPermission(String, String, String, String[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns the given role's access permission to a protection element defined by its application name, object ID and attribute.
hasPermission(String, String, String, String[], long[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns the given role's access permission to a protection element defined by its application name, object ID and attribute.
hasPermission(String, String[], String, String[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
 
hasPermission(String, String[], String, String[], long[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
 
hasPermission(String, String[], String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
 
HasPhysicalBioAssay - Interface in org.biomage.Interface
 
HasPhysicalBioAssayData - Interface in org.biomage.Interface
 
HasPhysicalBioAssayData.PhysicalBioAssayData_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute physicalBioAssayData.
HasPhysicalBioAssayData.PhysicalBioAssayData_list() - Constructor for class org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list
 
HasPhysicalBioAssaySource - Interface in org.biomage.Interface
 
HasPhysicalBioAssayTarget - Interface in org.biomage.Interface
 
HasPolymerType - Interface in org.biomage.Interface
 
HasPosition - Interface in org.biomage.Interface
 
HasPositionDelta - Interface in org.biomage.Interface
 
HasProducerTransformation - Interface in org.biomage.Interface
 
hasProperty(String) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
HasPropertySets - Interface in org.biomage.Interface
 
HasPropertySets.PropertySets_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute propertySets.
HasPropertySets.PropertySets_list() - Constructor for class org.biomage.Interface.HasPropertySets.PropertySets_list
 
HasProtocol - Interface in org.biomage.Interface
 
HasProtocolApplications - Interface in org.biomage.Interface
 
HasProtocolApplications.ProtocolApplications_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute protocolApplications.
HasProtocolApplications.ProtocolApplications_list() - Constructor for class org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
 
HasProviders - Interface in org.biomage.Interface
 
HasProviders.Providers_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute providers.
HasProviders.Providers_list() - Constructor for class org.biomage.Interface.HasProviders.Providers_list
 
HasQualityControlDescription - Interface in org.biomage.Interface
 
HasQualityControlStatistics - Interface in org.biomage.Interface
 
HasQualityControlStatistics.QualityControlStatistics_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute qualityControlStatistics.
HasQualityControlStatistics.QualityControlStatistics_list() - Constructor for class org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list
 
HasQuantitationDimension - Interface in org.biomage.Interface
 
HasQuantitationType - Interface in org.biomage.Interface
 
HasQuantitationTypeDimension - Interface in org.biomage.Interface
 
HasQuantitationTypeMapping - Interface in org.biomage.Interface
 
HasQuantitationTypeMaps - Interface in org.biomage.Interface
 
HasQuantitationTypeMaps.QuantitationTypeMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute quantitationTypeMaps.
HasQuantitationTypeMaps.QuantitationTypeMaps_list() - Constructor for class org.biomage.Interface.HasQuantitationTypeMaps.QuantitationTypeMaps_list
 
HasQuantitationTypes - Interface in org.biomage.Interface
 
HasQuantitationTypes.QuantitationTypes_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute quantitationTypes.
HasQuantitationTypes.QuantitationTypes_list() - Constructor for class org.biomage.Interface.HasQuantitationTypes.QuantitationTypes_list
 
HasQuantitationTypeTuples - Interface in org.biomage.Interface
 
HasQuantitationTypeTuples.QuantitationTypeTuples_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute quantitationTypeTuples.
HasQuantitationTypeTuples.QuantitationTypeTuples_list() - Constructor for class org.biomage.Interface.HasQuantitationTypeTuples.QuantitationTypeTuples_list
 
HasRegions - Interface in org.biomage.Interface
 
HasRegions.Regions_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute regions.
HasRegions.Regions_list() - Constructor for class org.biomage.Interface.HasRegions.Regions_list
 
HasReplicateDescription - Interface in org.biomage.Interface
 
HasReporter - Interface in org.biomage.Interface
 
HasReporterCompositeMaps - Interface in org.biomage.Interface
 
HasReporterCompositeMaps.ReporterCompositeMaps_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute reporterCompositeMaps.
HasReporterCompositeMaps.ReporterCompositeMaps_list() - Constructor for class org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list
 
HasReporterGroups - Interface in org.biomage.Interface
 
HasReporterGroups.ReporterGroups_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute reporterGroups.
HasReporterGroups.ReporterGroups_list() - Constructor for class org.biomage.Interface.HasReporterGroups.ReporterGroups_list
 
HasReporterPositionSources - Interface in org.biomage.Interface
 
HasReporterPositionSources.ReporterPositionSources_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute reporterPositionSources.
HasReporterPositionSources.ReporterPositionSources_list() - Constructor for class org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list
 
HasReporters - Interface in org.biomage.Interface
 
HasReporters.Reporters_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute reporters.
HasReporters.Reporters_list() - Constructor for class org.biomage.Interface.HasReporters.Reporters_list
 
HasRoles - Interface in org.biomage.Interface
 
HasRoles.Roles_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute roles.
HasRoles.Roles_list() - Constructor for class org.biomage.Interface.HasRoles.Roles_list
 
HasScale - Interface in org.biomage.Interface
 
HasSecurity - Interface in org.biomage.Interface
 
HasSecurityGroups - Interface in org.biomage.Interface
 
HasSecurityGroups.SecurityGroups_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute securityGroups.
HasSecurityGroups.SecurityGroups_list() - Constructor for class org.biomage.Interface.HasSecurityGroups.SecurityGroups_list
 
HasSeqFeatures - Interface in org.biomage.Interface
 
HasSeqFeatures.SeqFeatures_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute seqFeatures.
HasSeqFeatures.SeqFeatures_list() - Constructor for class org.biomage.Interface.HasSeqFeatures.SeqFeatures_list
 
HasSequenceDatabases - Interface in org.biomage.Interface
 
HasSequenceDatabases.SequenceDatabases_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute sequenceDatabases.
HasSequenceDatabases.SequenceDatabases_list() - Constructor for class org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list
 
HasSoftware - Interface in org.biomage.Interface
 
HasSoftwareApplications - Interface in org.biomage.Interface
 
HasSoftwareApplications.SoftwareApplications_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute softwareApplications.
HasSoftwareApplications.SoftwareApplications_list() - Constructor for class org.biomage.Interface.HasSoftwareApplications.SoftwareApplications_list
 
HasSoftwareManufacturers - Interface in org.biomage.Interface
 
HasSoftwareManufacturers.SoftwareManufacturers_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute softwareManufacturers.
HasSoftwareManufacturers.SoftwareManufacturers_list() - Constructor for class org.biomage.Interface.HasSoftwareManufacturers.SoftwareManufacturers_list
 
HasSoftwares - Interface in org.biomage.Interface
 
HasSoftwares.Softwares_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute softwares.
HasSoftwares.Softwares_list() - Constructor for class org.biomage.Interface.HasSoftwares.Softwares_list
 
HasSourceBioAssays - Interface in org.biomage.Interface
 
HasSourceBioAssays.SourceBioAssays_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute sourceBioAssays.
HasSourceBioAssays.SourceBioAssays_list() - Constructor for class org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list
 
HasSourceBioMaterialMeasurements - Interface in org.biomage.Interface
 
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute sourceBioMaterialMeasurements.
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list() - Constructor for class org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list
 
HasSourceContact - Interface in org.biomage.Interface
 
HasSourceContact.SourceContact_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute sourceContact.
HasSourceContact.SourceContact_list() - Constructor for class org.biomage.Interface.HasSourceContact.SourceContact_list
 
HasSourcesQuantitationType - Interface in org.biomage.Interface
 
HasSourcesQuantitationType.SourcesQuantitationType_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute sourcesQuantitationType.
HasSourcesQuantitationType.SourcesQuantitationType_list() - Constructor for class org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list
 
HasSpecies - Interface in org.biomage.Interface
 
HasSubregions - Interface in org.biomage.Interface
 
HasSubregions.Subregions_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute subregions.
HasSubregions.Subregions_list() - Constructor for class org.biomage.Interface.HasSubregions.Subregions_list
 
HasSubstrateType - Interface in org.biomage.Interface
 
HasSummaryStatistics - Interface in org.biomage.Interface
 
HasSummaryStatistics.SummaryStatistics_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute summaryStatistics.
HasSummaryStatistics.SummaryStatistics_list() - Constructor for class org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list
 
HasSurfaceType - Interface in org.biomage.Interface
 
HasTarget - Interface in org.biomage.Interface
 
HasTargetQuantitationType - Interface in org.biomage.Interface
 
HasTechnologyType - Interface in org.biomage.Interface
 
HasTopBioMaterial - Interface in org.biomage.Interface
 
HasTopBioMaterial.TopLevelBioMaterials_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute topLevelBioMaterials.
HasTopBioMaterial.TopLevelBioMaterials_list() - Constructor for class org.biomage.Interface.HasTopBioMaterial.TopLevelBioMaterials_list
 
HasTopLevelBioAssays - Interface in org.biomage.Interface
 
HasTopLevelBioAssays.TopLevelBioAssays_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute topLevelBioAssays.
HasTopLevelBioAssays.TopLevelBioAssays_list() - Constructor for class org.biomage.Interface.HasTopLevelBioAssays.TopLevelBioAssays_list
 
HasTreatments - Interface in org.biomage.Interface
 
HasTreatments.Treatments_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute treatments.
HasTreatments.Treatments_list() - Constructor for class org.biomage.Interface.HasTreatments.Treatments_list
 
HasType - Interface in org.biomage.Interface
 
HasTypes - Interface in org.biomage.Interface
 
HasTypes.Types_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute types.
HasTypes.Types_list() - Constructor for class org.biomage.Interface.HasTypes.Types_list
 
HasUnit - Interface in org.biomage.Interface
 
HasValue - Interface in org.biomage.Interface
 
HasWarningType - Interface in org.biomage.Interface
 
HasZone - Interface in org.biomage.Interface
 
HasZoneGroups - Interface in org.biomage.Interface
 
HasZoneGroups.ZoneGroups_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute zoneGroups.
HasZoneGroups.ZoneGroups_list() - Constructor for class org.biomage.Interface.HasZoneGroups.ZoneGroups_list
 
HasZoneLayout - Interface in org.biomage.Interface
 
HasZoneLocations - Interface in org.biomage.Interface
 
HasZoneLocations.ZoneLocations_list - Class in org.biomage.Interface
Inner list class for holding multiple entries for attribute zoneLocations.
HasZoneLocations.ZoneLocations_list() - Constructor for class org.biomage.Interface.HasZoneLocations.ZoneLocations_list
 
header_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
headerEndMarkerPattern_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
headerInformation(Element, Element, Map, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Obtains the information to generate the information for the package and the declaration of the class.
headerInformation() - Method in class org.biomage.tools.generate_classes.CreateInterfaceFile
Description: Obtains the information to generate the information for the package and the declaration of the class.
headerInformation() - Method in class org.biomage.tools.generate_classes.CreateMAGEFile
Description: Obtains the information to generate the information for the package and the declaration of the class.
headerInformation(Element, Map) - Method in class org.biomage.tools.generate_classes.CreatePackageFile
Description: Obtains the information to generate the information for the package and the declaration of the class.
headerParser_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
higherLevelAnalysis_package - Variable in class org.biomage.Common.MAGEJava
Describes the results of performing analysis on the result of the BioAssayData from an Experiment.
HigherLevelAnalysis_package - Class in org.biomage.HigherLevelAnalysis
Describes the results of performing analysis on the result of the BioAssayData from an Experiment.
HigherLevelAnalysis_package() - Constructor for class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Default constructor.
HigherLevelAnalysis_package(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Attribute constructor.
HigherLevelAnalysis_package.BioAssayDataCluster_list - Class in org.biomage.HigherLevelAnalysis
Inner list class for holding multiple entries for attribute bioAssayDataCluster.
HigherLevelAnalysis_package.BioAssayDataCluster_list() - Constructor for class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package.BioAssayDataCluster_list
 
histology_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
HISTOLOGY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
HolderBean - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
 
HolderBean() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.HolderBean
 
HomeAction - Class in gov.nih.nci.caarray.ui.login
 
HomeAction() - Constructor for class gov.nih.nci.caarray.ui.login.HomeAction
 
host_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
HOST_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
hours - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
htmlSpace - Static variable in class gov.nih.nci.caarray.ui.StringFormatter
 
HTTP_APPLET_ARRAYDESIGNADDUPDATEFORM - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_FILETYPE_GAL - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_FILEUPLOADDATAOBJECT - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_FILEUPLOADSESSIONDATA - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_JAR - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_APPLET_MODE_STOP - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_MODE_SUCCESS - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_MODULE_ARRAYDESIGN - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_MODULE_HYBRIDIZATION - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_MODULE_MAGEML - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_PARAMETER - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_REQUEST_ID - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_REQUEST_MODE - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_SOFTWARE_GENEPIX - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_APPLET_SOFTWARE_UCSFSPOT - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
HTTP_TUNNELING_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_AFFYMETRIX - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_AGILENT - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ARRAYDESIGN_AFFYMETRIX_CDF - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ARRAYDESIGN_DEFAULT_TO - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ARRAYDESIGN_GENEPIX - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ARRAYDESIGN_ILLUMINA - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ARRAYDESIGN_NOTIFY_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_GENEPIX - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_HYBRIDIZATION_DEFAULT_TO - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_HYBRIDIZATION_NOTIFY_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_ILLUMINA - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_IMAGENE - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_MAGEML - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_MAGEML_DEFAULT_TO - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_MAGEML_NOTIFY_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_SERVLET_URL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HTTP_UPLOAD_UCSF - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
HttpFileProperties - Class in gov.nih.nci.caarray.services.util.properties
This object serves as storage place for file upload annotation information and information about files acquired in different http sessions.
HttpFileProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
 
HttpFileUploadApplet - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
HttpFileUploadApplet() - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
 
HttpFileUploadApplet.HelpFrame - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
A popup window to display help text for the use of this upload applet.
HttpFileUploadApplet.ResultFrame - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
A popup window to display to the user upload summary that includes files uploaded, files failed to upload, time span and total bytes uploaded.
HttpFileUploadAppletParams - Class in gov.nih.nci.caarray.ui.core
 
HttpFileUploadAppletParams() - Constructor for class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
Default constructor
HttpFileUploadAppletParams - Class in gov.nih.nci.caarray.ui.experiment.data
 
HttpFileUploadAppletParams() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
Default constructor
HttpFileUploadCache - Class in gov.nih.nci.caarray.ui.experiment.data
This class serves as a container for hybridization file annotation data gathered before the file upload operation.
HttpFileUploadCache() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
The default constructor.
HttpFileUploader - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
This object is the central part of the file upload implementation.
HttpFileUploader(Vector, HttpUploadParameters) - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
constructor
HttpFileUploadSessionData - Class in gov.nih.nci.caarray.ui.core
This class serves as a container for hybridization file annotation data gathered before the file upload operation.
HttpFileUploadSessionData() - Constructor for class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
The default constructor.
HttpFileUploadThread - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
HttpFileUploadThread(Vector, HttpUploadParameters) - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
CONSTRUCTOR
HttpTunnelingFetchFileList - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
HttpTunnelingFetchFileList() - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpTunnelingFetchFileList
 
HttpUploadedFileData - Class in gov.nih.nci.caarray.ui.core
A simple java bean class to store meta data about the uploaded file received from the applet.
HttpUploadedFileData() - Constructor for class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
Default constructor.
HttpUploadedFileData - Class in gov.nih.nci.caarray.ui.experiment.data
A simple java bean class to store meta data about the uploaded file received from the applet.
HttpUploadedFileData() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
Default constructor.
HttpUploadFile - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
This Java bean class is used to hold file information user selected for upload.
HttpUploadFile() - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
HttpUploadParameters - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
This Java bean class encapsulates all the parameters received from the server that will be used to configure the upload process.
HttpUploadParameters() - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
The default constructor
humidity_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
HUMIDITY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
Hybridization - Class in gov.nih.nci.caarray.ui.experiment.data
 
Hybridization() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
Hybridization - Class in org.biomage.BioAssay
The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
Hybridization() - Constructor for class org.biomage.BioAssay.Hybridization
Default constructor.
Hybridization(Attributes) - Constructor for class org.biomage.BioAssay.Hybridization
Attribute constructor.
HYBRIDIZATION_FILE_MESSAGE - Static variable in class gov.nih.nci.caarray.services.fileparse.FileMessageTypes
 
HybridizationAnnotationForm - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationAnnotationForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
hybridizationAnnotationHome(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
HybridizationAnnotationMiniForm - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationAnnotationMiniForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
HybridizationCommonData - Class in gov.nih.nci.caarray.ui.experiment.data
 
HybridizationCommonData() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
HybridizationDataJob - Class in gov.nih.nci.caarray.services.hybridization
Contains information for hybridization data files to be parsed.
HybridizationDataJob(HybridizationFileUploadEntry[], String) - Constructor for class gov.nih.nci.caarray.services.hybridization.HybridizationDataJob
Creates a new job.
HybridizationDataJobHandlerImpl - Class in gov.nih.nci.caarray.services.fileupload2
 
HybridizationDataJobHandlerImpl() - Constructor for class gov.nih.nci.caarray.services.fileupload2.HybridizationDataJobHandlerImpl
 
HybridizationDataObj - Class in gov.nih.nci.caarray.ui.experiment.data
 
HybridizationDataObj() - Constructor for class gov.nih.nci.caarray.ui.experiment.data.HybridizationDataObj
 
HybridizationDataObject - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationDataObject() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
HybridizationDataTableMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
HybridizationDataTableMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
hybridizationDelete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
HybridizationDeletionConfiguration - Class in gov.nih.nci.caarray.services.experiment.ejb
Contains data about hybridizations to delete for an experiment.
HybridizationDeletionConfiguration() - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
HybridizationDeletionConfiguration(long, String) - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
HybridizationDeletionResult - Class in gov.nih.nci.caarray.services.experiment.ejb
Results from hybridization deletion.
HybridizationDeletionResult() - Constructor for class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionResult
 
HybridizationDelimitedFileParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
HybridizationDelimitedFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDelimitedFileParser
 
hybridizationDetail(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
HybridizationDetailForm - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationDetailForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
HybridizationFactorDataObject - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationFactorDataObject() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationFactorDataObject
 
HybridizationFileHandler - Interface in gov.nih.nci.caarray.services.hybridization
Interface to HybrdidizationFileHandler subsystem, allows clients to attempt to parse and store data contained in uploaded hybridization data files.
HybridizationFileHandlerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
HybridizationFileHandlerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
HybridizationFileHandlerEJB - Class in gov.nih.nci.caarray.services.hybridization.ejb
Allows direct, synchronous access to the hybridization data file parsing subsystem.
HybridizationFileHandlerEJB() - Constructor for class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
HybridizationFileHandlerFactory - Class in gov.nih.nci.caarray.services.hybridization
Allows clients to access an instance of the HybridizationFileHandler subsystem.
HybridizationFileParserMDB - Class in gov.nih.nci.caarray.services.fileparse2.mdb
 
HybridizationFileParserMDB() - Constructor for class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB
 
HybridizationFileParsingEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
HybridizationFileParsingEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.HybridizationFileParsingEntry
 
HybridizationFileParsingEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
HybridizationFileParsingEntryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileParsingEntryData
 
HybridizationFileParsingService - Class in gov.nih.nci.caarray.services.fileparse2
 
HybridizationFileParsingService() - Constructor for class gov.nih.nci.caarray.services.fileparse2.HybridizationFileParsingService
 
HybridizationFileProcessAction - Class in gov.nih.nci.caarray.ui.experiment
This action class is responsible for starting file parsing service, forwarding to a designated page upon user's request and cleaning up uploaded files when user requests a stop action.
HybridizationFileProcessAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationFileProcessAction
 
HybridizationFileType - Class in gov.nih.nci.caarray.common.data.fileupload2
 
HybridizationFileType() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileType
 
HybridizationFileUpload - Class in org.biomage.Experiment
Deprecated. This bean is replaced by HybridizationFileUploadGroup and HybridizationFileUploadEntry for version 1.3
HybridizationFileUpload() - Constructor for class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
HybridizationFileUploadAction - Class in gov.nih.nci.caarray.ui.experiment
The Action class that handles hybridization annotation data input from the users and launches the file upload applet so users will be be able to select files they want to be stored by the CaArray application through file uploading process.
HybridizationFileUploadAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
 
HybridizationFileUploadAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
HybridizationFileUploadAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadAssembler
 
HybridizationFileUploadData - Class in gov.nih.nci.caarray.common.data.experiment
Deprecated. This bean is replaced by HybridizationFileUploadGroupData and HybridizationFileUploadEntryData for version 1.3
HybridizationFileUploadData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
HybridizationFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
HybridizationFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
HybridizationFileUploadEntryAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
HybridizationFileUploadEntryAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadEntryAssembler
 
HybridizationFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
HybridizationFileUploadEntryData(String, FileType, String, String) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
HybridizationFileUploadEntrySummaryData - Class in gov.nih.nci.caarray.common.data.fileupload2
This class provides the summary information about hybridization file such as the file name and the failure/success flag excluding the annotation data such as experiment, labeled extracts, and factor values.
HybridizationFileUploadEntrySummaryData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
HybridizationFileUploadForm - Class in gov.nih.nci.caarray.ui.experiment
 
HybridizationFileUploadForm() - Constructor for class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
HybridizationFileUploadGroup - Class in gov.nih.nci.caarray.services.fileupload2
 
HybridizationFileUploadGroup() - Constructor for class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
HybridizationFileUploadGroupData - Class in gov.nih.nci.caarray.common.data.fileupload2
This class represents a group of files that are parsed to one or more bioassays.
HybridizationFileUploadGroupData(HybridizationFileType[]) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
hybridizationIndividualFileDownload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
HybridizationManagerDB - Class in gov.nih.nci.caarray.services.fileparse2
 
HybridizationManagerDB() - Constructor for class gov.nih.nci.caarray.services.fileparse2.HybridizationManagerDB
 
hybridizationProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method is the combined form of getHybridizationProtocolDesc method and saveHybridizationProtocolInfo method due to the change in the jsp page where a single method parameter is used for submitting the form data.
HybridizationRowWrapper - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
 
HybridizationRowWrapper(Object, String[], String[]) - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 

I

IAccess - Interface in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
 
id - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
id - Variable in class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean
 
id - Variable in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
id - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
id - Variable in class org.biomage.Common.Extendable
 
ID - Static variable in class org.biomage.tools.generate_er.CreateMageER
name of the primary key for tables
Id2ObjectFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
This custom field mapper allows setting NULL to the target field when the source field that is a long attribute and represents the target field value's identifying information is a zero.
Id2ObjectFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Id2ObjectFieldMapper
 
id_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
id_ - Variable in class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
 
ID_UNSET - Static variable in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
Identifiable - Class in org.biomage.Common
An Identifiable class is one that has an unambiguous reference within the scope.
Identifiable() - Constructor for class org.biomage.Common.Identifiable
Default constructor.
Identifiable(Attributes) - Constructor for class org.biomage.Common.Identifiable
Attribute constructor.
identifierLIMS - Variable in class org.biomage.Array.ManufactureLIMS
Association to a LIMS data source for further information on the manufacturing process.
identifierMap - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
IdFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
IdFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.IdFieldMapper
 
idOfConnection(Connection) - Method in class org.biomage.tools.helpers.DbConnectionBroker
Returns the local JDBC ID for a connection.
ignorableWhitespace(char[], int, int) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
ignorableWhitespace(char[], int, int) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
IlluminaArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.illumina
Loads array designs from an Illumina content descriptor CSV.
IlluminaCsvFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.illumina
Indicates an error in an Illumina array design content descriptor file.
IlluminaCsvFormatException() - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaCsvFormatException
 
IlluminaCsvFormatException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaCsvFormatException
 
IlluminaCsvFormatException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaCsvFormatException
 
IlluminaCsvFormatException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaCsvFormatException
 
IlluminaDataHandlerDataSourceManagerDB - Class in gov.nih.nci.caarray.services.bioassaydata
 
IlluminaDataHandlerDataSourceManagerDB() - Constructor for class gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB
 
IlluminaDbDataHanderDataSource - Class in gov.nih.nci.caarray.services.bioassaydata
 
IlluminaDbDataHanderDataSource() - Constructor for class gov.nih.nci.caarray.services.bioassaydata.IlluminaDbDataHanderDataSource
 
Image - Class in org.biomage.BioAssay
An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
Image() - Constructor for class org.biomage.BioAssay.Image
Default constructor.
Image(Attributes) - Constructor for class org.biomage.BioAssay.Image
Attribute constructor.
ImageAcquisition - Class in org.biomage.BioAssay
The process by which an image is generated (typically scanning).
ImageAcquisition() - Constructor for class org.biomage.BioAssay.ImageAcquisition
Default constructor.
ImageAcquisition(Attributes) - Constructor for class org.biomage.BioAssay.ImageAcquisition
Attribute constructor.
ImageneTxtArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.imagene
Loads an array design from an Imagene text data file.
ImageneTxtFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.imagene
Indicates an error in an Imagene txt data file.
ImageneTxtFormatException() - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtFormatException
 
ImageneTxtFormatException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtFormatException
 
ImageneTxtFormatException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtFormatException
 
ImageneTxtFormatException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtFormatException
 
ImageneTxtReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
 
imageProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
This method is the combined form of getImageProtocolData method and saveImageProtocolInfo method due to the change in the jsp page where a single method parameter is used for submitting the form data.
images - Variable in class org.biomage.BioAssay.ImageAcquisition
The images produced by the ImageAcquisition event.
implementParsedFeatureClass(Map) - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ClassGenerator
Create access class for getting and setting a bean-style property value.
importArrayDesign(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
 
importArrayDesign(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
Imports a MAGEML array design
importDate - Variable in class org.biomage.tools.generate_classes.CreateFile
 
importDate() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether the class needs to import Date.
imported - Variable in class org.biomage.BioMaterial.BioMaterial
caARRAY internal flag to indicate if this BioMaterial is imported.
ImportException - Exception in gov.nih.nci.caarray.common.exception
 
ImportException(String) - Constructor for exception gov.nih.nci.caarray.common.exception.ImportException
Creates a new instance of ImportException with a reason.
ImportException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.common.exception.ImportException
 
ImportException(Throwable) - Constructor for exception gov.nih.nci.caarray.common.exception.ImportException
 
importExperiment(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
 
importExperiment(String, String[], String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
 
importExperiment(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
importExperiment(String, String[], String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
importExperiment(String, String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
ImportExportTest - Class in org.biomage.tools.xmlutils
Description: Demonstration class that imports a MAGE-ML document into a MAGE-OM model and then writes it back out again.
ImportExportTest() - Constructor for class org.biomage.tools.xmlutils.ImportExportTest
 
importFileData(Set, String) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
Queues the file uploads corresponding to the ids given for data parsing and storage.
importMAGEML(String, String, String) - Method in class gov.nih.nci.caarray.services.security.test.MAGEMLImportSecuredElementBuilder
 
importProtocols(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
For testing only
importProtocols(String, String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
For testing only
importRecord(PagePanel, String) - Method in interface org.biomage.tools.apps.annot.data.DataLoader
 
importSerializable - Variable in class org.biomage.tools.generate_classes.CreateFile
 
importSerializable() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether the class needs to import Serializable.
importVector - Variable in class org.biomage.tools.generate_classes.CreateFile
 
importVector() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether the class needs to import Vector.
InContainerTest - Interface in gov.nih.nci.caarray.services.test
 
indent(int) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
INDENT - Static variable in class org.biomage.tools.generate_er.CreateMageER
one indent: a tab key
Index - Class in org.biomage.tools.generate_er
 
Index() - Constructor for class org.biomage.tools.generate_er.Index
Description: Constructor for the Index object.
Index(String, AssociationColumn) - Constructor for class org.biomage.tools.generate_er.Index
Description: Constructor for the Index object.
IndexAction - Class in gov.nih.nci.caarray.ui.core
 
IndexAction() - Constructor for class gov.nih.nci.caarray.ui.core.IndexAction
 
indexOfInstanceOfClass(List, Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
individual_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
INDIVIDUAL_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
information - Variable in class org.biomage.Array.Array
Association between the manufactured array and the information on that manufacture.
InheritedAccessDeniedException - Exception in gov.nih.nci.caarray.services.exception
 
InheritedAccessDeniedException(Object, Object) - Constructor for exception gov.nih.nci.caarray.services.exception.InheritedAccessDeniedException
 
init() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
Component initialization
init() - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
init(FilterConfig) - Method in class gov.nih.nci.caarray.ui.core.SecurityContextFilter
Initializes the filter.
initial() - Method in class org.biomage.tools.apps.annot.PagePanel
Description: initialize a generic interface t
INITIAL_TIME_POINT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
initialCap(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
initialCap(String) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the string and returns a new string based on the input but with the first letter capitalized.
initialize(Subject, CallbackHandler, Map, Map) - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
Initialize this LoginModule.
initialize(int, int, int, int, int, boolean, Integer, boolean, boolean, boolean, boolean) - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Initializer for class.
initialize(String, String, String, String) - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: C'tor for class.
initialize() - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Obtains the top node of the document.
initialLower(String) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the string and returns a new string based on the input but with the first letter in lower case.
initialTimePointId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
initialTimePointName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
initialTimePoints_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
INSERT_OBJECT_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
insertMtoNRelation(Object, Object, String) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Inserts a many-to-many association between two objects.
insertMtoNRelation(Object, Object, String, boolean) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
insertObject(Object) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Inserts an object.
insertObject(Object, boolean) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Inserts an object.
insertObject(Object, PersistenceBroker, boolean) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Inserts an object.
insertObject(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Inserts an object.
insertObject(Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
InsertObjectException - Exception in gov.nih.nci.caarray.services.exception
 
InsertObjectException() - Constructor for exception gov.nih.nci.caarray.services.exception.InsertObjectException
 
InsertObjectException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.InsertObjectException
 
InsertObjectException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.InsertObjectException
 
InsertObjectException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.InsertObjectException
 
insertObjectsInBatch(List, int, PersistenceBroker) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
Inserts the specified list of objects in batch mode.
instance() - Static method in class gov.nih.nci.caarray.services.fileparse2.BeanProvider
 
INTEGER - Static variable in class org.biomage.tools.generate_er.CreateMageER
association column type is int, and also columns in linking table
interfaceInfo - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Interfaces, if any, that this class implements.
InternalFeatureIdGenerator - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
InternalFeatureIdGenerator() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.InternalFeatureIdGenerator
 
InternalTable - Class in gov.nih.nci.caarray.services.util.parse
 
InternalTable() - Constructor for class gov.nih.nci.caarray.services.util.parse.InternalTable
 
IntValidator - Class in org.biomage.tools.apps.annot.validator
 
IntValidator() - Constructor for class org.biomage.tools.apps.annot.validator.IntValidator
 
invokeWriteMAGEMLOnMAGEIdentifiables(List, Writer, int) - Static method in class gov.nih.nci.caarray.services.util.mage.MAGEWriter
Invokes method writeMAGEML on the specified list of identifiables AND surround the writing of each of the batchSize of Identifiables with a transaction.
isAbstract() - Method in class org.biomage.tools.generate_classes.CreateFile.IdentifierAttrInformation
Description: Method that returns whether the role's class is abstract.
isAbstract - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Variables to indicate whether class is abstract.
isAbstract() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether the class is abstract.
isArrayDesignProvidedByAffymetrix(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
isArrayDesignProvidedByAffymetrix(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
isArrayDesignProvidedByAffymetrix(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Checks if the specified ArrayDesign was made/provided by Affymetrix.
isAssignable - Variable in class org.biomage.tools.helpers.MGEDOntologyEntry
 
isAssignable() - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
isAssigned - Variable in class org.biomage.tools.helpers.MGEDOntologyEntry
 
isAssigned() - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
isAssociationEndNavigable(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns whether the association end is navigable.
isAssociationEndOrdered(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns whether the association end is ordered.
isAuthenticationSuccessful(String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthenticationDAItf
Returns the result of the user authentication.
isAuthenticationSuccessful(String, String) - Method in class gov.nih.nci.caarray.services.security.LdapAuthenticationDAObj
Returns the result of the user authentication using a LDAP server as data repository.
isAuthenticationSuccessful(String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthenticationDAObj
Returns the result of the user authentication using a RDBMS as data repository.
isBackground() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
isBaseClass - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Indicates whether this class is a base class.
isBaseClass() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether this is a base class.
isCategoryForNonReusableVocab(String) - Static method in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
isCompressing() - Method in class gov.nih.nci.caarray.services.util.file.FileZipper
Is this object currently compressing data files ?
isCompressing() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
Is this object currently compressing data files ?
isDateFormatValid(String) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
isDeleted() - Method in class org.biomage.ArrayDesign.ArrayDesign
 
isDeleted() - Method in class org.biomage.BioAssay.BioAssay
 
isDeleted() - Method in class org.biomage.Experiment.Experiment
 
isDoneParsing() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
 
isDoneParsing() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
 
isEditable - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
isEditable - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
isEditable - Variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
isEditable() - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
isEditable - Variable in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
isEditable - Variable in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
isEditable() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
isEditable() - Method in interface gov.nih.nci.caarray.common.data.util.DataDescInterface
 
isEditable() - Method in interface gov.nih.nci.caarray.services.security.intf.SecuredElementItf
 
isEditable - Variable in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
isEditable() - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
isEditable - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
isEditable - Variable in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
isEditable() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
isEditable - Variable in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
isEditable - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
isEditable() - Method in class org.biomage.Common.Extendable
 
isEnum() - Method in class org.biomage.tools.generate_classes.CreateFile.AttrInformation
Description: Get method for whether the datatype is an enumeration.
isFailed() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Returns the value isFailed set dynamically during the cause of file upload.
isFailed() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
isFloat(String, int, int) - Method in class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
Description: checks if a string is a float number.
isGroupNameUnique(String, long) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
isHybridizationFile() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
isIdentifiable - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Is this class ultimately identifiable.
isIdentifiable(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns whether or not a given class is Identifiable -- useful in the C++ generation code.
isIdentifiableClass() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns whether this class is identifiable.
isIgnoreCopy() - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
isIncludeHeaders() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Returns the includeHeaders.
isIndependent - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Will this class need a package list?
isIndependentClass() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Will this class need a package list?
isInstantiable(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
isInteger(String, int) - Method in class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
Description: checks if a string is an integer.
isInterface - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on whether this is an interface.
isLDAPAuthorization() - Static method in class gov.nih.nci.caarray.services.security.SecurityObjFactory
 
isLoaded() - Method in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
isLocalMode() - Method in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
isLoginNameUnique(String) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
isMeasuredBioAssay() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileType
 
isMultiParent() - Method in class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
isNewBioDataCube() - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
isNewDesignElementDimension(DerivedBioAssay) - Method in class gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB
 
isNewDesignElementDimension(MeasuredBioAssay) - Method in class gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB
 
isOkay() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
isOrdered - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
isOwner(String, String, String) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns an item's ownership for the given user.
isOwner(String, String, String[], long[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns an users ownership for a collection of items.
isOwner(String, String, String[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns an users ownership for a collection of items.
isOwner(String, String, String) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns an item's ownership for the given user.
isOwner(String, String, String[], long[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns an item's ownership for the given user.
isOwner(String, String, String[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns an item's ownership for the given user.
isOwner - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
isOwner() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Returns whether this associations end class owns this class.
isOwnerOnly(String, String, String[]) - Method in interface gov.nih.nci.caarray.services.security.intf.AuthorizationDAItf
Returns an item's ownership for the given user.
isOwnerOnly(String, String, String[]) - Method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Returns an item's ownership for the given user.
isReadDataLineTabs() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
isReadHeaderTabs() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
isReferenced - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Whether any association needs a reference to this class.
isReferenced() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Whether this class is referenced by an association.
isReferenced(boolean) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Sets whether this class is referenced by an association.
isReferencedClass(CreateFile) - Static method in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: Utility method to verify whether class has roles or is top-level.
isRequired() - Method in class org.biomage.tools.generate_classes.CreateClassFile.DataTypeAttrInformation
Description: method to determine if the attribute is required.
isStartDateBeforeEndDate(String, String) - Static method in class gov.nih.nci.caarray.services.useradmin.AdminUtils
 
isStopped() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
 
isSubclassOf(Class, Class) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
Check if a class is a super class or an interface of another class.
isTransactionActive() - Method in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
isUnrestricted() - Method in class gov.nih.nci.caarray.common.data.security.RoleAssignmentData
 
isUploadComplete() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
isUploadFile() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
isUploadFile() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
isUploadPreparationDone() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
isUserAuthenticated(String, String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
 
isUserAuthenticated(String, String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
 
isUserAuthenticated(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Authenticates the user
isUserAuthenticated(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Authenticates the user
isUserElementOwner(String, String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Deprecated.  
isUserElementOwner(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Checks if the user is owner of the Object SecuredElement.
isUserElementOwner(String, String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Deprecated.  
isUserElementOwner(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Checks if the user is owner of the Object SecuredElement.
isUserElementOwner(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Deprecated.  
isUserElementOwner(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Checks if the user is owner of the Object SecuredElement.
isUserElementOwner(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Deprecated.  
isUserElementOwner(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Checks if the user is owner of the Object SecuredElement.
isUserOwner(String, String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Returns if the user is owner of given securedElement.
IsUsrElementOwner - Class in gov.nih.nci.caarray.services.security.test.usecases
 
IsUsrElementOwner() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.IsUsrElementOwner
 
isValid() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
isValidDate(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
isZip() - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
 
isZipFile(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileZipper
Checks if the specified file is a compressed zip file.
isZipFile() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
isZipped() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
 
itemStateChanged(ItemEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
This ItemListener method uses various File methods to obtain information about a file or directory.
itemStateChanged(ItemEvent) - Method in class gov.nih.nci.caarray.ui.experiment.UploadApplet
This ItemListener method uses various File methods to obtain information about a file or directory.

J

JAVA_INTERFACE - Static variable in class org.biomage.tools.generate_classes.CreateFile
 
javaBodyIndent - Static variable in class org.biomage.tools.helpers.StringOutputHelpers
 
JavassistCalls - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
 
JavassistCalls() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.JavassistCalls
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Action2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Basis2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Boolean2IntFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.KindCV2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Long2LongObjectFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Order2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.OrientationMarkPosition2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.SourceType2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Type2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion
 
javaToSql(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Value2StringFieldConversion
 
JCSHelper - Class in gov.nih.nci.caarray.services.util.cache
 
JCSHelper() - Constructor for class gov.nih.nci.caarray.services.util.cache.JCSHelper
 
JdbcAccessImpl - Class in gov.nih.nci.caarray.services.util.ojb
 
JdbcAccessImpl(PersistenceBroker) - Constructor for class gov.nih.nci.caarray.services.util.ojb.JdbcAccessImpl
Creates a new instance of JdbcAccessImpl
JDBCConnection2 - Class in org.biomage.tools.helpers
 
JDBCConnection2() - Constructor for class org.biomage.tools.helpers.JDBCConnection2
 
JDBCConnectionImpl2 - Class in org.biomage.tools.helpers
 
JDBCParms - Class in gov.nih.nci.caarray.services.security.db
Encapsulates JDBC params used in the implementation of a JDBC Connection Pool via the Object Pool Pattern.
JDBCParms() - Constructor for class gov.nih.nci.caarray.services.security.db.JDBCParms
 
JDBCParms - Class in org.biomage.tools.helpers
Author: Wiebe deJong Date: May 9, 2000 REF: Implement a JDBC Connection Pool via the Object Pool Pattern www.earthweb.com
JDBCParms() - Constructor for class org.biomage.tools.helpers.JDBCParms
 
JMSMessageCollection - Interface in gov.nih.nci.caarray.services.util.jms
 
JMSMessageHandler - Interface in gov.nih.nci.caarray.services.util.jms
 
JMSMessageManagerDB - Class in gov.nih.nci.caarray.services.util.jms
 
JMSMessageManagerDB() - Constructor for class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
Default Constructor
JMSMessageManagerDB(String) - Constructor for class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
join(Object[], String, String) - Static method in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Joins the elements of the provided array into a single String containing the provided list of elements.

K

K - Variable in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
kg - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
kind - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation.ParamInfo
 
KindCV2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
KindCV2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.KindCV2StringFieldConversion
 

L

L - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
label(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
LABEL_COMPOUND - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
LabelAddUpdateAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabelAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
labelBioSample(TreatmentData, LabeledExtractData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
labelBioSample(TreatmentData, LabeledExtractData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Labels a BioMaterial to create a LabeledExtract.
LabeledExtract - Class in org.biomage.BioMaterial
LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties).
LabeledExtract() - Constructor for class org.biomage.BioMaterial.LabeledExtract
Default constructor.
LabeledExtract(Attributes) - Constructor for class org.biomage.BioMaterial.LabeledExtract
Attribute constructor.
LabeledExtractBaseForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabeledExtractBaseForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
LabeledExtractData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
LabeledExtractData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData
 
labeledExtractData - Variable in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
LabeledExtractDesc - Class in gov.nih.nci.caarray.common.data.biomaterial
 
LabeledExtractDesc() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractDesc
 
LabeledExtractDetailAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabeledExtractDetailAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailAction
 
LabeledExtractDetailForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabeledExtractDetailForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailForm
 
LabeledExtractManagementTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
LabeledExtractManagementTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
LabeledExtractSearchAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabeledExtractSearchAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
LabeledExtractSearchForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
LabeledExtractSearchForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
LabeledExtractView - Class in gov.nih.nci.caarray.common.data.biomaterial
 
LabeledExtractView() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
LabelFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
LabelFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.LabelFieldMapper
 
labelName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
labels - Variable in class org.biomage.BioAssay.Channel
The compound used to label the extract.
labels - Variable in class org.biomage.BioMaterial.LabeledExtract
Compound used to label the extract.
lastDocument - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
lastDocument - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
ldapAuthenticateUser(String, String) - Method in class gov.nih.nci.caarray.services.security.db.LDAPConnection
Return the result of user authentication with LDAP server
LdapAuthenticationDAObj - Class in gov.nih.nci.caarray.services.security
This authentication data service class is a local implementation of AuthenticationDAItf using NCI Directory Server as the data repository.
LdapAuthenticationDAObj() - Constructor for class gov.nih.nci.caarray.services.security.LdapAuthenticationDAObj
Constructor for a new LdapAuthenticationDAObj object.
LDAPConnection - Class in gov.nih.nci.caarray.services.security.db
Provides the LDAP connection and user authentication service.
LDAPConnection() - Constructor for class gov.nih.nci.caarray.services.security.db.LDAPConnection
 
LED_SIZE - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
left - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
legalValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyClassEntry
 
legalValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
legalValue(Object) - Method in class org.biomage.tools.helpers.MGEDOntologyPropertyEntry
 
length - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
lengthExceeded(String, int) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
light_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
LIGHT_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
LineSplitter - Interface in gov.nih.nci.caarray.services.util.file
 
LineSplitterImpl - Class in gov.nih.nci.caarray.services.util.file
Helper class used to split CSV or tab-separated lines into lists of Strings.
LineSplitterImpl(char, char) - Constructor for class gov.nih.nci.caarray.services.util.file.LineSplitterImpl
 
link(Object, String, boolean) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
link(Object, boolean) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
link(Object, String, boolean) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
LINKING - Static variable in class org.biomage.tools.generate_er.CreateMageER
table type is linking
LINKING_FKEY - Static variable in class org.biomage.tools.generate_er.CreateMageER
foreign key type is many to many
LinkingKey - Class in org.biomage.tools.generate_er
 
LinkingKey() - Constructor for class org.biomage.tools.generate_er.LinkingKey
Description: Constructor for the LinkingKey object.
LinkingKey(AssociationColumn, AssociationColumn) - Constructor for class org.biomage.tools.generate_er.LinkingKey
Description: Constructor for the LinkingKey object.
LIST_MATERIAL_TYPES - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
LIST_TAXON_TYPES - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
LIST_TREATMENT_TYPES - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
LIST_UNIT_TYPES - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
listDirectory(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
This method uses the list() method to get all entries in a directory and then displays them in the List component.
listDirectory(String) - Method in class gov.nih.nci.caarray.ui.experiment.UploadApplet
This method uses the list() method to get all entries in a directory and then displays them in the List component.
listenerAbstractClassPKPersistence_ - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
listenerCompoundResolver_ - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
listenerMAGEIdentifierAssigner_ - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
listenerOntologyEntryResolver_ - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
load() - Static method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
load(String, byte[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ClassGenerator.DirectLoader
 
load(String, byte[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls.DirectLoader
 
loadArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.AffymetrixArrayDesignLoader
Creates and returns the id of the new array design.
loadArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaArrayDesignLoader
 
loadData(BioAssayDataInfo) - Method in interface gov.nih.nci.caarray.services.bioassaydata.BioAssayDataLoader
Parses and saves the data referred to by the data information object.
LoadDuplicateFileNameProcessor - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
LoadDuplicateFileNameProcessor(String[], ArrayList) - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.LoadDuplicateFileNameProcessor
 
loaded_ - Variable in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
loadInformation(ExperimentCleaningConfiguration) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
loadInformation(ExperimentCleaningConfiguration) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
loadList(String[]) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.ProcessDuplicatedFileName
 
loadProperties() - Method in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
loadProviderNames(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
loadUnitNames(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
loadUnits(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
This method is used to get the correct units for the type of measurement specified by the user in the bodyTreatmentPageTwo.
loadUnits(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
loadUnits(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
loadUnits(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
This method is used to get the correct units for the type of measurement specified by the user in the bodyTreatmentPageTwo.
LOCAL - Static variable in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
 
LOCAL - Static variable in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
 
LOCAL_MODE - Static variable in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
LOCAL_MODE - Static variable in class gov.nih.nci.caarray.services.security.test.Tester
 
LOCAL_MODE - Static variable in class gov.nih.nci.caarray.services.test.Tester
 
LOCAL_MODE - Static variable in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
LocalDynaBean - Interface in gov.nih.nci.caarray.services.fileparse2.parsers
An equivalent of common-beanutils's DynaBean with extra support to get the property's value as String, Double, or Long.
LocalDynaBean - Interface in gov.nih.nci.caarray.services.util.parse
Simple wrappper for the apache dynabean
LocalDynaBeanImpl - Class in gov.nih.nci.caarray.services.fileparse2.parsers
An equivalent of common-beanutils's BasicDynaBean with extra support to get the property's value as String, Double, or Long.
LocalDynaBeanImpl(BasicDynaClass) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
LocalDynaBeanImpl - Class in gov.nih.nci.caarray.services.util.parse
 
LocalDynaBeanImpl(BasicDynaClass) - Constructor for class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl
 
LocalDynaBeanWrapper - Class in gov.nih.nci.caarray.services.fileparse2.parsers
An equivalent of common-beanutils's BasicDynaBean with extra support to get the property's value as String, Double, or Long.
LocalDynaBeanWrapper(Object) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
LocalDynaBeanWrapper - Class in gov.nih.nci.caarray.services.util.parse
 
LocalDynaBeanWrapper(Object) - Constructor for class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanWrapper
 
lock(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
lockExperiment(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
lockExperiment(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Locks a particular experiment by changing the visibility to public and relinquishing ownership.
log - Static variable in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Commons Logging instance.
logger_ - Variable in class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
logger_ - Static variable in class gov.nih.nci.caarray.services.bioassaydata.DesignElementDimensionCreator
Logger used by this class.
logger_ - Variable in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSampleTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSourceTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.biomaterial.test.DeleteTreatmentFromBioMaterial
 
logger_ - Variable in class gov.nih.nci.caarray.services.biomaterial.test.DuplicateBioSourceTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.biomaterial.test.UpdateBioSourceCharacteristicsTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.BioAssayService
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.CaArrayToMageConversion
Logger used by an instance of this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.CubeCreator
Logger used by an instance of this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.DataFileProcessorFactory
Logger used by an instance of this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.FileParsingService
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElementService
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantificationService
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse2.hybridization.BioDataCubeCreator
Logger used by an instance of this class.
logger_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
Logger used by this class.
logger_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeFactory
Logger used by an instance of this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Logger used by this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Logger used by this class.
logger_ - Variable in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerUpdateTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerUpdateTest
 
logger_ - Static variable in class gov.nih.nci.caarray.services.util.AbstractSessionBean
Logger used by an instance of this class.
logger_ - Static variable in class gov.nih.nci.caarray.services.util.mage.MAGEWriter
Logger used by this class.
logger_ - Variable in class gov.nih.nci.caarray.services.util.ojb.CaArraySequenceManagerHighLowImpl
Logger used by an instance of this class.
logger_ - Variable in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
Logger used by this class.
logger_ - Variable in class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
 
logger_ - Variable in class gov.nih.nci.caarray.services.vocab.test.VocabManagerUpdateTest
 
LoggingSecuredElementOrphanHandler - Class in gov.nih.nci.caarray.services.security.mageom
 
LoggingSecuredElementOrphanHandler() - Constructor for class gov.nih.nci.caarray.services.security.mageom.LoggingSecuredElementOrphanHandler
 
LoggingUserTransaction - Class in gov.nih.nci.caarray.services.util
 
LoggingUserTransaction(UserTransaction) - Constructor for class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
login() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
Authenticate the user by prompting for a user name and password.
login() - Method in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
LoginAction - Class in gov.nih.nci.caarray.ui.login
 
LoginAction() - Constructor for class gov.nih.nci.caarray.ui.login.LoginAction
 
LoginForm - Class in gov.nih.nci.caarray.ui.login
 
LoginForm() - Constructor for class gov.nih.nci.caarray.ui.login.LoginForm
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignFileProcessAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
Determines whether a log in is required to access this action
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionOne
Determines whether a log in is required to access this action
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionThree
Determines whether a log in is required to access this action
loginRequired() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
Determines whether a log in is required to access this action
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.ContactsAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.core.BaseAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.core.BaseDispatchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.core.IndexAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.AddExperimentFactorAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.AddExperimentPublicationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAddAdditionalHybPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAddHybPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalQualifierAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalUploadFilePageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBatchDownloadAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentContactPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDataProcessingPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationDetailDoneAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentImportMageMLAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewAdditionalQualifierAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageContinueAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentUploadAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileProcessAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadAction
To make sure that calling to any method in this class requires security check.
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentAdditionalQualifierAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentContactAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentFactorAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentGeneralInfoAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentPublicationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentQualityAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAdditionalUploadFileAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAddPublicationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentDataProcessingAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentImportMageMLAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewAdditionalQualifierAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewPageContinueAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.HomeAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.LoginAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.LogoutAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.PublicExperimentDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.PublicSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.login.RegisterAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAction
This method returns a boolean value, which determines if the action is accesseble with or without log in True = LogIn required to access this page False = LogIn not required
loginRequired() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
This method returns a boolean value, which determines if the action is accesseble with or without log in True = LogIn required to access this page False = LogIn not required
loginRequired() - Method in class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
This method returns a boolean value, which determines if the action is accesseble with or without log in True = LogIn required to access this page False = LogIn not required
loginRequired() - Method in class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
This method returns a boolean value, which determines if the action is accesseble with or without log in True = LogIn required to access this page False = LogIn not required
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolActionMappingsAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserAdminAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserManagementAction
 
loginRequired() - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
logout() - Method in class gov.nih.nci.caarray.services.security.CaArrayLoginModule
Logout the user.
LogoutAction - Class in gov.nih.nci.caarray.ui.login
 
LogoutAction() - Constructor for class gov.nih.nci.caarray.ui.login.LogoutAction
 
logTA - Static variable in class org.biomage.tools.apps.annot.MageXMLConverter
 
Long2LongObjectFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Long2LongObjectFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Long2LongObjectFieldConversion
 
lookup(String, Class) - Method in class gov.nih.nci.caarray.services.security.test.MAGEMLImportSecuredElementBuilder
 
lookup(String, Class) - Method in class gov.nih.nci.caarray.services.security.test.SecurityTester
 
lookup(Identity) - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
Lookup object with Identity oid in objectTable.
LOOKUP_FKEY - Static variable in class org.biomage.tools.generate_er.CreateMageER
foreign key type is for look up table
LoopNames(CreateFile, CreateCPPFile.specificWriter) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Loops through the Attributes and Associations so that we can write based on context.
lowerCaseFirstLetter(String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: change the first letter of a string to be lower case

M

M - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
m - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
MAGE_IDENTIFIER_NAME_SPACE - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
MAGEContentHandler - Class in org.biomage.tools.xmlutils
Description: Content handler for MAGE.
MAGEContentHandler() - Constructor for class org.biomage.tools.xmlutils.MAGEContentHandler
 
MAGEContentHandler.UnresolvedRef - Class in org.biomage.tools.xmlutils
Basic structure to hold unresolved references.
MAGEContentHandler.UnresolvedRef(MAGEContentHandler.Association, Object, String, String) - Constructor for class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
 
MAGECubeBuilder - Class in gov.nih.nci.caarray.services.mageloader
 
MAGECubeBuilder(BioAssayData, String) - Constructor for class gov.nih.nci.caarray.services.mageloader.MAGECubeBuilder
Construtor for a new Cube Builder for MAGE
MAGEException - Exception in org.biomage.Common
 
MAGEException(String) - Constructor for exception org.biomage.Common.MAGEException
Description: Constructor for the MAGEException object.
MAGEException() - Constructor for exception org.biomage.Common.MAGEException
Description: Default constructor for the MAGEException object.
MAGEException(Throwable, String) - Constructor for exception org.biomage.Common.MAGEException
Description: Specialized constructor for the MAGEException object.
mageJava - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
MAGEJava - Class in org.biomage.Common
Top-level object that represents the model.
MAGEJava() - Constructor for class org.biomage.Common.MAGEJava
Default constructor.
MAGEJava(Attributes) - Constructor for class org.biomage.Common.MAGEJava
Attribute constructor.
mageJava - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
MAGEManagerDB - Class in gov.nih.nci.caarray.services.util.mage
This class provides methods to retrieve collections of DesignElement and NameValueType objects associated with a parent MAGE object without their associations for MAGE-ML.
MAGEManagerDB() - Constructor for class gov.nih.nci.caarray.services.util.mage.MAGEManagerDB
Default Constructor
MAGEML_DTD_LOCATION - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
MAGEML_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
MAGEML_MESSAGE - Static variable in class gov.nih.nci.caarray.services.fileparse.FileMessageTypes
 
MAGEML_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
MAGEML_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
MAGEML_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
MAGEMLExportManagerDB - Class in gov.nih.nci.caarray.services.mageml
 
MAGEMLExportManagerDB() - Constructor for class gov.nih.nci.caarray.services.mageml.MAGEMLExportManagerDB
Default Constructor
MAGEMLFileUploadEntry - Class in gov.nih.nci.caarray.services.fileupload2
 
MAGEMLFileUploadEntry() - Constructor for class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
MAGEMLFileUploadEntryData - Class in gov.nih.nci.caarray.common.data.fileupload2
 
MAGEMLFileUploadEntryData(String, FileType, String, String) - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
MAGEMLFileUploadSearchCriteria - Class in gov.nih.nci.caarray.common.data.fileupload2
 
MAGEMLFileUploadSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
MAGEMLFileValues - Class in gov.nih.nci.caarray.services.mageml
 
MAGEMLFileValues(Long, Integer, String, boolean) - Constructor for class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues
Constructs the argument containing MAGEML generation information to provide to MAGEML generator.
MAGEMLGeneratorDelegate - Class in gov.nih.nci.caarray.services.mageml
 
MAGEMLGeneratorDelegate() - Constructor for class gov.nih.nci.caarray.services.mageml.MAGEMLGeneratorDelegate
 
MAGEMLGeneratorMDB - Class in gov.nih.nci.caarray.services.mageml.mdb
 
MAGEMLGeneratorMDB() - Constructor for class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB
 
MAGEMLImportManagerDB - Class in gov.nih.nci.caarray.services.mageloader
Specialized ManagerDB for MAGEML import shared.
MAGEMLImportManagerDB() - Constructor for class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Default Constructor
MAGEMLImportSecuredElementBuilder - Class in gov.nih.nci.caarray.services.security.test
 
MAGEMLImportSecuredElementBuilder() - Constructor for class gov.nih.nci.caarray.services.security.test.MAGEMLImportSecuredElementBuilder
 
MAGEMLManagerDelegate - Class in gov.nih.nci.caarray.services.mageml
 
MAGEMLManagerDelegate() - Constructor for class gov.nih.nci.caarray.services.mageml.MAGEMLManagerDelegate
 
MAGEMLManagerEJB - Class in gov.nih.nci.caarray.services.mageml.ejb
MAGEMLManagerEJB
MAGEMLManagerEJB() - Constructor for class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
 
mageObj - Variable in class org.biomage.tools.xmlutils.MAGEReader
 
MAGEReader - Class in gov.nih.nci.caarray.services.util.mage
Deprecated. Use mageloader.DatabaseImportMAGEReader instead
MAGEReader(String, String[]) - Constructor for class gov.nih.nci.caarray.services.util.mage.MAGEReader
Deprecated. Reading multiple MAGE-ML files.
MAGEReader - Class in org.biomage.tools.xmlutils
 
MAGEReader(String) - Constructor for class org.biomage.tools.xmlutils.MAGEReader
Creates a new instance of MAGEReader
MAGEResolver - Class in gov.nih.nci.caarray.services.mageloader
 
MAGEResolver() - Constructor for class gov.nih.nci.caarray.services.mageloader.MAGEResolver
 
MAGEWriter - Class in gov.nih.nci.caarray.services.util.mage
 
MAGEWriter(Identifiable) - Constructor for class gov.nih.nci.caarray.services.util.mage.MAGEWriter
 
MageXMLConverter - Class in org.biomage.tools.apps.annot
 
MageXMLConverter() - Constructor for class org.biomage.tools.apps.annot.MageXMLConverter
Description: Generic constructor.
main(String[]) - Static method in class gov.nih.nci.caarray.loader.ArrayDesignLoaderClient
 
main(String[]) - Static method in class gov.nih.nci.caarray.loader.DataFileLoaderClient
 
main(String[]) - Static method in class gov.nih.nci.caarray.loader.ExperimentCleanerClient
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Used for test only.
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSampleTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSourceTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.DeleteTreatmentFromBioMaterial
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.DuplicateBioSourceTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.GetTreatmentTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateBioSourceCharacteristicsTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.FileParsingService
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElementService
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantificationService
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gpr.GprFileParseHandler
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ClassGenerator
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.BCELCalls
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.JavassistCalls
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.ReflectAccess
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.hybridization.DesignElementFinder
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDelimitedFileParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanWrapper
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayDelimitedFileParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
short example of how to use the api, note UploadFileTypes is used to communicate the file types
main(String[]) - Static method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEReader
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.mageloader.MAGEResolver
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.mageloader.test.ArrayDesignFixer
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.mageloader.test.PerfTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerAddTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerGetTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerParameterAddTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerUpdateTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerAddTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerGetTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerUpdateTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.LoggingSecuredElementOrphanHandler
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.PathElement
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementIdUpdaterFactory
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.mageom.SecuredElementOrphanHandlerFactory
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Used for test only.
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.SecurityServiceObj
Used for test only.
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.test.GeneralSecuredElementUpdateTester
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.test.MAGEMLImportSecuredElementBuilder
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.test.SecurityTester
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.security.test.Tester
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.test.FetchFileListTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.test.Tester
 
main(String[]) - Static method in exception gov.nih.nci.caarray.services.test.TestException
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestArrayDesignConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestTreatmentConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.file.FileLocatorUtils
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.file.FileZipper
Use this for testing.
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.file.ReadZipFileContent
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
I should use this to test this.
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
Test driver.
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageCollection
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.mage.MAGEReader
Deprecated.  
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.parse.InternalTable
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanWrapper
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerAddTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerDeleteTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerUpdateTest
 
main(String[]) - Static method in class gov.nih.nci.caarray.ui.test.ExperimentSearchTest
 
main(String[]) - Static method in class org.biomage.tools.apps.annot.MageXMLConverter
Description: Start point to lauch the application.
main(String[]) - Static method in class org.biomage.tools.generate_classes.CreateMageClasses
Description: The main entry point for the XMLLoaderTestServer.
main(String[]) - Static method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: The main entry point for the XMLLoaderTestServer.
main(String[]) - Static method in class org.biomage.tools.helpers.OntologyHelper
 
main(String[]) - Static method in class org.biomage.tools.helpers.OntologyImport
 
main(String[]) - Static method in class org.biomage.tools.xmlutils.ImportExportTest
Description: Program entry point.
main(String[]) - Static method in class org.biomage.tools.xmlutils.MAGEReader
 
makeArrayPage() - Method in class org.biomage.tools.apps.annot.pages.ArrayPage
Description: initialized an interface for Array page.
makeAssociation(DatabaseImportMAGEContentHandler.Association, Object, Object) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
Method to make an association between object via reflection.
makeAssociation(MAGEContentHandler.Association, Object, Object) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
Method to make an association between object via reflection.
makeOptional() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Writes the name of the association role, capitulized.
makeProtocolApplicationData(ProtocolData) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
makePublic(PhysicalArrayDesign, String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Makes an array design public.
makePublic(PhysicalArrayDesign, String) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignSecurityHelper
 
makePublic(PhysicalArrayDesign, String) - Method in class gov.nih.nci.caarray.services.arraydesign.CaArrayArrayDesignSecurityHelper
 
makePublic(PhysicalArrayDesign, String) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
ManagerDB - Class in gov.nih.nci.caarray.services.util.db
The super class of all ManagerDB classes to allow common OJB operations to be shared.
ManagerDB() - Constructor for class gov.nih.nci.caarray.services.util.db.ManagerDB
Creates a new instance of ManagerDB
ManagerDB(String) - Constructor for class gov.nih.nci.caarray.services.util.db.ManagerDB
Creates a new instance of ManagerDB
manageUserGroups(long, String[]) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
manageUserGroups(long, String[]) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
manageUserGroups(long, String[]) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Updates the User's Group assignments.
MandatoryFloat - Class in org.biomage.tools.apps.annot.validator
 
MandatoryFloat() - Constructor for class org.biomage.tools.apps.annot.validator.MandatoryFloat
 
MandatoryInt - Class in org.biomage.tools.apps.annot.validator
 
MandatoryInt() - Constructor for class org.biomage.tools.apps.annot.validator.MandatoryInt
 
MandatoryText - Class in org.biomage.tools.apps.annot.validator
 
MandatoryText() - Constructor for class org.biomage.tools.apps.annot.validator.MandatoryText
 
manufactureDate - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
ManufactureLIMS - Class in org.biomage.Array
Information on the physical production of arrays within the laboratory.
ManufactureLIMS() - Constructor for class org.biomage.Array.ManufactureLIMS
Default constructor.
ManufactureLIMS(Attributes) - Constructor for class org.biomage.Array.ManufactureLIMS
Attribute constructor.
ManufactureLIMSBiomaterial - Class in org.biomage.Array
Stores the location from which a biomaterial was obtained.
ManufactureLIMSBiomaterial() - Constructor for class org.biomage.Array.ManufactureLIMSBiomaterial
Default constructor.
ManufactureLIMSBiomaterial(Attributes) - Constructor for class org.biomage.Array.ManufactureLIMSBiomaterial
Attribute constructor.
ManyToMany(CreateFile, String) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create an association column for many to many relationship
ManyToOne(Table, AssociationColumn, CreateFile, CreateFile.AssociationAttrInformation, FileWriter) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create an association column for one to one relationship
map - Static variable in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
Represents a map of
map - Static variable in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
Represents a map of
map - Static variable in class gov.nih.nci.caarray.services.bioassaydata.reader.UCSFSpotGprReader
Represents a map of
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
Converts the value contained in the source field of the source object specified by this converter to be the value for the target field of the target object specified by this converter.
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ArrayManufacturerFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BibliographicReferenceAccessionFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BioMaterialParentsFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.BioSourceProviderFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Date2NameValueTypeFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Date2StringFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.DescriptionFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ExperimentTypeFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.HardwaresSoftwaresParameterTypesFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.Id2ObjectFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.IdFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.LabelFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.NumberOfChannelsFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ParsingSucceededFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProtocolApplicationFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProtocolApplicationPerformerFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProviderFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.SoftwareOrHardwareManufacturerFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.SqlDate2JavaDateFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.TechnologyTypeFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.UnitDataFieldMapper
 
map(Object, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.VocabDataFieldMapper
 
Map - Class in org.biomage.BioEvent
A Map is the description of how sources are transformed into a target.
Map() - Constructor for class org.biomage.BioEvent.Map
Default constructor.
Map(Attributes) - Constructor for class org.biomage.BioEvent.Map
Attribute constructor.
mark(int) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
markSupported() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
mass - Variable in class org.biomage.Measurement.Measurement.KindCV
 
MASS_UNIT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
MassUnit - Class in org.biomage.Measurement
Mass
MassUnit() - Constructor for class org.biomage.Measurement.MassUnit
Default constructor.
MassUnit(Attributes) - Constructor for class org.biomage.Measurement.MassUnit
Attribute constructor.
MassUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
match(String, String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
matchDatabase(Database, PersistenceBroker) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
 
matchHeaderEndMarkerPattern(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
matchOntologyEntry(OntologyEntry) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
matchOntologyEntry(OntologyEntry, PersistenceBroker) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
 
matchType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Examines the file name is of this type by matching its normal extension and zip version extension.
matchZone(Map, ParsedFeature) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ZoneMatcher
 
matchZone(Map, ParsedFeature) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.DefaultZoneMatcher
 
matchZone(Map, ParsedFeature) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.GenePixGALZoneMatcher
 
matchZone(Map, ParsedFeature) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.UCSFSpotZoneMatcher
 
matchZone(Map, ParsedFeature) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.ZoneLocationZoneMatcher
 
MATERIAL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
materialType - Variable in class org.biomage.BioMaterial.BioMaterial
The type of material used, i.e.
materialType_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
materialTypeId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
materialTypeName_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
materialTypes - Static variable in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
materialTypes - Static variable in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
materialTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
MAX_IN_CLAUSE_SIZE - Static variable in class gov.nih.nci.caarray.services.security.mageom.DefaultSecuredElementIdUpdater
 
maxCard - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
MeasuredBioAssay - Class in org.biomage.BioAssay
A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
MeasuredBioAssay() - Constructor for class org.biomage.BioAssay.MeasuredBioAssay
Default constructor.
MeasuredBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.MeasuredBioAssay
Attribute constructor.
MeasuredBioAssayAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
MeasuredBioAssayAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.MeasuredBioAssayAssembler
 
measuredBioAssayData - Variable in class org.biomage.BioAssay.MeasuredBioAssay
The data associated with the MeasuredBioAssay.
MeasuredBioAssayData - Class in org.biomage.BioAssayData
The data associated with the MeasuredBioAssay produced by FeatureExtraction.
MeasuredBioAssayData() - Constructor for class org.biomage.BioAssayData.MeasuredBioAssayData
Default constructor.
MeasuredBioAssayData(Attributes) - Constructor for class org.biomage.BioAssayData.MeasuredBioAssayData
Attribute constructor.
measuredBioAssayTarget - Variable in class org.biomage.BioAssay.FeatureExtraction
The association between the MeasuredBioAssay and the FeatureExtraction Event.
MeasuredSignal - Class in org.biomage.QuantitationType
Best measure from feature extraction as to the presence and intensity of the signal.
MeasuredSignal() - Constructor for class org.biomage.QuantitationType.MeasuredSignal
Default constructor.
MeasuredSignal(Attributes) - Constructor for class org.biomage.QuantitationType.MeasuredSignal
Attribute constructor.
measurement - Variable in class org.biomage.BioMaterial.BioMaterialMeasurement
The amount of the BioMaterial.
measurement - Variable in class org.biomage.BioMaterial.CompoundMeasurement
The amount of the Compound.
measurement - Variable in class org.biomage.Experiment.FactorValue
The measured value for this factor.
Measurement - Class in org.biomage.Measurement
A Measurement is a quantity with a unit.
Measurement() - Constructor for class org.biomage.Measurement.Measurement
Default constructor.
Measurement(Attributes) - Constructor for class org.biomage.Measurement.Measurement
Attribute constructor.
Measurement.KindCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute kindCV can assume.
Measurement.Type - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute type can assume.
measurement_package - Variable in class org.biomage.Common.MAGEJava
The classes of this package provide utility information on the quantities of other classes to each other.
Measurement_package - Class in org.biomage.Measurement
The classes of this package provide utility information on the quantities of other classes to each other.
Measurement_package() - Constructor for class org.biomage.Measurement.Measurement_package
Default constructor.
Measurement_package(Attributes) - Constructor for class org.biomage.Measurement.Measurement_package
Attribute constructor.
MeasurementData - Class in gov.nih.nci.caarray.common.data.measurement
 
MeasurementData() - Constructor for class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
MeasurementManagerDB - Class in gov.nih.nci.caarray.services.protocol
This class does not support adding Measurement because Measurement is intended to be cascade-stored with the objects it is associated with.
MeasurementManagerDB() - Constructor for class gov.nih.nci.caarray.services.protocol.MeasurementManagerDB
 
MEDIA - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
media_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
mediaId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
mediaTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
members - Variable in class org.biomage.AuditAndSecurity.SecurityGroup
The members of the Security Group.
mergePckgs(Object, Object) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
MessageData - Class in gov.nih.nci.caarray.services.util.jms
 
MessageData() - Constructor for class gov.nih.nci.caarray.services.util.jms.MessageData
 
methodInfo - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on the methods for this class.
methodInformation(Element, Map, Map, Map, Map) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: Puts together the information on the class methods.
methodsMap - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
methodsMap - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
mg - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
mg_per_mL - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
MGEDOntologyClassEntry - Class in org.biomage.tools.helpers
 
MGEDOntologyClassEntry() - Constructor for class org.biomage.tools.helpers.MGEDOntologyClassEntry
 
MGEDOntologyClassEntry(String, OntologyHelper) - Constructor for class org.biomage.tools.helpers.MGEDOntologyClassEntry
Creates a new instance of MGEDOntologyClassEntry
MGEDOntologyClassEntry(String, OntologyHelper, HashMap) - Constructor for class org.biomage.tools.helpers.MGEDOntologyClassEntry
Creates a new instance of MGEDOntologyClassEntry
MGEDOntologyEntry - Class in org.biomage.tools.helpers
 
MGEDOntologyEntry() - Constructor for class org.biomage.tools.helpers.MGEDOntologyEntry
 
MGEDOntologyEntry.OntologyDatabaseEntry - Class in org.biomage.tools.helpers
 
MGEDOntologyEntry.OntologyDatabaseEntry() - Constructor for class org.biomage.tools.helpers.MGEDOntologyEntry.OntologyDatabaseEntry
 
MGEDOntologyPropertyEntry - Class in org.biomage.tools.helpers
 
MGEDOntologyPropertyEntry(String, String, OntologyHelper) - Constructor for class org.biomage.tools.helpers.MGEDOntologyPropertyEntry
Creates a new instance of MGEDOntologyEntry
MicroarrayDelimitedFileParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
MicroarrayDelimitedFileParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayDelimitedFileParser
 
MicroarrayTextFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
MicroarrayTextFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
Constructs a parser to parse a text file's header section.
MicroarrayTextFileHeaderParser(DataSetMapper, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
Constructs a parser to parse a text file's header section.
minCard - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
minutes - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
mismatchInformation - Variable in class org.biomage.DesignElement.CompositePosition
Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
mismatchInformation - Variable in class org.biomage.DesignElement.FeatureInformation
Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match.
MismatchInformation - Class in org.biomage.DesignElement
Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
MismatchInformation() - Constructor for class org.biomage.DesignElement.MismatchInformation
Default constructor.
MismatchInformation(Attributes) - Constructor for class org.biomage.DesignElement.MismatchInformation
Attribute constructor.
mismatchInformation - Variable in class org.biomage.DesignElement.ReporterPosition
Differences in how the reporter matches its compositeSequence's sequence.
MissingSecuredElementIdException - Exception in gov.nih.nci.caarray.services.exception
 
MissingSecuredElementIdException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.MissingSecuredElementIdException
 
ml - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
mL_per_L - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
mM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
mm - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
mode - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
mode_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
modification - Variable in class org.biomage.AuditAndSecurity.Audit.Action
 
modifyAdditionalQualifier(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
modifyCompound(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
modifyContact(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ModifyExperimentAdditionalQualifierAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentAdditionalQualifierAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentAdditionalQualifierAction
 
ModifyExperimentContactAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentContactAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentContactAction
 
ModifyExperimentDetailAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentDetailAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ModifyExperimentFactorAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentFactorAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentFactorAction
 
ModifyExperimentGeneralInfoAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentGeneralInfoAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentGeneralInfoAction
 
ModifyExperimentPublicationAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentPublicationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentPublicationAction
 
ModifyExperimentQualityAction - Class in gov.nih.nci.caarray.ui.experiment
 
ModifyExperimentQualityAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.ModifyExperimentQualityAction
 
modifyGeneralInfomation(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ModifyProtocolApplicationAction - Class in gov.nih.nci.caarray.ui.protocol
 
ModifyProtocolApplicationAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
modifyPublicationPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
modifyqualityControl(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
ModifyTreatmentAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
ModifyTreatmentAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
mol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
molecules - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
months - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
moveArrayDesignFilesToFinalLocation(ArrayDesignFileUploadGroup, long) - Static method in class gov.nih.nci.caarray.services.fileparse2.ArrayDesignFileParsingService
 
ms - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
MultiHashMap - Class in org.biomage.tools.xmlutils
Utility class for associating multiple values with a key in a Synchronized Map.
MultiHashMap() - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
MultiHashMap(int) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
MultiHashMap(int, float) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
MultiHashMap(MultiHashMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
Constructs a new MultiHashMap with the same mappings as the given MultiHashMap.
MultiHashMap(MultiMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
Constructs a new MultiHashMap with the same mappings as the given MultiMap.
MultiHashMap(Map) - Constructor for class org.biomage.tools.xmlutils.MultiHashMap
MultiHashtable - Class in org.biomage.tools.xmlutils
Utility class for associating multiple values with a key in a Synchronized Map.
MultiHashtable() - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
MultiHashtable(int) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
MultiHashtable(int, float) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
MultiHashtable(MultiHashtable) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
Constructs a new MultiHashtable with the same mappings as the given MultiHashtable.
MultiHashtable(MultiMap) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
Constructs a new MultiHashtable with the same mappings as the given MultiMap.
MultiHashtable(Map) - Constructor for class org.biomage.tools.xmlutils.MultiHashtable
MultiMap - Interface in org.biomage.tools.xmlutils
Utility interface for associating multiple values with a key.

N

N - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
NA - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
name - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
name - Variable in class org.biomage.tools.helpers.OntologyHelper.InstanceInformation
 
name_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
name_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
name_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
nameAndDatabase - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
NameValueType - Class in org.biomage.Common
A tuple designed to store data, keyed by a name and type.
NameValueType() - Constructor for class org.biomage.Common.NameValueType
Default constructor.
NameValueType(Attributes) - Constructor for class org.biomage.Common.NameValueType
Attribute constructor.
navigateToChildren(Extendable, String) - Static method in class gov.nih.nci.caarray.services.security.mageom.DefaultSecuredElementIdUpdater
 
NE - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
NETCDFCreator - Class in gov.nih.nci.caarray.services.util.netcdf
Creates netcdf files for the application.
NETCDFCreator(DesignElement[], QuantitationType[], BioAssay[]) - Constructor for class gov.nih.nci.caarray.services.util.netcdf.NETCDFCreator
Constructs the class with the neccessary items as arrays
NETCDFCreator(List, List, List) - Constructor for class gov.nih.nci.caarray.services.util.netcdf.NETCDFCreator
Constructs the class with the neccessary items as lists
NETCDFException - Exception in gov.nih.nci.caarray.services.util.netcdf
 
NETCDFException() - Constructor for exception gov.nih.nci.caarray.services.util.netcdf.NETCDFException
 
NETCDFException(String) - Constructor for exception gov.nih.nci.caarray.services.util.netcdf.NETCDFException
 
NETCDFException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.netcdf.NETCDFException
 
NETCDFException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.netcdf.NETCDFException
 
NETCDFFileReader - Class in gov.nih.nci.caarray.services.util.netcdf
Class for reading items from a netcdf file
NETCDFFileReader() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.NETCDFFileReader
 
NEW_LINE - Static variable in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
Indicator for the new line delimiter.
newAdditionalQualifier(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
newCaArrayCache(String) - Static method in class gov.nih.nci.caarray.services.util.cache.EHCacheHelper
 
newInstance(String) - Static method in class gov.nih.nci.caarray.services.util.cache.EHCacheHelper
 
newInstance(String) - Static method in class gov.nih.nci.caarray.services.util.cache.JCSHelper
 
newInstance(ExtractDropDownData) - Static method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
Alternative style for a copy constructor, using a static newInstance method.
newInstance(FactorDropDownData) - Static method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
Alternative style for a copy constructor, using a static newInstance method.
newline - Static variable in class gov.nih.nci.caarray.ui.StringFormatter
 
NEWLINE - Static variable in class org.biomage.tools.generate_classes.CreateFile
Description: The environment specific new line.
NEWLINE - Static variable in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: The environment specific new line.
NEWLINE - Static variable in class org.biomage.tools.generate_dtd.WriteDTDClassElement
 
NEWLINE - Static variable in class org.biomage.tools.generate_er.CreateMageER
a new line character
NEWLINE - Static variable in class org.biomage.tools.helpers.StringOutputHelpers
Description: The environment specific new line.
newPublicationPage(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
This method performs the intial search for the
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
newSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
next() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
 
next() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
next() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
next(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewPageContinueAction
 
nextRow() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileReader
 
nextRow(LocalDynaBean) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportDefaultListener
 
nextRow(LocalDynaBean) - Method in interface gov.nih.nci.caarray.services.util.parse.DelimitedImportListener
 
ng - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
nl - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
nM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
nm - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
nmol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
NO_BASE_CLASS - Static variable in class org.biomage.tools.generate_er.CreateMageER
the object (table) does not have base class
NO_SPACE - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
Node - Class in org.biomage.HigherLevelAnalysis
An individual component of a clustering.
Node() - Constructor for class org.biomage.HigherLevelAnalysis.Node
Default constructor.
Node(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.Node
Attribute constructor.
nodeContents - Variable in class org.biomage.HigherLevelAnalysis.Node
The contents of the node, expressed as either a one, two or three dimensional object.
NodeContents - Class in org.biomage.HigherLevelAnalysis
The contents of a node for any or all of the three Dimensions.
NodeContents() - Constructor for class org.biomage.HigherLevelAnalysis.NodeContents
Default constructor.
NodeContents(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.NodeContents
Attribute constructor.
nodes - Variable in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
The nodes of the cluster.
nodes - Variable in class org.biomage.HigherLevelAnalysis.Node
Nested nodes of the BioAssayDataCluster.
nodeValue - Variable in class org.biomage.HigherLevelAnalysis.Node
Values or measurements for this node that may be produced by the clustering algorithm.
NodeValue - Class in org.biomage.HigherLevelAnalysis
A value associated with the Node that can rank it in relation to the other nodes produced by the clustering algorithm.
NodeValue() - Constructor for class org.biomage.HigherLevelAnalysis.NodeValue
Default constructor.
NodeValue(Attributes) - Constructor for class org.biomage.HigherLevelAnalysis.NodeValue
Attribute constructor.
NONE - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
NonNumericQuantitationTypes - Class in gov.nih.nci.caarray.services.util.netcdf
Class provides resolution of code to value and value to code for a given quantitation type
NonNumericQuantitationTypes() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypes
 
NonNumericQuantitationTypesService - Class in gov.nih.nci.caarray.services.util.netcdf
This class serves up resolution for non-numeric expression values such as affy calls
NonNumericQuantitationTypesService() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
normalizationDescription - Variable in class org.biomage.Experiment.ExperimentDesign
Description of the normalization strategy of the Experiment.
NOT_ABSTRACT - Static variable in class org.biomage.tools.generate_er.CreateMageER
the object (table) is not abstract
NOT_AGGR - Static variable in class org.biomage.tools.generate_classes.XMIParseHelpers
Is Independent
NOT_ASSIGNED - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
NOT_NULL - Static variable in class org.biomage.tools.generate_er.CreateMageER
the column can not be null
Notifiable - Interface in gov.nih.nci.caarray.services.util.parse
 
notifyCuratorOfFileUploadProcessingError(String, String) - Static method in class gov.nih.nci.caarray.common.util.SendMail
 
notifyOfFileUploadProcessing(String, String, String, boolean) - Static method in class gov.nih.nci.caarray.common.util.SendMail
 
notifyServer(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
After a upload, notify the server to start process uploaded files, or clean up the cache if failed.
notifyServer(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
NULL - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
NULL - Static variable in class org.biomage.tools.generate_er.CreateMageER
the column can be null
NumberOfChannelsFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
NumberOfChannelsFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.NumberOfChannelsFieldMapper
 
NumberOfColumns() - Method in class org.biomage.tools.generate_er.Unique
Description: get the number of columns for the Unique
NumberOfIds() - Method in class org.biomage.tools.generate_er.Unique
Description: get the number of columns for the Unique
nutrients_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
NUTRIENTS_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
NW - Static variable in class org.biomage.tools.apps.annot.GuiSet
 

O

OBJECT_IN_USE_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
OBJECT_NOT_FOUND_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
ObjectCacheEHCacheImpl - Class in gov.nih.nci.caarray.services.util.cache
This has been adapted to use EHCache
ObjectCacheEHCacheImpl(PersistenceBroker, Properties) - Constructor for class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
Constructor for the MetaObjectCachePerClassImpl object
ObjectCacheEHCacheImpl(String) - Constructor for class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
Constructor used by the ObjectCacheEHCachePerClassImpl
ObjectCacheEHCachePerClassImpl - Class in gov.nih.nci.caarray.services.util.cache
This has been adapted to use EHCache.
ObjectCacheEHCachePerClassImpl(PersistenceBroker, Properties) - Constructor for class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCachePerClassImpl
Constructor for the MetaObjectCachePerClassImpl object
ObjectInUseException - Exception in gov.nih.nci.caarray.services.exception
 
ObjectInUseException() - Constructor for exception gov.nih.nci.caarray.services.exception.ObjectInUseException
Creates a new default ObjectInUseException
ObjectInUseException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.ObjectInUseException
Creates an ObjectInUseException with the specified message.
ObjectNotExistException - Exception in gov.nih.nci.caarray.services.exception
This exception is used when an object cannot be found.
ObjectNotExistException() - Constructor for exception gov.nih.nci.caarray.services.exception.ObjectNotExistException
Creates a new default ObjectNotExistException
ObjectNotExistException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.ObjectNotExistException
Creates an ObjectNotExistException with the specified message.
objectStack - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
objectStack - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
ODMGImplementationManager - Class in gov.nih.nci.caarray.services.util.db
 
OJB_MAGEML_EXPORT_REPOSITORY - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
OJB_MAGEML_IMPORT_REPOSITORY - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
OJB_MAGEML_JCD_ALIAS - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
OJB_TX_MODE - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
ojbConcreteClass - Variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
ojbConcreteClass - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
ojbConcreteClass - Variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
ojbConcreteClass - Variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
ojbConcreteClass - Variable in class org.biomage.Array.ManufactureLIMS
 
ojbConcreteClass - Variable in class org.biomage.ArrayDesign.DesignElementGroup
 
ojbConcreteClass - Variable in class org.biomage.BioAssay.BioAssay
 
ojbConcreteClass - Variable in class org.biomage.BioAssay.BioAssayCreation
 
ojbConcreteClass - Variable in class org.biomage.BioAssay.BioAssayTreatment
 
ojbConcreteClass - Variable in class org.biomage.BioAssayData.BioDataValues
 
ojbConcreteClass - Variable in class org.biomage.BioAssayData.DesignElementDimension
 
ojbConcreteClass - Variable in class org.biomage.BioAssayData.DesignElementMap
 
ojbConcreteClass - Variable in class org.biomage.BioMaterial.BioMaterial
 
ojbConcreteClass - Variable in class org.biomage.BioSequence.SequencePosition
 
ojbConcreteClass - Variable in class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
ojbConcreteClass - Variable in class org.biomage.Measurement.Unit
 
ojbConcreteClass - Variable in class org.biomage.QuantitationType.QuantitationType
 
OjbInitializer - Class in gov.nih.nci.caarray.services.util.db
Ensures that OJB is initialized on application startup
OjbInitializer() - Constructor for class gov.nih.nci.caarray.services.util.db.OjbInitializer
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
This method is used when returning to the original search page after looking at details of a particular search result.
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
oldSearch(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
ONE_TO_MANY - Static variable in class org.biomage.tools.generate_er.CreateMageER
foreign key type is one to many
ONE_TO_ONE - Static variable in class org.biomage.tools.generate_er.CreateMageER
foreign key type is one to one
oneIndent - Static variable in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Size of indentation.
oneIndent - Static variable in class org.biomage.tools.generate_er.CreateMageER
one indent: a tab key
oneIndent - Static variable in class org.biomage.tools.helpers.StringOutputHelpers
Description: Size of indentation.
OneToMany(Table, AssociationColumn, CreateFile, CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create an association column for one to one relationship
OneToOne(Table, AssociationColumn, CreateFile, CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: create an association column for one to one relationship
onMessage(Message) - Method in class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB
 
onMessage(Message) - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
ONT_SEARCH_ACCNUM - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
ONT_SEARCH_DBNAME - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
ONT_SEARCH_ECOCULT - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
ONT_SEARCH_NAME - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
ONT_SEARCH_RESULTS - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
OntologyAction - Class in gov.nih.nci.caarray.ui.ontology
 
OntologyAction() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyAction
 
OntologyActionForm - Class in gov.nih.nci.caarray.ui.ontology
This ActionForm is used by the OntologyActions and pages and stores the attributes for each of the ontologys except Strain or Line, which extends this class to add attributes and further validation
OntologyActionForm() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
OntologyAddUpdateAction - Class in gov.nih.nci.caarray.ui.ontology
 
OntologyAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
 
OntologyCategoriesProperties - Class in gov.nih.nci.caarray.services.util.properties
This class reads a properties file that describes an ontology category and its sub-categories.
OntologyCategoriesProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.OntologyCategoriesProperties
 
OntologyConstants - Class in gov.nih.nci.caarray.ui.ontology
This class contains the constants used by the Ontology pages and actions
OntologyConstants() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
OntologyDetailAction - Class in gov.nih.nci.caarray.ui.ontology
This Action uses the id value from the intial search page as passed in the request to perform a new search and provide more details regarding the specific search result selected by the user.
OntologyDetailAction() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyDetailAction
 
OntologyEntry - Class in org.biomage.Description
A single entry from an ontology or a controlled vocabulary.
OntologyEntry() - Constructor for class org.biomage.Description.OntologyEntry
Default constructor.
OntologyEntry(Attributes) - Constructor for class org.biomage.Description.OntologyEntry
Attribute constructor.
OntologyEntryAttrsProperties - Class in gov.nih.nci.caarray.services.util.properties
 
OntologyEntryAttrsProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.OntologyEntryAttrsProperties
 
OntologyHelper - Class in org.biomage.tools.helpers
 
OntologyHelper(String) - Constructor for class org.biomage.tools.helpers.OntologyHelper
 
OntologyHelper.ClassInformation - Class in org.biomage.tools.helpers
 
OntologyHelper.ClassInformation(String) - Constructor for class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
OntologyHelper.InstanceInformation - Class in org.biomage.tools.helpers
 
OntologyHelper.InstanceInformation(String) - Constructor for class org.biomage.tools.helpers.OntologyHelper.InstanceInformation
 
OntologyImport - Class in org.biomage.tools.helpers
 
OntologyImport() - Constructor for class org.biomage.tools.helpers.OntologyImport
 
ontologyReference - Variable in class org.biomage.Description.OntologyEntry
Many ontology entries will not yet have formalized ontologies.
OntologySearchAction - Class in gov.nih.nci.caarray.ui.ontology
 
OntologySearchAction() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
 
OntologyStrainLineActionForm - Class in gov.nih.nci.caarray.ui.ontology
 
OntologyStrainLineActionForm() - Constructor for class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm
 
OptionData - Class in gov.nih.nci.caarray.ui.useradmin
 
OptionData(int, String) - Constructor for class gov.nih.nci.caarray.ui.useradmin.OptionData
 
Order2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Order2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Order2StringFieldConversion
 
org.biomage.Array - package org.biomage.Array
 
org.biomage.ArrayDesign - package org.biomage.ArrayDesign
 
org.biomage.AuditAndSecurity - package org.biomage.AuditAndSecurity
 
org.biomage.BioAssay - package org.biomage.BioAssay
 
org.biomage.BioAssayData - package org.biomage.BioAssayData
 
org.biomage.BioEvent - package org.biomage.BioEvent
 
org.biomage.BioMaterial - package org.biomage.BioMaterial
 
org.biomage.BioSequence - package org.biomage.BioSequence
 
org.biomage.BQS - package org.biomage.BQS
 
org.biomage.Common - package org.biomage.Common
 
org.biomage.Description - package org.biomage.Description
 
org.biomage.Description.Ontology - package org.biomage.Description.Ontology
 
org.biomage.DesignElement - package org.biomage.DesignElement
 
org.biomage.Experiment - package org.biomage.Experiment
 
org.biomage.HigherLevelAnalysis - package org.biomage.HigherLevelAnalysis
 
org.biomage.Interface - package org.biomage.Interface
 
org.biomage.Measurement - package org.biomage.Measurement
 
org.biomage.Protocol - package org.biomage.Protocol
 
org.biomage.QuantitationType - package org.biomage.QuantitationType
 
org.biomage.tools.apps.annot - package org.biomage.tools.apps.annot
 
org.biomage.tools.apps.annot.data - package org.biomage.tools.apps.annot.data
 
org.biomage.tools.apps.annot.pages - package org.biomage.tools.apps.annot.pages
 
org.biomage.tools.apps.annot.validator - package org.biomage.tools.apps.annot.validator
 
org.biomage.tools.generate_classes - package org.biomage.tools.generate_classes
 
org.biomage.tools.generate_cpp - package org.biomage.tools.generate_cpp
 
org.biomage.tools.generate_doc - package org.biomage.tools.generate_doc
 
org.biomage.tools.generate_dtd - package org.biomage.tools.generate_dtd
 
org.biomage.tools.generate_er - package org.biomage.tools.generate_er
 
org.biomage.tools.generate_java - package org.biomage.tools.generate_java
 
org.biomage.tools.helpers - package org.biomage.tools.helpers
 
org.biomage.tools.xmlutils - package org.biomage.tools.xmlutils
 
ORGANISM_PART - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ORGANISM_STATUS - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
organismPart_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
organismPartId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
organismParts_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
organismStatus_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
organismStatuses_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
organismStatusId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
Organization - Class in org.biomage.AuditAndSecurity
Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
Organization() - Constructor for class org.biomage.AuditAndSecurity.Organization
Default constructor.
Organization(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Organization
Attribute constructor.
OrganizationAddUpdateAction - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
OrganizationAddUpdateForm - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
OrganizationComparator - Class in gov.nih.nci.caarray.ui.core
 
OrganizationComparator() - Constructor for class gov.nih.nci.caarray.ui.core.OrganizationComparator
 
OrganizationData - Class in gov.nih.nci.caarray.common.data.contact
 
OrganizationData() - Constructor for class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
OrganizationDesc - Class in gov.nih.nci.caarray.common.data.contact
 
OrganizationDesc() - Constructor for class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
OrganizationDescriptor - Enum in gov.nih.nci.caarray.services.contact
Data for known organizations referenced in code.
OrganizationDetailAction - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationDetailAction() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationDetailAction
 
OrganizationDetailForm - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationDetailForm() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationDetailForm
 
OrganizationSearchAction - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationSearchAction() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
OrganizationSearchCriteria - Class in gov.nih.nci.caarray.common.data.contact
 
OrganizationSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.contact.OrganizationSearchCriteria
 
OrganizationSearchForm - Class in gov.nih.nci.caarray.ui.contact
 
OrganizationSearchForm() - Constructor for class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
organizeByFileTypes(UploadFileValues) - Static method in class gov.nih.nci.caarray.services.fileupload.FileTypeManager
 
ORGPART_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
ORIENTATION_MARK_POSITION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
OrientationMarkPosition2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
OrientationMarkPosition2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.OrientationMarkPosition2StringFieldConversion
 
originalType - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
other - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
other - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
other - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
other - Variable in class org.biomage.Measurement.Measurement.KindCV
 
other - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
other - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
other - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
OTHER_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
OTHER_TYPE - Static variable in class gov.nih.nci.caarray.common.data.experiment.ExperimentFileTypeConstants
 
OTHER_TYPE - Static variable in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
OTHER_TYPE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
otherNav - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
OtherUnit - Class in org.biomage.Measurement
 
OtherUnit() - Constructor for class org.biomage.Measurement.OtherUnit
 
owner - Variable in class org.biomage.AuditAndSecurity.Security
The owner of the security rights.

P

packageDoc - Variable in class org.biomage.tools.generate_classes.CreateFile
 
packageElement - Variable in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
Description: For outputting the MAGE-OM element to the file.
packageImports - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: List of Packages needed in the import list.
packageInformation(Element, Map) - Method in class org.biomage.tools.generate_classes.CreateMageClassFileList
Description: Obtains the PackageInformation (name and documentation) and puts it on a map keyed by the model element id.
packageName - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Package this class belongs to.
packageName() - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
packFiles(String[], String, String) - Method in class gov.nih.nci.caarray.services.util.file.FilePacker
 
PAGE_X - Static variable in class org.biomage.tools.apps.annot.MageXMLConverter
 
PAGE_Y - Static variable in class org.biomage.tools.apps.annot.MageXMLConverter
 
PagePanel - Class in org.biomage.tools.apps.annot
 
PagePanel() - Constructor for class org.biomage.tools.apps.annot.PagePanel
 
PageRecord - Class in org.biomage.tools.apps.annot.data
 
PageRecord(String[], Hashtable) - Constructor for class org.biomage.tools.apps.annot.data.PageRecord
 
param(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
paramData - Variable in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
Parameter - Class in org.biomage.Protocol
A Parameter is a replaceable value in a Parameterizable class.
Parameter() - Constructor for class org.biomage.Protocol.Parameter
Default constructor.
Parameter(Attributes) - Constructor for class org.biomage.Protocol.Parameter
Attribute constructor.
ParameterAddAction - Class in gov.nih.nci.caarray.ui.protocol
 
ParameterAddAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
ParameterAddForm - Class in gov.nih.nci.caarray.ui.protocol
 
ParameterAddForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
ParameterData - Class in gov.nih.nci.caarray.common.data.protocol
 
ParameterData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
Parameterizable - Class in org.biomage.Protocol
The Parameterizable interface encapsulates the association of Parameters with ParameterValues.
Parameterizable() - Constructor for class org.biomage.Protocol.Parameterizable
Default constructor.
Parameterizable(Attributes) - Constructor for class org.biomage.Protocol.Parameterizable
Attribute constructor.
ParameterizableApplication - Class in org.biomage.Protocol
The interface that is the use of a Parameterizable class.
ParameterizableApplication() - Constructor for class org.biomage.Protocol.ParameterizableApplication
Default constructor.
ParameterizableApplication(Attributes) - Constructor for class org.biomage.Protocol.ParameterizableApplication
Attribute constructor.
ParameterizableApplicationData - Class in gov.nih.nci.caarray.common.data.protocol
 
ParameterizableApplicationData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData
 
parameters - Variable in class org.biomage.BQS.BibliographicReference
Criteria that can be used to look up the reference in a repository.
parameterType - Variable in class org.biomage.Protocol.ParameterValue
The parameter this value is for.
parameterTypes - Variable in class org.biomage.Protocol.Parameterizable
The description of the parameters for the Parameterizable class instance.
ParameterValue - Class in org.biomage.Protocol
The value of a Parameter.
ParameterValue() - Constructor for class org.biomage.Protocol.ParameterValue
Default constructor.
ParameterValue(Attributes) - Constructor for class org.biomage.Protocol.ParameterValue
Attribute constructor.
ParameterValueData - Class in gov.nih.nci.caarray.common.data.protocol
 
ParameterValueData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
parameterValues - Variable in class org.biomage.Protocol.ParameterizableApplication
The parameter values for this Parameterizable Application.
paramInfos - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
 
parent - Variable in class org.biomage.AuditAndSecurity.Organization
The containing organization (the university or business which a lab belongs to, etc.)
parent - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
 
parents - Variable in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
parents_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
parse(SequenceInputFile) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.GenePixGALFileHeaderParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.UCSFSpotFileHeaderParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.AffyCelFileParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.AffyChpFileParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayDelimitedFileParser
 
parse(SequenceInputFile) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
parse() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
parse(String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
parseArgs(String) - Static method in class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
 
parseArgs(String, String) - Static method in class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
 
parseArgs(String) - Static method in class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
 
parseArgs(String, String) - Static method in class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
 
parseArgs(String) - Static method in class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
 
parseArgs(String, String) - Static method in class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
 
parseArgs(String) - Static method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
 
parseArgs(String, String) - Static method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
 
parsed_ - Variable in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
ParsedFeature - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
This class is intended to be dynamically implemented
ParsedFeature(Object, Map) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
ParseException - Exception in gov.nih.nci.caarray.services.exception
This is top-most level checked exception for the microarray parsing services.
ParseException() - Constructor for exception gov.nih.nci.caarray.services.exception.ParseException
DBException constructor comment.
ParseException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.ParseException
Constructs a new ParseException with the specified detail message.
ParseException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.ParseException
 
ParseException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.ParseException
ParseException constructor comment.
parseFile() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
Run the parser
parseFile() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
Run the parser
parseFiles(String) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
parse the list of filename from the given string.
PARSER_NAME - Static variable in class org.biomage.tools.helpers.OntologyHelper
 
ParserBeanPropertiesInterface - Interface in gov.nih.nci.caarray.services.util.parse
 
ParserUtils - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
PARSING_TRANSACTION_TIMEOUT - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
ParsingBioAssay - Class in gov.nih.nci.caarray.services.fileparse
 
ParsingBioAssay() - Constructor for class gov.nih.nci.caarray.services.fileparse.ParsingBioAssay
 
ParsingDataMatrix - Interface in gov.nih.nci.caarray.services.fileparse
 
ParsingDesignElement - Interface in gov.nih.nci.caarray.services.fileparse
 
ParsingProperties - Class in gov.nih.nci.caarray.services.util.properties
 
ParsingProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.ParsingProperties
 
ParsingQuantitationType - Interface in gov.nih.nci.caarray.services.fileparse
 
ParsingSucceededFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
ParsingSucceededFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ParsingSucceededFieldMapper
 
ParsingTest - Class in gov.nih.nci.caarray.services.fileparse2.parsers.test
Testing caArray's EJB by logging in the application with a test account.
ParsingTest() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
ParsingTest(String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
PathElement - Class in gov.nih.nci.caarray.services.security.mageom
 
PathElement() - Constructor for class gov.nih.nci.caarray.services.security.mageom.PathElement
 
PathElement(String, String) - Constructor for class gov.nih.nci.caarray.services.security.mageom.PathElement
 
PathInfo - Class in gov.nih.nci.caarray.services.security.mageom
 
PathInfo() - Constructor for class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
PathInfo(int) - Constructor for class gov.nih.nci.caarray.services.security.mageom.PathInfo
 
PATHOGEN_TEST_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
pathogenTest_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
PBLifeCycleAdapter - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleAdapter() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
PBLifeCycleListenerAbstractClassPKPersistence - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleListenerAbstractClassPKPersistence() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerAbstractClassPKPersistence
 
PBLifeCycleListenerCompoundResolver - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleListenerCompoundResolver() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerCompoundResolver
 
PBLifeCycleListenerDescriptorModifier - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleListenerDescriptorModifier() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerDescriptorModifier
 
PBLifeCycleListenerMAGEIdentifierAssigner - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleListenerMAGEIdentifierAssigner() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerMAGEIdentifierAssigner
 
PBLifeCycleListenerOntologyEntryResolver - Class in gov.nih.nci.caarray.services.util.ojb
 
PBLifeCycleListenerOntologyEntryResolver() - Constructor for class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleListenerOntologyEntryResolver
 
PCData - Interface in org.biomage.tools.xmlutils
 
PCDataImpl - Class in org.biomage.tools.xmlutils
 
PCDataImpl() - Constructor for class org.biomage.tools.xmlutils.PCDataImpl
Creates a new instance of PCData
pcDataStack - Variable in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
pcDataStack - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
PeopleSearchAction - Class in gov.nih.nci.caarray.ui.contact
 
PeopleSearchAction() - Constructor for class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
PeopleSearchForm - Class in gov.nih.nci.caarray.ui.contact
 
PeopleSearchForm() - Constructor for class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
percent_vol_per_vol - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
percent_weight_per_vol - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
percent_weight_per_weight - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
perform(ComponentContext, HttpServletRequest, HttpServletResponse, ServletContext) - Method in class gov.nih.nci.caarray.ui.core.TilesController
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.ContactsAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.core.BaseAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.core.IndexAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.AddExperimentPublicationAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalQualifierAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentAdditionalUploadFilePageAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentContactPageAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDataProcessingPageAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailPageAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentImportMageMLAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewAdditionalQualifierAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewPageContinueAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentUploadAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentSearchAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.HomeAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.LoginAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.LogoutAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.PublicExperimentDetailAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.PublicSearchAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.login.RegisterAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAction
 
performAction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAdminAction
 
performer - Variable in class org.biomage.AuditAndSecurity.Audit
The contact for creating or changing the instance referred to by the Audit.
performers - Variable in class org.biomage.Protocol.ProtocolApplication
The people who performed the protocol.
PerformExperimentAdditionalUploadFileAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentAdditionalUploadFileAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentAdditionalUploadFileAction
 
PerformExperimentAddPublicationAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentAddPublicationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentAddPublicationAction
 
PerformExperimentDataProcessingAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentDataProcessingAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentDataProcessingAction
 
PerformExperimentImportMageMLAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentImportMageMLAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentImportMageMLAction
 
PerformExperimentNewAdditionalQualifierAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentNewAdditionalQualifierAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewAdditionalQualifierAction
 
PerformExperimentNewPageContinueAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentNewPageContinueAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewPageContinueAction
 
PerformExperimentSearchAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentSearchAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentSearchAction
 
PerformExperimentUploadHybridizationAction - Class in gov.nih.nci.caarray.ui.experiment
 
PerformExperimentUploadHybridizationAction() - Constructor for class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
performService() - Method in class gov.nih.nci.caarray.services.fileparse.FileParsingService
Actually perform the parsing service
performService() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalImportService
Do the parsing
PerfTest - Class in gov.nih.nci.caarray.services.mageloader.test
This class performs test of INSERT queries performance
PerfTest() - Constructor for class gov.nih.nci.caarray.services.mageloader.test.PerfTest
 
PersistArrayDesign - Class in gov.nih.nci.caarray.services.test.usecases
 
PersistArrayDesign() - Constructor for class gov.nih.nci.caarray.services.test.usecases.PersistArrayDesign
 
PersistenceBrokerManager - Class in gov.nih.nci.caarray.services.util.db
A singleton
PersistenceBrokerManagerInitializationException - Exception in gov.nih.nci.caarray.services.util.db
 
PersistenceBrokerManagerInitializationException() - Constructor for exception gov.nih.nci.caarray.services.util.db.PersistenceBrokerManagerInitializationException
 
PersistExperiment - Class in gov.nih.nci.caarray.services.test.usecases
 
PersistExperiment() - Constructor for class gov.nih.nci.caarray.services.test.usecases.PersistExperiment
 
PersistProtocol - Class in gov.nih.nci.caarray.services.test.usecases
 
PersistProtocol() - Constructor for class gov.nih.nci.caarray.services.test.usecases.PersistProtocol
 
Person - Class in org.biomage.AuditAndSecurity
A person for which the attributes are self describing.
Person() - Constructor for class org.biomage.AuditAndSecurity.Person
Default constructor.
Person(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Person
Attribute constructor.
PersonAddUpdateAction - Class in gov.nih.nci.caarray.ui.contact
 
PersonAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
PersonAddUpdateForm - Class in gov.nih.nci.caarray.ui.contact
 
PersonAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
PersonComparator - Class in gov.nih.nci.caarray.ui.core
 
PersonComparator() - Constructor for class gov.nih.nci.caarray.ui.core.PersonComparator
 
PersonData - Class in gov.nih.nci.caarray.common.data.contact
 
PersonData() - Constructor for class gov.nih.nci.caarray.common.data.contact.PersonData
 
PersonDesc - Class in gov.nih.nci.caarray.common.data.contact
 
PersonDesc() - Constructor for class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
PersonDetailAction - Class in gov.nih.nci.caarray.ui.contact
 
PersonDetailAction() - Constructor for class gov.nih.nci.caarray.ui.contact.PersonDetailAction
 
PersonDetailForm - Class in gov.nih.nci.caarray.ui.contact
 
PersonDetailForm() - Constructor for class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
PersonSearchCriteria - Class in gov.nih.nci.caarray.common.data.contact
 
PersonSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
pg - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
phenotype_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
PHENOTYPE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
phone_ - Variable in class gov.nih.nci.caarray.common.data.contact.ContactData
 
PhysicalArrayDesign - Class in org.biomage.ArrayDesign
A design that is expected to be used to manufacture physical arrays.
PhysicalArrayDesign() - Constructor for class org.biomage.ArrayDesign.PhysicalArrayDesign
Default constructor.
PhysicalArrayDesign(Attributes) - Constructor for class org.biomage.ArrayDesign.PhysicalArrayDesign
Attribute constructor.
physicalBioAssay - Variable in class org.biomage.BioAssay.BioAssayTreatment
The set of treatments undergone by this PhysicalBioAssay.
PhysicalBioAssay - Class in org.biomage.BioAssay
A bioAssay created by the bioAssayCreation event (e.g.
PhysicalBioAssay() - Constructor for class org.biomage.BioAssay.PhysicalBioAssay
Default constructor.
PhysicalBioAssay(Attributes) - Constructor for class org.biomage.BioAssay.PhysicalBioAssay
Attribute constructor.
physicalBioAssayData - Variable in class org.biomage.BioAssay.PhysicalBioAssay
The Images associated with this PhysicalBioAssay by ImageAcquisition.
physicalBioAssaySource - Variable in class org.biomage.BioAssay.FeatureExtraction
The PhysicalBioAssay used in the FeatureExtraction event.
physicalBioAssayTarget - Variable in class org.biomage.BioAssay.BioAssayCreation
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.
pl - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
PLOIDY - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ploidy_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ploidyId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
ploidys_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
pM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
pmol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
pointsToIdentifiable - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
pointsToIdentifiableClass() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Does this association point to an Identifiable class? This is a necessary question for the cPP code generation as that changes the container used underneath.
POLYMER_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
polymerType - Variable in class org.biomage.BioSequence.BioSequence
A choice of protein, RNA, or DNA.
pool(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
PoolAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
PoolAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
poolBioSamples(TreatmentData, BioSampleData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
poolBioSamples(TreatmentData, BioSampleData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Pools bioMaterials into a single biomaterial
PoolException - Exception in gov.nih.nci.caarray.services.security.db
Throws when there is a failure in JDBC Connection Pool.
PoolException() - Constructor for exception gov.nih.nci.caarray.services.security.db.PoolException
 
PoolException(String) - Constructor for exception gov.nih.nci.caarray.services.security.db.PoolException
 
PoolForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
PoolForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
POPULATION_DENSITY_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
populationDensity_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
position - Variable in class org.biomage.Array.Fiducial
The position, relative to the upper left corner, of the fiducial
position - Variable in class org.biomage.DesignElement.Feature
The position of the feature on the array, relative to the top, left corner.
Position - Class in org.biomage.DesignElement
Specifies a position on an array.
Position() - Constructor for class org.biomage.DesignElement.Position
Default constructor.
Position(Attributes) - Constructor for class org.biomage.DesignElement.Position
Attribute constructor.
positionDelta - Variable in class org.biomage.Array.FeatureDefect
How the feature deviates in position from the ArrayDesign.
PositionDelta - Class in org.biomage.Array
The delta the feature was actually printed on the array from the position specified for the feature in the array design.
PositionDelta() - Constructor for class org.biomage.Array.PositionDelta
Default constructor.
PositionDelta(Attributes) - Constructor for class org.biomage.Array.PositionDelta
Attribute constructor.
positionDelta - Variable in class org.biomage.Array.ZoneDefect
How the zone deviates in position from the ArrayDesign.
postconditions - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
 
preconditions - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
 
prependItemToArray(String, String[]) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
Inserts the specified item at the head of the array.
prepForApplyProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
 
PresentAbsent - Class in org.biomage.QuantitationType
Indicates relative presence or absence.
PresentAbsent() - Constructor for class org.biomage.QuantitationType.PresentAbsent
Default constructor.
PresentAbsent(Attributes) - Constructor for class org.biomage.QuantitationType.PresentAbsent
Attribute constructor.
previous(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewPageContinueAction
 
PRIMARY_KEY - Static variable in class org.biomage.tools.generate_er.CreateMageER
full name of the primary key for tables
PRIMARY_PATH_DELIMITER - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
PrimaryInfo - Class in gov.nih.nci.caarray.services.security.mageom
 
PrimaryInfo() - Constructor for class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
PrimaryInfo(String, String) - Constructor for class gov.nih.nci.caarray.services.security.mageom.PrimaryInfo
 
PrimaryKey - Class in org.biomage.tools.generate_er
 
PrimaryKey() - Constructor for class org.biomage.tools.generate_er.PrimaryKey
Description: Constructor for the PrimaryKey object.
PrimaryKey(DataColumn) - Constructor for class org.biomage.tools.generate_er.PrimaryKey
Description: Constructor for the PrimaryKey object.
print(int) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
printCPPClassFile(CreateFile, String, String, File, String, String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: From the parsed information creates the file itself.
printCPPClassImpl(CreateFile, String, String, File, String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: This Method creates the CPP implementation file.
printInstances(int) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
printJavaClassFile(String, String, File) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: From the parsed information creates the file itself.
printJavaClassFile(String, String, File) - Method in class org.biomage.tools.generate_java.CreateJavaMAGEFile
Description: From the parsed information creates the file itself.
printOutArray(Object[][][]) - Static method in class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
 
printProperties(int) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
printProtocol(Protocol) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
printProtocolData(ProtocolData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
PRIVATE_VISIBILITY - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
process(long) - Method in class gov.nih.nci.caarray.services.fileparse2.ArrayDesignFileParsingService
 
process(long, String) - Method in class gov.nih.nci.caarray.services.fileparse2.ArrayDesignFileParsingService
 
process(long, boolean) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationFileParsingService
 
process(long, boolean, String) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationFileParsingService
 
processArrayDesignFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.FileParserDelegate
 
ProcessBatchFileDownload - Class in gov.nih.nci.caarray.services.util.file
 
ProcessBatchFileDownload() - Constructor for class gov.nih.nci.caarray.services.util.file.ProcessBatchFileDownload
 
ProcessDuplicatedFileName - Class in gov.nih.nci.caarray.services.util.httpfileuploadapplet
 
ProcessDuplicatedFileName(String[], ArrayList) - Constructor for class gov.nih.nci.caarray.services.util.httpfileuploadapplet.ProcessDuplicatedFileName
Construct the frame
ProcessFetchFileList - Class in gov.nih.nci.caarray.services.util.file
 
ProcessFetchFileList() - Constructor for class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList
 
processFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignFileProcessAction
This method deals with the requests from the upload applet as a notify operation.
processFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileProcessAction
This method deals with the requests from the upload applet as a notify operation.
ProcessFileUpload - Class in gov.nih.nci.caarray.services.util.file
This servlet is called up by the HttpFileUploadApplet to process files that are sent from the client machines.
ProcessFileUpload() - Constructor for class gov.nih.nci.caarray.services.util.file.ProcessFileUpload
 
processHybridizationFileUploadGroup(long) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.FileParserDelegate
 
PROCESSING - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
PROCESSING - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
PROCESSING - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
PROCESSING - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
PROCESSING_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
PROCESSING_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
PROCESSING_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
PROCESSING_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
PROCESSING_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
PROCESSING_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
PROCESSING_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
PROCESSING_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
processingInstruction(String, String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
processingInstruction(String, String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
processWindowEvent(WindowEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
Overridden so we can exit when window is closed
processWindowEvent(WindowEvent) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.ProcessDuplicatedFileName
Overridden so we can exit when window is closed
processWindowEvent(WindowEvent) - Method in class gov.nih.nci.caarray.ui.experiment.UploadApplet
Overridden so we can exit when window is closed
producerTransformation - Variable in class org.biomage.BioAssayData.DerivedBioAssayData
The association between the DerivedBioAssayData and the Transformation event that produced it.
PROFILE_CAARRAY - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
PROFILE_MAGEML_EXPORT - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
PROFILE_MAGEML_IMPORT - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
PropertiesReader - Class in gov.nih.nci.caarray.services.util.properties
 
PropertiesReader(String) - Constructor for class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
PropertiesReader(InputStream) - Constructor for class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
propertyHash_ - Variable in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
propertySets - Variable in class org.biomage.Common.NameValueType
Allows nested specification of name/value pairs
propInStream_ - Variable in class gov.nih.nci.caarray.services.util.properties.PropertiesReader
 
PROTECTION_GROUP_PRIVATE - Static variable in class gov.nih.nci.caarray.services.util.SecurityUtils
 
PROTECTION_GROUP_PUBLIC - Static variable in class gov.nih.nci.caarray.services.util.SecurityUtils
 
ProtectionAppGroupElement - Class in gov.nih.nci.caarray.services.security.db
 
ProtectionAppGroupElement() - Constructor for class gov.nih.nci.caarray.services.security.db.ProtectionAppGroupElement
 
ProtectionElement - Class in gov.nih.nci.caarray.services.security.db
 
ProtectionElement() - Constructor for class gov.nih.nci.caarray.services.security.db.ProtectionElement
 
ProtectionGroupData - Class in gov.nih.nci.caarray.common.data.security
 
ProtectionGroupData() - Constructor for class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
ProtectionGroupData(long) - Constructor for class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
protectionGroups_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
Protocol - Class in org.biomage.Protocol
A Protocol is a parameterizable description of a method.
Protocol() - Constructor for class org.biomage.Protocol.Protocol
Default constructor.
Protocol(Attributes) - Constructor for class org.biomage.Protocol.Protocol
Attribute constructor.
protocol - Variable in class org.biomage.Protocol.ProtocolApplication
The protocol that is being used.
PROTOCOL_ARRAY_MANUF - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PROTOCOL_DATA_TRANSFORMATION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PROTOCOL_FEATURE_EXTRACTION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PROTOCOL_HIGH_LEVEL_ANALYSIS - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PROTOCOL_HYBRIDIZATION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PROTOCOL_IMAGE_ACQUISITION - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
protocol_list - Variable in class org.biomage.Protocol.Protocol_package
A Protocol is a parameterizable description of a method.
PROTOCOL_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
protocol_package - Variable in class org.biomage.Common.MAGEJava
Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.
Protocol_package - Class in org.biomage.Protocol
Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol.
Protocol_package() - Constructor for class org.biomage.Protocol.Protocol_package
Default constructor.
Protocol_package(Attributes) - Constructor for class org.biomage.Protocol.Protocol_package
Attribute constructor.
Protocol_package.Hardware_list - Class in org.biomage.Protocol
Inner list class for holding multiple entries for attribute hardware.
Protocol_package.Hardware_list() - Constructor for class org.biomage.Protocol.Protocol_package.Hardware_list
 
Protocol_package.Protocol_list - Class in org.biomage.Protocol
Inner list class for holding multiple entries for attribute protocol.
Protocol_package.Protocol_list() - Constructor for class org.biomage.Protocol.Protocol_package.Protocol_list
 
Protocol_package.Software_list - Class in org.biomage.Protocol
Inner list class for holding multiple entries for attribute software.
Protocol_package.Software_list() - Constructor for class org.biomage.Protocol.Protocol_package.Software_list
 
PROTOCOL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ProtocolAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolAction
 
ProtocolActionMappingsAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolActionMappingsAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolActionMappingsAction
 
ProtocolActionMappingsForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolActionMappingsForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolActionMappingsForm
 
ProtocolAddUpdateAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
ProtocolAddUpdateForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
ProtocolApplication - Class in org.biomage.Protocol
The use of a protocol with the requisite Parameters and ParameterValues.
ProtocolApplication() - Constructor for class org.biomage.Protocol.ProtocolApplication
Default constructor.
ProtocolApplication(Attributes) - Constructor for class org.biomage.Protocol.ProtocolApplication
Attribute constructor.
ProtocolApplicationAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolApplicationAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
ProtocolApplicationData - Class in gov.nih.nci.caarray.common.data.protocol
 
ProtocolApplicationData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
ProtocolApplicationFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
This class forces overwriting of a target ProtocolApplication with the source ProtocolApplicationData since the conversion is only intended for adding a new ProtocolApplication.
ProtocolApplicationFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProtocolApplicationFieldMapper
 
ProtocolApplicationForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolApplicationForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
ProtocolApplicationPerformerFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
ProtocolApplicationPerformerFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProtocolApplicationPerformerFieldMapper
 
protocolApplications - Variable in class org.biomage.Array.ArrayManufacture
The protocols followed in the manufacturing of the arrays.
protocolApplications - Variable in class org.biomage.ArrayDesign.ArrayDesign
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
ProtocolBaseForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolBaseForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
ProtocolData - Class in gov.nih.nci.caarray.common.data.protocol
 
ProtocolData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
ProtocolDesc - Class in gov.nih.nci.caarray.common.data.protocol
 
ProtocolDesc() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
ProtocolDetailAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolDetailAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
ProtocolDetailForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolDetailForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
protocolId_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
ProtocolManagerAddTest - Class in gov.nih.nci.caarray.services.protocol.test
 
ProtocolManagerAddTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerAddTest
Constructor for ProtocolManagerDelegateTest.
ProtocolManagerDB - Class in gov.nih.nci.caarray.services.protocol
 
ProtocolManagerDB() - Constructor for class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Default Constructor
ProtocolManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
ProtocolManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
ProtocolManagerEJB - Class in gov.nih.nci.caarray.services.protocol.ejb
ProtocolManagerEJB
ProtocolManagerEJB() - Constructor for class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
ProtocolManagerGetTest - Class in gov.nih.nci.caarray.services.protocol.test
 
ProtocolManagerGetTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerGetTest
Constructor for ProtocolManagerDelegateTest.
ProtocolManagerParameterAddTest - Class in gov.nih.nci.caarray.services.protocol.test
 
ProtocolManagerParameterAddTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerParameterAddTest
Constructor for ProtocolManagerParameterAddTest.
ProtocolManagerUpdateTest - Class in gov.nih.nci.caarray.services.protocol.test
 
ProtocolManagerUpdateTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerUpdateTest
Constructor for ProtocolManagerDelegateTest.
ProtocolSearchAction - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolSearchAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
ProtocolSearchCriteria - Class in gov.nih.nci.caarray.common.data.protocol
 
ProtocolSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
ProtocolSearchForm - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolSearchForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
protocolTypeId_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
protocolTypeName_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
protocolTypes_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
ProtocolUIUtils - Class in gov.nih.nci.caarray.ui.protocol
 
ProtocolUIUtils() - Constructor for class gov.nih.nci.caarray.ui.protocol.ProtocolUIUtils
 
ProtocolUtils - Class in gov.nih.nci.caarray.services.protocol
 
provider - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
ProviderFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
ProviderFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.ProviderFieldMapper
 
providerRoles - Variable in class org.biomage.Experiment.Experiment
The providers of the Experiment that have a role which describes how he/she contributes the experiment, e.g.
prune() - Method in class org.biomage.tools.helpers.MGEDOntologyClassEntry
 
prune() - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
prune() - Method in class org.biomage.tools.helpers.MGEDOntologyPropertyEntry
 
PUBLIC_GROUP - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
PUBLICATION_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
PublicationData - Class in gov.nih.nci.caarray.common.data.experiment
 
PublicationData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
PublicExperimentDetailAction - Class in gov.nih.nci.caarray.ui.login
 
PublicExperimentDetailAction() - Constructor for class gov.nih.nci.caarray.ui.login.PublicExperimentDetailAction
 
PublicSearchAction - Class in gov.nih.nci.caarray.ui.login
 
PublicSearchAction() - Constructor for class gov.nih.nci.caarray.ui.login.PublicSearchAction
 
publish(String, Message) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
publish(String, Message) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
purgeMap(int) - Static method in class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
To remove items stored in the map after a certain period of time as specified by the passed in days.
put(Object, Object) - Method in class gov.nih.nci.caarray.services.util.cache.CaArrayCache
 
put(Object, Object) - Method in class gov.nih.nci.caarray.services.util.cache.CaArrayCache2
makes object obj persistent to the Objectcache under the key.
put(Object, Object) - Method in class org.biomage.tools.xmlutils.MultiHashMap
Note that this method will always return null.
put(Object, Object) - Method in class org.biomage.tools.xmlutils.MultiHashtable
Note that this method will always return null.
putObjectInCache(Object) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
putQuantitationTypeNameJavaPropertyNameMapping(String, String) - Method in class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
PValue - Class in org.biomage.QuantitationType
Measurement of the accuracy of a quantitation.
PValue() - Constructor for class org.biomage.QuantitationType.PValue
Default constructor.
PValue(Attributes) - Constructor for class org.biomage.QuantitationType.PValue
Attribute constructor.

Q

QBD - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
QDB - Variable in class org.biomage.BioAssayData.BioDataCube.Order
 
QUALITY_CONTROL_DESCRIPTION_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
QualityControlData - Class in gov.nih.nci.caarray.common.data.experiment
 
QualityControlData() - Constructor for class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
qualityControlDescription - Variable in class org.biomage.Experiment.ExperimentDesign
Description of the quality control aspects of the Experiment.
qualityControlStatistics - Variable in class org.biomage.Array.ArrayManufacture
Information on the quality of the ArrayManufacture.
qualityControlStatistics - Variable in class org.biomage.BioMaterial.BioMaterial
Measures of the quality of the BioMaterial.
quantitationDimension - Variable in class org.biomage.HigherLevelAnalysis.NodeContents
The relevant QuantitationTypes for this NodeContents from the BioAssayData.
QuantitationNamesProperties - Class in gov.nih.nci.caarray.services.util.properties
 
QuantitationNamesProperties() - Constructor for class gov.nih.nci.caarray.services.util.properties.QuantitationNamesProperties
 
quantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeTuple
The QuantitationType associated with the value of the BioAssayDatum.
QuantitationType - Class in org.biomage.QuantitationType
A method for calculating a single datum of the matrix (e.g.
QuantitationType() - Constructor for class org.biomage.QuantitationType.QuantitationType
Default constructor.
QuantitationType(Attributes) - Constructor for class org.biomage.QuantitationType.QuantitationType
Attribute constructor.
quantitationType_list - Variable in class org.biomage.QuantitationType.QuantitationType_package
A method for calculating a single datum of the matrix (e.g.
quantitationType_package - Variable in class org.biomage.Common.MAGEJava
This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue.
QuantitationType_package - Class in org.biomage.QuantitationType
This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue.
QuantitationType_package() - Constructor for class org.biomage.QuantitationType.QuantitationType_package
Default constructor.
QuantitationType_package(Attributes) - Constructor for class org.biomage.QuantitationType.QuantitationType_package
Attribute constructor.
QuantitationType_package.QuantitationType_list - Class in org.biomage.QuantitationType
Inner list class for holding multiple entries for attribute quantitationType.
QuantitationType_package.QuantitationType_list() - Constructor for class org.biomage.QuantitationType.QuantitationType_package.QuantitationType_list
 
QuantitationTypeColumnsMap - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
QuantitationTypeColumnsMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.QuantitationTypeColumnsMap
 
QuantitationTypeDescriptor - Enum in gov.nih.nci.caarray.services.bioassaydata.descriptor
Enumeration (and descriptions) of all QuantitationTypes handled by the system.
quantitationTypeDimension - Variable in class org.biomage.BioAssayData.BioAssayData
The QuantitationTypes of the BioAssayData.
QuantitationTypeDimension - Class in org.biomage.BioAssayData
An ordered list of quantitationTypes.
QuantitationTypeDimension() - Constructor for class org.biomage.BioAssayData.QuantitationTypeDimension
Default constructor.
QuantitationTypeDimension(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeDimension
Attribute constructor.
quantitationTypeDimension_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
An ordered list of quantitationTypes.
QuantitationTypeFinder - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
Service quantitation types
QuantitationTypeFinder() - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.QuantitationTypeFinder
 
QuantitationTypeManagerDB - Class in gov.nih.nci.caarray.services.fileparse2
 
QuantitationTypeManagerDB() - Constructor for class gov.nih.nci.caarray.services.fileparse2.QuantitationTypeManagerDB
Default Constructor
QuantitationTypeMap - Class in org.biomage.BioAssayData
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
QuantitationTypeMap() - Constructor for class org.biomage.BioAssayData.QuantitationTypeMap
Default constructor.
QuantitationTypeMap(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeMap
Attribute constructor.
quantitationTypeMap_list - Variable in class org.biomage.BioAssayData.BioAssayData_package
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
QuantitationTypeMapping - Class in org.biomage.BioAssayData
Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
QuantitationTypeMapping() - Constructor for class org.biomage.BioAssayData.QuantitationTypeMapping
Default constructor.
QuantitationTypeMapping(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeMapping
Attribute constructor.
quantitationTypeMapping - Variable in class org.biomage.BioAssayData.Transformation
The collection of mappings for the QuantitationTypes.
quantitationTypeMaps - Variable in class org.biomage.BioAssayData.QuantitationTypeMapping
The maps for the QuantitationTypes.
quantitationTypeMaps - Variable in class org.biomage.QuantitationType.QuantitationType
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
QuantitationTypeName2JavaPropertyNameMap - Class in gov.nih.nci.caarray.services.fileparse2.util
This class allows a quantitation name to be translated to a valid Java simple property.
QuantitationTypeName2JavaPropertyNameMap() - Constructor for class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
quantitationTypeName2JavaPropertyNameMap_ - Static variable in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
 
quantitationTypes - Variable in class org.biomage.BioAssayData.QuantitationTypeDimension
The QuantitationTypes for this Dimension.
QuantitationTypeService - Interface in gov.nih.nci.caarray.services.fileparse
 
QuantitationTypeServiceFactory - Class in gov.nih.nci.caarray.services.fileparse
 
QuantitationTypeServiceFactory() - Constructor for class gov.nih.nci.caarray.services.fileparse.QuantitationTypeServiceFactory
 
QuantitationTypeTuple - Class in org.biomage.BioAssayData
Transformed container to specify a Quantitation Type and the value for that Type.
QuantitationTypeTuple() - Constructor for class org.biomage.BioAssayData.QuantitationTypeTuple
Default constructor.
QuantitationTypeTuple(Attributes) - Constructor for class org.biomage.BioAssayData.QuantitationTypeTuple
Attribute constructor.
quantity - Variable in class org.biomage.Measurement.Measurement.KindCV
 
QuantityUnit - Class in org.biomage.Measurement
Quantity
QuantityUnit() - Constructor for class org.biomage.Measurement.QuantityUnit
Default constructor.
QuantityUnit(Attributes) - Constructor for class org.biomage.Measurement.QuantityUnit
Attribute constructor.
QuantityUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
query(String) - Static method in class gov.nih.nci.caarray.services.security.db.SecurityDSConnectionUtil
 
QueryCustomizerExcludingObjectsMarkedAsDeleted - Class in gov.nih.nci.caarray.services.util.ojb
 
QueryCustomizerExcludingObjectsMarkedAsDeleted() - Constructor for class gov.nih.nci.caarray.services.util.ojb.QueryCustomizerExcludingObjectsMarkedAsDeleted
 
QUEUE_CONN_FACTORY - Static variable in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
QUEUE_NAME - Static variable in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
QUEUE_NAME - Static variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
QUEUE_NAME - Static variable in class gov.nih.nci.caarray.services.security.mageom.SecuredElementUpdateListener
 
quote(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 

R

rank - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
Ratio - Class in org.biomage.QuantitationType
The ratio of two or more signals, typically between two channels.
Ratio() - Constructor for class org.biomage.QuantitationType.Ratio
Default constructor.
Ratio(Attributes) - Constructor for class org.biomage.QuantitationType.Ratio
Attribute constructor.
RdbmsAuthenticationDAObj - Class in gov.nih.nci.caarray.services.security
This authentication data service class is a local implementation of AuthenticationDAItf using SPOREs database schema and RDBMS as data repository.
RdbmsAuthenticationDAObj() - Constructor for class gov.nih.nci.caarray.services.security.RdbmsAuthenticationDAObj
Constructor for a new LdapAuthenticationDAObj object.
RdbmsAuthorizationDAObj - Class in gov.nih.nci.caarray.services.security
This authorization data service class is a local implementation of AuthorizationDAItf using the common security RDBMS as the data repository.
RdbmsAuthorizationDAObj() - Constructor for class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
Constructor for a new RdbmsAuthorizationDAObj object.
read() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
read(byte[]) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
read(byte[], int, int) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
readExternalDataCubeFromFile(int, int, int, String) - Static method in class gov.nih.nci.caarray.services.mageloader.CustomDataCubeIOHelpers
Description: Method for reading a text file formatted and written by the saveExternalDataCubeToFile method.
readExternalDataCubeFromFile(int, int, int, String) - Static method in class org.biomage.tools.helpers.ExternalDataCubeIOHelpers
Description: Method for reading a text file formatted and written by the saveExternalDataCubeToFile method.
readFile(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
readLine(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
Read a line
readLine(String) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
read a line
readLineWithMessage(String) - Method in class gov.nih.nci.caarray.services.fileparse.test.usecases.AbstractUseCase
Deprecated. Used for interactive command prompt
readLineWithMessage(String) - Method in class gov.nih.nci.caarray.services.security.test.usecases.AbstractUseCase
Deprecated. Used for interactive command prompt
readLineWithMessage(String) - Method in class gov.nih.nci.caarray.services.test.usecases.AbstractUseCase
Deprecated. Used for interactive command prompt
readLineWithMessage(String) - Method in class gov.nih.nci.caarray.services.util.netcdf.test.usecases.AbstractUseCase
Deprecated. Used for interactive command prompt
readObjectArrayFrom(ResultSet, Map) - Method in class gov.nih.nci.caarray.services.util.ojb.RowReaderUnit
 
readPkValuesFrom(ResultSet, Map) - Method in class gov.nih.nci.caarray.services.util.ojb.RowReaderBioSequence
 
readRows() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
 
ReadZipFileContent - Class in gov.nih.nci.caarray.services.util.file
 
ReadZipFileContent() - Constructor for class gov.nih.nci.caarray.services.util.file.ReadZipFileContent
default constructor
ref(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
ReflectAccess - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
Simple example of program using reflection.
ReflectAccess() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.ReflectAccess
 
regions - Variable in class org.biomage.BioSequence.SeqFeature
Association to classes that describe the location with the sequence of the SeqFeature.
RegisterAction - Class in gov.nih.nci.caarray.ui.login
 
RegisterAction() - Constructor for class gov.nih.nci.caarray.ui.login.RegisterAction
 
registerArrayDesignFileTypeGroupMapping(String, List) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
registerDataSetMapper(String, DataSetMapper) - Method in class gov.nih.nci.caarray.services.fileparse2.util.DataSetMapperMap
 
RegisterForm - Class in gov.nih.nci.caarray.ui.login
 
RegisterForm() - Constructor for class gov.nih.nci.caarray.ui.login.RegisterForm
 
registerHybridizationFileTypeGroupMapping(String, List) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
registerSubClassName(CreateFile, Map, boolean) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Called to add a subclass name to the vector.
registerWithBaseClass(Map) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: If the class is a subclass, registers with its base class.
REGISTRATION_EMAIL - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
REGISTRATION_EMAIL_SUBJECT - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
RELATIVE - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
releaseConnection() - Method in class org.biomage.tools.helpers.JDBCConnection2
 
releaseDate_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
reloadArrayDesign(ArrayDesignDesc, int) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
reloadArrayDesign(ArrayDesignDesc, int) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Reloads design information for the given array design.
reloadArrayDesign(ArrayDesignDesc, int) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Reloads design information for existing array designs.
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.AffymetrixArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGalArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGprArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGalArrayDesignLoader
 
reloadArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprArrayDesignLoader
 
reloadDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
reloadDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
REMAINDER - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
REMOTE - Static variable in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
 
REMOTE - Static variable in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
 
REMOTE_MODE - Static variable in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
REMOTE_MODE - Static variable in class gov.nih.nci.caarray.services.security.test.Tester
 
REMOTE_MODE - Static variable in class gov.nih.nci.caarray.services.test.Tester
 
REMOTE_MODE - Static variable in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
remove(Identity) - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
removes an Object from the cache.
remove(File) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
Removes a file from SelectedFiles.
remove(Object) - Static method in class gov.nih.nci.caarray.services.util.properties.HttpFileProperties
 
remove(Object, Object) - Method in class org.biomage.tools.xmlutils.MultiHashMap
Remove the given ( key, value ) pair from this MultiMap.
remove(Object, Object) - Method in class org.biomage.tools.xmlutils.MultiHashtable
Remove the given ( key, value ) pair from this MultiMap.
remove(Object, Object) - Method in interface org.biomage.tools.xmlutils.MultiMap
Remove the given ( key, value ) pair from this MultiMap.
removeAdditionalQualifier(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeAdditionalUploadFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeAll(Object) - Method in class org.biomage.tools.xmlutils.MultiHashMap
Remove all references to an Object (all values and a key, if any).
removeAll(Object) - Method in class org.biomage.tools.xmlutils.MultiHashtable
Remove all references to an Object (all values and a key, if any).
removeAll(Object) - Method in interface org.biomage.tools.xmlutils.MultiMap
Remove all references to an Object (all values and a key, if any).
removeCompositeGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Remove the specified CompositeGroup from the specified ArrayDesign.
removeCompositeGroupFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
removeDataProcessData(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeDesignElements(ArrayDesignDesc, int) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
removeDesignElements(ArrayDesignDesc, int) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Removes the design elements associated with an array design in preparation for reloading.
removeDesignElements(ArrayDesignDesc, int) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Removes the design elements associated with an array design in preparation for reloading.
removeDesignElements(PhysicalArrayDesign) - Static method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignCleaner
 
removeDesignProvider(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
removeDesignProviderFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
removeDesignProviderFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
removeElementAtFromAccessions(int) - Method in class org.biomage.BQS.BibliographicReference
Method to remove by position from Accessions_list
removeElementAtFromAccessions(int) - Method in interface org.biomage.Interface.HasAccessions
Method to remove by position from Accessions_list
removeElementAtFromAdjustments(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove by position from Adjustments_list
removeElementAtFromAdjustments(int) - Method in interface org.biomage.Interface.HasAdjustments
Method to remove by position from Adjustments_list
removeElementAtFromAnalysisResults(int) - Method in class org.biomage.Experiment.Experiment
Method to remove by position from AnalysisResults_list
removeElementAtFromAnalysisResults(int) - Method in interface org.biomage.Interface.HasAnalysisResults
Method to remove by position from AnalysisResults_list
removeElementAtFromAnnotations(int) - Method in class org.biomage.Description.Description
Method to remove by position from Annotations_list
removeElementAtFromAnnotations(int) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to remove by position from Annotations_list
removeElementAtFromAnnotations(int) - Method in interface org.biomage.Interface.HasAnnotations
Method to remove by position from Annotations_list
removeElementAtFromArray_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from Array_list
removeElementAtFromArrayDesign_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove by position from ArrayDesign_list
removeElementAtFromArrayGroup_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from ArrayGroup_list
removeElementAtFromArrayManufacture_list(int) - Method in class org.biomage.Array.Array_package
Method to remove by position from ArrayManufacture_list
removeElementAtFromArrayManufactureDeviations(int) - Method in class org.biomage.Array.Array
Method to remove by position from ArrayManufactureDeviations_list
removeElementAtFromArrayManufactureDeviations(int) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Method to remove by position from ArrayManufactureDeviations_list
removeElementAtFromArrayManufacturers(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from ArrayManufacturers_list
removeElementAtFromArrayManufacturers(int) - Method in interface org.biomage.Interface.HasArrayManufacturers
Method to remove by position from ArrayManufacturers_list
removeElementAtFromArrays(int) - Method in class org.biomage.Array.ArrayGroup
Method to remove by position from Arrays_list
removeElementAtFromArrays(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from Arrays_list
removeElementAtFromArrays(int) - Method in interface org.biomage.Interface.HasArrays
Method to remove by position from Arrays_list
removeElementAtFromAssociations(int) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Method to remove by position from Associations_list
removeElementAtFromAssociations(int) - Method in class org.biomage.Description.OntologyEntry
Method to remove by position from Associations_list
removeElementAtFromAssociations(int) - Method in interface org.biomage.Interface.HasAssociations
Method to remove by position from Associations_list
removeElementAtFromAuditTrail(int) - Method in class org.biomage.Common.Describable
Method to remove by position from AuditTrail_list
removeElementAtFromAuditTrail(int) - Method in interface org.biomage.Interface.HasAuditTrail
Method to remove by position from AuditTrail_list
removeElementAtFromBibliographicReferences(int) - Method in class org.biomage.Description.Description
Method to remove by position from BibliographicReferences_list
removeElementAtFromBibliographicReferences(int) - Method in interface org.biomage.Interface.HasBibliographicReferences
Method to remove by position from BibliographicReferences_list
removeElementAtFromBioAssay_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
Method to remove by position from BioAssay_list
removeElementAtFromBioAssayData(int) - Method in class org.biomage.Experiment.Experiment
Method to remove by position from BioAssayData_list
removeElementAtFromBioAssayData(int) - Method in interface org.biomage.Interface.HasBioAssayData
Method to remove by position from BioAssayData_list
removeElementAtFromBioAssayData_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from BioAssayData_list
removeElementAtFromBioAssayDataCluster_list(int) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Method to remove by position from BioAssayDataCluster_list
removeElementAtFromBioAssayDataSources(int) - Method in class org.biomage.BioAssayData.Transformation
Method to remove by position from BioAssayDataSources_list
removeElementAtFromBioAssayDataSources(int) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Method to remove by position from BioAssayDataSources_list
removeElementAtFromBioAssayDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from BioAssayDimension_list
removeElementAtFromBioAssayFactorValues(int) - Method in class org.biomage.BioAssay.BioAssay
Method to remove by position from BioAssayFactorValues_list
removeElementAtFromBioAssayFactorValues(int) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Method to remove by position from BioAssayFactorValues_list
removeElementAtFromBioAssayMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from BioAssayMap_list
removeElementAtFromBioAssayMaps(int) - Method in class org.biomage.BioAssayData.BioAssayMapping
Method to remove by position from BioAssayMaps_list
removeElementAtFromBioAssayMaps(int) - Method in interface org.biomage.Interface.HasBioAssayMaps
Method to remove by position from BioAssayMaps_list
removeElementAtFromBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayDimension
Method to remove by position from BioAssays_list
removeElementAtFromBioAssays(int) - Method in class org.biomage.Experiment.Experiment
Method to remove by position from BioAssays_list
removeElementAtFromBioAssays(int) - Method in interface org.biomage.Interface.HasBioAssays
Method to remove by position from BioAssays_list
removeElementAtFromBioAssayTreatments(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to remove by position from BioAssayTreatments_list
removeElementAtFromBioAssayTreatments(int) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Method to remove by position from BioAssayTreatments_list
removeElementAtFromBioAssayTuples(int) - Method in class org.biomage.BioAssayData.BioDataTuples
Method to remove by position from BioAssayTuples_list
removeElementAtFromBioAssayTuples(int) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Method to remove by position from BioAssayTuples_list
removeElementAtFromBiologicalCharacteristics(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove by position from BiologicalCharacteristics_list
removeElementAtFromBiologicalCharacteristics(int) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Method to remove by position from BiologicalCharacteristics_list
removeElementAtFromBioMaterial_list(int) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to remove by position from BioMaterial_list
removeElementAtFromBioSequence_list(int) - Method in class org.biomage.BioSequence.BioSequence_package
Method to remove by position from BioSequence_list
removeElementAtFromChannel_list(int) - Method in class org.biomage.BioAssay.BioAssay_package
Method to remove by position from Channel_list
removeElementAtFromChannels(int) - Method in class org.biomage.BioAssay.BioAssay
Method to remove by position from Channels_list
removeElementAtFromChannels(int) - Method in class org.biomage.BioAssay.Image
Method to remove by position from Channels_list
removeElementAtFromChannels(int) - Method in interface org.biomage.Interface.HasChannels
Method to remove by position from Channels_list
removeElementAtFromCharacteristics(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove by position from Characteristics_list
removeElementAtFromCharacteristics(int) - Method in interface org.biomage.Interface.HasCharacteristics
Method to remove by position from Characteristics_list
removeElementAtFromComponentCompounds(int) - Method in class org.biomage.BioMaterial.Compound
Method to remove by position from ComponentCompounds_list
removeElementAtFromComponentCompounds(int) - Method in interface org.biomage.Interface.HasComponentCompounds
Method to remove by position from ComponentCompounds_list
removeElementAtFromCompositeCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove by position from CompositeCompositeMap_list
removeElementAtFromCompositeCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove by position from CompositeCompositeMaps_list
removeElementAtFromCompositeCompositeMaps(int) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Method to remove by position from CompositeCompositeMaps_list
removeElementAtFromCompositeGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove by position from CompositeGroup_list
removeElementAtFromCompositeGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove by position from CompositeGroups_list
removeElementAtFromCompositeGroups(int) - Method in interface org.biomage.Interface.HasCompositeGroups
Method to remove by position from CompositeGroups_list
removeElementAtFromCompositePositionSources(int) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Method to remove by position from CompositePositionSources_list
removeElementAtFromCompositePositionSources(int) - Method in interface org.biomage.Interface.HasCompositePositionSources
Method to remove by position from CompositePositionSources_list
removeElementAtFromCompositeSequence_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove by position from CompositeSequence_list
removeElementAtFromCompositeSequences(int) - Method in class org.biomage.ArrayDesign.CompositeGroup
Method to remove by position from CompositeSequences_list
removeElementAtFromCompositeSequences(int) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Method to remove by position from CompositeSequences_list
removeElementAtFromCompositeSequences(int) - Method in interface org.biomage.Interface.HasCompositeSequences
Method to remove by position from CompositeSequences_list
removeElementAtFromCompound_list(int) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to remove by position from Compound_list
removeElementAtFromCompoundIndices(int) - Method in class org.biomage.BioMaterial.Compound
Method to remove by position from CompoundIndices_list
removeElementAtFromCompoundIndices(int) - Method in interface org.biomage.Interface.HasCompoundIndices
Method to remove by position from CompoundIndices_list
removeElementAtFromCompoundMeasurements(int) - Method in class org.biomage.BioMaterial.Treatment
Method to remove by position from CompoundMeasurements_list
removeElementAtFromCompoundMeasurements(int) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Method to remove by position from CompoundMeasurements_list
removeElementAtFromConfidenceIndicators(int) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Method to remove by position from ConfidenceIndicators_list
removeElementAtFromConfidenceIndicators(int) - Method in class org.biomage.QuantitationType.QuantitationType
Method to remove by position from ConfidenceIndicators_list
removeElementAtFromContact_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove by position from Contact_list
removeElementAtFromContacts(int) - Method in class org.biomage.Description.Database
Method to remove by position from Contacts_list
removeElementAtFromContacts(int) - Method in interface org.biomage.Interface.HasContacts
Method to remove by position from Contacts_list
removeElementAtFromContainedFeatures(int) - Method in class org.biomage.BioAssayData.FeatureDimension
Method to remove by position from ContainedFeatures_list
removeElementAtFromContainedFeatures(int) - Method in interface org.biomage.Interface.HasContainedFeatures
Method to remove by position from ContainedFeatures_list
removeElementAtFromControlFeatures(int) - Method in class org.biomage.DesignElement.Feature
Method to remove by position from ControlFeatures_list
removeElementAtFromControlFeatures(int) - Method in interface org.biomage.Interface.HasControlFeatures
Method to remove by position from ControlFeatures_list
removeElementAtFromControlledFeatures(int) - Method in class org.biomage.DesignElement.Feature
Method to remove by position from ControlledFeatures_list
removeElementAtFromControlledFeatures(int) - Method in interface org.biomage.Interface.HasControlledFeatures
Method to remove by position from ControlledFeatures_list
removeElementAtFromDatabase_list(int) - Method in class org.biomage.Description.Description_package
Method to remove by position from Database_list
removeElementAtFromDatabaseReferences(int) - Method in class org.biomage.Description.Description
Method to remove by position from DatabaseReferences_list
removeElementAtFromDatabaseReferences(int) - Method in interface org.biomage.Interface.HasDatabaseReferences
Method to remove by position from DatabaseReferences_list
removeElementAtFromDerivedBioAssayData(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to remove by position from DerivedBioAssayData_list
removeElementAtFromDerivedBioAssayData(int) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Method to remove by position from DerivedBioAssayData_list
removeElementAtFromDerivedBioAssayMap(int) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to remove by position from DerivedBioAssayMap_list
removeElementAtFromDerivedBioAssayMap(int) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Method to remove by position from DerivedBioAssayMap_list
removeElementAtFromDescriptions(int) - Method in class org.biomage.Common.Describable
Method to remove by position from Descriptions_list
removeElementAtFromDescriptions(int) - Method in interface org.biomage.Interface.HasDescriptions
Method to remove by position from Descriptions_list
removeElementAtFromDesignElementDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from DesignElementDimension_list
removeElementAtFromDesignElementMaps(int) - Method in class org.biomage.BioAssayData.DesignElementMapping
Method to remove by position from DesignElementMaps_list
removeElementAtFromDesignElementMaps(int) - Method in interface org.biomage.Interface.HasDesignElementMaps
Method to remove by position from DesignElementMaps_list
removeElementAtFromDesignElementTuples(int) - Method in class org.biomage.BioAssayData.BioAssayTuple
Method to remove by position from DesignElementTuples_list
removeElementAtFromDesignElementTuples(int) - Method in interface org.biomage.Interface.HasDesignElementTuples
Method to remove by position from DesignElementTuples_list
removeElementAtFromDesignProviderRoles(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
removeElementAtFromDesignProviders(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove by position from DesignProviders_list
removeElementAtFromDesignProviders(int) - Method in interface org.biomage.Interface.HasDesignProviders
Method to remove by position from DesignProviders_list
removeElementAtFromExperiment_list(int) - Method in class org.biomage.Experiment.Experiment_package
Method to remove by position from Experiment_list
removeElementAtFromExperimentalFactors(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove by position from ExperimentalFactors_list
removeElementAtFromExperimentalFactors(int) - Method in interface org.biomage.Interface.HasExperimentalFactors
Method to remove by position from ExperimentalFactors_list
removeElementAtFromExperimentDesigns(int) - Method in class org.biomage.Experiment.Experiment
Method to remove by position from ExperimentDesigns_list
removeElementAtFromExperimentDesigns(int) - Method in interface org.biomage.Interface.HasExperimentDesigns
Method to remove by position from ExperimentDesigns_list
removeElementAtFromFactorValues(int) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to remove by position from FactorValues_list
removeElementAtFromFactorValues(int) - Method in interface org.biomage.Interface.HasFactorValues
Method to remove by position from FactorValues_list
removeElementAtFromFailTypes(int) - Method in class org.biomage.DesignElement.Reporter
Method to remove by position from FailTypes_list
removeElementAtFromFailTypes(int) - Method in interface org.biomage.Interface.HasFailTypes
Method to remove by position from FailTypes_list
removeElementAtFromFeatureDefects(int) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove by position from FeatureDefects_list
removeElementAtFromFeatureDefects(int) - Method in interface org.biomage.Interface.HasFeatureDefects
Method to remove by position from FeatureDefects_list
removeElementAtFromFeatureGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove by position from FeatureGroups_list
removeElementAtFromFeatureGroups(int) - Method in interface org.biomage.Interface.HasFeatureGroups
Method to remove by position from FeatureGroups_list
removeElementAtFromFeatureInformationSources(int) - Method in class org.biomage.DesignElement.FeatureReporterMap
Method to remove by position from FeatureInformationSources_list
removeElementAtFromFeatureInformationSources(int) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Method to remove by position from FeatureInformationSources_list
removeElementAtFromFeatureLIMSs(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from FeatureLIMSs_list
removeElementAtFromFeatureLIMSs(int) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Method to remove by position from FeatureLIMSs_list
removeElementAtFromFeatureReporterMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove by position from FeatureReporterMap_list
removeElementAtFromFeatureReporterMaps(int) - Method in class org.biomage.DesignElement.Reporter
Method to remove by position from FeatureReporterMaps_list
removeElementAtFromFeatureReporterMaps(int) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Method to remove by position from FeatureReporterMaps_list
removeElementAtFromFeatures(int) - Method in class org.biomage.ArrayDesign.FeatureGroup
Method to remove by position from Features_list
removeElementAtFromFeatures(int) - Method in interface org.biomage.Interface.HasFeatures
Method to remove by position from Features_list
removeElementAtFromFiducials(int) - Method in class org.biomage.Array.ArrayGroup
Method to remove by position from Fiducials_list
removeElementAtFromFiducials(int) - Method in interface org.biomage.Interface.HasFiducials
Method to remove by position from Fiducials_list
removeElementAtFromHardware_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to remove by position from Hardware_list
removeElementAtFromHardwareApplications(int) - Method in interface org.biomage.Interface.HasHardwareApplications
Method to remove by position from HardwareApplications_list
removeElementAtFromHardwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove by position from HardwareApplications_list
removeElementAtFromHardwareManufacturers(int) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Method to remove by position from HardwareManufacturers_list
removeElementAtFromHardwareManufacturers(int) - Method in class org.biomage.Protocol.Hardware
Method to remove by position from HardwareManufacturers_list
removeElementAtFromHardwares(int) - Method in interface org.biomage.Interface.HasHardwares
Method to remove by position from Hardwares_list
removeElementAtFromHardwares(int) - Method in class org.biomage.Protocol.Protocol
Method to remove by position from Hardwares_list
removeElementAtFromImages(int) - Method in class org.biomage.BioAssay.ImageAcquisition
Method to remove by position from Images_list
removeElementAtFromImages(int) - Method in interface org.biomage.Interface.HasImages
Method to remove by position from Images_list
removeElementAtFromImmobilizedCharacteristics(int) - Method in class org.biomage.DesignElement.Reporter
Method to remove by position from ImmobilizedCharacteristics_list
removeElementAtFromImmobilizedCharacteristics(int) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Method to remove by position from ImmobilizedCharacteristics_list
removeElementAtFromLabels(int) - Method in class org.biomage.BioAssay.Channel
Method to remove by position from Labels_list
removeElementAtFromLabels(int) - Method in class org.biomage.BioMaterial.LabeledExtract
Method to remove by position from Labels_list
removeElementAtFromLabels(int) - Method in interface org.biomage.Interface.HasLabels
Method to remove by position from Labels_list
removeElementAtFromMeasuredBioAssayData(int) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Method to remove by position from MeasuredBioAssayData_list
removeElementAtFromMeasuredBioAssayData(int) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Method to remove by position from MeasuredBioAssayData_list
removeElementAtFromMembers(int) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Method to remove by position from Members_list
removeElementAtFromMembers(int) - Method in interface org.biomage.Interface.HasMembers
Method to remove by position from Members_list
removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.CompositePosition
Method to remove by position from MismatchInformation_list
removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.FeatureInformation
Method to remove by position from MismatchInformation_list
removeElementAtFromMismatchInformation(int) - Method in class org.biomage.DesignElement.ReporterPosition
Method to remove by position from MismatchInformation_list
removeElementAtFromMismatchInformation(int) - Method in interface org.biomage.Interface.HasMismatchInformation
Method to remove by position from MismatchInformation_list
removeElementAtFromNodeContents(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove by position from NodeContents_list
removeElementAtFromNodeContents(int) - Method in interface org.biomage.Interface.HasNodeContents
Method to remove by position from NodeContents_list
removeElementAtFromNodes(int) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Method to remove by position from Nodes_list
removeElementAtFromNodes(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove by position from Nodes_list
removeElementAtFromNodes(int) - Method in interface org.biomage.Interface.HasNodes
Method to remove by position from Nodes_list
removeElementAtFromNodeValue(int) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove by position from NodeValue_list
removeElementAtFromNodeValue(int) - Method in interface org.biomage.Interface.HasNodeValue
Method to remove by position from NodeValue_list
removeElementAtFromOntologyEntries(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from OntologyEntries_list
removeElementAtFromOntologyEntries(int) - Method in interface org.biomage.Interface.HasOntologyEntries
Method to remove by position from OntologyEntries_list
removeElementAtFromOwner(int) - Method in class org.biomage.AuditAndSecurity.Security
Method to remove by position from Owner_list
removeElementAtFromOwner(int) - Method in interface org.biomage.Interface.HasOwner
Method to remove by position from Owner_list
removeElementAtFromParameters(int) - Method in class org.biomage.BQS.BibliographicReference
Method to remove by position from Parameters_list
removeElementAtFromParameters(int) - Method in interface org.biomage.Interface.HasParameters
Method to remove by position from Parameters_list
removeElementAtFromParameterTypes(int) - Method in interface org.biomage.Interface.HasParameterTypes
Method to remove by position from ParameterTypes_list
removeElementAtFromParameterTypes(int) - Method in class org.biomage.Protocol.Parameterizable
Method to remove by position from ParameterTypes_list
removeElementAtFromParameterValues(int) - Method in interface org.biomage.Interface.HasParameterValues
Method to remove by position from ParameterValues_list
removeElementAtFromParameterValues(int) - Method in class org.biomage.Protocol.ParameterizableApplication
Method to remove by position from ParameterValues_list
removeElementAtFromPerformers(int) - Method in interface org.biomage.Interface.HasPerformers
Method to remove by position from Performers_list
removeElementAtFromPerformers(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove by position from Performers_list
removeElementAtFromPhysicalBioAssayData(int) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to remove by position from PhysicalBioAssayData_list
removeElementAtFromPhysicalBioAssayData(int) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Method to remove by position from PhysicalBioAssayData_list
removeElementAtFromPropertySets(int) - Method in class org.biomage.Common.Extendable
Method to remove by position from PropertySets_list
removeElementAtFromPropertySets(int) - Method in class org.biomage.Common.NameValueType
Method to remove by position from PropertySets_list
removeElementAtFromPropertySets(int) - Method in interface org.biomage.Interface.HasPropertySets
Method to remove by position from PropertySets_list
removeElementAtFromProtocol_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to remove by position from Protocol_list
removeElementAtFromProtocolApplications(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from ProtocolApplications_list
removeElementAtFromProtocolApplications(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove by position from ProtocolApplications_list
removeElementAtFromProtocolApplications(int) - Method in class org.biomage.BioEvent.BioEvent
Method to remove by position from ProtocolApplications_list
removeElementAtFromProtocolApplications(int) - Method in interface org.biomage.Interface.HasProtocolApplications
Method to remove by position from ProtocolApplications_list
removeElementAtFromProviders(int) - Method in class org.biomage.Experiment.Experiment
Method to remove by position from Providers_list
removeElementAtFromProviders(int) - Method in interface org.biomage.Interface.HasProviders
Method to remove by position from Providers_list
removeElementAtFromQualityControlStatistics(int) - Method in class org.biomage.Array.ArrayManufacture
Method to remove by position from QualityControlStatistics_list
removeElementAtFromQualityControlStatistics(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove by position from QualityControlStatistics_list
removeElementAtFromQualityControlStatistics(int) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Method to remove by position from QualityControlStatistics_list
removeElementAtFromQuantitationType_list(int) - Method in class org.biomage.QuantitationType.QuantitationType_package
Method to remove by position from QuantitationType_list
removeElementAtFromQuantitationTypeDimension_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from QuantitationTypeDimension_list
removeElementAtFromQuantitationTypeMap_list(int) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove by position from QuantitationTypeMap_list
removeElementAtFromQuantitationTypeMaps(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Method to remove by position from QuantitationTypeMaps_list
removeElementAtFromQuantitationTypeMaps(int) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Method to remove by position from QuantitationTypeMaps_list
removeElementAtFromQuantitationTypeMaps(int) - Method in class org.biomage.QuantitationType.QuantitationType
Method to remove by position from QuantitationTypeMaps_list
removeElementAtFromQuantitationTypes(int) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Method to remove by position from QuantitationTypes_list
removeElementAtFromQuantitationTypes(int) - Method in interface org.biomage.Interface.HasQuantitationTypes
Method to remove by position from QuantitationTypes_list
removeElementAtFromQuantitationTypeTuples(int) - Method in class org.biomage.BioAssayData.DesignElementTuple
Method to remove by position from QuantitationTypeTuples_list
removeElementAtFromQuantitationTypeTuples(int) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Method to remove by position from QuantitationTypeTuples_list
removeElementAtFromRegions(int) - Method in class org.biomage.BioSequence.SeqFeature
Method to remove by position from Regions_list
removeElementAtFromRegions(int) - Method in interface org.biomage.Interface.HasRegions
Method to remove by position from Regions_list
removeElementAtFromReporter_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove by position from Reporter_list
removeElementAtFromReporterCompositeMap_list(int) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove by position from ReporterCompositeMap_list
removeElementAtFromReporterCompositeMaps(int) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove by position from ReporterCompositeMaps_list
removeElementAtFromReporterCompositeMaps(int) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Method to remove by position from ReporterCompositeMaps_list
removeElementAtFromReporterGroup_list(int) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove by position from ReporterGroup_list
removeElementAtFromReporterGroups(int) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove by position from ReporterGroups_list
removeElementAtFromReporterGroups(int) - Method in interface org.biomage.Interface.HasReporterGroups
Method to remove by position from ReporterGroups_list
removeElementAtFromReporterPositionSources(int) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Method to remove by position from ReporterPositionSources_list
removeElementAtFromReporterPositionSources(int) - Method in interface org.biomage.Interface.HasReporterPositionSources
Method to remove by position from ReporterPositionSources_list
removeElementAtFromReporters(int) - Method in class org.biomage.ArrayDesign.ReporterGroup
Method to remove by position from Reporters_list
removeElementAtFromReporters(int) - Method in class org.biomage.BioAssayData.ReporterDimension
Method to remove by position from Reporters_list
removeElementAtFromReporters(int) - Method in interface org.biomage.Interface.HasReporters
Method to remove by position from Reporters_list
removeElementAtFromRoles(int) - Method in class org.biomage.AuditAndSecurity.Contact
Method to remove by position from Roles_list
removeElementAtFromRoles(int) - Method in interface org.biomage.Interface.HasRoles
Method to remove by position from Roles_list
removeElementAtFromSecurity_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove by position from Security_list
removeElementAtFromSecurityGroup_list(int) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove by position from SecurityGroup_list
removeElementAtFromSecurityGroups(int) - Method in class org.biomage.AuditAndSecurity.Security
Method to remove by position from SecurityGroups_list
removeElementAtFromSecurityGroups(int) - Method in interface org.biomage.Interface.HasSecurityGroups
Method to remove by position from SecurityGroups_list
removeElementAtFromSeqFeatures(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from SeqFeatures_list
removeElementAtFromSeqFeatures(int) - Method in interface org.biomage.Interface.HasSeqFeatures
Method to remove by position from SeqFeatures_list
removeElementAtFromSequenceDatabases(int) - Method in class org.biomage.BioSequence.BioSequence
Method to remove by position from SequenceDatabases_list
removeElementAtFromSequenceDatabases(int) - Method in interface org.biomage.Interface.HasSequenceDatabases
Method to remove by position from SequenceDatabases_list
removeElementAtFromSoftware_list(int) - Method in class org.biomage.Protocol.Protocol_package
Method to remove by position from Software_list
removeElementAtFromSoftwareApplications(int) - Method in interface org.biomage.Interface.HasSoftwareApplications
Method to remove by position from SoftwareApplications_list
removeElementAtFromSoftwareApplications(int) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove by position from SoftwareApplications_list
removeElementAtFromSoftwareManufacturers(int) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Method to remove by position from SoftwareManufacturers_list
removeElementAtFromSoftwareManufacturers(int) - Method in class org.biomage.Protocol.Software
Method to remove by position from SoftwareManufacturers_list
removeElementAtFromSoftwares(int) - Method in interface org.biomage.Interface.HasSoftwares
Method to remove by position from Softwares_list
removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Hardware
Method to remove by position from Softwares_list
removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Protocol
Method to remove by position from Softwares_list
removeElementAtFromSoftwares(int) - Method in class org.biomage.Protocol.Software
Method to remove by position from Softwares_list
removeElementAtFromSourceBioAssays(int) - Method in class org.biomage.BioAssayData.BioAssayMap
Method to remove by position from SourceBioAssays_list
removeElementAtFromSourceBioAssays(int) - Method in interface org.biomage.Interface.HasSourceBioAssays
Method to remove by position from SourceBioAssays_list
removeElementAtFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioAssay.BioAssayCreation
Method to remove by position from SourceBioMaterialMeasurements_list
removeElementAtFromSourceBioMaterialMeasurements(int) - Method in class org.biomage.BioMaterial.Treatment
Method to remove by position from SourceBioMaterialMeasurements_list
removeElementAtFromSourceBioMaterialMeasurements(int) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Method to remove by position from SourceBioMaterialMeasurements_list
removeElementAtFromSourceContact(int) - Method in class org.biomage.BioMaterial.BioSource
Method to remove by position from SourceContact_list
removeElementAtFromSourceContact(int) - Method in interface org.biomage.Interface.HasSourceContact
Method to remove by position from SourceContact_list
removeElementAtFromSourcesQuantitationType(int) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Method to remove by position from SourcesQuantitationType_list
removeElementAtFromSourcesQuantitationType(int) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Method to remove by position from SourcesQuantitationType_list
removeElementAtFromSubregions(int) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to remove by position from Subregions_list
removeElementAtFromSubregions(int) - Method in interface org.biomage.Interface.HasSubregions
Method to remove by position from Subregions_list
removeElementAtFromSummaryStatistics(int) - Method in class org.biomage.BioAssayData.BioAssayData
Method to remove by position from SummaryStatistics_list
removeElementAtFromSummaryStatistics(int) - Method in interface org.biomage.Interface.HasSummaryStatistics
Method to remove by position from SummaryStatistics_list
removeElementAtFromTopLevelBioAssays(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove by position from TopLevelBioAssays_list
removeElementAtFromTopLevelBioAssays(int) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Method to remove by position from TopLevelBioAssays_list
removeElementAtFromTopLevelBioMaterials(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove by position from Treatments_list
removeElementAtFromTopLevelBioMaterials(int) - Method in interface org.biomage.Interface.HasTopBioMaterial
Method to remove by position from TopLevelBioMaterials_list
removeElementAtFromTreatments(int) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove by position from Treatments_list
removeElementAtFromTreatments(int) - Method in interface org.biomage.Interface.HasTreatments
Method to remove by position from Treatments_list
removeElementAtFromTypes(int) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Method to remove by position from Types_list
removeElementAtFromTypes(int) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove by position from Types_list
removeElementAtFromTypes(int) - Method in interface org.biomage.Interface.HasTypes
Method to remove by position from Types_list
removeElementAtFromZoneGroups(int) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Method to remove by position from ZoneGroups_list
removeElementAtFromZoneGroups(int) - Method in interface org.biomage.Interface.HasZoneGroups
Method to remove by position from ZoneGroups_list
removeElementAtFromZoneLocations(int) - Method in class org.biomage.ArrayDesign.ZoneGroup
Method to remove by position from ZoneLocations_list
removeElementAtFromZoneLocations(int) - Method in interface org.biomage.Interface.HasZoneLocations
Method to remove by position from ZoneLocations_list
removeEntryFromList(long, HttpServletRequest, Class<? extends BioMaterialDesc>) - Static method in class gov.nih.nci.caarray.ui.biomaterial.BioMaterialUIUtils
 
removeExistingDesignElements(PhysicalArrayDesign) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Clears all existing associated array design objects from the system, leaving only the top level PhysicalArrayDesign object.
removeExistingDesignElements(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
removeExistingDesignElements(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
removeFactor(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeFactorValue(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeFeatureGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Remove the specified FeatureGroup from the specified ArrayDesign.
removeFeatureGroupFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
removeFileUploadEntry(ArrayDesignFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
removeFileUploadEntry(int) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
removeFileUploadEntry(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
removeFileUploadEntry(int) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
removeForms(HttpSession) - Static method in class gov.nih.nci.caarray.ui.biomaterial.BioMaterialUIUtils
 
removeFromAccessions(DatabaseEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to remove first DatabaseEntry from Accessions_list
removeFromAccessions(DatabaseEntry) - Method in interface org.biomage.Interface.HasAccessions
Method to remove first DatabaseEntry from Accessions_list
removeFromAdjustments(ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove first ZoneDefect from Adjustments_list
removeFromAdjustments(ZoneDefect) - Method in interface org.biomage.Interface.HasAdjustments
Method to remove first ZoneDefect from Adjustments_list
removeFromAnalysisResults(BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment
Method to remove first BioAssayDataCluster from AnalysisResults_list
removeFromAnalysisResults(BioAssayDataCluster) - Method in interface org.biomage.Interface.HasAnalysisResults
Method to remove first BioAssayDataCluster from AnalysisResults_list
removeFromAnnotations(OntologyEntry) - Method in class org.biomage.Description.Description
Method to remove first OntologyEntry from Annotations_list
removeFromAnnotations(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to remove first OntologyEntry from Annotations_list
removeFromAnnotations(OntologyEntry) - Method in interface org.biomage.Interface.HasAnnotations
Method to remove first OntologyEntry from Annotations_list
removeFromArray_list(Array) - Method in class org.biomage.Array.Array_package
Method to remove first Array from Array_list
removeFromArrayDesign_list(ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove first ArrayDesign from ArrayDesign_list
removeFromArrayGroup_list(ArrayGroup) - Method in class org.biomage.Array.Array_package
Method to remove first ArrayGroup from ArrayGroup_list
removeFromArrayManufacture_list(ArrayManufacture) - Method in class org.biomage.Array.Array_package
Method to remove first ArrayManufacture from ArrayManufacture_list
removeFromArrayManufactureDeviations(ArrayManufactureDeviation) - Method in class org.biomage.Array.Array
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list
removeFromArrayManufactureDeviations(ArrayManufactureDeviation) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list
removeFromArrayManufacturers(Contact) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first Contact from ArrayManufacturers_list
removeFromArrayManufacturers(Contact) - Method in interface org.biomage.Interface.HasArrayManufacturers
Method to remove first Contact from ArrayManufacturers_list
removeFromArrays(Array) - Method in class org.biomage.Array.ArrayGroup
Method to remove first Array from Arrays_list
removeFromArrays(Array) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first Array from Arrays_list
removeFromArrays(Array) - Method in interface org.biomage.Interface.HasArrays
Method to remove first Array from Arrays_list
removeFromAssociations(OntologyEntry) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Method to remove first OntologyEntry from Associations_list
removeFromAssociations(OntologyEntry) - Method in class org.biomage.Description.OntologyEntry
Method to remove first OntologyEntry from Associations_list
removeFromAssociations(OntologyEntry) - Method in interface org.biomage.Interface.HasAssociations
Method to remove first OntologyEntry from Associations_list
removeFromAuditTrail(Audit) - Method in class org.biomage.Common.Describable
Method to remove first Audit from AuditTrail_list
removeFromAuditTrail(Audit) - Method in interface org.biomage.Interface.HasAuditTrail
Method to remove first Audit from AuditTrail_list
removeFromBibliographicReferences(BibliographicReference) - Method in class org.biomage.Description.Description
Method to remove first BibliographicReference from BibliographicReferences_list
removeFromBibliographicReferences(BibliographicReference) - Method in interface org.biomage.Interface.HasBibliographicReferences
Method to remove first BibliographicReference from BibliographicReferences_list
removeFromBioAssay_list(BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package
Method to remove first BioAssay from BioAssay_list
removeFromBioAssayData(BioAssayData) - Method in class org.biomage.Experiment.Experiment
Method to remove first BioAssayData from BioAssayData_list
removeFromBioAssayData(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayData
Method to remove first BioAssayData from BioAssayData_list
removeFromBioAssayData_list(BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first BioAssayData from BioAssayData_list
removeFromBioAssayDataCluster_list(BioAssayDataCluster) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Method to remove first BioAssayDataCluster from BioAssayDataCluster_list
removeFromBioAssayDataSources(BioAssayData) - Method in class org.biomage.BioAssayData.Transformation
Method to remove first BioAssayData from BioAssayDataSources_list
removeFromBioAssayDataSources(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Method to remove first BioAssayData from BioAssayDataSources_list
removeFromBioAssayDimension_list(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first BioAssayDimension from BioAssayDimension_list
removeFromBioAssayFactorValues(FactorValue) - Method in class org.biomage.BioAssay.BioAssay
Method to remove first FactorValue from BioAssayFactorValues_list
removeFromBioAssayFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Method to remove first FactorValue from BioAssayFactorValues_list
removeFromBioAssayMap_list(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first BioAssayMap from BioAssayMap_list
removeFromBioAssayMaps(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping
Method to remove first BioAssayMap from BioAssayMaps_list
removeFromBioAssayMaps(BioAssayMap) - Method in interface org.biomage.Interface.HasBioAssayMaps
Method to remove first BioAssayMap from BioAssayMaps_list
removeFromBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension
Method to remove first BioAssay from BioAssays_list
removeFromBioAssays(BioAssay) - Method in class org.biomage.Experiment.Experiment
Method to remove first BioAssay from BioAssays_list
removeFromBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasBioAssays
Method to remove first BioAssay from BioAssays_list
removeFromBioAssayTreatments(BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to remove first BioAssayTreatment from BioAssayTreatments_list
removeFromBioAssayTreatments(BioAssayTreatment) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Method to remove first BioAssayTreatment from BioAssayTreatments_list
removeFromBioAssayTuples(BioAssayTuple) - Method in class org.biomage.BioAssayData.BioDataTuples
Method to remove first BioAssayTuple from BioAssayTuples_list
removeFromBioAssayTuples(BioAssayTuple) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Method to remove first BioAssayTuple from BioAssayTuples_list
removeFromBiologicalCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove first BioSequence from BiologicalCharacteristics_list
removeFromBiologicalCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Method to remove first BioSequence from BiologicalCharacteristics_list
removeFromBioMaterial_list(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to remove first BioMaterial from BioMaterial_list
removeFromBioSequence_list(BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package
Method to remove first BioSequence from BioSequence_list
removeFromCache(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
removeFromChannel_list(Channel) - Method in class org.biomage.BioAssay.BioAssay_package
Method to remove first Channel from Channel_list
removeFromChannels(Channel) - Method in class org.biomage.BioAssay.BioAssay
Method to remove first Channel from Channels_list
removeFromChannels(Channel) - Method in class org.biomage.BioAssay.Image
Method to remove first Channel from Channels_list
removeFromChannels(Channel) - Method in interface org.biomage.Interface.HasChannels
Method to remove first Channel from Channels_list
removeFromCharacteristics(OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove first OntologyEntry from Characteristics_list
removeFromCharacteristics(OntologyEntry) - Method in interface org.biomage.Interface.HasCharacteristics
Method to remove first OntologyEntry from Characteristics_list
removeFromComponentCompounds(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Compound
Method to remove first CompoundMeasurement from ComponentCompounds_list
removeFromComponentCompounds(CompoundMeasurement) - Method in interface org.biomage.Interface.HasComponentCompounds
Method to remove first CompoundMeasurement from ComponentCompounds_list
removeFromCompositeCompositeMap_list(CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove first CompositeCompositeMap from CompositeCompositeMap_list
removeFromCompositeCompositeMaps(CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
removeFromCompositeCompositeMaps(CompositeCompositeMap) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
removeFromCompositeGroup_list(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove first CompositeGroup from CompositeGroup_list
removeFromCompositeGroups(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove first CompositeGroup from CompositeGroups_list
removeFromCompositeGroups(CompositeGroup) - Method in interface org.biomage.Interface.HasCompositeGroups
Method to remove first CompositeGroup from CompositeGroups_list
removeFromCompositePositionSources(CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Method to remove first CompositePosition from CompositePositionSources_list
removeFromCompositePositionSources(CompositePosition) - Method in interface org.biomage.Interface.HasCompositePositionSources
Method to remove first CompositePosition from CompositePositionSources_list
removeFromCompositeSequence_list(CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove first CompositeSequence from CompositeSequence_list
removeFromCompositeSequences(CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup
Method to remove first CompositeSequence from CompositeSequences_list
removeFromCompositeSequences(CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Method to remove first CompositeSequence from CompositeSequences_list
removeFromCompositeSequences(CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequences
Method to remove first CompositeSequence from CompositeSequences_list
removeFromCompound_list(Compound) - Method in class org.biomage.BioMaterial.BioMaterial_package
Method to remove first Compound from Compound_list
removeFromCompoundIndices(OntologyEntry) - Method in class org.biomage.BioMaterial.Compound
Method to remove first OntologyEntry from CompoundIndices_list
removeFromCompoundIndices(OntologyEntry) - Method in interface org.biomage.Interface.HasCompoundIndices
Method to remove first OntologyEntry from CompoundIndices_list
removeFromCompoundMeasurements(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to remove first CompoundMeasurement from CompoundMeasurements_list
removeFromCompoundMeasurements(CompoundMeasurement) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Method to remove first CompoundMeasurement from CompoundMeasurements_list
removeFromConfidenceIndicators(ConfidenceIndicator) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Method to remove first ConfidenceIndicator from ConfidenceIndicators_list
removeFromConfidenceIndicators(ConfidenceIndicator) - Method in class org.biomage.QuantitationType.QuantitationType
Method to remove first ConfidenceIndicator from ConfidenceIndicators_list
removeFromContact_list(Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove first Contact from Contact_list
removeFromContacts(Contact) - Method in class org.biomage.Description.Database
Method to remove first Contact from Contacts_list
removeFromContacts(Contact) - Method in interface org.biomage.Interface.HasContacts
Method to remove first Contact from Contacts_list
removeFromContainedFeatures(Feature) - Method in class org.biomage.BioAssayData.FeatureDimension
Method to remove first Feature from ContainedFeatures_list
removeFromContainedFeatures(Feature) - Method in interface org.biomage.Interface.HasContainedFeatures
Method to remove first Feature from ContainedFeatures_list
removeFromControlFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
Method to remove first Feature from ControlFeatures_list
removeFromControlFeatures(Feature) - Method in interface org.biomage.Interface.HasControlFeatures
Method to remove first Feature from ControlFeatures_list
removeFromControlledFeatures(Feature) - Method in class org.biomage.DesignElement.Feature
Method to remove first Feature from ControlledFeatures_list
removeFromControlledFeatures(Feature) - Method in interface org.biomage.Interface.HasControlledFeatures
Method to remove first Feature from ControlledFeatures_list
removeFromDatabase_list(Database) - Method in class org.biomage.Description.Description_package
Method to remove first Database from Database_list
removeFromDatabaseReferences(DatabaseEntry) - Method in class org.biomage.Description.Description
Method to remove first DatabaseEntry from DatabaseReferences_list
removeFromDatabaseReferences(DatabaseEntry) - Method in interface org.biomage.Interface.HasDatabaseReferences
Method to remove first DatabaseEntry from DatabaseReferences_list
removeFromDerivedBioAssayData(DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
removeFromDerivedBioAssayData(DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
removeFromDerivedBioAssayMap(BioAssayMap) - Method in class org.biomage.BioAssay.DerivedBioAssay
Method to remove first BioAssayMap from DerivedBioAssayMap_list
removeFromDerivedBioAssayMap(BioAssayMap) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Method to remove first BioAssayMap from DerivedBioAssayMap_list
removeFromDescriptions(Description) - Method in class org.biomage.Common.Describable
Method to remove first Description from Descriptions_list
removeFromDescriptions(Description) - Method in interface org.biomage.Interface.HasDescriptions
Method to remove first Description from Descriptions_list
removeFromDesignElementDimension_list(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first DesignElementDimension from DesignElementDimension_list
removeFromDesignElementMaps(DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping
Method to remove first DesignElementMap from DesignElementMaps_list
removeFromDesignElementMaps(DesignElementMap) - Method in interface org.biomage.Interface.HasDesignElementMaps
Method to remove first DesignElementMap from DesignElementMaps_list
removeFromDesignElementTuples(DesignElementTuple) - Method in class org.biomage.BioAssayData.BioAssayTuple
Method to remove first DesignElementTuple from DesignElementTuples_list
removeFromDesignElementTuples(DesignElementTuple) - Method in interface org.biomage.Interface.HasDesignElementTuples
Method to remove first DesignElementTuple from DesignElementTuples_list
removeFromDesignProviderRoles(DesignProviderRole) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
removeFromDesignProviders(Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove first Contact from DesignProviders_list
removeFromDesignProviders(Contact) - Method in interface org.biomage.Interface.HasDesignProviders
Method to remove first Contact from DesignProviders_list
removeFromExperiment_list(Experiment) - Method in class org.biomage.Experiment.Experiment_package
Method to remove first Experiment from Experiment_list
removeFromExperimentalFactors(ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove first ExperimentalFactor from ExperimentalFactors_list
removeFromExperimentalFactors(ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactors
Method to remove first ExperimentalFactor from ExperimentalFactors_list
removeFromExperimentDesigns(ExperimentDesign) - Method in class org.biomage.Experiment.Experiment
Method to remove first ExperimentDesign from ExperimentDesigns_list
removeFromExperimentDesigns(ExperimentDesign) - Method in interface org.biomage.Interface.HasExperimentDesigns
Method to remove first ExperimentDesign from ExperimentDesigns_list
removeFromFactorValues(FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor
Method to remove first FactorValue from FactorValues_list
removeFromFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasFactorValues
Method to remove first FactorValue from FactorValues_list
removeFromFailTypes(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
Method to remove first OntologyEntry from FailTypes_list
removeFromFailTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasFailTypes
Method to remove first OntologyEntry from FailTypes_list
removeFromFeatureDefects(FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation
Method to remove first FeatureDefect from FeatureDefects_list
removeFromFeatureDefects(FeatureDefect) - Method in interface org.biomage.Interface.HasFeatureDefects
Method to remove first FeatureDefect from FeatureDefects_list
removeFromFeatureGroups(FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove first FeatureGroup from FeatureGroups_list
removeFromFeatureGroups(FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroups
Method to remove first FeatureGroup from FeatureGroups_list
removeFromFeatureInformationSources(FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap
Method to remove first FeatureInformation from FeatureInformationSources_list
removeFromFeatureInformationSources(FeatureInformation) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Method to remove first FeatureInformation from FeatureInformationSources_list
removeFromFeatureLIMSs(ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first ManufactureLIMS from FeatureLIMSs_list
removeFromFeatureLIMSs(ManufactureLIMS) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Method to remove first ManufactureLIMS from FeatureLIMSs_list
removeFromFeatureReporterMap_list(FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove first FeatureReporterMap from FeatureReporterMap_list
removeFromFeatureReporterMaps(FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter
Method to remove first FeatureReporterMap from FeatureReporterMaps_list
removeFromFeatureReporterMaps(FeatureReporterMap) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Method to remove first FeatureReporterMap from FeatureReporterMaps_list
removeFromFeatures(Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup
Method to remove first Feature from Features_list
removeFromFeatures(Feature) - Method in interface org.biomage.Interface.HasFeatures
Method to remove first Feature from Features_list
removeFromFiducials(Fiducial) - Method in class org.biomage.Array.ArrayGroup
Method to remove first Fiducial from Fiducials_list
removeFromFiducials(Fiducial) - Method in interface org.biomage.Interface.HasFiducials
Method to remove first Fiducial from Fiducials_list
removeFromHardware_list(Hardware) - Method in class org.biomage.Protocol.Protocol_package
Method to remove first Hardware from Hardware_list
removeFromHardwareApplications(HardwareApplication) - Method in interface org.biomage.Interface.HasHardwareApplications
Method to remove first HardwareApplication from HardwareApplications_list
removeFromHardwareApplications(HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove first HardwareApplication from HardwareApplications_list
removeFromHardwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Method to remove first Contact from HardwareManufacturers_list
removeFromHardwareManufacturers(Contact) - Method in class org.biomage.Protocol.Hardware
Method to remove first Contact from HardwareManufacturers_list
removeFromHardwares(Hardware) - Method in interface org.biomage.Interface.HasHardwares
Method to remove first Hardware from Hardwares_list
removeFromHardwares(Hardware) - Method in class org.biomage.Protocol.Protocol
Method to remove first Hardware from Hardwares_list
removeFromImages(Image) - Method in class org.biomage.BioAssay.ImageAcquisition
Method to remove first Image from Images_list
removeFromImages(Image) - Method in interface org.biomage.Interface.HasImages
Method to remove first Image from Images_list
removeFromImmobilizedCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.Reporter
Method to remove first BioSequence from ImmobilizedCharacteristics_list
removeFromImmobilizedCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Method to remove first BioSequence from ImmobilizedCharacteristics_list
removeFromLabels(Compound) - Method in class org.biomage.BioAssay.Channel
Method to remove first Compound from Labels_list
removeFromLabels(Compound) - Method in class org.biomage.BioMaterial.LabeledExtract
Method to remove first Compound from Labels_list
removeFromLabels(Compound) - Method in interface org.biomage.Interface.HasLabels
Method to remove first Compound from Labels_list
removeFromMeasuredBioAssayData(MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
removeFromMeasuredBioAssayData(MeasuredBioAssayData) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
removeFromMembers(Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Method to remove first Contact from Members_list
removeFromMembers(Contact) - Method in interface org.biomage.Interface.HasMembers
Method to remove first Contact from Members_list
removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition
Method to remove first MismatchInformation from MismatchInformation_list
removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation
Method to remove first MismatchInformation from MismatchInformation_list
removeFromMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition
Method to remove first MismatchInformation from MismatchInformation_list
removeFromMismatchInformation(MismatchInformation) - Method in interface org.biomage.Interface.HasMismatchInformation
Method to remove first MismatchInformation from MismatchInformation_list
removeFromNodeContents(NodeContents) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove first NodeContents from NodeContents_list
removeFromNodeContents(NodeContents) - Method in interface org.biomage.Interface.HasNodeContents
Method to remove first NodeContents from NodeContents_list
removeFromNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Method to remove first Node from Nodes_list
removeFromNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove first Node from Nodes_list
removeFromNodes(Node) - Method in interface org.biomage.Interface.HasNodes
Method to remove first Node from Nodes_list
removeFromNodeValue(NodeValue) - Method in class org.biomage.HigherLevelAnalysis.Node
Method to remove first NodeValue from NodeValue_list
removeFromNodeValue(NodeValue) - Method in interface org.biomage.Interface.HasNodeValue
Method to remove first NodeValue from NodeValue_list
removeFromOntologyEntries(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first OntologyEntry from OntologyEntries_list
removeFromOntologyEntries(OntologyEntry) - Method in interface org.biomage.Interface.HasOntologyEntries
Method to remove first OntologyEntry from OntologyEntries_list
removeFromOwner(Contact) - Method in class org.biomage.AuditAndSecurity.Security
Method to remove first Contact from Owner_list
removeFromOwner(Contact) - Method in interface org.biomage.Interface.HasOwner
Method to remove first Contact from Owner_list
removeFromParameters(OntologyEntry) - Method in class org.biomage.BQS.BibliographicReference
Method to remove first OntologyEntry from Parameters_list
removeFromParameters(OntologyEntry) - Method in interface org.biomage.Interface.HasParameters
Method to remove first OntologyEntry from Parameters_list
removeFromParameterTypes(Parameter) - Method in interface org.biomage.Interface.HasParameterTypes
Method to remove first Parameter from ParameterTypes_list
removeFromParameterTypes(Parameter) - Method in class org.biomage.Protocol.Parameterizable
Method to remove first Parameter from ParameterTypes_list
removeFromParameterValues(ParameterValue) - Method in interface org.biomage.Interface.HasParameterValues
Method to remove first ParameterValue from ParameterValues_list
removeFromParameterValues(ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication
Method to remove first ParameterValue from ParameterValues_list
removeFromPerformers(Person) - Method in interface org.biomage.Interface.HasPerformers
Method to remove first Person from Performers_list
removeFromPerformers(Person) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove first Person from Performers_list
removeFromPhysicalBioAssayData(Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Method to remove first Image from PhysicalBioAssayData_list
removeFromPhysicalBioAssayData(Image) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Method to remove first Image from PhysicalBioAssayData_list
removeFromPropertySets(NameValueType) - Method in class org.biomage.Common.Extendable
Method to remove first NameValueType from PropertySets_list
removeFromPropertySets(NameValueType) - Method in class org.biomage.Common.NameValueType
Method to remove first NameValueType from PropertySets_list
removeFromPropertySets(NameValueType) - Method in interface org.biomage.Interface.HasPropertySets
Method to remove first NameValueType from PropertySets_list
removeFromProtocol_list(Protocol) - Method in class org.biomage.Protocol.Protocol_package
Method to remove first Protocol from Protocol_list
removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first ProtocolApplication from ProtocolApplications_list
removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove first ProtocolApplication from ProtocolApplications_list
removeFromProtocolApplications(ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent
Method to remove first ProtocolApplication from ProtocolApplications_list
removeFromProtocolApplications(ProtocolApplication) - Method in interface org.biomage.Interface.HasProtocolApplications
Method to remove first ProtocolApplication from ProtocolApplications_list
removeFromProviderRoles(ExperimentProviderRole) - Method in class org.biomage.Experiment.Experiment
 
removeFromProviders(Contact) - Method in class org.biomage.Experiment.Experiment
Method to remove first Contact from Providers_list
removeFromProviders(Contact) - Method in interface org.biomage.Interface.HasProviders
Method to remove first Contact from Providers_list
removeFromQualityControlStatistics(NameValueType) - Method in class org.biomage.Array.ArrayManufacture
Method to remove first NameValueType from QualityControlStatistics_list
removeFromQualityControlStatistics(NameValueType) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove first NameValueType from QualityControlStatistics_list
removeFromQualityControlStatistics(NameValueType) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Method to remove first NameValueType from QualityControlStatistics_list
removeFromQuantitationType_list(QuantitationType) - Method in class org.biomage.QuantitationType.QuantitationType_package
Method to remove first QuantitationType from QuantitationType_list
removeFromQuantitationTypeDimension_list(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list
removeFromQuantitationTypeMap_list(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package
Method to remove first QuantitationTypeMap from QuantitationTypeMap_list
removeFromQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list
removeFromQuantitationTypeMaps(QuantitationTypeMap) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list
removeFromQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.QuantitationType.QuantitationType
Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list
removeFromQuantitationTypes(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Method to remove first QuantitationType from QuantitationTypes_list
removeFromQuantitationTypes(QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationTypes
Method to remove first QuantitationType from QuantitationTypes_list
removeFromQuantitationTypeTuples(QuantitationTypeTuple) - Method in class org.biomage.BioAssayData.DesignElementTuple
Method to remove first QuantitationTypeTuple from QuantitationTypeTuples_list
removeFromQuantitationTypeTuples(QuantitationTypeTuple) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Method to remove first QuantitationTypeTuple from QuantitationTypeTuples_list
removeFromRegions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature
Method to remove first SeqFeatureLocation from Regions_list
removeFromRegions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasRegions
Method to remove first SeqFeatureLocation from Regions_list
removeFromReporter_list(Reporter) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove first Reporter from Reporter_list
removeFromReporterCompositeMap_list(ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package
Method to remove first ReporterCompositeMap from ReporterCompositeMap_list
removeFromReporterCompositeMaps(ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence
Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
removeFromReporterCompositeMaps(ReporterCompositeMap) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
removeFromReporterGroup_list(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Method to remove first ReporterGroup from ReporterGroup_list
removeFromReporterGroups(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign
Method to remove first ReporterGroup from ReporterGroups_list
removeFromReporterGroups(ReporterGroup) - Method in interface org.biomage.Interface.HasReporterGroups
Method to remove first ReporterGroup from ReporterGroups_list
removeFromReporterPositionSources(ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Method to remove first ReporterPosition from ReporterPositionSources_list
removeFromReporterPositionSources(ReporterPosition) - Method in interface org.biomage.Interface.HasReporterPositionSources
Method to remove first ReporterPosition from ReporterPositionSources_list
removeFromReporters(Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup
Method to remove first Reporter from Reporters_list
removeFromReporters(Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension
Method to remove first Reporter from Reporters_list
removeFromReporters(Reporter) - Method in interface org.biomage.Interface.HasReporters
Method to remove first Reporter from Reporters_list
removeFromRoles(OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact
Method to remove first OntologyEntry from Roles_list
removeFromRoles(OntologyEntry) - Method in interface org.biomage.Interface.HasRoles
Method to remove first OntologyEntry from Roles_list
removeFromSecurity_list(Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove first Security from Security_list
removeFromSecurityGroup_list(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Method to remove first SecurityGroup from SecurityGroup_list
removeFromSecurityGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security
Method to remove first SecurityGroup from SecurityGroups_list
removeFromSecurityGroups(SecurityGroup) - Method in interface org.biomage.Interface.HasSecurityGroups
Method to remove first SecurityGroup from SecurityGroups_list
removeFromSeqFeatures(SeqFeature) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first SeqFeature from SeqFeatures_list
removeFromSeqFeatures(SeqFeature) - Method in interface org.biomage.Interface.HasSeqFeatures
Method to remove first SeqFeature from SeqFeatures_list
removeFromSequenceDatabases(DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence
Method to remove first DatabaseEntry from SequenceDatabases_list
removeFromSequenceDatabases(DatabaseEntry) - Method in interface org.biomage.Interface.HasSequenceDatabases
Method to remove first DatabaseEntry from SequenceDatabases_list
removeFromSoftware_list(Software) - Method in class org.biomage.Protocol.Protocol_package
Method to remove first Software from Software_list
removeFromSoftwareApplications(SoftwareApplication) - Method in interface org.biomage.Interface.HasSoftwareApplications
Method to remove first SoftwareApplication from SoftwareApplications_list
removeFromSoftwareApplications(SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication
Method to remove first SoftwareApplication from SoftwareApplications_list
removeFromSoftwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Method to remove first Contact from SoftwareManufacturers_list
removeFromSoftwareManufacturers(Contact) - Method in class org.biomage.Protocol.Software
Method to remove first Contact from SoftwareManufacturers_list
removeFromSoftwares(Software) - Method in interface org.biomage.Interface.HasSoftwares
Method to remove first Software from Softwares_list
removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Hardware
Method to remove first Software from Softwares_list
removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Protocol
Method to remove first Software from Softwares_list
removeFromSoftwares(Software) - Method in class org.biomage.Protocol.Software
Method to remove first Software from Softwares_list
removeFromSourceBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
Method to remove first BioAssay from SourceBioAssays_list
removeFromSourceBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasSourceBioAssays
Method to remove first BioAssay from SourceBioAssays_list
removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioMaterial.Treatment
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
removeFromSourceContact(Contact) - Method in class org.biomage.BioMaterial.BioSource
Method to remove first Contact from SourceContact_list
removeFromSourceContact(Contact) - Method in interface org.biomage.Interface.HasSourceContact
Method to remove first Contact from SourceContact_list
removeFromSourcesQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Method to remove first QuantitationType from SourcesQuantitationType_list
removeFromSourcesQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Method to remove first QuantitationType from SourcesQuantitationType_list
removeFromSubregions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Method to remove first SeqFeatureLocation from Subregions_list
removeFromSubregions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasSubregions
Method to remove first SeqFeatureLocation from Subregions_list
removeFromSummaryStatistics(NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData
Method to remove first NameValueType from SummaryStatistics_list
removeFromSummaryStatistics(NameValueType) - Method in interface org.biomage.Interface.HasSummaryStatistics
Method to remove first NameValueType from SummaryStatistics_list
removeFromTopLevelBioAssays(BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove first BioAssay from TopLevelBioAssays_list
removeFromTopLevelBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Method to remove first BioAssay from TopLevelBioAssays_list
removeFromTopLevelBioMaterials(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove first Treatment from Treatments_list
removeFromTopLevelBioMaterials(BioMaterial) - Method in interface org.biomage.Interface.HasTopBioMaterial
Method to remove first BioMaterial from TopLevelBioMaterials_list
removeFromTreatments(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
removeFromTreatments(Treatment) - Method in class org.biomage.BioMaterial.BioMaterial
Method to remove first Treatment from Treatments_list
removeFromTreatments(Treatment) - Method in interface org.biomage.Interface.HasTreatments
Method to remove first Treatment from Treatments_list
removeFromTypes(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData
 
removeFromTypes(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Method to remove first OntologyEntry from Types_list
removeFromTypes(OntologyEntry) - Method in class org.biomage.Description.Ontology.ChromosomalAberration
 
removeFromTypes(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign
Method to remove first OntologyEntry from Types_list
removeFromTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasTypes
Method to remove first OntologyEntry from Types_list
removeFromZoneGroups(ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Method to remove first ZoneGroup from ZoneGroups_list
removeFromZoneGroups(ZoneGroup) - Method in interface org.biomage.Interface.HasZoneGroups
Method to remove first ZoneGroup from ZoneGroups_list
removeFromZoneLocations(Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup
Method to remove first Zone from ZoneLocations_list
removeFromZoneLocations(Zone) - Method in interface org.biomage.Interface.HasZoneLocations
Method to remove first Zone from ZoneLocations_list
removeHardware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
removeHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
removeHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Removes the specified Hardware from the specified Protocol.
removeHardwareFromSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
removeHardwareFromSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
removeHardwareFromSoftware(long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Disassociates a hardware from a software.
removeHybridization(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationDetailDoneAction
 
removeOntologyEntry(Object, String, List) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.VocabDataFieldMapper
 
removeProtocolApp(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
removeProtocolApp(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailAction
 
removeProvider(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
removePublication(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeQualityControl(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentDetailAction
 
removeQuotes(String) - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
 
removeReporterGroup(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Remove the specified ReporterGroup from the specified ArrayDesign.
removeReporterGroupFromArrayDesign(long, long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
removeSearch(Class, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
removeSecuredElement(String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
remove a secured element from security database
removeSecuredElement(String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
remove a secured element from security database
removeSecuredElement(String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
remove a secured element from security database
removeSecuredElement(String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
remove a secured element from security database
RemoveSecuredElement - Class in gov.nih.nci.caarray.services.security.test.usecases
 
RemoveSecuredElement() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.RemoveSecuredElement
 
removeSecuredElemProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
remove Protection/Group association from AS_PROTECTION_GROUP_ELEMENT table.
removeSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
removeSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
removeSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Removes the specified Software from the specified Protocol.
removeSoftwareFromHardware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
removeSoftwareFromHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
removeSoftwareFromHardware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Disassociates a software from a hardware.
removeSoftwareFromSoftware(long, long) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
removeSoftwareFromSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
removeSoftwareFromSoftware(long, long) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Removes a software from another software.
removeZoneLocation(Integer, Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
removeZoneLocation(Integer, Integer) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
removeZoneLocation(Integer, Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
repairDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.delegate.HybridizationFileHandlerDelegate
 
repairDataFile(HybridizationFileUploadEntryData) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB
 
replaceLinebreaker(StringBuffer) - Static method in class gov.nih.nci.caarray.ui.StringFormatter
 
replaceSpace(StringBuffer, int) - Static method in class gov.nih.nci.caarray.ui.StringFormatter
 
replicateDescription - Variable in class org.biomage.Experiment.ExperimentDesign
Description of the replicate strategy of the Experiment.
reporter - Variable in class org.biomage.DesignElement.FeatureReporterMap
Associates features with their reporter.
Reporter - Class in org.biomage.DesignElement
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
Reporter() - Constructor for class org.biomage.DesignElement.Reporter
Default constructor.
Reporter(Attributes) - Constructor for class org.biomage.DesignElement.Reporter
Attribute constructor.
reporter - Variable in class org.biomage.DesignElement.ReporterPosition
A reporter that comprises part of a CompositeSequence.
reporter_list - Variable in class org.biomage.DesignElement.DesignElement_package
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.
REPORTER_TYPE_GENBANK - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
REPORTER_TYPE_UNIGENE - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
ReporterCompositeMap - Class in org.biomage.DesignElement
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
ReporterCompositeMap() - Constructor for class org.biomage.DesignElement.ReporterCompositeMap
Default constructor.
ReporterCompositeMap(Attributes) - Constructor for class org.biomage.DesignElement.ReporterCompositeMap
Attribute constructor.
reporterCompositeMap_list - Variable in class org.biomage.DesignElement.DesignElement_package
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences.
ReporterDimension - Class in org.biomage.BioAssayData
Specialized DesignElementDimension to hold Reporters.
ReporterDimension() - Constructor for class org.biomage.BioAssayData.ReporterDimension
Default constructor.
ReporterDimension(Attributes) - Constructor for class org.biomage.BioAssayData.ReporterDimension
Attribute constructor.
reporterFileLocation - Variable in class org.biomage.ArrayDesign.ArrayDesign
 
reporterFileType - Variable in class org.biomage.ArrayDesign.ArrayDesign
 
ReporterGroup - Class in org.biomage.ArrayDesign
Allows specification of the type of Reporter Design Element.
ReporterGroup() - Constructor for class org.biomage.ArrayDesign.ReporterGroup
Default constructor.
ReporterGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.ReporterGroup
Attribute constructor.
reporterGroup_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package
Allows specification of the type of Reporter Design Element.
ReporterGroupData - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ReporterGroupData() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupData
 
ReporterGroupDesc - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ReporterGroupDesc() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
ReporterGroupManagerDB - Class in gov.nih.nci.caarray.services.arraydesign
 
ReporterGroupManagerDB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Default Constructor
reporterGroups - Variable in class org.biomage.ArrayDesign.ArrayDesign
The grouping of like Reporter together.
ReporterGroupSearchCriteria - Class in gov.nih.nci.caarray.common.data.arraydesign
 
ReporterGroupSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
ReporterPosition - Class in org.biomage.DesignElement
The location in the composite target's sequence to which a source reporter maps.
ReporterPosition() - Constructor for class org.biomage.DesignElement.ReporterPosition
Default constructor.
ReporterPosition(Attributes) - Constructor for class org.biomage.DesignElement.ReporterPosition
Attribute constructor.
reporters - Variable in class org.biomage.ArrayDesign.ReporterGroup
The reporters that belong to this group.
reporters - Variable in class org.biomage.BioAssayData.ReporterDimension
The reporters for this dimension.
ReporterTypeData - Class in gov.nih.nci.caarray.ui.arraydesign
 
ReporterTypeData(int, String) - Constructor for class gov.nih.nci.caarray.ui.arraydesign.ReporterTypeData
 
request - Variable in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
required - Variable in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
REQUIRED - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
reset() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AbstractDataFileReader
 
reset() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.AgilentTxtReader
 
reset() - Method in class gov.nih.nci.caarray.services.bioassaydata.reader.ImageneTxtReader
 
reset() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
reset(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
reset() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
reset() - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
reset(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
reset() - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
reset(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
reset(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
reset(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
reset() - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
reset() - Method in class org.biomage.tools.apps.annot.PagePanel
Description: called when Reset button is clicked
reset() - Method in class org.biomage.tools.apps.annot.pages.ArrayPage
Description: clean all entries
reset() - Method in class org.biomage.tools.apps.annot.pages.Contact
Description: called when Reset button is clicked
resetAttributes(Describable) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
Resets the ID and identifying attributes including audit trail, property set, and security typically useful for duplication
resetBtn - Variable in class org.biomage.tools.apps.annot.PagePanel
 
resetCollectionDescriptorCascadeToPreviousValue(ClassDescriptor, Map, String) - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
resetObjectDescriptorCascadeToPreviousValue(ClassDescriptor, Map, String) - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
resetParameterizableApplication(ParameterizableApplication) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Resets the specified ParameterizableApplication by setting its id, associated ParameterizableApplications' id, and their ParameterValues' id, to 0.
resetTreatmentEvent() - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
resolveEntity(String, String) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEResolver
 
resolveIdentifiable(Attributes, Identifiable) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Get object by identifier, if not there it makes it.
resolveOntologyClassNameFromModel(Extendable, String) - Method in class org.biomage.tools.helpers.OntologyHelper
 
response - Variable in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
retrieve(long, Class, ManagerDB) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
Get the object to be sure it exists.
retrieveAndCheckSecurity(long, Class, String[], ManagerDB) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
retrieveList(Class, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
retrieveList(String, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
retrieveReference(Object, String) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
retrieveReferences(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
retrieveSearch(Class, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
returnType - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
 
reverse() - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
reverse(ClassMapper) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
right - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
rightColor - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
Role - Class in gov.nih.nci.caarray.common.data.security
This class encapsulates the properties of a security role object
Role() - Constructor for class gov.nih.nci.caarray.common.data.security.Role
Constructor for a new Role object.
ROLE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ROLE_INVESTIGATOR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
ROLE_SUBMITTER - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
RoleAssignmentData - Class in gov.nih.nci.caarray.common.data.security
 
RoleAssignmentData(RoleData, ProtectionGroupData[]) - Constructor for class gov.nih.nci.caarray.common.data.security.RoleAssignmentData
 
RoleData - Class in gov.nih.nci.caarray.common.data.security
 
RoleData(long, String) - Constructor for class gov.nih.nci.caarray.common.data.security.RoleData
 
roleNames - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on the rolenames to create for this class's associstions.
roles - Variable in class org.biomage.AuditAndSecurity.Contact
The roles (lab equipment sales, contractor, etc.) the contact fills.
rollback() - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
rollback() - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Cleans up when a problem occurs during request processing.
rollBackTransaction() - Method in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
rollbackTransaction() - Method in class gov.nih.nci.caarray.services.util.transaction.CaArrayTransactionHandler
 
rollbackTransaction() - Method in interface gov.nih.nci.caarray.services.util.transaction.TransactionHandler
 
rollbackUserTx(ManagerDB, UserTransaction) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
rollbackUserTx(ManagerDB, TransactionHandler) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
RowReaderBioSequence - Class in gov.nih.nci.caarray.services.util.ojb
This custom OJB's RowReader reads a BioSequence object that has the "sequence" attribute stored as Oracle's LONG type which must be read as the FIRST and UNIQUE column from the row.
RowReaderBioSequence(ClassDescriptor) - Constructor for class gov.nih.nci.caarray.services.util.ojb.RowReaderBioSequence
 
RowReaderUnit - Class in gov.nih.nci.caarray.services.util.ojb
This custom OJB's RowReader creates the appropriate UnitNameCV object given the UnitNameCV string value and set it to the Unit being retrieved.
RowReaderUnit(ClassDescriptor) - Constructor for class gov.nih.nci.caarray.services.util.ojb.RowReaderUnit
 
run() - Method in class gov.nih.nci.caarray.services.fileparse.test.Tester
the applications main loop.
run(String, int) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls
 
run(String) - Method in class gov.nih.nci.caarray.services.security.test.GeneralSecuredElementUpdateTester
 
run() - Method in class gov.nih.nci.caarray.services.security.test.Tester
the applications main loop.
run(String) - Method in class gov.nih.nci.caarray.services.test.BaseInContainerTest
 
run(String) - Method in interface gov.nih.nci.caarray.services.test.InContainerTest
 
run() - Method in class gov.nih.nci.caarray.services.test.Tester
the applications main loop.
run() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
The run method to control the upload process.
run() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
the applications main loop.
run() - Method in class org.biomage.tools.helpers.DbConnectionBroker
Housekeeping thread.
runDeleteStatements(String, Object) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Runs delete statements for owned objects
runParser() - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
Run the parser
runParser() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprFileParseHandler
runs the parser
runTest(String, String, Properties) - Method in class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB
 
RuntimeCacheException - Exception in gov.nih.nci.caarray.services.util.cache
 
RuntimeCacheException() - Constructor for exception gov.nih.nci.caarray.services.util.cache.RuntimeCacheException
 
RuntimeCacheException(String) - Constructor for exception gov.nih.nci.caarray.services.util.cache.RuntimeCacheException
 
RuntimeCacheException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.cache.RuntimeCacheException
 
RuntimeCacheException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.cache.RuntimeCacheException
 

S

S - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
s_classLoader - Variable in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls
Class loader for access classes
SampleBaseForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleBaseForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
SampleDetailAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleDetailAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
SampleDetailForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleDetailForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
SampleSearchAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleSearchAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
SampleSearchForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleSearchForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
SampleUpdateAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateAction
 
SampleUpdateForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
SampleUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
save(PhysicalArrayDesign) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Saves an existing array design to the database.
save(PhysicalArrayDesign) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Stores the given array design to the database.
save(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
save(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Saves data for a HybridizationFileUploadEntry without saving (linking only) any associated MAGE objects.
save(CAFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
Saves data for a CAFileUploadEntry without saving (linking only) any associated MAGE objects.
save(HybridizationFileUploadEntry) - Method in class gov.nih.nci.caarray.services.hybridization.DbFileUploadEntrySaver
 
save(CAFileUploadEntry) - Method in class gov.nih.nci.caarray.services.hybridization.DbFileUploadEntrySaver
 
save(HybridizationFileUploadEntry) - Method in interface gov.nih.nci.caarray.services.hybridization.FileUploadEntrySaver
 
save(CAFileUploadEntry) - Method in interface gov.nih.nci.caarray.services.hybridization.FileUploadEntrySaver
 
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentFactorAction
 
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentGeneralInfoAction
 
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
saveAdditionalQualifier(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentAdditionalQualifierAction
 
saveAdditionalQualifier(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentNewAdditionalQualifierAction
 
saveAnnotation(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
saveArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
Alternate (to addArrayDesign) method for saving an array design -- assumes that the associated OntologyEntries are correct and stores all associated objects automatically.
saveBioAssay(BioAssay) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationManagerDB
 
saveBioAssayData(BioAssayData) - Method in class gov.nih.nci.caarray.services.fileparse2.HybridizationManagerDB
 
saveCompositeSequence(CompositeSequence, CompositeGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
saveContactor(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentContactAction
 
saveExperimentData(ExperimentData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
saveExperimentData(ExperimentData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
saveExternalDataCubeToFile(double[][][], String, boolean) - Static method in class gov.nih.nci.caarray.services.mageloader.CustomDataCubeIOHelpers
Description: Method for writing a cube of doubles to a text file.
saveExternalDataCubeToFile(double[][][], String, boolean) - Static method in class org.biomage.tools.helpers.ExternalDataCubeIOHelpers
Description: Method for writing a cube of doubles to a text file.
saveFeature(Feature, FeatureGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
savefeatureProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
saveFileData(HybridizationFileUploadEntrySummaryData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
saveHybridizationProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
saveImageProtocolInfo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentUploadHybridizationAction
 
saveList(Class, Object[], HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
saveList(String, Object[], HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
saveMAGEMLCallBack(Identifiable) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEReader
 
saveMeasurement(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
saveOriginal(Class, String, boolean) - Method in class gov.nih.nci.caarray.services.arraydesign.DesignElementRetrievalSettings
 
savePublication(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentPublicationAction
 
savePublication(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAddPublicationAction
 
saveQuality(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentQualityAction
 
saveReporter(Reporter, ReporterGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
saveSearch(Class, Object, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
saveTopLevelElements(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaver
 
SCALE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
scale - Variable in class org.biomage.HigherLevelAnalysis.NodeValue
The scale (linear, log10, ln, etc.) of the value.
scale - Variable in class org.biomage.QuantitationType.QuantitationType
Indication of how to interpret the value.
ScaleEnum - Enum in gov.nih.nci.caarray.services.bioassaydata.descriptor
Scale values used in QuantitationTypeDescriptors.
Scope(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
screenSize - Static variable in class org.biomage.tools.apps.annot.MageXMLConverter
 
SE - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
search(UserSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
search(GroupSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
search(ArrayDesignSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
search(ArraySearchCriteria, int, int) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
search(ArraySearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
search(PersonSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
search(OrganizationSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
search(HardwareSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
search(ProtocolSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
search(SoftwareSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
search(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
search(ArraySearchCriteria) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
search(ArraySearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
search(ArrayDesignSearchCriteria) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Searches ArrayDesign's that match the specifed ArrayDesignSearchCriteria.
search(HardwareSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
search(ProtocolSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
Searchs for Protocol's that match the specifed ProtocolSearchCriteria.
search(SoftwareSearchCriteria) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
search(VocabSearchCriteria) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
search(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
searchBioMaterials(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Deprecated. No uses appear to be found, possible dead code
searchBioMaterials(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioMaterials
searchBioSamples(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchBioSamples(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
deprecated No uses appear to be found, possible dead code
searchBioSamples(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchBioSamples(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSamples
searchBioSamples(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSamples
searchBioSamples(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSamples
searchBioSamples(BioMaterialSearchCriteria, int, int, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSamples
searchBioSamplesShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Perform a shallow search (used typically to populate pull-down lists in UI)
searchBioSamplesShallow(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Perform a shallow search (used typically to populate pull-down lists in UI)
searchBioSamplesShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Shallow search for BioSamples
searchBioSamplesShallow(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Shallow search for BioSamples
searchBioSources(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchBioSources(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Deprecated. No uses appear to be found, possible dead code
searchBioSources(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchBioSources(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSources
searchBioSources(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSources
searchBioSources(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSources
searchBioSources(BioMaterialSearchCriteria, int, int, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Searches BioSources
searchBioSourcesShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Perform a shallow search (used typically to populate pull-down lists in UI)
searchBioSourcesShallow(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
Perform a shallow search (used typically to populate pull-down lists in UI)
searchBioSourcesShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Shallow search for BioSources
searchBioSourcesShallow(BioMaterialSearchCriteria, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Shallow search for BioSources
SearchCriteriaConverter - Class in gov.nih.nci.caarray.services.util
 
SearchCriteriaConverter() - Constructor for class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
searchExperiments(ExperimentSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
searchExperiments(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
searchExperiments(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Searches Experiments
searchExperiments(ExperimentSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Searches Experiments pagesize 0 imples return averything.
searchFiles(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBatchDownloadAction
 
searchFileUploadHistory(FileUploadHistorySearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
searchFileUploadHistory(FileUploadHistorySearchCriteria) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
Searches FileUploadHistory
searchFileUploadHistory(FileUploadHistorySearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
Searches MAGEMLFileUploadEntries pagesize 0 imples return averything.
searchGroups(GroupSearchCriteria) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Gets a list of groups matching the criteria and returns a GroupData object for each.
searchLabeledExtracts(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchLabeledExtracts(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchLabeledExtracts(BioMaterialSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Search Label Extract
searchLabeledExtracts(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Search Label Extract
searchLabeledExtractsShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
searchLabeledExtractsShallow(BioMaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Shallow search for Label Extract
searchMAGEMLFileUploadEntries(MAGEMLFileUploadSearchCriteria) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
searchMAGEMLFileUploadEntries(MAGEMLFileUploadSearchCriteria) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
Searches Experiments
searchMAGEMLFileUploadEntries(MAGEMLFileUploadSearchCriteria, int, int) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
Searches MAGEMLFileUploadEntries pagesize 0 imples return averything.
searchOrganizations(OrganizationSearchCriteria) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Gets a list of users matching the criteria and returns a OrganizationDesc object for each.
searchOwner(SecuredElementItf[]) - Static method in class gov.nih.nci.caarray.services.util.SecurityUtils
 
searchOwnerOnly(SecuredElementItf[]) - Static method in class gov.nih.nci.caarray.services.util.SecurityUtils
 
searchPersons(PersonSearchCriteria) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Gets a list of users matching the criteria and returns a PersonDesc object for each.
searchResults - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
searchUsers(UserSearchCriteria) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Gets a list of users matching the criteria and returns a UserData object for each.
searchVisibility(ProtectionGroupData, SecuredElementItf[], String[]) - Static method in class gov.nih.nci.caarray.services.util.SecurityUtils
 
SecondaryInfo - Class in gov.nih.nci.caarray.services.security.mageom
 
SecondaryInfo() - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
SecondaryInfo(String, boolean) - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecondaryInfo
 
SECONDLINE - Static variable in class org.biomage.tools.generate_er.CreateMageER
second line in the MAGE_ER.xml file
seconds - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
SecuredElementBuilder - Interface in gov.nih.nci.caarray.services.security.test
 
securedElementClassName - Variable in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
SecuredElementData - Class in gov.nih.nci.caarray.common.data.security
 
SecuredElementData() - Constructor for class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
securedElementId - Variable in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
securedElementId - Variable in class org.biomage.Common.Extendable
 
SecuredElementIdUpdater - Interface in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementIdUpdaterFactory - Class in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementIdUpdaterFactory() - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecuredElementIdUpdaterFactory
 
SecuredElementIdUpdaterMDB - Class in gov.nih.nci.caarray.services.security.mageom.mdb
 
SecuredElementIdUpdaterMDB() - Constructor for class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
SecuredElementInfo - Class in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementInfo() - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecuredElementInfo
 
SecuredElementItf - Interface in gov.nih.nci.caarray.services.security.intf
An interface defines the get/set methods to be implemented by all objects which are secured elements.
SecuredElementOrphanHandler - Interface in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementOrphanHandlerFactory - Class in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementOrphanHandlerFactory() - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecuredElementOrphanHandlerFactory
 
SecuredElementUpdateListener - Class in gov.nih.nci.caarray.services.security.mageom
 
SecuredElementUpdateListener() - Constructor for class gov.nih.nci.caarray.services.security.mageom.SecuredElementUpdateListener
 
SecuredElementUpdateMessage - Class in gov.nih.nci.caarray.services.security.mageom.mdb
 
SecuredElementUpdateMessage(String, String) - Constructor for class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
Security - Class in org.biomage.AuditAndSecurity
Permission information for an object as to ownership, write and read permissions.
Security() - Constructor for class org.biomage.AuditAndSecurity.Security
Default constructor.
Security(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Security
Attribute constructor.
security - Variable in class org.biomage.Common.Describable
Information on the security for the instance of the class.
SECURITY_DATASOURCE - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
SECURITY_DATASOURCE_PASSWORD - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
SECURITY_DATASOURCE_USER - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
SECURITY_EXCEPTION_MSG - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
security_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Permission information for an object as to ownership, write and read permissions.
SecurityAdminService - Class in gov.nih.nci.caarray.services.security
This class provides the security admin services such as the creation/update/deletion of a protection element and assigning/de-assigning a protection element to a role.
SecurityAdminService() - Constructor for class gov.nih.nci.caarray.services.security.SecurityAdminService
Constructor for a new SecurityAdminService object.
SecurityConstants - Class in gov.nih.nci.caarray.services.util
This class defines constants that will be used in the application.
SecurityConstants() - Constructor for class gov.nih.nci.caarray.services.util.SecurityConstants
 
SecurityContextFilter - Class in gov.nih.nci.caarray.ui.core
Filter that sets the security information for the scope of the current request.
SecurityContextFilter() - Constructor for class gov.nih.nci.caarray.ui.core.SecurityContextFilter
 
SecurityDSConnectionUtil - Class in gov.nih.nci.caarray.services.security.db
Provides a means to perform database queries and updates against the Security XA datasource (Formerly known as JDBCConnection2 and refactored to current class)
SecurityDSConnectionUtil.CustomRowMap - Interface in gov.nih.nci.caarray.services.security.db
 
SecurityException - Exception in gov.nih.nci.caarray.services.exception
A generic Exception thrown by Security Services.
SecurityException() - Constructor for exception gov.nih.nci.caarray.services.exception.SecurityException
 
SecurityException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.SecurityException
 
SecurityException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.SecurityException
 
SecurityException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.exception.SecurityException
 
SecurityGroup - Class in org.biomage.AuditAndSecurity
Groups contacts together based on their security privileges.
SecurityGroup() - Constructor for class org.biomage.AuditAndSecurity.SecurityGroup
Default constructor.
SecurityGroup(Attributes) - Constructor for class org.biomage.AuditAndSecurity.SecurityGroup
Attribute constructor.
securityGroup_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Groups contacts together based on their security privileges.
securityGroups - Variable in class org.biomage.AuditAndSecurity.Security
Specifies which security groups have permission to view the associated object.
SecurityManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
Delegate class for security manager.
SecurityManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
 
SecurityManagerDelegate(int) - Constructor for class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Overloaded contructor to support Local/Remote EJB lookups.
SecurityManagerEJB - Class in gov.nih.nci.caarray.services.security.ejb
This class contains the implemention of the SecurityManager EJB.
SecurityManagerEJB() - Constructor for class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
 
SecurityObjFactory - Class in gov.nih.nci.caarray.services.security
This factory class creates security data service objects based on the environment configuration.
SecurityObjFactory() - Constructor for class gov.nih.nci.caarray.services.security.SecurityObjFactory
Constructor for a new SecurityObjFactory object.
SecurityServiceItf - Interface in gov.nih.nci.caarray.services.security.intf
An interface defines the generic properties of a security service object.
SecurityServiceObj - Class in gov.nih.nci.caarray.services.security
This class which implements SecurityServiceItf provides the authentication and authorization services and is independent of underlying security infrastructures.
SecurityServiceObj() - Constructor for class gov.nih.nci.caarray.services.security.SecurityServiceObj
Constructor for a new SecurityServiceObj object.
SecurityTester - Class in gov.nih.nci.caarray.services.security.test
 
SecurityTester() - Constructor for class gov.nih.nci.caarray.services.security.test.SecurityTester
 
SecurityTester(String) - Constructor for class gov.nih.nci.caarray.services.security.test.SecurityTester
 
SecurityUtils - Class in gov.nih.nci.caarray.services.util
 
SecurityUtils() - Constructor for class gov.nih.nci.caarray.services.util.SecurityUtils
 
selectBiomaterial(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAnnotationAction
 
selectedCharacteristics_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
SelectedFiles - Class in gov.nih.nci.caarray.services.util.fileuploadapplet
The SelectedFiles class is basically a list of the files to be uploaded and validates that all the required files are present.
SelectedFiles() - Constructor for class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
 
selectUseCase() - Method in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
selectUseCase() - Method in class gov.nih.nci.caarray.services.security.test.Tester
 
selectUseCase() - Method in class gov.nih.nci.caarray.services.test.Tester
 
selectUseCase() - Method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
semantics - Variable in class org.biomage.tools.generate_classes.CreateClassFile.MethodInformation
 
send(String, String, String, String) - Static method in class gov.nih.nci.caarray.common.util.SendMail
 
send(String, String, String, String, String) - Static method in class gov.nih.nci.caarray.common.util.SendMail
 
send(String, Message, long) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
send(String, Message) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
send(String, Message) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
send(String, Message, long) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
sendArrayDesignUploadMessage(ArrayDesignValues) - Method in class gov.nih.nci.caarray.services.fileparse.FileParsingDelegate
 
sendExperimentUploadMessage(UploadFileValues) - Method in class gov.nih.nci.caarray.services.fileparse.FileParsingDelegate
 
sendHybridizationUploadMessage(UploadFileValues) - Method in class gov.nih.nci.caarray.services.fileparse.FileParsingDelegate
 
sendMAGEMLGenerationMessage(MAGEMLFileValues) - Method in class gov.nih.nci.caarray.services.mageml.MAGEMLGeneratorDelegate
 
SendMail - Class in gov.nih.nci.caarray.common.util
 
sendMessage(String, String, String) - Method in class gov.nih.nci.caarray.services.fileupload2.DataJobHandlerImpl
 
sendRequest(String) - Method in class org.biomage.tools.helpers.JDBCConnection2
 
sendRequest2(String) - Method in class org.biomage.tools.helpers.JDBCConnection2
 
SeqFeature - Class in org.biomage.BioSequence
Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
SeqFeature() - Constructor for class org.biomage.BioSequence.SeqFeature
Default constructor.
SeqFeature(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeature
Attribute constructor.
SeqFeature.Basis - Class in org.biomage.BioSequence
Inner class for the enumeration values that the attribute basis can assume.
SeqFeatureLocation - Class in org.biomage.BioSequence
The location of the SeqFeature annotation.
SeqFeatureLocation() - Constructor for class org.biomage.BioSequence.SeqFeatureLocation
Default constructor.
SeqFeatureLocation(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeatureLocation
Attribute constructor.
SequenceInputFile - Class in gov.nih.nci.caarray.services.fileparse2.parsers
 
SequenceInputFile(String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
SequenceInputFile(String, String) - Constructor for class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
SequencePosition - Class in org.biomage.BioSequence
Designates the position of the Feature in its BioSequence.
SequencePosition() - Constructor for class org.biomage.BioSequence.SequencePosition
Default constructor.
SequencePosition(Attributes) - Constructor for class org.biomage.BioSequence.SequencePosition
Attribute constructor.
SERIAL - Static variable in class org.biomage.tools.generate_er.CreateMageER
type of the primary key for tables
SerializableFileUploadBean - Class in gov.nih.nci.caarray.services.fileupload2
The base/super class from which all persistable beans used for managing the file upload and parsing processes extend so only one OJB's sequence can be used to generate the objects' primary key.
SerializableFileUploadBean() - Constructor for class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean
 
SerializableFileUploadDataBean - Class in gov.nih.nci.caarray.common.data.fileupload2
 
SerializableFileUploadDataBean() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
 
serialVersionUID - Static variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
serialVersionUID - Static variable in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
ServerMessageConstants - Class in gov.nih.nci.caarray.services.exception
 
service(HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentFileDownloadServlet
 
ServiceLocator - Class in gov.nih.nci.caarray.services.util
This class is an implementation of the Service Locator pattern.
ServiceLookupException - Exception in gov.nih.nci.caarray.services.exception
This exception is used to indicate that an error occurs when a service is looked up using ServiceLocator.
ServiceLookupException(String) - Constructor for exception gov.nih.nci.caarray.services.exception.ServiceLookupException
Creates a new ServiceLookupException with the specified reason.
ServiceLookupException(Exception) - Constructor for exception gov.nih.nci.caarray.services.exception.ServiceLookupException
 
sessionCtx_ - Variable in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
setAbsoluteFilePath(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setAccession(String) - Method in class org.biomage.Description.DatabaseEntry
Set method for accession
setAccession(String) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry.OntologyDatabaseEntry
 
setAccessionNumber(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setAccessionNumber(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setAccessionNumber(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setAccessions(HasAccessions.Accessions_list) - Method in class org.biomage.BQS.BibliographicReference
Set method for accessions
setAccessions(HasAccessions.Accessions_list) - Method in interface org.biomage.Interface.HasAccessions
Set method for accessions
setAccessionVersion(String) - Method in class org.biomage.Description.DatabaseEntry
Set method for accessionVersion
setAction(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData
 
setAction(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm
 
setAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setAction(Audit.Action) - Method in class org.biomage.AuditAndSecurity.Audit
Set method for action
setAction(OntologyEntry) - Method in class org.biomage.BioMaterial.ActionProtocolTypeMap
 
setAction(OntologyEntry) - Method in class org.biomage.BioMaterial.Treatment
Set method for action
setAction(OntologyEntry) - Method in interface org.biomage.Interface.HasAction
Set method for action
setActionCommand(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setActionMeasurement(Measurement) - Method in class org.biomage.BioMaterial.Treatment
Set method for actionMeasurement
setActionMeasurement(Measurement) - Method in interface org.biomage.Interface.HasActionMeasurement
Set method for actionMeasurement
setActivityDate(Date) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setActivityDate(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setActivityDate(Date) - Method in class org.biomage.Protocol.ProtocolApplication
Set method for activityDate
setActivityDateAsString(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setAdditionalDataApplyProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalDataProcessData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalDataProcessDownloadPath(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalDataProcessingFile(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalDataProcessings(AdditionalDataProcessingData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setAdditionalFeatureColumns(List) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
setAdditionalFileUploadCancel(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalQualifierData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalQualifierDataID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalQualifierName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalQualifiers(AdditionalQualifierData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setAdditionalQualifierSource(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalQualifierValue(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalReporterFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setAdditionalReporterFileLocation(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setAdditionalReporterFileLocation(String) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
setAdditionalUploadedFileData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalUploadedFiles(AdditionalUploadedFileData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setAdditionalUploadFile(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAdditionalUploadFileDesc(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setAddress(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
setAddress(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
setAddress(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setAddress(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setAddress(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setAddress(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for address
setAddress1(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setAddress2(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setAdjustments(HasAdjustments.Adjustments_list) - Method in class org.biomage.Array.ArrayManufactureDeviation
Set method for adjustments
setAdjustments(HasAdjustments.Adjustments_list) - Method in interface org.biomage.Interface.HasAdjustments
Set method for adjustments
setAffiliation(long) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setAffiliation(long) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setAffiliation(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setAffiliation(Organization) - Method in class org.biomage.AuditAndSecurity.Person
Set method for affiliation
setAffiliation(Organization) - Method in interface org.biomage.Interface.HasAffiliation
Set method for affiliation
setAffiliationId(long) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setAffiliationName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setAffiliations(Collection) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setAge(Integer) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setAge(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMax(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMaxUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMaxUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMin(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMinUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeMinUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeOrRange(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setAgeTypes(String[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAgeValue(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setAllCharacteristics(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setAllele(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAllGroups(Collection) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setAllGroupsSelection(String[]) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setAllHardware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setAllHardware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setAllSoftware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setAllSoftware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setAllSoftware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setAllValues(ExtractData[]) - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
setAllValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
setAmount(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setAmountUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setAnalysisResults(HasAnalysisResults.AnalysisResults_list) - Method in class org.biomage.Experiment.Experiment
Set method for analysisResults
setAnalysisResults(HasAnalysisResults.AnalysisResults_list) - Method in interface org.biomage.Interface.HasAnalysisResults
Set method for analysisResults
setAnnotationId(int) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setAnnotations(HasAnnotations.Annotations_list) - Method in class org.biomage.Description.Description
Set method for annotations
setAnnotations(HasAnnotations.Annotations_list) - Method in class org.biomage.Experiment.ExperimentalFactor
Set method for annotations
setAnnotations(HasAnnotations.Annotations_list) - Method in interface org.biomage.Interface.HasAnnotations
Set method for annotations
setApplicationId(long) - Method in class gov.nih.nci.caarray.common.data.security.Role
Sets the applicationId for this Role object
setApplicationId(Long) - Static method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setApplyMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setApplyProtocol(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setApplyProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArchive_value(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setArchiveValue(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setArchiveValue(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setArray(ArrayData) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setArray(Array) - Method in class org.biomage.BioAssay.BioAssayCreation
Set method for array
setArray(Array) - Method in interface org.biomage.Interface.HasArray
Set method for array
setArray_list(Array_package.Array_list) - Method in class org.biomage.Array.Array_package
Set method for array_list
setArray_package(Array_package) - Method in class org.biomage.Common.MAGEJava
Set method for array_package
setArrayBatch(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayBatch(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayBatchName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setArrayBatchName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setArrayBatchName(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setArrayDesign(ArrayDesignData) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setArrayDesign(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setArrayDesign(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
 
setArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
 
setArrayDesign(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setArrayDesign(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayDesign(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayDesign(ArrayDesign) - Method in class org.biomage.Array.Array
Set method for arrayDesign
setArrayDesign(ArrayDesign) - Method in interface org.biomage.Interface.HasArrayDesign
Set method for arrayDesign
setArrayDesign_list(ArrayDesign_package.ArrayDesign_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Set method for arrayDesign_list
setArrayDesign_package(ArrayDesign_package) - Method in class org.biomage.Common.MAGEJava
Set method for arrayDesign_package
setArrayDesignDesc(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
setArrayDesignFile(ArrayDesignUploadedFileData) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setArrayDesignFileToken(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setArrayDesignFileTypeGroupMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
setArrayDesignFileUploadEntryData(ArrayDesignFileUploadEntryData) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
setArrayDesignId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setArrayDesignId(long) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setArrayDesignID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayDesignID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setArrayDesignID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setArrayDesignName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayDesigns(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setArrayGroup(ArrayGroup) - Method in class org.biomage.Array.Array
Set method for arrayGroup
setArrayGroup(ArrayGroup) - Method in interface org.biomage.Interface.HasArrayGroup
Set method for arrayGroup
setArrayGroup_list(Array_package.ArrayGroup_list) - Method in class org.biomage.Array.Array_package
Set method for arrayGroup_list
setArrayGroupBarCode(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayGroupDescription(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayGroupSpacingX(float) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayGroupSpacingY(float) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayGroupTemplateName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setArrayIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setArrayIdentifier(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setArrayIdentifier(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayIdentifier(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setArrayIdentifier(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setArrayIdentifier(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayIdentifier(String) - Method in class org.biomage.Array.Array
Set method for arrayIdentifier
setArrayIdentifier(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setArrayIdentifierId(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setArrayIdentifiers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setArrayIdentifiers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setArrayIdentifiers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setArrayLength(float) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayManufacture_list(Array_package.ArrayManufacture_list) - Method in class org.biomage.Array.Array_package
Set method for arrayManufacture_list
setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list) - Method in class org.biomage.Array.Array
Set method for arrayManufactureDeviations
setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations
Set method for arrayManufactureDeviations
setArrayManufacturers(OrganizationData[]) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for arrayManufacturers
setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list) - Method in interface org.biomage.Interface.HasArrayManufacturers
Set method for arrayManufacturers
setArrayName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setArrayNameArrayDesignName(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setArrayOrientationMark(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayOrientationMarkPosition(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrays(ArrayData[]) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayGroup
Set method for arrays
setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for arrays
setArrays(HasArrays.Arrays_list) - Method in interface org.biomage.Interface.HasArrays
Set method for arrays
setArraySearchPage(String, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
setArraySpacingX(Float) - Method in class org.biomage.Array.ArrayGroup
Set method for arraySpacingX
setArraySpacingY(Float) - Method in class org.biomage.Array.ArrayGroup
Set method for arraySpacingY
setArrayWidth(float) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setArrayXOrigin(Float) - Method in class org.biomage.Array.Array
Set method for arrayXOrigin
setArrayYOrigin(Float) - Method in class org.biomage.Array.Array
Set method for arrayYOrigin
setAssignedGroups(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setAsso(AssociationColumn) - Method in class org.biomage.tools.generate_er.Table
Description: set one association column
setAssociatedHardware(HardwareDesc) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setAssociatedSoftware(SoftwareDesc[]) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setAssociatedSoftware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setAssociations(HasAssociations.Associations_list) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Set method for associations
setAssociations(HasAssociations.Associations_list) - Method in class org.biomage.Description.OntologyEntry
Set method for associations
setAssociations(HasAssociations.Associations_list) - Method in interface org.biomage.Interface.HasAssociations
Set method for associations
setAssoColumnVec(Vector) - Method in class org.biomage.tools.generate_er.Table
Description: set the vector containing all association columns
setAtmosphere(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setAttachmentType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setAttachmentType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setAttachmentTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setAttachmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setAttachmentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setAttempts(int) - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
setAttributes(Attributes) - Method in class org.biomage.Array.Array
 
setAttributes(Attributes) - Method in class org.biomage.Array.ArrayGroup
 
setAttributes(Attributes) - Method in class org.biomage.Array.ArrayManufacture
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.CompositeGroup
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.DesignElementGroup
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.FeatureGroup
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.ReporterGroup
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.Zone
 
setAttributes(Attributes) - Method in class org.biomage.ArrayDesign.ZoneGroup
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.Contact
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.Organization
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.Person
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.Security
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
 
setAttributes(Attributes) - Method in class org.biomage.AuditAndSecurity.User
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.BioAssay
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.BioAssayCreation
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.BioAssayTreatment
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.Channel
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.DerivedBioAssay
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.FeatureExtraction
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.Hybridization
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.Image
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.ImageAcquisition
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.MeasuredBioAssay
 
setAttributes(Attributes) - Method in class org.biomage.BioAssay.PhysicalBioAssay
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.BioAssayData
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.BioAssayDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.BioAssayMap
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.DesignElementDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.DesignElementMap
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.FeatureDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.ReporterDimension
 
setAttributes(Attributes) - Method in class org.biomage.BioAssayData.Transformation
 
setAttributes(Attributes) - Method in class org.biomage.BioEvent.BioEvent
 
setAttributes(Attributes) - Method in class org.biomage.BioEvent.Map
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.BioMaterial
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.BioSample
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.BioSource
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.Compound
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.LabeledExtract
 
setAttributes(Attributes) - Method in class org.biomage.BioMaterial.Treatment
 
setAttributes(Attributes) - Method in class org.biomage.BioSequence.BioSequence
 
setAttributes(Attributes) - Method in class org.biomage.Common.Describable
 
setAttributes(Attributes) - Method in class org.biomage.Common.Extendable
 
setAttributes(Attributes) - Method in class org.biomage.Common.Identifiable
 
setAttributes(Attributes) - Method in class org.biomage.Description.Database
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.CompositeCompositeMap
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.CompositeSequence
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.DesignElement
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.Feature
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.FeatureReporterMap
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.Reporter
 
setAttributes(Attributes) - Method in class org.biomage.DesignElement.ReporterCompositeMap
 
setAttributes(Attributes) - Method in class org.biomage.Experiment.Experiment
 
setAttributes(Attributes) - Method in class org.biomage.Experiment.ExperimentalFactor
 
setAttributes(Attributes) - Method in class org.biomage.Experiment.FactorValue
 
setAttributes(Attributes) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
 
setAttributes(Attributes) - Method in class org.biomage.Protocol.Hardware
 
setAttributes(Attributes) - Method in class org.biomage.Protocol.Parameter
 
setAttributes(Attributes) - Method in class org.biomage.Protocol.Parameterizable
 
setAttributes(Attributes) - Method in class org.biomage.Protocol.Protocol
 
setAttributes(Attributes) - Method in class org.biomage.Protocol.Software
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.ConfidenceIndicator
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.DerivedSignal
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.Error
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.ExpectedValue
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.Failed
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.MeasuredSignal
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.PresentAbsent
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.PValue
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.QuantitationType
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.Ratio
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
 
setAttributes(Attributes) - Method in class org.biomage.QuantitationType.StandardQuantitationType
 
setAuditAndSecurity_package(AuditAndSecurity_package) - Method in class org.biomage.Common.MAGEJava
Set method for auditAndSecurity_package
setAuditTrail(HasAuditTrail.AuditTrail_list) - Method in class org.biomage.Common.Describable
Set method for auditTrail
setAuditTrail(HasAuditTrail.AuditTrail_list) - Method in interface org.biomage.Interface.HasAuditTrail
Set method for auditTrail
setAuthors(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setAuthors(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for authors
setBack(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setBack(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setBarcode(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setBarcode(String) - Method in class org.biomage.Array.ArrayGroup
Set method for barcode
setBarrierFacility(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBaseClass(String) - Method in class org.biomage.tools.generate_er.Table
Description: set the BaseClass of this table
setBaseClassCreateFile(CreateFile) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: sets the base class createFile.
setBasis(SeqFeature.Basis) - Method in class org.biomage.BioSequence.SeqFeature
Set method for basis
setBatch(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setBatchFileName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setBatchFileResults(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setBatchSize(int) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
setBedding(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list) - Method in class org.biomage.Description.Description
Set method for bibliographicReferences
setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list) - Method in interface org.biomage.Interface.HasBibliographicReferences
Set method for bibliographicReferences
setBioAssay(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayTuple
Set method for bioAssay
setBioAssay(BioAssay) - Method in interface org.biomage.Interface.HasBioAssay
Set method for bioAssay
setBioAssay_list(BioAssay_package.BioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package
Set method for bioAssay_list
setBioAssay_package(BioAssay_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioAssay_package
setBioAssayCreation(BioAssayCreation) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Set method for bioAssayCreation
setBioAssayCreation(BioAssayCreation) - Method in interface org.biomage.Interface.HasBioAssayCreation
Set method for bioAssayCreation
setBioAssayData(HasBioAssayData.BioAssayData_list) - Method in class org.biomage.Experiment.Experiment
Set method for bioAssayData
setBioAssayData(HasBioAssayData.BioAssayData_list) - Method in interface org.biomage.Interface.HasBioAssayData
Set method for bioAssayData
setBioAssayData_list(BioAssayData_package.BioAssayData_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for bioAssayData_list
setBioAssayData_package(BioAssayData_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioAssayData_package
setBioAssayDataCluster_list(HigherLevelAnalysis_package.BioAssayDataCluster_list) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
Set method for bioAssayDataCluster_list
setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list) - Method in class org.biomage.BioAssayData.Transformation
Set method for bioAssayDataSources
setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list) - Method in interface org.biomage.Interface.HasBioAssayDataSources
Set method for bioAssayDataSources
setBioAssayDimension(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData
Set method for bioAssayDimension
setBioAssayDimension(BioAssayDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Set method for bioAssayDimension
setBioAssayDimension(BioAssayDimension) - Method in interface org.biomage.Interface.HasBioAssayDimension
Set method for bioAssayDimension
setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for bioAssayDimension_list
setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list) - Method in class org.biomage.BioAssay.BioAssay
Set method for bioAssayFactorValues
setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list) - Method in interface org.biomage.Interface.HasBioAssayFactorValues
Set method for bioAssayFactorValues
setBioAssayId(Long) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
setBioAssayId(String) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
setBioAssayMap_list(BioAssayData_package.BioAssayMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for bioAssayMap_list
setBioAssayMapping(BioAssayMapping) - Method in class org.biomage.BioAssayData.Transformation
Set method for bioAssayMapping
setBioAssayMapping(BioAssayMapping) - Method in interface org.biomage.Interface.HasBioAssayMapping
Set method for bioAssayMapping
setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list) - Method in class org.biomage.BioAssayData.BioAssayMapping
Set method for bioAssayMaps
setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list) - Method in interface org.biomage.Interface.HasBioAssayMaps
Set method for bioAssayMaps
setBioAssayMapTarget(DerivedBioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap
Set method for bioAssayMapTarget
setBioAssayMapTarget(DerivedBioAssay) - Method in interface org.biomage.Interface.HasBioAssayMapTarget
Set method for bioAssayMapTarget
setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayDimension
Set method for bioAssays
setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.Experiment.Experiment
Set method for bioAssays
setBioAssays(HasBioAssays.BioAssays_list) - Method in interface org.biomage.Interface.HasBioAssays
Set method for bioAssays
setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Set method for bioAssayTreatments
setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list) - Method in interface org.biomage.Interface.HasBioAssayTreatments
Set method for bioAssayTreatments
setBioAssayTuples(HasBioAssayTupleData.BioAssayTuples_list) - Method in class org.biomage.BioAssayData.BioDataTuples
Set method for bioAssayTuples
setBioAssayTuples(HasBioAssayTupleData.BioAssayTuples_list) - Method in interface org.biomage.Interface.HasBioAssayTupleData
Set method for bioAssayTuples
setBioDataValues(BioDataValues) - Method in class org.biomage.BioAssayData.BioAssayData
Set method for bioDataValues
setBioDataValues(BioDataValues) - Method in interface org.biomage.Interface.HasBioDataValues
Set method for bioDataValues
setBioEvent_package(BioEvent_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioEvent_package
setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list) - Method in class org.biomage.DesignElement.CompositeSequence
Set method for biologicalCharacteristics
setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics
Set method for biologicalCharacteristics
setBioMaterial(BioMaterial) - Method in class org.biomage.Array.ManufactureLIMS
Set method for bioMaterial
setBioMaterial(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
Set method for bioMaterial
setBioMaterial(BioMaterial) - Method in interface org.biomage.Interface.HasBioMaterial
Set method for bioMaterial
setBioMaterial_list(BioMaterial_package.BioMaterial_list) - Method in class org.biomage.BioMaterial.BioMaterial_package
Set method for bioMaterial_list
setBioMaterial_package(BioMaterial_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioMaterial_package
setBiomaterialCharacteristics(VocabData[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiomaterialCharacteristics(VocabData[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setBiomaterialCharacteristics(VocabData[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setBiomaterialId(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setBioMaterialName(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setBioMaterialPlateCol(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateCol
setBioMaterialPlateIdentifier(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateIdentifier
setBioMaterialPlateRow(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
Set method for bioMaterialPlateRow
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setBiometricHeight(float) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricHeightUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricHeightUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricHeightUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricWeight(float) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricWeightUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricWeightUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiometricWeightUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setBiosampleId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setBiosamples(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setBioSampleType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleDesc
 
setBioSequence_list(BioSequence_package.BioSequence_list) - Method in class org.biomage.BioSequence.BioSequence_package
Set method for bioSequence_list
setBioSequence_package(BioSequence_package) - Method in class org.biomage.Common.MAGEJava
Set method for bioSequence_package
setBiosourceId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setBiosourceName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setBiosources(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setBiosourceType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setBioSourceType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceDesc
 
setBiosourceType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setBiosourceTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setBiosourceTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setBlock(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setBQS_package(BQS_package) - Method in class org.biomage.Common.MAGEJava
Set method for bQS_package
setButton(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setButtonName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setCaArrayDesignFileEntry(CAArrayDesignFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
setCaArrayDesignFileEntryData(CAArrayDesignFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setCaFileEntryData(CAFileUploadEntryData) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
setCaFileUploadHistory(CAFileUploadHistory) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
setCaFileUploadHistoryData(CAFileUploadHistoryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setCallBack(DatabaseImportMAGEReader) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
setCaMagemlFileEntry(CAMagemlFileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
setCaMagemlFileEntryData(CAMagemlFileUploadEntryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setCanBeNull(String) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the canBeNull field of this column
setCancel(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setCancelURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setCanReload(boolean) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
setCanRepair(boolean) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
setCascade(String) - Method in class org.biomage.tools.generate_er.ForeignKey
Description: set if the foreign table owns this table
setCascadeDelete(PersistenceBroker, Class, String, int) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
setCascadeRetrieve(PersistenceBroker, Class, String, boolean) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
setCascadeStore(PersistenceBroker, Class, String, int) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
setCascadingStore(ClassDescriptor, String, int) - Static method in class gov.nih.nci.caarray.services.util.ojb.PBLifeCycleAdapter
 
setCategory(String) - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
setCategory(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setCategory(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setCategory(String) - Method in class org.biomage.Description.Database
 
setCategory(String) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
setCategory(String) - Method in class org.biomage.Description.OntologyEntry
Set method for category
setCategory(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor
Set method for category
setCategory(OntologyEntry) - Method in interface org.biomage.Interface.HasCategory
Set method for category
setCategory(String) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
setCel_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setCelFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setCelFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setCelFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setCellLine(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCellLineId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCellLines(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCellType(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCellTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCellTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setChannel(Channel) - Method in interface org.biomage.Interface.HasChannel
Set method for channel
setChannel(Channel) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for channel
setChannel_list(BioAssay_package.Channel_list) - Method in class org.biomage.BioAssay.BioAssay_package
Set method for channel_list
setChannelId(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setChannelOne(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setChannelOneExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelOneExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelOneExtract(LabeledExtract) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannelOneFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelOneFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelOneFactorValues(FactorValue[]) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannelOneSpike(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setChannelOneSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelOneSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelOneSpikedControl(LabeledExtract) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.BioAssay
Set method for channels
setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.Image
Set method for channels
setChannels(HasChannels.Channels_list) - Method in interface org.biomage.Interface.HasChannels
Set method for channels
setChannelTwo(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setChannelTwoExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setChannelTwoExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelTwoExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelTwoExtract(LabeledExtract) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannelTwoExtract(LabeledExtract) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setChannelTwoFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setChannelTwoFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelTwoFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelTwoFactorValues(FactorValue[]) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannelTwoFactorValues(ArrayList) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setChannelTwoSpike(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setChannelTwoSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setChannelTwoSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setChannelTwoSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setChannelTwoSpikedControl(LabeledExtract) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setChannelTwoSpikedControl(LabeledExtract) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setCharacteristics(VocabData[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
setCharacteristics(HasCharacteristics.Characteristics_list) - Method in class org.biomage.BioMaterial.BioMaterial
Set method for characteristics
setCharacteristics(HasCharacteristics.Characteristics_list) - Method in interface org.biomage.Interface.HasCharacteristics
Set method for characteristics
setCharList(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setChp_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setChpFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setChpFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setChpFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setChromosomalAberrationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setChromosomalAberrations(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setChromosomalAberrationTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setChromosomalAberrationTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setCity(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setCity(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setCity(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setClinicalHistory(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setClinicalTest(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setClinicalTreatment(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setClusterBioAssayData(BioAssayData) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Set method for clusterBioAssayData
setClusterBioAssayData(BioAssayData) - Method in interface org.biomage.Interface.HasClusterBioAssayData
Set method for clusterBioAssayData
setColumn(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setColumn(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
setColumn(Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setColumn(Integer) - Method in class org.biomage.ArrayDesign.Zone
Set method for column
setColumn(Integer) - Method in class org.biomage.DesignElement.FeatureLocation
Set method for column
setColumnDelimiter(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTableMap
 
setColumnId(String) - Method in class org.biomage.tools.generate_er.ForeignKey
Description: set the column id of the foreign key
setColumnNames(String[]) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Sets the column names that are to be read.
setColumnNumber(long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
setColumnOrder(String[]) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method setColumnOrder.
setComment(String) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the Comment of this column
setComment(String) - Method in class org.biomage.tools.generate_er.Table
Description: set the Comment of this table
setCompleteDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setCompletionDate(Date) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setComponentCompounds(HasComponentCompounds.ComponentCompounds_list) - Method in class org.biomage.BioMaterial.Compound
Set method for componentCompounds
setComponentCompounds(HasComponentCompounds.ComponentCompounds_list) - Method in interface org.biomage.Interface.HasComponentCompounds
Set method for componentCompounds
setComposite(CompositeSequence) - Method in class org.biomage.DesignElement.CompositePosition
Set method for composite
setComposite(CompositeSequence) - Method in interface org.biomage.Interface.HasComposite
Set method for composite
setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
Set method for compositeCompositeMap_list
setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence
Set method for compositeCompositeMaps
setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps
Set method for compositeCompositeMaps
setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Set method for compositeGroup_list
setCompositeGroupId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
setCompositeGroups(HasCompositeGroups.CompositeGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for compositeGroups
setCompositeGroups(HasCompositeGroups.CompositeGroups_list) - Method in interface org.biomage.Interface.HasCompositeGroups
Set method for compositeGroups
setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Set method for compositePositionSources
setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list) - Method in interface org.biomage.Interface.HasCompositePositionSources
Set method for compositePositionSources
setCompositeSequence(CompositeSequence) - Method in class org.biomage.DesignElement.CompositeCompositeMap
Set method for compositeSequence
setCompositeSequence(CompositeSequence) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Set method for compositeSequence
setCompositeSequence(CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequence
Set method for compositeSequence
setCompositeSequence_list(DesignElement_package.CompositeSequence_list) - Method in class org.biomage.DesignElement.DesignElement_package
Set method for compositeSequence_list
setCompositeSequences(CompositeSequenceData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.ArrayDesign.CompositeGroup
Set method for compositeSequences
setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
Set method for compositeSequences
setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in interface org.biomage.Interface.HasCompositeSequences
Set method for compositeSequences
setCompound(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData
 
setCompound(Compound) - Method in class org.biomage.BioMaterial.CompoundMeasurement
Set method for compound
setCompound(Compound) - Method in interface org.biomage.Interface.HasCompound
Set method for compound
setCompound_list(BioMaterial_package.Compound_list) - Method in class org.biomage.BioMaterial.BioMaterial_package
Set method for compound_list
setCompoundData(CompoundMeasurementData) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundID(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundIndices(HasCompoundIndices.CompoundIndices_list) - Method in class org.biomage.BioMaterial.Compound
Set method for compoundIndices
setCompoundIndices(HasCompoundIndices.CompoundIndices_list) - Method in interface org.biomage.Interface.HasCompoundIndices
Set method for compoundIndices
setCompoundMData(CompoundMeasurementData[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setCompoundMData(CompoundMeasurementData[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setCompoundMeasurements(CompoundMeasurementData[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setCompoundMeasurements(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundMeasurements(List) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list) - Method in class org.biomage.BioMaterial.Treatment
Set method for compoundMeasurements
setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list) - Method in interface org.biomage.Interface.HasCompoundMeasurements
Set method for compoundMeasurements
setCompoundmeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundmeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundmeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundmeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundmeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundmeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundmeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundmeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundmeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundModifyUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompoundOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompoundOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setCompounds(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCompounds(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list) - Method in interface org.biomage.Interface.HasConfidenceIndicators
Set method for confidenceIndicators
setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for confidenceIndicators
setConfirmPassword(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setContact(ContactData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData
 
setContact(ContactData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData
 
setContact(long) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setContact(PersonData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setContact(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setContact(Person) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setContact(Contact) - Method in class org.biomage.ArrayDesign.DesignProviderRole
 
setContact(Contact) - Method in class org.biomage.Experiment.ExperimentProviderRole
 
setContact_list(AuditAndSecurity_package.Contact_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Set method for contact_list
setContactId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setContactId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setContactID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setContactor(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setContactor(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setContacts(HasContacts.Contacts_list) - Method in class org.biomage.Description.Database
Set method for contacts
setContacts(HasContacts.Contacts_list) - Method in interface org.biomage.Interface.HasContacts
Set method for contacts
setContainedFeatures(HasContainedFeatures.ContainedFeatures_list) - Method in class org.biomage.BioAssayData.FeatureDimension
Set method for containedFeatures
setContainedFeatures(HasContainedFeatures.ContainedFeatures_list) - Method in interface org.biomage.Interface.HasContainedFeatures
Set method for containedFeatures
setContentType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setContentType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setContentType(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setContentType(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setContentType(String) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setContentType(String) - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Sets the content type for this file.
setControlFeatures(HasControlFeatures.ControlFeatures_list) - Method in class org.biomage.DesignElement.Feature
Set method for controlFeatures
setControlFeatures(HasControlFeatures.ControlFeatures_list) - Method in interface org.biomage.Interface.HasControlFeatures
Set method for controlFeatures
setControlledFeatures(HasControlledFeatures.ControlledFeatures_list) - Method in class org.biomage.DesignElement.Feature
Set method for controlledFeatures
setControlledFeatures(HasControlledFeatures.ControlledFeatures_list) - Method in interface org.biomage.Interface.HasControlledFeatures
Set method for controlledFeatures
setControlType(OntologyEntry) - Method in class org.biomage.DesignElement.DesignElement
Set method for controlType
setControlType(OntologyEntry) - Method in interface org.biomage.Interface.HasControlType
Set method for controlType
setCoordinate(SequencePosition) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for coordinate
setCoordinate(SequencePosition) - Method in interface org.biomage.Interface.HasCoordinate
Set method for coordinate
setCopied(Boolean) - Method in class org.biomage.BioMaterial.BioMaterial
 
setCopyLabelExtract(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setCopyLabelExtractChannel2(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setCopySpikeControl(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setCopySpikeControlChannel2(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setCountry(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setCountry(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setCountry(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setCrc32(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setCreatingSoftware(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setCreatingSoftwareVersion(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setCreationDate(Date) - Method in class gov.nih.nci.caarray.common.data.util.FileData
 
setCreationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setCreationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setCreationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setCreationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setCreationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setCube(Object[][][], String) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFCreator
The cube has our expression data, the order tells us the dimensions
setCultivarOrEcotype(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm
 
setCuratorMessage(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setCurrentSelection(long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
setDarrayDesignID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setData(byte[]) - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
setData(DataColumn) - Method in class org.biomage.tools.generate_er.Table
Description: set one simple data column
setDataAccessMode(String) - Static method in class gov.nih.nci.caarray.services.fileparse.test.Tester
 
setDataAccessMode(String) - Static method in class gov.nih.nci.caarray.services.security.test.Tester
 
setDataAccessMode(String) - Static method in class gov.nih.nci.caarray.services.test.Tester
 
setDataAccessMode(String) - Static method in class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
setDatabase(DatabaseData) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
setDatabase(Database) - Method in class org.biomage.Description.DatabaseEntry
Set method for database
setDatabase(Database) - Method in interface org.biomage.Interface.HasDatabase
Set method for database
setDatabase_list(Description_package.Database_list) - Method in class org.biomage.Description.Description_package
Set method for database_list
setDatabaseId(long) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDatabaseName(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDatabaseReference(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setDatabaseReference(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list) - Method in class org.biomage.Description.Description
Set method for databaseReferences
setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list) - Method in interface org.biomage.Interface.HasDatabaseReferences
Set method for databaseReferences
setDatabases(DatabaseData[]) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDatabases(int, Object) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDatabaseVersion(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDataColumn(DataColumn) - Method in class org.biomage.tools.generate_er.PrimaryKey
Description: set the primary key column
setDataColumnVec(Vector) - Method in class org.biomage.tools.generate_er.Table
Description: set the vector containing all simple data columns
setDataExternal(DataExternal) - Method in class org.biomage.BioAssayData.BioDataCube
Set method for dataExternal
setDataFile(File) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
setDataFormat(String) - Method in class org.biomage.BioAssayData.DataExternal
Set method for dataFormat
setDataFormatInfoURI(String) - Method in class org.biomage.BioAssayData.DataExternal
Set method for dataFormatInfoURI
setDataHeader(BasicDynaBean) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSet
 
setDataHeaderMap(DataHeaderMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
setDataIdsInForm(ArrayDesignData, ArrayDesignAddUpdateForm) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
setDataInternal(DataInternal) - Method in class org.biomage.BioAssayData.BioDataCube
Set method for dataInternal
setDataNamesInForm(ArrayDesignData, ArrayDesignBaseForm) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
setDataNamesInForm(ArrayDesignView, ArrayDesignDetailForm) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
setDataProcessHardwareParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessHardwareSerialNumber(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessProtocolDescription(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessProtocolParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessProtocolPerformers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessSoftwareParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessSoftwareReleaseDate(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessSoftwareVersion(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataProcessURI(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDataSetMapperMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.util.DataSetMapperMap
 
setDataTable(DataTable) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSet
 
setDataTableMap(DataTableMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
setDataType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
setDataType(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setDataType(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Set method for dataType
setDataType(OntologyEntry) - Method in interface org.biomage.Interface.HasDataType
Set method for dataType
setDataType(OntologyEntry) - Method in class org.biomage.Protocol.Parameter
Set method for dataType
setDataType(OntologyEntry) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for dataType
setDataTypeId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setDataTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setDate(Date) - Method in class org.biomage.AuditAndSecurity.Audit
Set method for date
setDatum(Datum) - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
Set method for datum
setDbName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
setDefaultURL(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setDefaultURL(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setDefaultURL(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setDefaultValue(MeasurementData) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
setDefaultValue(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setDefaultValue(Measurement) - Method in interface org.biomage.Interface.HasDefaultValue
Set method for defaultValue
setDefaultValue(Measurement) - Method in class org.biomage.Protocol.Parameter
Set method for defaultValue
setDefectType(OntologyEntry) - Method in class org.biomage.Array.FeatureDefect
Set method for defectType
setDefectType(OntologyEntry) - Method in class org.biomage.Array.ZoneDefect
Set method for defectType
setDefectType(OntologyEntry) - Method in interface org.biomage.Interface.HasDefectType
Set method for defectType
setDeleteAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setDeleted(boolean) - Method in class org.biomage.ArrayDesign.ArrayDesign
Mark this ArrayDesign as deleted.
setDeleted(boolean) - Method in class org.biomage.BioAssay.BioAssay
Marks if this BioAssay is deleted.
setDeleted(boolean) - Method in class org.biomage.Experiment.Experiment
Sets if this Experiment is deleted.
setDeleteLabel(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setDeltaX(Float) - Method in class org.biomage.Array.PositionDelta
Set method for deltaX
setDeltaY(Float) - Method in class org.biomage.Array.PositionDelta
Set method for deltaY
setDepartment(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setDepartment(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setDepartment(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setDept(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setDerivedBioAssay(DerivedBioAssay) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setDerivedBioAssay(DerivedBioAssay) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list) - Method in class org.biomage.BioAssay.DerivedBioAssay
Set method for derivedBioAssayData
setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list) - Method in interface org.biomage.Interface.HasDerivedBioAssayData
Set method for derivedBioAssayData
setDerivedBioAssayDataTarget(DerivedBioAssayData) - Method in class org.biomage.BioAssayData.Transformation
Set method for derivedBioAssayDataTarget
setDerivedBioAssayDataTarget(DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayDataTarget
Set method for derivedBioAssayDataTarget
setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list) - Method in class org.biomage.BioAssay.DerivedBioAssay
Set method for derivedBioAssayMap
setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list) - Method in interface org.biomage.Interface.HasDerivedBioAssayMap
Set method for derivedBioAssayMap
setDesc(ArrayGroupDesc) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setDesc(ArrayDesignDesc) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setDesc(CompositeGroupDesc) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData
 
setDesc(FeatureGroupDesc) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupData
 
setDesc(ReporterGroupDesc) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupData
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleData
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData
 
setDesc(BioMaterialDesc) - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
setDesc(OrganizationDesc) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
setDesc(PersonDesc) - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
setDesc(CompositeSequenceDesc) - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceData
 
setDesc(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
setDesc(HardwareDesc) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
setDesc(ProtocolDesc) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setDesc(SoftwareDesc) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setDesc(UserDesc) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setDesc(VocabDesc) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Sets the description of the specific status change for the uploaded file (can be null)
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Sets the description of the specific status change for the uploaded file (can be null)
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setDescription(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
setDescription(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Sets the description of the specific status change for the uploaded file (can be null)
setDescription(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setDescription(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Sets the description of the specific status change for the uploaded file (can be null)
setDescription(String) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setDescription(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setDescription(String) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Set method for description
setDescription(String) - Method in class org.biomage.Description.OntologyEntry
Set method for description
setDescription(String) - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
setDescription_(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setDescription_package(Description_package) - Method in class org.biomage.Common.MAGEJava
Set method for description_package
setDescriptions(HasDescriptions.Descriptions_list) - Method in class org.biomage.Common.Describable
Set method for descriptions
setDescriptions(HasDescriptions.Descriptions_list) - Method in interface org.biomage.Interface.HasDescriptions
Set method for descriptions
setDesignElement(DesignElement) - Method in class org.biomage.BioAssayData.DesignElementTuple
Set method for designElement
setDesignElement(DesignElement) - Method in interface org.biomage.Interface.HasDesignElement
Set method for designElement
setDesignElement_package(DesignElement_package) - Method in class org.biomage.Common.MAGEJava
Set method for designElement_package
setDesignElementColumn2PropertyMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
setDesignElementColumnsMap(DesignElementColumnsMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
setDesignElementDimension(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData
Set method for designElementDimension
setDesignElementDimension(DesignElementDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Set method for designElementDimension
setDesignElementDimension(DesignElementDimension) - Method in interface org.biomage.Interface.HasDesignElementDimension
Set method for designElementDimension
setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for designElementDimension_list
setDesignElementId(long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
setDesignElementId(long) - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingDesignElement
 
setDesignElementMapping(DesignElementMapping) - Method in class org.biomage.BioAssayData.Transformation
Set method for designElementMapping
setDesignElementMapping(DesignElementMapping) - Method in interface org.biomage.Interface.HasDesignElementMapping
Set method for designElementMapping
setDesignElementMaps(HasDesignElementMaps.DesignElementMaps_list) - Method in class org.biomage.BioAssayData.DesignElementMapping
Set method for designElementMaps
setDesignElementMaps(HasDesignElementMaps.DesignElementMaps_list) - Method in interface org.biomage.Interface.HasDesignElementMaps
Set method for designElementMaps
setDesignElementProperties(String[]) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
setDesignElementTuples(HasDesignElementTuples.DesignElementTuples_list) - Method in class org.biomage.BioAssayData.BioAssayTuple
Set method for designElementTuples
setDesignElementTuples(HasDesignElementTuples.DesignElementTuples_list) - Method in interface org.biomage.Interface.HasDesignElementTuples
Set method for designElementTuples
setDesignProviderRoles(DesignProviderRoleData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
setDesignProviderRoles(ArrayList) - Method in class org.biomage.ArrayDesign.ArrayDesign
The specified providerRoles must be instantiable List subclass for creation by reflection to work.
setDesignProviders(HasDesignProviders.DesignProviders_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for designProviders
setDesignProviders(HasDesignProviders.DesignProviders_list) - Method in interface org.biomage.Interface.HasDesignProviders
Set method for designProviders
setDestination(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setDevelopmentalStage(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDevelopmentalStageId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDevelopmentalStages(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDfactorNameID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDfactorValueID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setDirectory(String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
setDiseaseLocation(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseLocationId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseLocations(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseStage(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseStageId(long[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseStages(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseState(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseStateId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDiseaseStates(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setDisplayName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
setDistanceUnit(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setDistanceUnit(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.ArrayGroup
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.Fiducial
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.PositionDelta
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.Zone
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneLayout
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in class org.biomage.DesignElement.Position
Set method for distanceUnit
setDistanceUnit(DistanceUnit) - Method in interface org.biomage.Interface.HasDistanceUnit
Set method for distanceUnit
setDocumentLocator(Locator) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
This method is called by the parser to set the current file location information for this class for use to track line numbers being parsed.
setDocumentLocator(Locator) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
setDoneParsing(boolean) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
 
setDoneParsing(boolean) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
 
setDoneParsing(boolean) - Method in interface gov.nih.nci.caarray.services.util.parse.Notifiable
 
setEditable(boolean) - Method in interface gov.nih.nci.caarray.common.data.util.DataDescInterface
 
setEditable(boolean) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setEditable(boolean) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setEditor(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setEditor(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for editor
setEfficientDesignElementRetrieval() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Changes OJB auto-retrieval for design elements to false for all objects associated with design elements.
setEfficientDesignElementRetrieval() - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Changes OJB auto-retrieval for design elements to false for all objects associated with design elements.
setEfficientDesignElementRetrieval() - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
setEfficientDesignElementRetrieval() - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
setElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
set ProtectionGroups for a securedElement/Object
setElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
set ProtectionGroups for a securedElement/Object
setElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
set ProtectionGroups for a securedElement/Object
setElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
set ProtectionGroups for a securedElement/Object
setElementTypes(List) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.CollectionField
 
setEmail(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
setEmail(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
setEmail(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setEmail(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setEmail(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setEmail(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setEmail(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setEmail(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for email
setEmailAddress(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setEmailAddress(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setEmailAddress(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setEmailAddress(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setEmailAddress(String) - Method in class org.biomage.AuditAndSecurity.User
 
setEmailSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setEnd(Integer) - Method in class org.biomage.BioSequence.SequencePosition
Set method for end
setEndAtLine(int) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Sets the endAtLine.
setEndDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setEndDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setEndDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setEndDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setEndJumptoUrl(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setEndManufactureDate(Date) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setEnumVector(Vector) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the all enum values
setEnvironmentalHistoryDesign(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setError(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setErrorCode(String) - Method in exception gov.nih.nci.caarray.common.exception.GeneralException
 
setErrors(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setEventOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setEventOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setExp_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperiment(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
setExperiment(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
setExperiment(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setExperiment(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setExperiment(ExperimentDesc) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setExperiment(Experiment) - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
setExperiment(Experiment) - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
setExperiment(Experiment) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setExperiment_list(Experiment_package.Experiment_list) - Method in class org.biomage.Experiment.Experiment_package
Set method for experiment_list
setExperiment_package(Experiment_package) - Method in class org.biomage.Common.MAGEJava
Set method for experiment_package
setExperimentalFactor(ExperimentalFactor) - Method in class org.biomage.Experiment.FactorValue
Set method for experimentalFactor
setExperimentalFactor(ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactor
Set method for experimentalFactor
setExperimentalFactors(ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for experimentalFactors
setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list) - Method in interface org.biomage.Interface.HasExperimentalFactors
Set method for experimentalFactors
setExperimentCompleteDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentCompleteDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentCompleteDate_(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentDesc(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setExperimentDesigns(HasExperimentDesigns.ExperimentDesigns_list) - Method in class org.biomage.Experiment.Experiment
Set method for experimentDesigns
setExperimentDesigns(HasExperimentDesigns.ExperimentDesigns_list) - Method in interface org.biomage.Interface.HasExperimentDesigns
Set method for experimentDesigns
setExperimentFactorData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentFactorScaleID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentFactorTypeID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentId(Long) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
setExperimentMAGEMLData(FileData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setExperimentName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setExperimentOwnedByCurrentUser(boolean) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentProviderRoles(ExperimentProviderRoleData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setExperimentSearchTypeID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setExperimentTitle(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentTitle(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setExperimentTitle(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentTitle_(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentType(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setExperimentType(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExperimentType(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setExperimentType(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentType_(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setExperimentTypeID(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setExperimentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setExperimentVisibilities(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setExpFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setExpFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setExpFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setExpId(String) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setExpId(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExpId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
` * @param expId The expId to set.
setExpId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setExpId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setExportedFromDB(String) - Method in class org.biomage.Description.ExternalReference
Set method for exportedFromDB
setExportedFromServer(String) - Method in class org.biomage.Description.ExternalReference
Set method for exportedFromServer
setExportID(String) - Method in class org.biomage.Description.ExternalReference
Set method for exportID
setExportName(String) - Method in class org.biomage.Description.ExternalReference
Set method for exportName
setExternalLIMS(DatabaseEntry) - Method in class org.biomage.BioMaterial.Compound
Set method for externalLIMS
setExternalLIMS(DatabaseEntry) - Method in interface org.biomage.Interface.HasExternalLIMS
Set method for externalLIMS
setExternalReference(ExternalReference) - Method in class org.biomage.Description.Description
Set method for externalReference
setExternalReference(ExternalReference) - Method in interface org.biomage.Interface.HasExternalReference
Set method for externalReference
setExtract(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setExtract(ExtractDropDownData) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setExtract(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExtract(LabeledExtract) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setExtractCh2(ExtractDropDownData) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setExtractID(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setExtractID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setExtractIDCh2(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFactorForChannelOne(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFactorForChannelOne(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setFactorForChannelTwo(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFactorForChannelTwo(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setFactorID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorLevel(FactorDropDownData[]) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setFactorLevelCh2(FactorDropDownData[]) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setFactorLevelChOne(FactorDropDownData[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFactorLevelChTwo(FactorDropDownData[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFactorLevels(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setFactorName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFactorDataObject
 
setFactorNames(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorNames(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setFactorTypes(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorValue(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorValue(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFactorDataObject
 
setFactorValueID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
setFactorValues(FactorValueData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setFactorValues(HasFactorValues.FactorValues_list) - Method in class org.biomage.Experiment.ExperimentalFactor
Set method for factorValues
setFactorValues(ArrayList) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setFactorValues(HasFactorValues.FactorValues_list) - Method in interface org.biomage.Interface.HasFactorValues
Set method for factorValues
setFactTypes(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFactTypes(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setFailTypes(HasFailTypes.FailTypes_list) - Method in class org.biomage.DesignElement.Reporter
Set method for failTypes
setFailTypes(HasFailTypes.FailTypes_list) - Method in interface org.biomage.Interface.HasFailTypes
Set method for failTypes
setFailureDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
setFailureDescription(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setFailureDescription(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
setFailureMessage() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
 
setFamilyHistory(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setFax(String) - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
setFax(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for fax
setFaxNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setFaxNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setFaxNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setFeature(Feature) - Method in class org.biomage.Array.FeatureDefect
Set method for feature
setFeature(Feature) - Method in class org.biomage.Array.ManufactureLIMS
Set method for feature
setFeature(Feature) - Method in class org.biomage.DesignElement.FeatureInformation
Set method for feature
setFeature(Feature) - Method in interface org.biomage.Interface.HasFeature
Set method for feature
setFeatureActivateDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureActivateDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setFeatureData(GalFeatureData[]) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
 
setFeatureDefects(HasFeatureDefects.FeatureDefects_list) - Method in class org.biomage.Array.ArrayManufactureDeviation
Set method for featureDefects
setFeatureDefects(HasFeatureDefects.FeatureDefects_list) - Method in interface org.biomage.Interface.HasFeatureDefects
Set method for featureDefects
setFeatureDiameter(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setFeatureExtraction(FeatureExtraction) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Set method for featureExtraction
setFeatureExtraction(FeatureExtraction) - Method in interface org.biomage.Interface.HasFeatureExtraction
Set method for featureExtraction
setFeatureExtractionProtocol(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setFeatureExtractionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setFeatureExtractionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setFeatureExtractionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setFeatureGroup(FeatureGroup) - Method in class org.biomage.DesignElement.Feature
Set method for featureGroup
setFeatureGroup(FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroup
Set method for featureGroup
setFeatureGroupId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setFeatureGroups(HasFeatureGroups.FeatureGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for featureGroups
setFeatureGroups(HasFeatureGroups.FeatureGroups_list) - Method in interface org.biomage.Interface.HasFeatureGroups
Set method for featureGroups
setFeatureHeight(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setFeatureHeight(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setFeatureHeight(Float) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for featureHeight
setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list) - Method in class org.biomage.DesignElement.FeatureReporterMap
Set method for featureInformationSources
setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list) - Method in interface org.biomage.Interface.HasFeatureInformationSources
Set method for featureInformationSources
setFeatureLength(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setFeatureLength(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setFeatureLength(Float) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for featureLength
setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for featureLIMSs
setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list) - Method in interface org.biomage.Interface.HasFeatureLIMSs
Set method for featureLIMSs
setFeatureLocation(FeatureLocation) - Method in class org.biomage.DesignElement.Feature
Set method for featureLocation
setFeatureLocation(FeatureLocation) - Method in interface org.biomage.Interface.HasFeatureLocation
Set method for featureLocation
setFeatureParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setFeaturePerformerID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setFeatureProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureProtocol(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setFeatureProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFeatureProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFeatureProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setFeatureProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFeatureProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFeatureProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setFeatureProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFeatureProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFeatureProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
Set method for featureReporterMap_list
setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list) - Method in class org.biomage.DesignElement.Reporter
Set method for featureReporterMaps
setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list) - Method in interface org.biomage.Interface.HasFeatureReporterMaps
Set method for featureReporterMaps
setFeatures(HasFeatures.Features_list) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for features
setFeatures(HasFeatures.Features_list) - Method in interface org.biomage.Interface.HasFeatures
Set method for features
setFeatureShape(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setFeatureShape(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for featureShape
setFeatureShape(OntologyEntry) - Method in interface org.biomage.Interface.HasFeatureShape
Set method for featureShape
setFeatureWidth(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setFeatureWidth(double) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setFeatureWidth(Float) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for featureWidth
setFetchPath(String, String) - Static method in class gov.nih.nci.caarray.services.security.mageom.DefaultSecuredElementIdUpdater
 
setFiducials(HasFiducials.Fiducials_list) - Method in class org.biomage.Array.ArrayGroup
Set method for fiducials
setFiducials(HasFiducials.Fiducials_list) - Method in interface org.biomage.Interface.HasFiducials
Set method for fiducials
setFiducialType(OntologyEntry) - Method in class org.biomage.Array.Fiducial
Set method for fiducialType
setFiducialType(OntologyEntry) - Method in interface org.biomage.Interface.HasFiducialType
Set method for fiducialType
setFileAdditional(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setFileArrayDesignData(ArrayDesignFileUploadGroupData) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
setFileCategory(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setFileData(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
setFileData(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
setFileEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
setFileEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
setFileEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
 
setFileEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setFileEntryId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
setFileEntryId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
 
setFileEntryId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setFileExtension(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setFileExtension(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setFileExtension(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setFileGAL(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setFileGroupId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
setFileGroupId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
setFileGroupId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
setFileGroupId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFileGroupId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setFileHeaderParserFactory(AbstractBeanFactoryBasedTargetSource) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setFileId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setFileList(List) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
setFileList(List) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
setFileList(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFileMAGE(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setFileMAGEML(CustomFormFile) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFileMappingType(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the name of the file, not the full path.
setFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
setFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setFileName(String) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
setFileName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the name of the file, not the full path.
setFileName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the name of the file, not the full path.
setFileName(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setFileName(String) - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Sets the (client-side) file name for this file.
setFileName(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setFileName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setFileName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setFileNameMap(TreeMap) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
set the list of selected fiels using a map.
setFilenameURI(String) - Method in class org.biomage.BioAssayData.DataExternal
Set method for filenameURI
setFileParserFactory(AbstractBeanFactoryBasedTargetSource) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataSetMapper
 
setFileParsingEntry(ArrayDesignFileParsingEntryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadEntryData
 
setFileParsingEntry(HybridizationFileParsingEntryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setFileParsingEntry(ArrayDesignFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
 
setFileParsingEntry(ArrayDesignFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
setFileParsingEntry(HybridizationFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setFileParsingEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
setFileParsingEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData
 
setFileParsingEntryId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setFileParsingEntryId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry
 
setFileParsingEntryId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setFilePath(String) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
setFilePath(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setFilePath(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setFiles(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setFiles(String, File[]) - Method in class gov.nih.nci.caarray.services.util.file.FileZipper
This method establishes the set of files to be put into the zip file, and then actually places them in there.
setFiles(SelectedFiles) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
This method establishes the set of files to be put into the zip file, and then actually places them in there.
setFileSize(int) - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Sets the size, in bytes, for this file.
setFileType(FileType) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
setFileType(HybridizationFileType) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setFileType(UploadFileTypes.MICROARRAY_FILE_TYPE) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFile
 
setFileType(FileType) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
setFileType(String) - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.FileDataObject
 
setFileType(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setFileType(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFileType(int) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFileTypeId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setFileTypeId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setFileTypeId(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
setFileTypeMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap
 
setFileTypeName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setFileUploadEntries(ArrayDesignFileUploadEntryData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData
Sets the fileUploadEntries from which DesignElements are extracted and populated into the ArrayDesign set for this fileUploadGroup.
setFileUploadEntries(HybridizationFileUploadEntryData[]) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setFileUploadEntries(ArrayDesignFileUploadEntry[]) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup
 
setFileUploadEntries(HybridizationFileUploadEntry[]) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup
 
setFileUploadEntry(FileUploadEntryData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Sets the id for the FileUploadEntry record associated with this history record, foreigh key.
setFileUploadEntry(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistorySearchCriteria
 
setFileUploadEntry(FileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
Sets the FileUploadEntry record associated with this ArrayDesignFileUpload record, foreigh key.
setFileUploadEntry(FileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Sets the id for the FileUploadEntry record associated with this history record, foreigh key.
setFileUploadEntry(FileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
Sets the FileUploadEntry record associated with this HybridizationFileUpload record, foreigh key.
setFileUploadEntry(FileUploadEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
Sets the FileUploadEntry record associated with this MAGEMLFileUpload record, foreigh key.
setFileZipExtension(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setFirstName(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
setFirstName(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
setFirstName(String) - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
setFirstName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setFirstName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setFirstName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setFirstName(String) - Method in class org.biomage.AuditAndSecurity.Person
Set method for firstName
setFirstName(String) - Method in class org.biomage.AuditAndSecurity.User
 
setFirstNameSearch(String) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
setFirstNameSearch(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setFirstNameSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setForeignKey(ForeignKey) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the foreign key object of this table
setForeignKeyType(String) - Method in class org.biomage.tools.generate_er.ForeignKey
Description: set the type of the foreign key
setForeignTable(String) - Method in class org.biomage.tools.generate_er.ForeignKey
Description: set the foreign table object for this table
setForeignTablePrimaryKey(String) - Method in class org.biomage.tools.generate_er.ForeignKey
Description: set the primary key of the foreign table object
setFormat(OntologyEntry) - Method in class org.biomage.BioAssay.Image
Set method for format
setFormat(OntologyEntry) - Method in interface org.biomage.Interface.HasFormat
Set method for format
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
setFreeText(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
setFrom(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setFullName(String) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the full name of this column
setGalBlocks_(GalBlockData[]) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFileParseHandler
 
setGalFileLocation(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setGeneIdentifier(String) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setGeneration(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGeneticModificationDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGeneticModificationId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGeneticModificationName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGeneticModifications(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGenotype(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGeographicLocation(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setGpr_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setGprFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setGprFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setGprFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setGprFromSpotFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setGprFromSpotFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setGprFromSpotFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setGps_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setGpsFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setGpsFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setGpsFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setGroup(GroupData) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setGroupName(String) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setGroupName(String) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setGroupName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setGroupName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupSearchCriteria
 
setGroupName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
setGroupName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setGroupName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setGroupName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setGroupNameSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm
 
setGroups(Vector) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setGroups(Collection) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setGroups(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setHardware(HardwareData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData
 
setHardware(HardwareDesc) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setHardware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setHardware(Hardware) - Method in interface org.biomage.Interface.HasHardware
Set method for hardware
setHardware(Hardware) - Method in class org.biomage.Protocol.HardwareApplication
Set method for hardware
setHardware(Hardware) - Method in class org.biomage.Protocol.Software
Set method for hardware
setHardware_list(Protocol_package.Hardware_list) - Method in class org.biomage.Protocol.Protocol_package
Set method for hardware_list
setHardwareApplications(HardwareApplicationData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setHardwareApplications(HasHardwareApplications.HardwareApplications_list) - Method in interface org.biomage.Interface.HasHardwareApplications
Set method for hardwareApplications
setHardwareApplications(HasHardwareApplications.HardwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication
Set method for hardwareApplications
setHardwareId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setHardwareId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareID(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setHardwareMake(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareManufacturerId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setHardwareManufacturerId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareManufacturerName(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareManufacturers(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareManufacturers(HasHardwareManufacturers.HardwareManufacturers_list) - Method in interface org.biomage.Interface.HasHardwareManufacturers
Set method for hardwareManufacturers
setHardwareManufacturers(HasHardwareManufacturers.HardwareManufacturers_list) - Method in class org.biomage.Protocol.Hardware
Set method for hardwareManufacturers
setHardwareModel(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareName(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwares(HardwareData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setHardwares(HasHardwares.Hardwares_list) - Method in interface org.biomage.Interface.HasHardwares
Set method for hardwares
setHardwares(HasHardwares.Hardwares_list) - Method in class org.biomage.Protocol.Protocol
Set method for hardwares
setHardwareTypeId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHardwareTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setHeaderNames(ArrayList) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
setHeaderNameValueDelimiter(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
setHeaderRecordDelimiter(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataHeaderMap
 
setHeight(Float) - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
setHeight(OntologyEntry) - Method in class org.biomage.Description.Ontology.Biometrics
 
setHeightMeasurement(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
setHeightMeasurement(OntologyEntry) - Method in class org.biomage.Description.Ontology.Biometrics
 
setHeightUnitId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setHigherLevelAnalysis_package(HigherLevelAnalysis_package) - Method in class org.biomage.Common.MAGEJava
Set method for higherLevelAnalysis_package
setHistology(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setHost(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setHostIP(String) - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
setHttpTunnelingURL(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setHumidity(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setHybridizationActiveityDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationData(HybridizationFileUploadData[]) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationDataObj
 
setHybridizationData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationFactors(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationFactorValues(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationFileTypeGroupMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.util.FileTypeGroupMap
 
setHybridizationFileUploads(HybridizationFileUploadData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setHybridizationGroupName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationGroupName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setHybridizationId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setHybridizationMappingType(int) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setHybridizationParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setHybridizationPerformerID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setHybridizationProtocol(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setHybridizationProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationProtocol(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setHybridizationProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setHybridizationProtocolActiveDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setHybridizationProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setHybridizationProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setHybridizationProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setHybridizationProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setHybridizationProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setHybridizationProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setHybridizationProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setHybridizationProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setHybridizationProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
sethybridizationProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizationProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setHybridizations(Hybridization[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setHybridizations(Hybridization[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.array.ArrayData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
 
setId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.security.VisibilityData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
setId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
setId(long) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setID(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setId(long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantitationType
 
setId(long) - Method in class gov.nih.nci.caarray.services.fileparse.ParsingBioAssay
 
setId(long) - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingQuantitationType
 
setId(long) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
setId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
setId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
 
setId(long) - Method in class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean
 
setId(long) - Method in class gov.nih.nci.caarray.services.security.db.ProtectionAppGroupElement
 
setId(long) - Method in class gov.nih.nci.caarray.services.security.db.ProtectionElement
 
setId(Object) - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
setId(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setId(Long) - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
setId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ReporterTypeData
 
setId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
setId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setId(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setId(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractData
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setId(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setId(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setId(int) - Method in class gov.nih.nci.caarray.ui.useradmin.OptionData
 
setId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setId(long) - Method in class org.biomage.Common.Extendable
 
setId(long) - Method in class org.biomage.Common.NameValueType
 
setId(long) - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
setId(long) - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
setId(long) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setIdentifiable(Element, boolean) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Sets up a class as identifiable or not.
setIdentifiable(Element, String) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Sets up a class as identifiable or not.
setIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setIdentifier(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setIdentifier(String) - Method in class org.biomage.Common.Identifiable
Set method for identifier
setIdentifier(String) - Method in class org.biomage.Common.MAGEJava
 
setIdentifierLIMS(DatabaseEntry) - Method in class org.biomage.Array.ManufactureLIMS
Set method for identifierLIMS
setIdentifierLIMS(DatabaseEntry) - Method in interface org.biomage.Interface.HasIdentifierLIMS
Set method for identifierLIMS
setIgnoreCopy(boolean) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setImageAcquisitionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setImageAcquisitionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
 
setImageAcquisitionProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData
 
setImageActivateDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageActivateDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setImageParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageParameters(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setImagePerformerID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setImageProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageProtocol(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setImageProtocol(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setImageProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageProtocolData(ProtocolData) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setImageProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setImageProtocolID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setImageProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setImageProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setImageProtocolName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setImageProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setImageProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setImages(HasImages.Images_list) - Method in class org.biomage.BioAssay.ImageAcquisition
Set method for images
setImages(HasImages.Images_list) - Method in interface org.biomage.Interface.HasImages
Set method for images
setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list) - Method in class org.biomage.DesignElement.Reporter
Set method for immobilizedCharacteristics
setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics
Set method for immobilizedCharacteristics
setImported(boolean) - Method in class org.biomage.BioMaterial.BioMaterial
Flags this BioMaterial if it is imported from MAGEML.
setIncludeAllSubCategories(boolean) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setIncludeHeaders(boolean) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Sets the includeHeaders.
setIndex(Index) - Method in class org.biomage.tools.generate_er.Table
Description: set one index
setIndexColumn(AssociationColumn) - Method in class org.biomage.tools.generate_er.Index
Description: set column id for the index
setIndexVector(Vector) - Method in class org.biomage.tools.generate_er.Table
Description: set the vector for all index
setIndividual(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setIndividualTreatmentId(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setInformation(ArrayManufacture) - Method in class org.biomage.Array.Array
Set method for information
setInformation(ArrayManufacture) - Method in interface org.biomage.Interface.HasInformation
Set method for information
setInitialTimePoint(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setInitialTimePoint(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setInitialTimePointId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setInitialTimePointName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setInitialTimePoints(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setInstitutionName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setInstitutionName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setInstitutionName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setInstitutionName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setInstitutionName(String) - Method in class org.biomage.AuditAndSecurity.User
 
setInstitutionSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setInternalId(long) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setInvestigator(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setInvestigatorID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setInvestigators(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setIsAbstract(String) - Method in class org.biomage.tools.generate_er.Table
Description: set if the table is for an abstract class
setIsAdminUser(boolean) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setIsAdminUser(boolean) - Method in class gov.nih.nci.caarray.ui.core.UserInfo
 
setIsAdminUser(boolean) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setIsAdminUser(boolean) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setIsApproximateLength(Boolean) - Method in class org.biomage.BioSequence.BioSequence
Set method for isApproximateLength
setIsBackground(Boolean) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for isBackground
setIsCancel(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setIsCancel(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setIsCircular(Boolean) - Method in class org.biomage.BioSequence.BioSequence
Set method for isCircular
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabData
 
setIsEditable(boolean) - Method in interface gov.nih.nci.caarray.services.security.intf.SecuredElementItf
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setIsEditable(boolean) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setIsEditable(boolean) - Method in class org.biomage.Common.Extendable
 
setIsFactorEmpty(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setIsIndependentClass(boolean) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Allows the isIndependent Variable to be set in this class.
setIsLDAPAuthorization(boolean) - Static method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setIsNew(boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setIsSolvent(Boolean) - Method in class org.biomage.BioMaterial.Compound
Set method for isSolvent
setIsStopped(boolean) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData
 
setIsStopped(boolean) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache
 
setIssue(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setIssue(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for issue
setKindCV(Measurement.KindCV) - Method in class org.biomage.Measurement.Measurement
Set method for kindCV
setLabel(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData
 
setLabel(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
setLabel(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setLabeledExtractID(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setLabeledExtractName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setLabelId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setLabelName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setLabels(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setLabels(HasLabels.Labels_list) - Method in class org.biomage.BioAssay.Channel
Set method for labels
setLabels(HasLabels.Labels_list) - Method in class org.biomage.BioMaterial.LabeledExtract
Set method for labels
setLabels(HasLabels.Labels_list) - Method in interface org.biomage.Interface.HasLabels
Set method for labels
setLargeElementCountFlag(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setLargeElementCountFlag(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setLargeElementCountFlag(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setLastDocument(boolean) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
setLastDocument(boolean) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
setLastName(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
setLastName(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
setLastName(String) - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
setLastName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setLastName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setLastName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setLastName(String) - Method in class org.biomage.AuditAndSecurity.Person
Set method for lastName
setLastName(String) - Method in class org.biomage.AuditAndSecurity.User
 
setLastNameSearch(String) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
setLastNameSearch(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setLastNameSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setLDAPAuthorization(boolean) - Static method in class gov.nih.nci.caarray.services.security.SecurityObjFactory
 
setLength(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setLength(Float) - Method in class org.biomage.Array.ArrayGroup
Set method for length
setLength(Integer) - Method in class org.biomage.BioSequence.BioSequence
Set method for length
setLevels(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setLight(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setLinkingKey(LinkingKey) - Method in class org.biomage.tools.generate_er.Table
Description: set linking key column
setLinkOne(AssociationColumn) - Method in class org.biomage.tools.generate_er.LinkingKey
Description: set one linking key for the table
setLinkTwo(AssociationColumn) - Method in class org.biomage.tools.generate_er.LinkingKey
Description: set the other linking key for the table
setListener(GalHeaderListener) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderParser
 
setListener(GprHeaderListener) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderParser
 
setListener(DelimitedImportListener) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Sets the listener.
setLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
setLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData
 
setLocation(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setLocation(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setLocation(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setLocation(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setLocation(String) - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
setLocation(String) - Method in class org.biomage.Experiment.AdditionalUploadedFile
 
setLog(String, Color) - Static method in class org.biomage.tools.apps.annot.MageXMLConverter
 
setLoginName(String) - Method in class gov.nih.nci.caarray.common.data.security.UserDesc
 
setLoginName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setLoginName(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setLoginName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setLoginName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setLoginName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
setLoginName(String) - Method in class org.biomage.AuditAndSecurity.User
 
setLoginNameSearch(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setLowerRightX(Float) - Method in class org.biomage.ArrayDesign.Zone
Set method for lowerRightX
setLowerRightY(Float) - Method in class org.biomage.ArrayDesign.Zone
Set method for lowerRightY
setMageFileLocation(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationData
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setMageIdentifier(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setMagellFileGroupId(long) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setMagellFileGroupId(Long) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setMAGEMLSecurity(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
setMake(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setMake(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setMake(String) - Method in class org.biomage.Protocol.Hardware
Set method for make
setManufacture(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setManufacture(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setManufactureDate(Date) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setManufactureDate(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setManufactureDateEnd(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
setManufactureDateStart(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
setManufactureID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setManufactureID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setManufacturer(OrganizationDesc) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setManufacturer(OrganizationData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setManufacturer(OrganizationData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setManufacturer(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setManufacturerId(long) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setManufacturerId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setManufacturerId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setManufacturerId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
setManufacturerName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
setManufacturerName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
setManufacturers(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setManufacturingDate(Date) - Method in class org.biomage.Array.ArrayManufacture
 
setManufacturingProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.array.ArrayData
 
setManufacturingProtocolId(long) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setMapperClassName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setMapping(ActionMapping) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Sets the action mapping with which this handler is associated.
setMaterialType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setMaterialType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setMaterialType(OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial
Set method for materialType
setMaterialType(OntologyEntry) - Method in interface org.biomage.Interface.HasMaterialType
Set method for materialType
setMaterialTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMaterialTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setMaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setMaterialTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMaterialTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setMaterialTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setMaterialTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMaterialTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMax(Integer) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setMaxCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the maximum cardinality of the assocaition class
setMaxFilesToProcess(int) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
setMaxMeasurement(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setMaxMeasurement(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setMaxValue(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setMeasuredBioAssay(MeasuredBioAssay) - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
 
setMeasuredBioAssay(MeasuredBioAssay) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list) - Method in class org.biomage.BioAssay.MeasuredBioAssay
Set method for measuredBioAssayData
setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData
Set method for measuredBioAssayData
setMeasuredBioAssayTarget(MeasuredBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction
Set method for measuredBioAssayTarget
setMeasuredBioAssayTarget(MeasuredBioAssay) - Method in interface org.biomage.Interface.HasMeasuredBioAssayTarget
Set method for measuredBioAssayTarget
setMeasurement(MeasurementData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData
 
setMeasurement(MeasurementData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.SplitBioSampleData
 
setMeasurement(MeasurementData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setMeasurement(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setMeasurement(Measurement) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
Set method for measurement
setMeasurement(Measurement) - Method in class org.biomage.BioMaterial.CompoundMeasurement
Set method for measurement
setMeasurement(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setMeasurement(Measurement) - Method in class org.biomage.Experiment.FactorValue
Set method for measurement
setMeasurement(Measurement) - Method in interface org.biomage.Interface.HasMeasurement
Set method for measurement
setMeasurement_package(Measurement_package) - Method in class org.biomage.Common.MAGEJava
Set method for measurement_package
setMeasurementType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setMeasurementTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setMeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setMeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMeasurementUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMeasurementUnit1(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnit2(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnitName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setMeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setMeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMeasurementUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMeasurementUnits1(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnits2(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMeasurementUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMeasurementUnitType1(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnitType2(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMeasurementUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setMeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMeasurementValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMeasurementValue1(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMeasurementValue2(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMedia(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMediaId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMediaTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMembers(HasMembers.Members_list) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
Set method for members
setMembers(HasMembers.Members_list) - Method in interface org.biomage.Interface.HasMembers
Set method for members
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB
 
setMessageDrivenContext(MessageDrivenContext) - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB
 
SetMeth(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
setMethod(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setMethod(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setMethod(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm
 
setMethod(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setMethod(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setMiddleInitial(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setMiddleInitial(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setMiddleInitials(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setMiddleInitials(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setMidInitials(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
setMidInitials(String) - Method in class org.biomage.AuditAndSecurity.Person
Set method for midInitials
setMin(Integer) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setMinCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the minimum cardinality of the assocaition class
setMinMeasurement(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.AgeData
 
setMinMeasurement(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setMinutesToRun(int) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
setMinValue(OntologyEntry) - Method in class org.biomage.Description.Ontology.Age
 
setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.CompositePosition
Set method for mismatchInformation
setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.FeatureInformation
Set method for mismatchInformation
setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.ReporterPosition
Set method for mismatchInformation
setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in interface org.biomage.Interface.HasMismatchInformation
Set method for mismatchInformation
setMode(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setMode(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setMode_(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setModel(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setModel(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setModel(String) - Method in class org.biomage.Protocol.Hardware
Set method for model
setModifyUnit(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setModifyUnitType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setModifyUnitValue(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setModule(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setModule(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setModule(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setMsgToCurator(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setMsgToCurator(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setMsgToCurator(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setMsgToCurator(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setMsgToCurator(String) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setMultipleIds(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setName(VocabData) - Method in class gov.nih.nci.caarray.common.data.measurement.UnitData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setName(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setName(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setName(String) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixQuantitationType
 
setName(String) - Method in interface gov.nih.nci.caarray.services.fileparse.ParsingQuantitationType
 
setName(String) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
setName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
setName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ReporterTypeData
 
setName(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractData
 
setName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
setName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
setName(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setName(String) - Method in class gov.nih.nci.caarray.ui.useradmin.OptionData
 
setName(String) - Method in class org.biomage.Common.Identifiable
Set method for name
setName(String) - Method in class org.biomage.Common.MAGEJava
 
setName(String) - Method in class org.biomage.Common.NameValueType
Set method for name
setName(String) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Set method for name
setName(String) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the name of this column
setName(String) - Method in class org.biomage.tools.generate_er.Index
Description: set name of the index
setName(String) - Method in class org.biomage.tools.generate_er.Table
Description: set the name of this table
setName(String) - Method in class org.biomage.tools.helpers.OntologyHelper.ClassInformation
 
setNameByValue(int) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
setNameByValue(int) - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
setNameByValue(int) - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
setNameByValue(int) - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
setNameByValue(int) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.Measurement.KindCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.Measurement.Type
 
setNameByValue(int) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
setNameByValue(int) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
setNameByValueAction(int) - Method in class org.biomage.AuditAndSecurity.Audit
For Action set the Name of the Enumeration type by passing a value (int)
setNameByValueBasis(int) - Method in class org.biomage.BioSequence.SeqFeature
For Basis set the Name of the Enumeration type by passing a value (int)
setNameByValueKindCV(int) - Method in class org.biomage.Measurement.Measurement
For KindCV set the Name of the Enumeration type by passing a value (int)
setNameByValueOrder(int) - Method in class org.biomage.BioAssayData.BioDataCube
For Order set the Name of the Enumeration type by passing a value (int)
setNameByValueOrientationMarkPosition(int) - Method in class org.biomage.Array.ArrayGroup
For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)
setNameByValueType(int) - Method in class org.biomage.Measurement.Measurement
For Type set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.ConcentrationUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.DistanceUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.MassUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.QuantityUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TemperatureUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TimeUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.VolumeUnit
For UnitNameCV set the Name of the Enumeration type by passing a value (int)
setNameOrientationMarkPosition(String) - Method in class org.biomage.Array.ArrayGroup
Return the current name of the Enumeration type of OrientationMarkPosition.
setNameSearch(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
setNeedsRepair(boolean) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment
 
setNestedProperty(Object, String, Object) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
setNewBioDataCube(boolean) - Method in class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo
 
setNewDesignElementDimension(boolean) - Method in class gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB
 
setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly(boolean) - Method in class gov.nih.nci.caarray.services.bioassaydata.IlluminaDbDataHanderDataSource
 
setNewHardwareId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setNewLabel(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setNewMaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setNewMaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setNewSequence(String) - Method in class org.biomage.DesignElement.MismatchInformation
Set method for newSequence
setNewSoftwareId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setNewSoftwareId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setNewTaxonTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setNewTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setNewTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
setNewTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setNewTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
setNodeContents(HasNodeContents.NodeContents_list) - Method in class org.biomage.HigherLevelAnalysis.Node
Set method for nodeContents
setNodeContents(HasNodeContents.NodeContents_list) - Method in interface org.biomage.Interface.HasNodeContents
Set method for nodeContents
setNodes(HasNodes.Nodes_list) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
Set method for nodes
setNodes(HasNodes.Nodes_list) - Method in class org.biomage.HigherLevelAnalysis.Node
Set method for nodes
setNodes(HasNodes.Nodes_list) - Method in interface org.biomage.Interface.HasNodes
Set method for nodes
setNodeValue(HasNodeValue.NodeValue_list) - Method in class org.biomage.HigherLevelAnalysis.Node
Set method for nodeValue
setNodeValue(HasNodeValue.NodeValue_list) - Method in interface org.biomage.Interface.HasNodeValue
Set method for nodeValue
setNonNumericMap(HashMap) - Method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
setNormalDesignElementRetrieval(DesignElementRetrievalSettings) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSource
Restores OJB design element auto-retrieve settings to their original values.
setNormalDesignElementRetrieval(DesignElementRetrievalSettings) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignManager
Restores OJB design element auto-retrieve settings to their original values.
setNormalDesignElementRetrieval(DesignElementRetrievalSettings) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
setNormalDesignElementRetrieval(DesignElementRetrievalSettings) - Method in class gov.nih.nci.caarray.services.arraydesign.DbArrayDesignDataSource
 
setNormalizationDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for normalizationDescription
setNormalizationDescription(Description) - Method in interface org.biomage.Interface.HasNormalizationDescription
Set method for normalizationDescription
setNotify(Notifiable) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalHeaderListener
 
setNotify(Notifiable) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprHeaderListener
 
setNotifyURL(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setNotifyURL(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setNotifyURL(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setNumArrays(int) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setNumArrays(Integer) - Method in class org.biomage.Array.ArrayGroup
Set method for numArrays
setNumberChanels(int) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setNumberCopies(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
setNumberHybridization(int) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDataObject
 
setNumberOfChannels(Integer) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setNumberOfChannels(int) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setNumberOfChannels(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setNumberOfChannels(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setNumberOfChannels(int) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setNumberOfFactor(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setNumberOfFeatures(int) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setNumberOfFeatures(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setNumberOfFeatures(Integer) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for numberOfFeatures
setNumberOfHybridization(int) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setNumberOfHybridization(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setNumberOfHybridizations(int) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setNumberOfXFeatures(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setNumberOfYFeatures(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setNumberSamples(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setNumChannels(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setNumFactors(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setNumFeaturesPerCol(Integer) - Method in class org.biomage.ArrayDesign.ZoneLayout
Set method for numFeaturesPerCol
setNumFeaturesPerRow(Integer) - Method in class org.biomage.ArrayDesign.ZoneLayout
Set method for numFeaturesPerRow
setNumHybridizations(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setNutrients(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setObject(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setObject(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setObjectId(String) - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
setObjectId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setOneColumn(DataColumn) - Method in class org.biomage.tools.generate_er.Unique
Description: set the one of the columns consisting the Unique
setOntologyEntries(HasOntologyEntries.OntologyEntries_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for ontologyEntries
setOntologyEntries(HasOntologyEntries.OntologyEntries_list) - Method in interface org.biomage.Interface.HasOntologyEntries
Set method for ontologyEntries
setOntologyReference(DatabaseEntry) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
 
setOntologyReference(DatabaseEntry) - Method in class org.biomage.Description.OntologyEntry
Set method for ontologyReference
setOntologyReference(DatabaseEntry) - Method in interface org.biomage.Interface.HasOntologyReference
Set method for ontologyReference
setOrder(BioDataCube.Order) - Method in class org.biomage.BioAssayData.BioDataCube
Set method for order
setOrder(Integer) - Method in class org.biomage.BioMaterial.Treatment
Set method for order
setOrgAddress(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setOrganismPart(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganismPartId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganismParts(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganismStatus(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganismStatuses(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganismStatusId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setOrganization(OrganizationData) - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
setOrganization(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setOrganizationName(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationSearchCriteria
 
setOrganizationName(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria
 
setOrientationMark(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setOrientationMark(String) - Method in class org.biomage.Array.ArrayGroup
Set method for orientationMark
setOrientationMarkPosition(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition) - Method in class org.biomage.Array.ArrayGroup
Set method for orientationMarkPosition
setOrientationMarkPositionName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
setOrientationMarkPositions(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the original file name for the uploaded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Sets the original file name for the uploaded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
Sets the original file name of the uploaded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the original file name for the uploaded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the original file name for the uploaded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
Sets the original file name for the uplaoded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
Sets the original file name for the uplaoded file
setOriginalFileName(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setOriginalName(String) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
setOriginalProtocolId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setOriginalProtocolsApp(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setOriginRelativeTo(String) - Method in class org.biomage.Array.Array
Set method for originRelativeTo
setOther_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setOtherCompoundModifyUnit(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOtherCompoundModifyUnitTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOtherCompoundUnit(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherCompoundUnit(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOtherCompoundUnitType(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherCompoundUnitTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherCompoundUnitTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOtherExperimentType(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setOtherExperimentType(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setOtherKind(String) - Method in class org.biomage.Measurement.Measurement
Set method for otherKind
setOtherProperties(Hashtable) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setOtherPropertyNames(String[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
Intended to be implemented dynamically by a subclass to set a list of main property names that are mapped to the defined getter and setters so other unmapped properties could be recognized as returned by the method getOtherProperties().
setOtherUnit(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherUnit(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOtherUnitType(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherUnitTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setOtherUnitTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setOutputDesc(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setOutputDesc1(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setOutputDesc2(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setOutputName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setOutputName1(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setOutputName2(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setOwner(String) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
setOwner(String) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
setOwner(String) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
setOwner(HasOwner.Owner_list) - Method in class org.biomage.AuditAndSecurity.Security
Set method for owner
setOwner(HasOwner.Owner_list) - Method in interface org.biomage.Interface.HasOwner
Set method for owner
setOwner(String) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the owner of the association relationship
setOwnerClass(Class) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
setOwnerUserName(String) - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
 
setPackageOrder(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
Description: Method to read the XML configuration for the ordering of the packages.
setPages(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setPages(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for pages
setParameter(ParameterData) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
setParameterId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setParameters(ParameterData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
setParameters(ParameterData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setParameters(ParameterData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setParameters(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setParameters(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setParameters(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setParameters(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setParameters(HasParameters.Parameters_list) - Method in class org.biomage.BQS.BibliographicReference
Set method for parameters
setParameters(HasParameters.Parameters_list) - Method in interface org.biomage.Interface.HasParameters
Set method for parameters
setParameterType(Parameter) - Method in interface org.biomage.Interface.HasParameterType
Set method for parameterType
setParameterType(Parameter) - Method in class org.biomage.Protocol.ParameterValue
Set method for parameterType
setParameterTypes(HasParameterTypes.ParameterTypes_list) - Method in interface org.biomage.Interface.HasParameterTypes
Set method for parameterTypes
setParameterTypes(HasParameterTypes.ParameterTypes_list) - Method in class org.biomage.Protocol.Parameterizable
Set method for parameterTypes
setParameterValues(ParameterValueData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData
 
setParameterValues(String[]) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setParameterValues(HasParameterValues.ParameterValues_list) - Method in interface org.biomage.Interface.HasParameterValues
Set method for parameterValues
setParameterValues(HasParameterValues.ParameterValues_list) - Method in class org.biomage.Protocol.ParameterizableApplication
Set method for parameterValues
setParent(Organization) - Method in class org.biomage.AuditAndSecurity.Organization
Set method for parent
setParent(Organization) - Method in interface org.biomage.Interface.HasParent
Set method for parent
setParentBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setParentBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setParentBioSampleId(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setParentBioSourceId(long) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setParents(BioMaterialDesc[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setParents(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setParsedFeatureColumn2PropertyMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataTableMap
 
setParsingEndDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
setParsingEndDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
setParsingEndDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setParsingEndDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
setParsingEndDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
setParsingStartDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
setParsingStartDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
setParsingStartDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setParsingStartDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
setParsingStartDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
setParsingSucceeded(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData
 
setParsingSucceeded(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData
 
setParsingSucceeded(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setParsingSucceeded(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry
 
setParsingSucceeded(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup
 
setPassword(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setPassword(String) - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
setPassword(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setPathName(String) - Method in class gov.nih.nci.caarray.common.data.util.FileData
 
setPathogenTest(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPcData(PCData) - Method in class org.biomage.BioAssayData.DataInternal
Set method for pcData
setPerformer(PersonData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setPerformer(Contact) - Method in class org.biomage.AuditAndSecurity.Audit
Set method for performer
setPerformer(Contact) - Method in interface org.biomage.Interface.HasPerformer
Set method for performer
setPerformerID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPerformerId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setPerformers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPerformers(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setPerformers(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setPerformers(HasPerformers.Performers_list) - Method in interface org.biomage.Interface.HasPerformers
Set method for performers
setPerformers(HasPerformers.Performers_list) - Method in class org.biomage.Protocol.ProtocolApplication
Set method for performers
setPermissibleFileExtension(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setPermissibleFileExtension(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setPermissibleFileExtention(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setPhenotype(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPhone(String) - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
setPhone(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setPhone(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for phone
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setPhoneNumber(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setPhysicalBioAssay(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayTreatment
Set method for physicalBioAssay
setPhysicalBioAssay(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssay
Set method for physicalBioAssay
setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay
Set method for physicalBioAssayData
setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData
Set method for physicalBioAssayData
setPhysicalBioAssaySource(PhysicalBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction
Set method for physicalBioAssaySource
setPhysicalBioAssaySource(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssaySource
Set method for physicalBioAssaySource
setPhysicalBioAssayTarget(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayCreation
Set method for physicalBioAssayTarget
setPhysicalBioAssayTarget(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssayTarget
Set method for physicalBioAssayTarget
setPK(PrimaryKey) - Method in class org.biomage.tools.generate_er.Table
Description: set the primary key for the table
setPloidy(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPloidyId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPloidys(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPolymerType(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for polymerType
setPolymerType(OntologyEntry) - Method in interface org.biomage.Interface.HasPolymerType
Set method for polymerType
setPopulationDensity(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setPosition(Position) - Method in class org.biomage.Array.Fiducial
Set method for position
setPosition(Position) - Method in class org.biomage.DesignElement.Feature
Set method for position
setPosition(Position) - Method in interface org.biomage.Interface.HasPosition
Set method for position
setPositionDelta(PositionDelta) - Method in class org.biomage.Array.FeatureDefect
Set method for positionDelta
setPositionDelta(PositionDelta) - Method in class org.biomage.Array.ZoneDefect
Set method for positionDelta
setPositionDelta(PositionDelta) - Method in interface org.biomage.Interface.HasPositionDelta
Set method for positionDelta
setPrevious(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPrincipalInvestigator(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setProducerTransformation(Transformation) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
Set method for producerTransformation
setProducerTransformation(Transformation) - Method in interface org.biomage.Interface.HasProducerTransformation
Set method for producerTransformation
setProperty(String, String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setProperty(Object, String, Object) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
setProperty(String, String) - Method in interface gov.nih.nci.caarray.services.util.parse.ParserBeanPropertiesInterface
 
setPropertyDefaultStringValueIfEmpty(Object[], String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.Extendable
Set method for propertySets
setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.NameValueType
Set method for propertySets
setPropertySets(HasPropertySets.PropertySets_list) - Method in interface org.biomage.Interface.HasPropertySets
Set method for propertySets
setProtectionElementId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setProtectionElementOwner(String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Update a protection element owner.
setProtectionGroupId(long) - Method in class gov.nih.nci.caarray.common.data.security.ProtectionGroupData
 
setProtectionGroupId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.data.security.SecuredElementData
Sets protection groups.
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
setProtectionGroups(ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
setProtectionGroups(ProtectionGroupData[], String) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
setProtectionGroupTypeId(long) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setProtectionGroupTypeId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setProtectionGroupTypeId(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setProtectionTypeId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setProtocol(ProtocolData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setProtocol(Protocol) - Method in interface org.biomage.Interface.HasProtocol
Set method for protocol
setProtocol(Protocol) - Method in class org.biomage.Protocol.ProtocolApplication
Set method for protocol
setProtocol_list(Protocol_package.Protocol_list) - Method in class org.biomage.Protocol.Protocol_package
Set method for protocol_list
setProtocol_package(Protocol_package) - Method in class org.biomage.Common.MAGEJava
Set method for protocol_package
setProtocolActivityDate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setProtocolApplication(ProtocolApplication) - Method in class org.biomage.Experiment.AdditionalDataProcessing
 
setProtocolApplicationId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProtocolApplications(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView
 
setProtocolApplications(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProtocolApplications(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for protocolApplications
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for protocolApplications
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.BioEvent.BioEvent
Set method for protocolApplications
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in interface org.biomage.Interface.HasProtocolApplications
Set method for protocolApplications
setProtocolId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setProtocolId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setProtocolPerformerID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setProtocols(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setProtocolsApp(ProtocolApplicationData[]) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setProtocolType(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
setProtocolTypeId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setProtocolTypeId(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setProtocolTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setProtocolTypes(VocabData[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData
 
setProtocolTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setProtocolTypes(ArrayList) - Method in class org.biomage.BioMaterial.ActionProtocolTypeMap
 
setProtocolVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setProtocolVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setProvidedByAffymetrix() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
Returns true if this ArrayDesign is made/provided by Affymetrix.
setProvidedByAffymetrix(boolean) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
Sets if this ArrayDesign is made/provided by Affymetrix.
setProvidedByAffymetrix(boolean) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProvider(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setProvider(ContactData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData
 
setProvider(ContactData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView
 
setProvider(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setProviderId(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setProviderId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setProviderId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProviderId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setProviderName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setProviderRoles(ArrayList) - Method in class org.biomage.Experiment.Experiment
The specified providerRoles must be instantiable List subclass for creation by reflection to work.
setProviders(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setProviders(DesignProviderRoleData[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setProviders(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setProviders(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setProviders(HasProviders.Providers_list) - Method in class org.biomage.Experiment.Experiment
Set method for providers
setProviders(HasProviders.Providers_list) - Method in interface org.biomage.Interface.HasProviders
Set method for providers
setProvidersOrgs(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setProvidersOrgs(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setProviderType(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setPublication(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setPublication(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublication(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for publication
setPublicationAuthor(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationCancel(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationData(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationDataID(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationEditor(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationIssue(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationMedID(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationPage(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublications(PublicationData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setPublicationTitle(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationURI(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublicationVolume(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublisher(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setPublisher(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPublisher(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for publisher
setPublishYear(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPubMedId(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setPubMedLink(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setPubMedLink_(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setPwd(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setQuality(String) - Method in class org.biomage.Array.ManufactureLIMS
Set method for quality
setQualityControl(QualityControlData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentView
 
setQualityControlData(QualityControlData) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setQualityControlDescription(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setQualityControlDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for qualityControlDescription
setQualityControlDescription(Description) - Method in interface org.biomage.Interface.HasQualityControlDescription
Set method for qualityControlDescription
setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in class org.biomage.Array.ArrayManufacture
Set method for qualityControlStatistics
setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in class org.biomage.BioMaterial.BioMaterial
Set method for qualityControlStatistics
setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in interface org.biomage.Interface.HasQualityControlStatistics
Set method for qualityControlStatistics
setQualityControlType(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setQuantitation(String, String) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
setQuantitationDimension(QuantitationTypeDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
Set method for quantitationDimension
setQuantitationDimension(QuantitationTypeDimension) - Method in interface org.biomage.Interface.HasQuantitationDimension
Set method for quantitationDimension
setQuantitations(LocalDynaBean) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
Set the values from a dynabean
setQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
Set method for quantitationType
setQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationType
Set method for quantitationType
setQuantitationType_list(QuantitationType_package.QuantitationType_list) - Method in class org.biomage.QuantitationType.QuantitationType_package
Set method for quantitationType_list
setQuantitationType_package(QuantitationType_package) - Method in class org.biomage.Common.MAGEJava
Set method for quantitationType_package
setQuantitationTypeColumn2SimpleQuantitationTypeMappings(LinkedHashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.QuantitationTypeColumnsMap
 
setQuantitationTypeColumnsMap(QuantitationTypeColumnsMap) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.HybridizationDataTableMap
 
setQuantitationTypeDimension(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData
Set method for quantitationTypeDimension
setQuantitationTypeDimension(QuantitationTypeDimension) - Method in interface org.biomage.Interface.HasQuantitationTypeDimension
Set method for quantitationTypeDimension
setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for quantitationTypeDimension_list
setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package
Set method for quantitationTypeMap_list
setQuantitationTypeMapping(QuantitationTypeMapping) - Method in class org.biomage.BioAssayData.Transformation
Set method for quantitationTypeMapping
setQuantitationTypeMapping(QuantitationTypeMapping) - Method in interface org.biomage.Interface.HasQuantitationTypeMapping
Set method for quantitationTypeMapping
setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
Set method for quantitationTypeMaps
setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps
Set method for quantitationTypeMaps
setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for quantitationTypeMaps
setQuantitationTypeName2JavaPropertyNameMappings(HashMap) - Method in class gov.nih.nci.caarray.services.fileparse2.util.QuantitationTypeName2JavaPropertyNameMap
 
setQuantitationTypeProperties(String[]) - Method in class gov.nih.nci.caarray.services.fileparse2.hybridization.HybridizationRowWrapper
 
setQuantitationTypes(HasQuantitationTypes.QuantitationTypes_list) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
Set method for quantitationTypes
setQuantitationTypes(HasQuantitationTypes.QuantitationTypes_list) - Method in interface org.biomage.Interface.HasQuantitationTypes
Set method for quantitationTypes
setQuantitationTypeTuples(HasQuantitationTypeTuples.QuantitationTypeTuples_list) - Method in class org.biomage.BioAssayData.DesignElementTuple
Set method for quantitationTypeTuples
setQuantitationTypeTuples(HasQuantitationTypeTuples.QuantitationTypeTuples_list) - Method in interface org.biomage.Interface.HasQuantitationTypeTuples
Set method for quantitationTypeTuples
setQueueName(String) - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
setReadDataLineTabs(boolean) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
setReadHeaderTabs(boolean) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
 
setRealColumnNames(String[]) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Sets all the column names that appear in the data file's data table.
setReason(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
set
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setReason(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
set
setRegions(HasRegions.Regions_list) - Method in class org.biomage.BioSequence.SeqFeature
Set method for regions
setRegions(HasRegions.Regions_list) - Method in interface org.biomage.Interface.HasRegions
Set method for regions
setReleaseDate(Date) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
setReleaseDate(Date) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setReleaseDate(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setReleaseDate(Date) - Method in class org.biomage.Protocol.SoftwareApplication
Set method for releaseDate
setReleaseDateAsString(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
setReload(boolean) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
setRepair(boolean) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
setReplacedLength(Integer) - Method in class org.biomage.DesignElement.MismatchInformation
Set method for replacedLength
setReplicateDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for replicateDescription
setReplicateDescription(Description) - Method in interface org.biomage.Interface.HasReplicateDescription
Set method for replicateDescription
setReporter(Reporter) - Method in class org.biomage.DesignElement.FeatureReporterMap
Set method for reporter
setReporter(Reporter) - Method in class org.biomage.DesignElement.ReporterPosition
Set method for reporter
setReporter(Reporter) - Method in interface org.biomage.Interface.HasReporter
Set method for reporter
setReporter_list(DesignElement_package.Reporter_list) - Method in class org.biomage.DesignElement.DesignElement_package
Set method for reporter_list
setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package
Set method for reporterCompositeMap_list
setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence
Set method for reporterCompositeMaps
setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list) - Method in interface org.biomage.Interface.HasReporterCompositeMaps
Set method for reporterCompositeMaps
setReporterFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setReporterFileLocation(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setReporterFileLocation(String) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
setReporterFileType(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setReporterFileType(String) - Method in class org.biomage.ArrayDesign.ArrayDesign
 
setReporterGroup_list(ArrayDesign_package.ReporterGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
Set method for reporterGroup_list
setReporterGroupId_(long) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
setReporterGroups(HasReporterGroups.ReporterGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for reporterGroups
setReporterGroups(HasReporterGroups.ReporterGroups_list) - Method in interface org.biomage.Interface.HasReporterGroups
Set method for reporterGroups
setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list) - Method in class org.biomage.DesignElement.ReporterCompositeMap
Set method for reporterPositionSources
setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list) - Method in interface org.biomage.Interface.HasReporterPositionSources
Set method for reporterPositionSources
setReporters(HasReporters.Reporters_list) - Method in class org.biomage.ArrayDesign.ReporterGroup
Set method for reporters
setReporters(HasReporters.Reporters_list) - Method in class org.biomage.BioAssayData.ReporterDimension
Set method for reporters
setReporters(HasReporters.Reporters_list) - Method in interface org.biomage.Interface.HasReporters
Set method for reporters
setReporterTypeId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setReporterTypeId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setReporterTypeID(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setReporterTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setReporterTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setReporterTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setRequestAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setRequired(Boolean) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
 
setResultingBiomaterialType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setResultingBiomaterialType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setResultingBiomaterialType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setResultingBiomaterialTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setResultingBiomaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setResultingBiomaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setResultingBiomaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setResultingBiomaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setResultingBiomaterialTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setResultingDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setResultingDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setResultingDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setResultingDescription(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setResultingName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setResultingName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setResultingName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setResultingName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setResultingName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setResults(Collection) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm
 
setResults(Collection) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchForm
 
setResults(Collection) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm
 
setResults(Collection) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setReturnFwd(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
setRole(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData
 
setRole(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData
 
setRole(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setRole(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setRole(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
setRole(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setRole(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignProviderRole
 
setRole(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentProviderRole
 
setRoleDesc(String) - Method in class gov.nih.nci.caarray.common.data.security.Role
Sets the roleDesc for this Role object
setRoleId(long) - Method in class gov.nih.nci.caarray.common.data.security.Role
Sets the roleId for this Role object
setRoleId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setRoleId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setRoleName(String) - Method in class gov.nih.nci.caarray.common.data.security.Role
Sets the roleName for this Role object
setRoles(Vector) - Method in class gov.nih.nci.caarray.common.data.security.UserRoleData
 
setRoles(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setRoles(HasRoles.Roles_list) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for roles
setRoles(HasRoles.Roles_list) - Method in interface org.biomage.Interface.HasRoles
Set method for roles
setRoleSelection(int) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setRollbackOnly() - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
setRow(String) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalFeatureData
 
setRow(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
setRow(Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setRow(Integer) - Method in class org.biomage.ArrayDesign.Zone
Set method for row
setRow(Integer) - Method in class org.biomage.DesignElement.FeatureLocation
Set method for row
setRowNumber(long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
setRows(LocalDynaBean[]) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DataTable
Method setRows.
setSampleId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
setSampleName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
setSampleName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setSampleName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setSampleType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setSampleType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
setSampleType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setSampleTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setSampleTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
setSampleTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setScale(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
setScale(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Set method for scale
setScale(OntologyEntry) - Method in interface org.biomage.Interface.HasScale
Set method for scale
setScale(OntologyEntry) - Method in class org.biomage.QuantitationType.QuantitationType
Set method for scale
setScales(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setScaleType(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentNewDataObject
 
setScaleTypes(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setScanningProtocol(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HybridizationCommonData
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
setSearchResults(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setSecuredElement(SecuredElementData) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setSecuredElementClassName(String) - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
setSecuredElementId(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setSecuredElementId(String) - Method in interface gov.nih.nci.caarray.services.security.intf.SecuredElementItf
 
setSecuredElementId(String) - Method in class gov.nih.nci.caarray.services.util.BaseSecuredElement
 
setSecuredElementId(String) - Method in class org.biomage.Common.Extendable
 
setSecuredElementOwner(String, String) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
Set New Secured Elemetn Owner
setSecuredElementOwner(String, String) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
Set New Secured Elemetn Owner
setSecuredElementOwner(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
Set New Secured Element Owner
setSecuredElementOwner(String, String) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
Set New Secured Element Owner
SetSecuredElementOwner - Class in gov.nih.nci.caarray.services.security.test.usecases
 
SetSecuredElementOwner() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementOwner
 
setSecuredElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
update the protectionGroups associated with a Secured Element
setSecuredElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
update the protectionGroups associated with a Secured Element
SetSecuredElementProtectionGroups - Class in gov.nih.nci.caarray.services.security.test.usecases
 
SetSecuredElementProtectionGroups() - Constructor for class gov.nih.nci.caarray.services.security.test.usecases.SetSecuredElementProtectionGroups
 
setSecuredElemProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Insert a protection element to AS_PROTECTION_GROUP_ELEMENT table.
setSecurity(Security) - Method in class org.biomage.Common.Describable
Set method for security
setSecurity(Security) - Method in interface org.biomage.Interface.HasSecurity
Set method for security
setSecurity_list(AuditAndSecurity_package.Security_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Set method for security_list
setSecurityGroup_list(AuditAndSecurity_package.SecurityGroup_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
Set method for securityGroup_list
setSecurityGroups(HasSecurityGroups.SecurityGroups_list) - Method in class org.biomage.AuditAndSecurity.Security
Set method for securityGroups
setSecurityGroups(HasSecurityGroups.SecurityGroups_list) - Method in interface org.biomage.Interface.HasSecurityGroups
Set method for securityGroups
setSelectedBiomaterial(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setSelectedBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setSelectedBiomaterials(String[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolForm
 
setSelectedCharacteristics(String[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setSelectedManufacturers(String[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setSelectedQualityControlTypeID(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setSelectedVisibilities(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setSelectedVisibilities(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setSelectedVisibilityIds(String[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setSelectedVisibilityNames(String[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setSelectedVisibilityNames(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setSelectedVisibilitys(String[]) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
setSeqFeatures(HasSeqFeatures.SeqFeatures_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for seqFeatures
setSeqFeatures(HasSeqFeatures.SeqFeatures_list) - Method in interface org.biomage.Interface.HasSeqFeatures
Set method for seqFeatures
setSequence(String) - Method in class org.biomage.BioSequence.BioSequence
Set method for sequence
setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list) - Method in class org.biomage.BioSequence.BioSequence
Set method for sequenceDatabases
setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list) - Method in interface org.biomage.Interface.HasSequenceDatabases
Set method for sequenceDatabases
setSerialNumber(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData
 
setSerialNumber(String) - Method in class org.biomage.Protocol.HardwareApplication
Set method for serialNumber
setServerURL(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setServlet(ActionServlet) - Method in class gov.nih.nci.caarray.ui.core.CustomMultipartRequestHandler
Sets the servlet with which this handler is associated.
setSessionContext(SessionContext) - Method in class gov.nih.nci.caarray.services.util.AbstractSessionBean
 
setSex(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setSexId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setSexTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setShouldBeAdminUser(boolean) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setSid(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setSid(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setSid(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setSize(long) - Method in class gov.nih.nci.caarray.common.data.util.FileData
 
setSobject(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setSoftware(SoftwareData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
setSoftware(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setSoftware(Software) - Method in interface org.biomage.Interface.HasSoftware
Set method for software
setSoftware(Software) - Method in class org.biomage.Protocol.SoftwareApplication
Set method for software
setSoftware_list(Protocol_package.Software_list) - Method in class org.biomage.Protocol.Protocol_package
Set method for software_list
setSoftwareApplications(SoftwareApplicationData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData
 
setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list) - Method in interface org.biomage.Interface.HasSoftwareApplications
Set method for softwareApplications
setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication
Set method for softwareApplications
setSoftwareId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setSoftwareId(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareManufacturerId(long) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setSoftwareManufacturerId(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareManufacturerName(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareManufacturers(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list) - Method in interface org.biomage.Interface.HasSoftwareManufacturers
Set method for softwareManufacturers
setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list) - Method in class org.biomage.Protocol.Software
Set method for softwareManufacturers
setSoftwareName(String) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MICROARRAY_FILE_TYPE
 
setSoftwares(SoftwareDesc[]) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
setSoftwares(SoftwareData[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setSoftwares(SoftwareDesc[]) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setSoftwares(HasSoftwares.Softwares_list) - Method in interface org.biomage.Interface.HasSoftwares
Set method for softwares
setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Hardware
Set method for softwares
setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Protocol
Set method for softwares
setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Software
Set method for softwares
setSoftwareTypeId(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareTypeName(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSoftwareTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
setSokey(String) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData
 
setSource(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayMap
Set method for sourceBioAssays
setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list) - Method in interface org.biomage.Interface.HasSourceBioAssays
Set method for sourceBioAssays
setSourceBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setSourceBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setSourceBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setSourceBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setSourceBiomaterialId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in class org.biomage.BioAssay.BioAssayCreation
Set method for sourceBioMaterialMeasurements
setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in class org.biomage.BioMaterial.Treatment
Set method for sourceBioMaterialMeasurements
setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements
Set method for sourceBioMaterialMeasurements
setSourceBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setSourceBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setSourceBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setSourceBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setSourceBiomaterialName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setSourceBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm
 
setSourceBiomaterials(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setSourceClassName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.DTOClass
 
setSourceContact(HasSourceContact.SourceContact_list) - Method in class org.biomage.BioMaterial.BioSource
Set method for sourceContact
setSourceContact(HasSourceContact.SourceContact_list) - Method in interface org.biomage.Interface.HasSourceContact
Set method for sourceContact
setSourceElementTypeNames(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setSourceField(SimpleField) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
setSourceFieldClassName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setSourceFieldName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Set method for sourcesQuantitationType
setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list) - Method in interface org.biomage.Interface.HasSourcesQuantitationType
Set method for sourcesQuantitationType
setSourceType(SourceType) - Method in class org.biomage.BioAssayData.BioDataCube
 
setSpacingBetweenCols(Float) - Method in class org.biomage.ArrayDesign.ZoneLayout
Set method for spacingBetweenCols
setSpacingBetweenRows(Float) - Method in class org.biomage.ArrayDesign.ZoneLayout
Set method for spacingBetweenRows
setSpacingsBetweenZonesX(Float) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for spacingsBetweenZonesX
setSpacingsBetweenZonesY(Float) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for spacingsBetweenZonesY
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setSpecies(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setSpecies(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setSpecies(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Set method for species
setSpecies(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for species
setSpecies(OntologyEntry) - Method in interface org.biomage.Interface.HasSpecies
Set method for species
setSpeciesLists(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setSpeciesType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setSpeciesTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSpeciesTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setSpeciesTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSpeciesTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSpeciesTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setSpikedControl(LabeledExtractDesc) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setSpikedControl(ExtractDropDownData) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setSpikedControl(LabeledExtract) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setSpikedControlCh2(ExtractDropDownData) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setSpikedControlID(long[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setSpikedControlID(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setSpikedControlIDCh2(long) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
setSpikedControls(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setSplitAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
setStart(Integer) - Method in class org.biomage.BioSequence.SequencePosition
Set method for start
setStartAtLine(int) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Sets the startAtLine.
setStartCoord(Integer) - Method in class org.biomage.DesignElement.MismatchInformation
Set method for startCoord
setStartDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setStartDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setStartDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setStartDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setStartManufactureDate(Date) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setState(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setState(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setState(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the status of the uploaded file
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Sets the status of the uploaded file for which this history record pertains.
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Sets the status of the uploaded file
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Sets the status of the uploaded file for which this history record pertains.
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setStatus(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setStatus(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the status of the uploaded file
setStatus(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Sets the status of the uploaded file for which this history record pertains.
setStatus(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the status of the uploaded file
setStatus(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Sets the status of the uploaded file for which this history record pertains.
setStatus(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setStatus(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the date the status of the uploaded file was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData
Sets the date the status of the uploaded file history was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Sets the date the status of the uploaded file was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Sets the date the status of the uploaded file history was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData
 
setStatusDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setStatusDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the date the status of the uploaded file was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory
Sets the date the status of the uploaded file history was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the date the status of the uploaded file was set
setStatusDate(Date) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Sets the date the status of the uploaded file history was set
setStatusSelection(int) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
setStopped(boolean) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
 
setStrainOrLine(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setStrainOrLineId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setStrainOrLines(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setStrandType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setStrandType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setStrandType(String) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for strandType
setStrandTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setStrandTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setStrandTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSubmitted(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setSubregions(HasSubregions.Subregions_list) - Method in class org.biomage.BioSequence.SeqFeatureLocation
Set method for subregions
setSubregions(HasSubregions.Subregions_list) - Method in interface org.biomage.Interface.HasSubregions
Set method for subregions
setSubSoftwareID(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setSubstrateType(VocabData) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setSubstrateType(VocabData) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setSubstrateType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setSubstrateType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setSubstrateType(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setSubstrateType(OntologyEntry) - Method in class org.biomage.Array.ArrayGroup
Set method for substrateType
setSubstrateType(OntologyEntry) - Method in interface org.biomage.Interface.HasSubstrateType
Set method for substrateType
setSubstrateTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSubstrateTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
setSubstrateTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSubstrateTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm
 
setSubstrateTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setSubstrateTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list) - Method in class org.biomage.BioAssayData.BioAssayData
Set method for summaryStatistics
setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list) - Method in interface org.biomage.Interface.HasSummaryStatistics
Set method for summaryStatistics
setSurfaceType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setSurfaceType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setSurfaceType(OntologyEntry) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Set method for surfaceType
setSurfaceType(OntologyEntry) - Method in interface org.biomage.Interface.HasSurfaceType
Set method for surfaceType
setSurfaceTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSurfaceTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setSurfaceTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setTarget(Object) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.test.IAccess
 
setTarget(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayTreatment
Set method for target
setTarget(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasTarget
Set method for target
setTargetClass(ClassMapperRepository.TargetClass) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.DTOClass
 
setTargetClassName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.TargetClass
 
setTargetDesignElementClassName(String) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DesignElementColumnsMap
 
setTargetedCellType(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTargetedCellTypeId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTargetedCellTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTargetElementTypeNames(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setTargetField(SimpleField) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
 
setTargetFieldClassName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setTargetFieldName(String) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapperRepository.ConvertField
 
setTargetQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
Set method for targetQuantitationType
setTargetQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasTargetQuantitationType
Set method for targetQuantitationType
setTargetQuantitationType(QuantitationType) - Method in class org.biomage.QuantitationType.ConfidenceIndicator
Set method for targetQuantitationType
setTaxonName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setTaxonType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTaxonTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTechnologyType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setTechnologyType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setTechnologyType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setTechnologyType(VocabData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setTechnologyType(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup
Set method for technologyType
setTechnologyType(OntologyEntry) - Method in interface org.biomage.Interface.HasTechnologyType
Set method for technologyType
setTechnologyTypeId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setTechnologyTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setTechnologyTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setTempDirectory(String) - Method in class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
setTemperature(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setText(String) - Method in class org.biomage.Description.Description
Set method for text
setText(String) - Method in class org.biomage.Protocol.Protocol
Set method for text
setTheDelimiter(String) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Sets the theDelimiter.
setTheDelimiter(String) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Sets the theDelimiter.
setTheFileName(String) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Sets the fileName.
setTheFileName(String) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedImportParser
Sets the theFileName.
setTheRows(LocalDynaBean[]) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method setTheRows.
setTheRows(Object[]) - Method in class gov.nih.nci.caarray.services.util.parse.InternalTable
Method setTheRows.
setTheTable(InternalTable) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Sets the theTable.
setThisMaxCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the maximum cardinality of this table for the association relationship
setThisMinCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn
Description: set the maximum cardinality of this table for the association relationship
setTitle(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setTitle(String) - Method in class gov.nih.nci.caarray.common.data.security.UserData
 
setTitle(String) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setTitle(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setTitle(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setTitle(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for title
setTitle(String) - Method in class org.biomage.Protocol.Protocol
Set method for title
setTolerance(Float) - Method in class org.biomage.Array.ArrayManufacture
Set method for tolerance
setTollFreePhone(String) - Method in class gov.nih.nci.caarray.common.data.contact.ContactData
 
setTollFreePhone(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for tollFreePhone
setTopElements(Element) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
 
setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for topLevelBioAssays
setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list) - Method in interface org.biomage.Interface.HasTopLevelBioAssays
Set method for topLevelBioAssays
setTopLevelBioMaterials(HasTopBioMaterial.TopLevelBioMaterials_list) - Method in class org.biomage.BioMaterial.BioMaterial
Set method for treatments
setTopLevelBioMaterials(HasTopBioMaterial.TopLevelBioMaterials_list) - Method in interface org.biomage.Interface.HasTopBioMaterial
F Set method for topLevelBioMaterials
setTransactionTimeout(int) - Method in class gov.nih.nci.caarray.services.util.LoggingUserTransaction
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentAction(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentActions(int, String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentActions(int, String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentEventId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setTreatmentEvents(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setTreatmentEvents(ArrayList) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setTreatmentEvents(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentEvents(ArrayList) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentEvents(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentEvents(ArrayList) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTreatmentId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTreatmentNumber(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
setTreatmentOrder(Integer) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setTreatmentOrder(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setTreatmentOrder(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatmentOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentOrder(int) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTreatments(TreatmentData[]) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
setTreatments(TreatmentEvent[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setTreatments(TreatmentEvent[]) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatments(HasTreatments.Treatments_list) - Method in class org.biomage.BioMaterial.BioMaterial
Set method for treatments
setTreatments(HasTreatments.Treatments_list) - Method in interface org.biomage.Interface.HasTreatments
Set method for treatments
setTreatmentType(VocabData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
setTreatmentType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setTreatmentType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatmentType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentType(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTreatmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
setTreatmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
setTreatmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentTypeName(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTreatmentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
 
setTreatmentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
setTreatmentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setTreatmentTypes(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
setTumorGrading(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTumorGradingId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTumorGradings(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setTunnelURL(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setTunnelURL(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setTxt_file_exist(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setTxtFile(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.Hybridization
 
setTxtFileLocation(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setTxtFileLocation(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.measurement.UnitData
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setType(VocabData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setType(Class) - Method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
setType(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setType(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setType(OntologyEntry) - Method in class org.biomage.BioAssay.DerivedBioAssay
Set method for type
setType(OntologyEntry) - Method in class org.biomage.BioMaterial.BioSample
Set method for type
setType(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence
Set method for type
setType(String) - Method in class org.biomage.Common.NameValueType
Set method for type
setType(OntologyEntry) - Method in class org.biomage.Description.DatabaseEntry
Set method for type
setType(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Set method for type
setType(OntologyEntry) - Method in interface org.biomage.Interface.HasType
Set method for type
setType(Measurement.Type) - Method in class org.biomage.Measurement.Measurement
Set method for type
setType(OntologyEntry) - Method in class org.biomage.Protocol.Hardware
Set method for type
setType(OntologyEntry) - Method in class org.biomage.Protocol.Protocol
Set method for type
setType(OntologyEntry) - Method in class org.biomage.Protocol.Software
Set method for type
setType(String) - Method in class org.biomage.tools.generate_er.DataColumn
Description: set the Type of this column
setType(String) - Method in class org.biomage.tools.generate_er.Table
Description: set the Type of this table
setTypes(VocabData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc
 
setTypes(VocabData[]) - Method in class gov.nih.nci.caarray.common.data.experiment.QualityControlData
 
setTypes(VocabData[]) - Method in class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData
 
setTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setTypes(HasTypes.Types_list) - Method in class org.biomage.ArrayDesign.DesignElementGroup
Set method for types
setTypes(ArrayList) - Method in class org.biomage.Description.Ontology.ChromosomalAberration
 
setTypes(HasTypes.Types_list) - Method in class org.biomage.Experiment.ExperimentDesign
Set method for types
setTypes(HasTypes.Types_list) - Method in interface org.biomage.Interface.HasTypes
Set method for types
setUnique(Unique) - Method in class org.biomage.tools.generate_er.Table
Description: set the unique column
setUniqueVector(Vector) - Method in class org.biomage.tools.generate_er.Unique
Description: set the vector holding all columns that consists the Unique
setUnit(UnitData) - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
setUnit(Unit) - Method in interface org.biomage.Interface.HasUnit
Set method for unit
setUnit(Unit) - Method in class org.biomage.Measurement.Measurement
Set method for unit
setUnitName(String) - Method in class org.biomage.Measurement.Unit
Set method for unitName
setUnitNameCV(ConcentrationUnit.UnitNameCV) - Method in class org.biomage.Measurement.ConcentrationUnit
Set method for unitNameCV
setUnitNameCV(DistanceUnit.UnitNameCV) - Method in class org.biomage.Measurement.DistanceUnit
Set method for unitNameCV
setUnitNameCV(MassUnit.UnitNameCV) - Method in class org.biomage.Measurement.MassUnit
Set method for unitNameCV
setUnitNameCV(QuantityUnit.UnitNameCV) - Method in class org.biomage.Measurement.QuantityUnit
Set method for unitNameCV
setUnitNameCV(TemperatureUnit.UnitNameCV) - Method in class org.biomage.Measurement.TemperatureUnit
Set method for unitNameCV
setUnitNameCV(TimeUnit.UnitNameCV) - Method in class org.biomage.Measurement.TimeUnit
Set method for unitNameCV
setUnitNameCV(VolumeUnit.UnitNameCV) - Method in class org.biomage.Measurement.VolumeUnit
Set method for unitNameCV
setUnitNameId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnitNameOther(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnitNames(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnitOtherId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnits(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm
 
setUnitTypeId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnitTypeOther(String) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUnitTypes(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
setUp() - Method in class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
 
setUp() - Method in class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
setUp() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerAddTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerGetTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerParameterAddTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerUpdateTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerAddTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerGetTest
 
setUp() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerUpdateTest
 
setUp(Properties) - Method in class gov.nih.nci.caarray.services.security.test.GeneralSecuredElementUpdateTester
 
setUp(Properties) - Method in class gov.nih.nci.caarray.services.test.BaseInContainerTest
 
setUp(Properties) - Method in interface gov.nih.nci.caarray.services.test.InContainerTest
 
setUp() - Method in class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestArrayDesignConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
setUp() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerAddTest
 
setUp() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerDeleteTest
 
setUp() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
 
setUp() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerUpdateTest
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionOne
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionThree
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PeopleSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentHybridizationAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologySearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolActionMappingsAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
setUp() - Method in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
setup(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
setupAdd(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
setupAddProvider(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
setupArray(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
setupArrayDesign(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
setupBiosampleList(LabeledExtractBaseForm) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
setupCharacteristicsDetail(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
setupCharacteristicsList(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
setUpdateDate(long) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setUpdateDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setUpdateDate(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setUpdateDate(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
setUpdateDate(long) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm
 
setUpdateDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setUpdateDate(String) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setUpdateDate(long) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setupForCreate(boolean) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setupForm(ExperimentDetailForm) - Static method in class gov.nih.nci.caarray.ui.experiment.ExperimentUtils
 
setupGroupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
setupLabeledExtract(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
setupList(ExperimentBaseForm) - Static method in class gov.nih.nci.caarray.ui.experiment.ExperimentUtils
 
setupLists(ArrayDesignBaseForm) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUtils
 
setupLists(ArrayBaseForm, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
setupLists(BiosourceSearchForm, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
setupLists(LabeledExtractBaseForm, boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
setupLists(LabeledExtractSearchForm, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
setupLists(PoolForm) - Method in class gov.nih.nci.caarray.ui.biomaterial.PoolAction
 
setupLists(HttpServletRequest, SampleSearchForm) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchAction
 
setupLists(SplitForm) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
setupLists(TreatmentFormOne, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionOne
 
setupLists(HardwareSearchForm) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchAction
 
setupListsTwo(SplitForm) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
setUploadDate(Date) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
setUploadedFileData(UploadedFileData) - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData
 
setUploadFile(UploadFile) - Method in class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues
 
setUploadFile(boolean) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
setUploadFile(boolean) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setUploadGroupName(String) - Method in class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData
Deprecated.  
setUploadGroupName(String) - Method in class org.biomage.Experiment.HybridizationFileUpload
Deprecated.  
setUploadTypeId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setUploadTypeId(int) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setUploadTypeName(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setUploadTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setUploadTypes(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm
 
setUploadURL(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadParameters
 
setUploadURL(String) - Method in class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams
 
setUploadURL(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams
 
setupModify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
setupModifyTreatment(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ModifyProtocolApplicationAction
 
setupNewTreatment(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.ModifyTreatmentAction
 
setupOldLists(ArrayBaseForm, HttpServletRequest) - Static method in class gov.nih.nci.caarray.ui.arraydesign.ArrayUtils
 
setupOldLists(BiosourceSearchForm, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchAction
 
setupOldLists(LabeledExtractSearchForm, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchAction
 
setUpperLeftX(Float) - Method in class org.biomage.ArrayDesign.Zone
Set method for upperLeftX
setUpperLeftY(Float) - Method in class org.biomage.ArrayDesign.Zone
Set method for upperLeftY
setUpperX(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setUpperY(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setupSearchCriteria(ExperimentSearchForm, ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentSearchAction
 
setupTreatment(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
setupUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
setupUpdateCharacteristicsDetail(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
setupUploadFile(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
setupVisibilityUpdate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
setupZoneMappings(Zone[]) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ZoneMatcher
 
setupZoneMappings(Zone[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.DefaultZoneMatcher
 
setupZoneMappings(Zone[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.UCSFSpotZoneMatcher
 
setupZoneMappings(Zone[]) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.ZoneLocationZoneMatcher
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.contact.OrganizationDesc
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareData
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolData
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
setURI(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
setURI(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setURI(String) - Method in class org.biomage.AuditAndSecurity.Contact
Set method for URI
setURI(String) - Method in class org.biomage.BioAssay.Image
Set method for URI
setURI(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for URI
setURI(String) - Method in class org.biomage.Description.Database
Set method for URI
setURI(String) - Method in class org.biomage.Description.DatabaseEntry
Set method for URI
setURI(String) - Method in class org.biomage.Description.Description
Set method for URI
setURI(String) - Method in class org.biomage.Protocol.Parameterizable
Set method for URI
setURI(String) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry.OntologyDatabaseEntry
 
setUrl(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setUrl(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
setUrl(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setUser(UserData) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setUserDefined(boolean) - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
setUserDefined(boolean) - Method in class org.biomage.Description.Database
 
setUserGroupData(Vector) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setUserId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the sumitters name for the uploaded file
setUserId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Sets the sumitters name for the uploaded file
setUserId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setUserId(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setUserId(Long) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
setUserId(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the sumitters name for the uploaded file
setUserId(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the sumitters name for the uploaded file
setUserId(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
 
setUserId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
 
setUserName(String) - Method in class gov.nih.nci.caarray.common.data.security.UserRoleData
 
setUserName(String) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setUserName(String) - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
setUserRoleCollection(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setUserRoles(Vector) - Method in class gov.nih.nci.caarray.common.data.useradmin.UserData
 
setUserRoles(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
setUserRoles(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
setUserRoleSelection(int) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setUsers(Vector) - Method in class gov.nih.nci.caarray.common.data.useradmin.GroupData
 
setUserStatusCollection(Vector) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setUserStatusSelection(int) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
setValid(boolean) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
setValidate(String) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setValidate(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
setValidatorCode(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
Sets the validatorCode for the uploaded file
setValidatorCode(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Sets the validatorCode for the uploaded file
setValidatorCode(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
setValidatorCode(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
Sets the validatorCode for the uploaded file
setValidatorCode(String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Sets the validatorCode for the uploaded file
setValidatorCode(String) - Method in class gov.nih.nci.caarray.ui.core.HttpUploadedFileData
Sets the CRC32 validatorCode for the uplaoded file
setValidatorCode(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData
Sets the CRC32 validatorCode for the uplaoded file
setValue(String) - Method in class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData
 
setValue(String) - Method in class gov.nih.nci.caarray.common.data.experiment.FactorValueData
 
setValue(String) - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
setValue(String) - Method in class gov.nih.nci.caarray.common.data.protocol.ParameterValueData
 
setValue(int) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.test.IAccess
 
setValue(Object) - Method in class org.biomage.BioAssayData.Datum
Set method for value
setValue(String) - Method in class org.biomage.Common.NameValueType
Set method for value
setValue(String) - Method in class org.biomage.Description.Ontology.BioMaterialCharacteristic
Set method for value
setValue(String) - Method in class org.biomage.Description.OntologyEntry
Set method for value
setValue(OntologyEntry) - Method in class org.biomage.Experiment.FactorValue
Set method for value
setValue(Object) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
Set method for value
setValue(OntologyEntry) - Method in interface org.biomage.Interface.HasValue
Set method for value
setValue(Object) - Method in class org.biomage.Measurement.Measurement
Set method for value
setValue(Object) - Method in class org.biomage.Protocol.ParameterValue
Set method for value
setValue(String) - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
setValue1(int) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.HolderBean
 
setValue2(int) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.HolderBean
 
setValueByName(String) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
setValueByName(String) - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
setValueByName(String) - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
setValueByName(String) - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
setValueByName(String) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.Measurement.KindCV
 
setValueByName(String) - Method in class org.biomage.Measurement.Measurement.Type
 
setValueByName(String) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
setValueByName(String) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
setValueByNameAction(String) - Method in class org.biomage.AuditAndSecurity.Audit
For Action set the Value of the Enumeration type by passing a Name to it.
setValueByNameBasis(String) - Method in class org.biomage.BioSequence.SeqFeature
For Basis set the Value of the Enumeration type by passing a Name to it.
setValueByNameKindCV(String) - Method in class org.biomage.Measurement.Measurement
For KindCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameOrder(String) - Method in class org.biomage.BioAssayData.BioDataCube
For Order set the Value of the Enumeration type by passing a Name to it.
setValueByNameOrientationMarkPosition(String) - Method in class org.biomage.Array.ArrayGroup
For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.
setValueByNameType(String) - Method in class org.biomage.Measurement.Measurement
For Type set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.ConcentrationUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.DistanceUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.MassUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.QuantityUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TemperatureUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TimeUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.VolumeUnit
For UnitNameCV set the Value of the Enumeration type by passing a Name to it.
setValueId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.ExtractDropDownData
 
setValueId(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
setValueName(String) - Method in class gov.nih.nci.caarray.ui.experiment.data.FactorDropDownData
 
setVerbose(int) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Looks for verboseness argument to set the level of output.
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData
 
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData
 
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
 
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria
 
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
setVersion(String) - Method in class gov.nih.nci.caarray.common.data.vocab.DatabaseData
 
setVersion(String) - Method in class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry
 
setVersion(String) - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
 
setVersion(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setVersion(String) - Method in class org.biomage.ArrayDesign.ArrayDesign
Set method for version
setVersion(String) - Method in class org.biomage.Description.Database
Set method for version
setVersion(String) - Method in class org.biomage.Protocol.SoftwareApplication
Set method for version
setVisibilities(Collection) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm
 
setVisibility(long) - Method in class gov.nih.nci.caarray.common.data.array.ArrayGroupData
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria
 
setVisibility(ProtectionGroupData) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
setVisibility(long) - Method in class gov.nih.nci.caarray.common.data.security.VisibilityData
 
setVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm
 
setVisibility(String[]) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
setVisibility(long) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm
 
setVisibility(String) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm
 
setVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
setVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm
 
setVisibility(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
setVisibility(String) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Sets the visibility.
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
setVisibilityId(long) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
setVisibilityName(String) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
setVisibilityName(String) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
setVisibilityName(String) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
setVisibilitys(long[]) - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
setVisibilitys(Collection) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
setVocabId(long) - Method in class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
setVolume(String) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setVolume(String) - Method in class org.biomage.BQS.BibliographicReference
Set method for volume
setWaitTime(long) - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
setWaitTime(Long) - Method in class gov.nih.nci.caarray.services.util.jms.MessageData
 
setWarningType(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter
Set method for warningType
setWarningType(OntologyEntry) - Method in interface org.biomage.Interface.HasWarningType
Set method for warningType
setWater(String) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
setWeight(Float) - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
setWeight(OntologyEntry) - Method in class org.biomage.Description.Ontology.Biometrics
 
setWeightMeasurement(VocabData) - Method in class gov.nih.nci.caarray.common.data.vocab.BiometricsData
 
setWeightMeasurement(OntologyEntry) - Method in class org.biomage.Description.Ontology.Biometrics
 
setWidth(String) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
setWidth(Float) - Method in class org.biomage.Array.ArrayGroup
Set method for width
setX(Float) - Method in class org.biomage.DesignElement.Position
Set method for x
setXSpacing(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setY(Float) - Method in class org.biomage.DesignElement.Position
Set method for y
setYear(Date) - Method in class gov.nih.nci.caarray.common.data.experiment.PublicationData
 
setYear(Date) - Method in class org.biomage.BQS.BibliographicReference
Set method for year
setYSpacing(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setZip(String) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
setZip(String) - Method in class gov.nih.nci.caarray.ui.contact.PersonDetailForm
 
setZip(String) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
setZipFileName(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setZipFilePath(String) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
 
setZone(Zone) - Method in class org.biomage.Array.ZoneDefect
Set method for zone
setZone(Zone) - Method in class org.biomage.DesignElement.Feature
Set method for zone
setZone(Zone) - Method in interface org.biomage.Interface.HasZone
Set method for zone
setZoneColumn(Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setZoneGroups(HasZoneGroups.ZoneGroups_list) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
Set method for zoneGroups
setZoneGroups(HasZoneGroups.ZoneGroups_list) - Method in interface org.biomage.Interface.HasZoneGroups
Set method for zoneGroups
setZoneIdentifier(String) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setZoneLayout(ZoneLayout) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
setZoneLayout(Float, Float, Integer, Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParser
 
setZoneLayout(ZoneLayout) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
setZoneLayout(Float, Float, Integer, Integer) - Method in interface gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignFileHeaderParserItf
 
setZoneLayout(ZoneLayout) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
setZoneLayout(Float, Float, Integer, Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ArrayDesignTextFileHeaderParser
 
setZoneLayout(ZoneLayout) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for zoneLayout
setZoneLayout(ZoneLayout) - Method in interface org.biomage.Interface.HasZoneLayout
Set method for zoneLayout
setZoneLocations(HasZoneLocations.ZoneLocations_list) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for zoneLocations
setZoneLocations(HasZoneLocations.ZoneLocations_list) - Method in interface org.biomage.Interface.HasZoneLocations
Set method for zoneLocations
setZoneMatcher(ZoneMatcher) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.ArrayDesignDataSetMapper
 
setZoneNumber(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gal.GalBlockData
 
setZoneNumber(long) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
setZoneNumber(Integer) - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GprDataRow
 
setZoneRow(Integer) - Method in class gov.nih.nci.caarray.services.fileparse2.arraydesign.ParsedFeature
 
setZonesPerX(Integer) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for zonesPerX
setZonesPerY(Integer) - Method in class org.biomage.ArrayDesign.ZoneGroup
Set method for zonesPerY
SEX - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
sex_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
sexId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
sexTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
shouldReload(String) - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration
 
showApplyProtocol(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
showCharacteristicsList(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
showUpdateCharacteristicsList(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
SimpleDesignElement - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
A wrapper to wrap a simplified DesignElement represented by a BasicDynaBean instance to allow for making a unique key by combining the values of the non-key properties specified when constructing an instance of this class.
SimpleDesignElement(Object, String, String[]) - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleDesignElement
 
SimpleField - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper
 
SimpleField(String, Class, Class) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.SimpleField
 
SimpleQuantitationType - Class in gov.nih.nci.caarray.services.fileparse2.hybridization
Represents a simplified QuantitationType
SimpleQuantitationType() - Constructor for class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleQuantitationType
 
skip(long) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.AppendInputStream
 
skippedEntity(String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
skippedEntity(String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
smartPointer(CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
SMTP_SERVER - Static variable in class gov.nih.nci.caarray.services.util.properties.CaArrayProperties
 
Software - Class in org.biomage.Protocol
Software represents the software used.
Software() - Constructor for class org.biomage.Protocol.Software
Default constructor.
Software(Attributes) - Constructor for class org.biomage.Protocol.Software
Attribute constructor.
software - Variable in class org.biomage.Protocol.SoftwareApplication
The underlying software.
software_list - Variable in class org.biomage.Protocol.Protocol_package
Software represents the software used.
SOFTWARE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
SoftwareAddUpdateAction - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
SoftwareAddUpdateForm - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
SoftwareApplication - Class in org.biomage.Protocol
The use of a piece of software with the requisite Parameters and ParameterValues.
SoftwareApplication() - Constructor for class org.biomage.Protocol.SoftwareApplication
Default constructor.
SoftwareApplication(Attributes) - Constructor for class org.biomage.Protocol.SoftwareApplication
Attribute constructor.
SoftwareApplicationData - Class in gov.nih.nci.caarray.common.data.protocol
 
SoftwareApplicationData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData
 
softwareApplications - Variable in class org.biomage.Protocol.ProtocolApplication
The use of software for the application of the protocol.
SoftwareBaseForm - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareBaseForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
SoftwareData - Class in gov.nih.nci.caarray.common.data.protocol
 
SoftwareData() - Constructor for class gov.nih.nci.caarray.common.data.protocol.SoftwareData
 
SoftwareDesc - Class in gov.nih.nci.caarray.common.data.protocol
 
SoftwareDesc() - Constructor for class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
SoftwareDetailAction - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareDetailAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareDetailAction
 
SoftwareDetailForm - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareDetailForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
softwareId_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
SoftwareManagerAddTest - Class in gov.nih.nci.caarray.services.protocol.test
 
SoftwareManagerAddTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerAddTest
Constructor for SoftwareManagerDelegateTest.
SoftwareManagerDB - Class in gov.nih.nci.caarray.services.protocol
 
SoftwareManagerDB() - Constructor for class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Default Constructor
SoftwareManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
SoftwareManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
SoftwareManagerEJB - Class in gov.nih.nci.caarray.services.protocol.ejb
SoftwareManagerEJB
SoftwareManagerEJB() - Constructor for class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
SoftwareManagerGetTest - Class in gov.nih.nci.caarray.services.protocol.test
 
SoftwareManagerGetTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerGetTest
Constructor for SoftwareManagerDelegateTest.
SoftwareManagerUpdateTest - Class in gov.nih.nci.caarray.services.protocol.test
 
SoftwareManagerUpdateTest(String) - Constructor for class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerUpdateTest
Constructor for SoftwareManagerDelegateTest.
softwareManufacturerId_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
softwareManufacturerName_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
softwareManufacturers - Variable in class org.biomage.Protocol.Software
Contact for information on the software.
softwareManufacturers_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
SoftwareOrHardwareManufacturerFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
SoftwareOrHardwareManufacturerFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.SoftwareOrHardwareManufacturerFieldMapper
 
softwares - Variable in class org.biomage.Protocol.Hardware
Associates Hardware and Software together.
softwares - Variable in class org.biomage.Protocol.Protocol
Software used by this Protocol.
softwares - Variable in class org.biomage.Protocol.Software
Software packages this software uses, i.e.
SoftwareSearchAction - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareSearchAction() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareSearchAction
 
SoftwareSearchCriteria - Class in gov.nih.nci.caarray.common.data.protocol
 
SoftwareSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria
 
SoftwareSearchForm - Class in gov.nih.nci.caarray.ui.protocol
 
SoftwareSearchForm() - Constructor for class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm
 
softwareTypeId_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
softwareTypeName_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
softwareTypes_ - Variable in class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm
 
sortBioSample(BioSampleDesc[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
sortDatabase(DatabaseData[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
sortOrganization(OrganizationData[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
sortPerson(PersonData[]) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
sortWriteFiles(Vector) - Static method in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: Create the write classes for each of the class files.
sourceBioAssays - Variable in class org.biomage.BioAssayData.BioAssayMap
The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.
sourceBioMaterialMeasurements - Variable in class org.biomage.BioAssay.BioAssayCreation
The BioSample and its amount used in the BioAssayCreation event.
sourceBioMaterialMeasurements - Variable in class org.biomage.BioMaterial.Treatment
The BioMaterials and the amounts used in the treatment
sourceContact - Variable in class org.biomage.BioMaterial.BioSource
The BioSource's source is the provider of the biological material (a cell line, strain, etc...).
sourcesQuantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeMap
The QuantitationType sources for values for the transformation.
SourceType - Enum in org.biomage.BioAssayData
Indicates the source of a BioAssayCube.
SourceType2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
SourceType2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.SourceType2StringFieldConversion
 
space - Static variable in class gov.nih.nci.caarray.ui.StringFormatter
 
SpecializedQuantitationType - Class in org.biomage.QuantitationType
User defined quantitation type.
SpecializedQuantitationType() - Constructor for class org.biomage.QuantitationType.SpecializedQuantitationType
Default constructor.
SpecializedQuantitationType(Attributes) - Constructor for class org.biomage.QuantitationType.SpecializedQuantitationType
Attribute constructor.
SPECIES - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
species - Variable in class org.biomage.ArrayDesign.DesignElementGroup
The organism from which the biosequences of this group are from.
species - Variable in class org.biomage.BioSequence.BioSequence
The organism from which this sequence was obtained.
species_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc
 
speciesTypeName_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
split(String) - Method in interface gov.nih.nci.caarray.services.util.file.LineSplitter
 
split(String) - Method in class gov.nih.nci.caarray.services.util.file.LineSplitterImpl
 
SplitAction - Class in gov.nih.nci.caarray.ui.biomaterial
 
SplitAction() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
splitBioSample(TreatmentData, SplitBioSampleData[]) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
splitBioSample(TreatmentData, SplitBioSampleData[]) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Splits a given bio sample to produce new bio samples represented by the specified output bio samples.
SplitBioSampleData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
SplitBioSampleData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.SplitBioSampleData
 
SplitForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
SplitForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.SplitForm
 
splitInClause(String, Collection, int, String) - Static method in class gov.nih.nci.caarray.services.util.db.SqlUtil
 
splitInClause(String, Collection, int) - Static method in class gov.nih.nci.caarray.services.util.db.SqlUtil
 
SQL_IN_LIMIT - Static variable in class gov.nih.nci.caarray.services.security.RdbmsAuthorizationDAObj
 
SqlDate2JavaDateFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
SqlDate2JavaDateFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.SqlDate2JavaDateFieldMapper
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Action2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Basis2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Boolean2IntFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.KindCV2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Long2LongObjectFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Order2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.OrientationMarkPosition2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.SourceType2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Type2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion
 
sqlToJava(Object) - Method in class gov.nih.nci.caarray.services.util.ojb.conversions.Value2StringFieldConversion
 
SqlUtil - Class in gov.nih.nci.caarray.services.util.db
 
StandardQuantitationType - Class in org.biomage.QuantitationType
Superclass for the named quantitation type.
StandardQuantitationType() - Constructor for class org.biomage.QuantitationType.StandardQuantitationType
Default constructor.
StandardQuantitationType(Attributes) - Constructor for class org.biomage.QuantitationType.StandardQuantitationType
Attribute constructor.
startDocument() - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
startDocument() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
startElement(String, String, String, Attributes) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
startElement(String, String, String, Attributes) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
startPrefixMapping(String, String) - Method in class gov.nih.nci.caarray.services.mageloader.DatabaseImportMAGEContentHandler
 
startPrefixMapping(String, String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler
 
startQueueSession(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
startQueueSession(String, String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
startQueueSession(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
startQueueSession(String, String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
startTopicSession(String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
startTopicSession(String, String) - Method in class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageHandler
 
startTopicSession(String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
startTopicSession(String, String) - Method in interface gov.nih.nci.caarray.services.util.jms.JMSMessageHandler
 
startTransaction(int) - Method in class gov.nih.nci.caarray.services.util.transaction.CaArrayTransactionHandler
 
startTransaction(int) - Method in interface gov.nih.nci.caarray.services.util.transaction.TransactionHandler
 
startUpload() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
 
stopUpload() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadThread
To stop the run method of this thread.
STORED_BIOSOURCE - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
STORED_TREATMENT2_FORM - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
storeMessage(MessageData) - Method in class gov.nih.nci.caarray.services.util.jms.JMSMessageManagerDB
 
storeObject(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Inserts or updates an object.
storeObject(Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
STRAIN_OR_LINE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
strainOrLine_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
STRAINORLINE_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
strainOrLineId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
strainOrLines_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
STRANDEDNESS - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
strandTypeName_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
streamBean(LocalDynaBean) - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Streams a bean to the file
streamRecords() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
To save memory you can use the streaming methods 1.
StringFormatter - Class in gov.nih.nci.caarray.ui
This class provides static methods to format a string as needed for web page text display.
StringFormatter() - Constructor for class gov.nih.nci.caarray.ui.StringFormatter
 
StringManipHelpers - Class in org.biomage.tools.helpers
 
StringManipHelpers() - Constructor for class org.biomage.tools.helpers.StringManipHelpers
Creates a new instance of StringManipHelpers
StringOutputHelpers - Class in org.biomage.tools.helpers
Description: Class that provides static helper metheds for outputting strings.
StringOutputHelpers() - Constructor for class org.biomage.tools.helpers.StringOutputHelpers
 
stripExtension(String) - Static method in class gov.nih.nci.caarray.services.util.file.FileUtility
Returns the given filename with the extension (if any) stripped out.
STRUTS_SUCCESS - Static variable in class gov.nih.nci.caarray.common.util.CaArrayConstants
 
subClassNames - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Vector of the subclasses' names.
SUBMISSION_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
SUBMISSION_ERROR - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
SUBMISSION_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
SUBMISSION_ERROR - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
SUBMISSION_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData
 
SUBMISSION_SUCCESS - Static variable in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
 
SUBMISSION_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry
 
SUBMISSION_SUCCESS - Static variable in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
 
submit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailAction
 
submitHybridizationFileUploadsForParsing(long, long[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
submitHybridizationFileUploadsForParsing(long, long[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This functionality is handled by FileUploadManagerEJB for 1.3
submitMAGEMLFile(String) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
submitMAGEMLFile(String) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
This method puts the specified zip file which is residing on the caARRAY server on the queue for the parsing and storing process of MAGEML's.
submitMAGEMLGeneration(long) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
submitMAGEMLGeneration(long) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
submitMAGEMLGeneration(long) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
Submits a MAGEML generation message to the responsible Message Driven Bean to generate MAGEML for the specified ArrayDesign.
submitMAGEMLGeneration(long) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Submits a MAGEML generation message to the responsible Message Driven Bean to generate MAGEML for the specified experiment.
submitPageOne(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
submitPageOne(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionOne
This Action method handles the request that is the submission of the first treatment page
submitPageThree(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionThree
 
submitPageTwo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SplitAction
 
submitPageTwo(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
This method handles the request from the Treatment add page it reviews the submitting action and determines the correct forward...
subregions - Variable in class org.biomage.BioSequence.SeqFeatureLocation
Regions within the SeqFeature.
SUBSET - Static variable in class org.biomage.tools.generate_er.CreateMageER
table type is subset
SUBSTRATE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
substrateType - Variable in class org.biomage.Array.ArrayGroup
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.
substrateTypeName_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
SUCCESS - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
suite() - Static method in class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
suite() - Static method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
suite() - Static method in class gov.nih.nci.caarray.services.security.test.SecurityTester
 
suite() - Static method in class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestArrayDesignConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestTreatmentConversion
 
suite() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
suite() - Static method in class gov.nih.nci.caarray.ui.test.ExperimentSearchTest
 
summaryStatistics - Variable in class org.biomage.BioAssayData.BioAssayData
Statistics on the Quality of the BioAssayData.
SURFACE_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
surfaceType - Variable in class org.biomage.ArrayDesign.PhysicalArrayDesign
The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
surfaceTypeName_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
SW - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
syncExperimentDesignTypes(ExperimentDesign) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
Add or synchronize the vocabularies that represent the annotations of the specified Describable object.
syncOntologyEntryOneToOneAssociation(Object, String) - Static method in class gov.nih.nci.caarray.services.util.DBUtils
 
syncVocabUnitTypeAndUnitName(UnitData) - Static method in class gov.nih.nci.caarray.services.vocab.VocabUtils
Synchronize the specified UnitData with the appropriate controlled vocabularies from the persistence store that represent its unit type and unit name.

T

TAB - Static variable in class gov.nih.nci.caarray.services.fileparse2.parsers.ParserUtils
 
tab - Static variable in class gov.nih.nci.caarray.ui.StringFormatter
 
TAB_DELIMITED - Static variable in interface gov.nih.nci.caarray.services.util.file.LineSplitter
 
TabDelimitedTxtReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Reader for tab-delimited txt files imported via caAMEL.
Table - Class in org.biomage.tools.generate_er
 
Table() - Constructor for class org.biomage.tools.generate_er.Table
Description: Constructor for the Table object.
target - Variable in class org.biomage.BioAssay.BioAssayTreatment
The PhysicalBioAssay that was treated.
TARGETED_CELL_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
targetedCellType_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
targetedCellTypeId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
targetedCellTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
targetQuantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeMap
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
targetQuantitationType - Variable in class org.biomage.QuantitationType.ConfidenceIndicator
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
taxonType_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
taxonTypes_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
tearDown() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
 
tearDown() - Method in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
TECHNOLOGY_TYPE - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
technologyType - Variable in class org.biomage.ArrayDesign.FeatureGroup
The technology type of this design.
TechnologyTypeFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
TechnologyTypeFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.TechnologyTypeFieldMapper
 
technologyTypeName_ - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
temperature - Variable in class org.biomage.Measurement.Measurement.KindCV
 
temperature_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
TEMPERATURE_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
TemperatureUnit - Class in org.biomage.Measurement
Temperature
TemperatureUnit() - Constructor for class org.biomage.Measurement.TemperatureUnit
Default constructor.
TemperatureUnit(Attributes) - Constructor for class org.biomage.Measurement.TemperatureUnit
Attribute constructor.
TemperatureUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
testAddArrayDesign() - Method in class gov.nih.nci.caarray.services.arraydesign.test.ArrayDesignManagementTest
 
testAddBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSampleTest
 
testAddBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.AddBioSourceTest
 
testAddBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testAddBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testAddBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testAddExperiment() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
testAddExperimentalFactors() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
testAddHybridizationFileUpload() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
testAddPerson() - Method in class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
testAddPerson() - Method in class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
testAddProtocolExistingType() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerAddTest
 
testAddSoftwareExistingType() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerAddTest
 
testAddVocabularyExistingType() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerAddTest
 
TestArrayDesignConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestArrayDesignConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestArrayDesignConversion
 
testArrayDesignData2ArrayDesign() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestArrayDesignConversion
 
TestBioMaterialConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestBioMaterialConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
testBioMaterialData2BioMaterial() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestBioMaterialConversion
 
TestCallbackHandler - Class in gov.nih.nci.caarray.services.util
 
TestCallbackHandler(TestCase, String, char[]) - Constructor for class gov.nih.nci.caarray.services.util.TestCallbackHandler
 
testCompareResult() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
 
testConvertBeans() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
testConvertHybridizationFileUploadEntry() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.BeanConversionTest
 
testCopyLabeledExtract() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testCopyLabeledExtract() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
TestDataConverter - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestDataConverter(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
testDeleteBioSamples() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testDeleteBioSamples() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testDeleteBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testDeleteDuplicatedBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testDeleteProducedBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testDeleteProducedBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testDeleteProducedBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testDeleteTreatmentFromBioMaterial() - Method in class gov.nih.nci.caarray.services.biomaterial.test.DeleteTreatmentFromBioMaterial
 
testDuplicateBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testDuplicateBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.DuplicateBioSourceTest
 
Tester - Class in gov.nih.nci.caarray.services.fileparse.test
 
Tester() - Constructor for class gov.nih.nci.caarray.services.fileparse.test.Tester
 
Tester - Class in gov.nih.nci.caarray.services.security.test
 
Tester() - Constructor for class gov.nih.nci.caarray.services.security.test.Tester
 
Tester - Class in gov.nih.nci.caarray.services.test
 
Tester() - Constructor for class gov.nih.nci.caarray.services.test.Tester
 
Tester - Class in gov.nih.nci.caarray.services.util.netcdf.test
 
Tester() - Constructor for class gov.nih.nci.caarray.services.util.netcdf.test.Tester
 
TestException - Exception in gov.nih.nci.caarray.services.test
 
TestException() - Constructor for exception gov.nih.nci.caarray.services.test.TestException
 
TestException(String) - Constructor for exception gov.nih.nci.caarray.services.test.TestException
 
TestException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.test.TestException
 
TestException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.test.TestException
 
testExperiment2ExperimentView() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
TestExperimentConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestExperimentConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestExperimentConversion
 
testExperimentSearch() - Method in class gov.nih.nci.caarray.ui.test.ExperimentSearchTest
 
testFileUploadManager() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testgetArrayGroup() - Method in class gov.nih.nci.caarray.services.array.test.ArrayGroupManagementTest
 
testGetBioSampleView() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testGetBioSampleViews() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testGetBioSampleViews() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testGetHyb() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testGetProtocol() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerGetTest
 
testGetProtocol() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerParameterAddTest
 
testGetProtocols() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerGetTest
 
testGetSoftware() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerGetTest
 
testGetSoftwares() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerGetTest
 
testGetTreatment() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
 
testGetTreatmentCompundMeasure() - Method in class gov.nih.nci.caarray.services.biomaterial.test.GetTreatmentTest
This method will test treatment Compound measurements
testGetTreatmentMeasure() - Method in class gov.nih.nci.caarray.services.biomaterial.test.GetTreatmentTest
This method will test treatment measurements
testGetTreatmentProtocolApplication() - Method in class gov.nih.nci.caarray.services.biomaterial.test.GetTreatmentTest
This method will test get treatment protocol application
testGetVocabulary() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
 
testHomeAddHybridizationFileUpload() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
testHomeSplitBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testHomeSplitBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testHomeTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
Phu's test for home db
testHomeTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
Phu's test for home db
testHomeTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
Phu's test for home db
testInContainer() - Method in class gov.nih.nci.caarray.services.security.test.SecurityTester
 
TestManagerEJB - Class in gov.nih.nci.caarray.services.test.ejb
 
TestManagerEJB() - Constructor for class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB
 
testOntologyEntry2VocabData() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
testParameter2ParameterData() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
TestParameterConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestParameterConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestParameterConversion
 
testParseCELDev() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseCHPDev() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseCHPStage() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseGAL() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseGPRDev() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseGPRDev2() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
This test tests two cases: 1.
testParseGPRFromUCSFSpotDev() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testParseImaGeneDev() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
 
testPoolBioSamples() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testPoolBioSamples() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testProtocol2ProtocolData() - Static method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestDataConverter
 
testProtocol2ProtocolData() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
TestProtocolConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestProtocolConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestProtocolConversion
 
testRemoveVocabulary() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerDeleteTest
 
testSecuredElement() - Method in class gov.nih.nci.caarray.services.security.test.GeneralSecuredElementUpdateTester
 
testSplitBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testSplitBioSample() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testTreatBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
TestTreatmentConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestTreatmentConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestTreatmentConversion
 
testTreatmentData2Treatment() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestTreatmentConversion
 
testUpdateBioMaterialCharacteristics() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSampleManagementTest
 
testUpdateBioMaterialCharacteristics() - Method in class gov.nih.nci.caarray.services.biomaterial.test.LabeledExtractManagementTest
 
testUpdateBioSource() - Method in class gov.nih.nci.caarray.services.biomaterial.test.BioSourceManagementTest
 
testUpdateBioSourceCharacteristics() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateBioSourceCharacteristicsTest
 
testUpdateExperiment() - Method in class gov.nih.nci.caarray.services.experiment.test.ExperimentManagementTest
 
testUpdatePerson() - Method in class gov.nih.nci.caarray.services.contact.test.ContactManagementTest
 
testUpdatePerson() - Method in class gov.nih.nci.caarray.services.useradmin.test.AdminManagementTest
 
testUpdateProtocol() - Method in class gov.nih.nci.caarray.services.protocol.test.ProtocolManagerUpdateTest
 
testUpdateSoftware() - Method in class gov.nih.nci.caarray.services.protocol.test.SoftwareManagerUpdateTest
 
testUpdateTreatment() - Method in class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
Test updating a treatment
testUpdateVocabulary() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerUpdateTest
 
TestUtils - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestUtils() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestUtils
 
TestVocabConversion - Class in gov.nih.nci.caarray.services.util.dataconverter.test
 
TestVocabConversion(String) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
testVocabData2OntologyEntry() - Method in class gov.nih.nci.caarray.services.util.dataconverter.test.TestVocabConversion
 
TEXT_GROUP_CURATOR - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
TEXT_GROUP_MEMBER - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
TEXT_NOT_ASSIGNED - Static variable in class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
TEXT_WIDTH - Static variable in class org.biomage.tools.apps.annot.PagePanel
 
theAuthenticationDAItf - Variable in class gov.nih.nci.caarray.services.security.SecurityServiceObj
 
theAuthorizationDAItf - Variable in class gov.nih.nci.caarray.services.security.SecurityServiceObj
 
thisMaxCard - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
thisMinCard - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
thisNav - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
thread2BrokerMap_ - Static variable in class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
ThreeDArrayTransformer - Class in gov.nih.nci.caarray.services.util.netcdf
 
ThreeDArrayTransformer(Object[][][]) - Constructor for class gov.nih.nci.caarray.services.util.netcdf.ThreeDArrayTransformer
 
TilesController - Class in gov.nih.nci.caarray.ui.core
 
TilesController() - Constructor for class gov.nih.nci.caarray.ui.core.TilesController
 
time - Variable in class org.biomage.Measurement.Measurement.KindCV
 
TIME_UNIT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
TimeCalls - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
Program demonstrating how runtime class generation can be used to replace reflection, with a substantial increase in performance for repeated calls.
TimeCalls() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls
 
TimeCalls.DirectLoader - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.test
Simple-minded loader for constructed classes.
TimeCalls.DirectLoader() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.test.TimeCalls.DirectLoader
 
TimeUnit - Class in org.biomage.Measurement
Time
TimeUnit() - Constructor for class org.biomage.Measurement.TimeUnit
Default constructor.
TimeUnit(Attributes) - Constructor for class org.biomage.Measurement.TimeUnit
Attribute constructor.
TimeUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.
TITLE - Static variable in class org.biomage.tools.apps.annot.MageXMLConverter
 
toAccessibleFieldName(String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.FieldMapper
Chops off the underscore (_) suffix from a simple field name if it's present as it is caARRAY's coding convention, so it can be used to form the getter/setter for this field.
tobeIdentifiable - Static variable in class org.biomage.tools.generate_classes.XMIParseHelpers
 
toClass(String) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.ClassMapper
 
tollFreePhone_ - Variable in class gov.nih.nci.caarray.common.data.contact.ContactData
 
toOJBCriteria(ProtocolSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a ProtocolSearchCriteria to an OJB Criteria
toOJBCriteria(HardwareSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a HardwareSearchCriteria to an OJB Criteria
toOJBCriteria(SoftwareSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a SoftwareSearchCriteria to an OJB Criteria
toOJBCriteria(VocabSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(ArrayDesignSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a ArrayDesignSearchCriteria to an OJB Criteria
toOJBCriteria(CompositeGroupSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(FeatureGroupSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(ReporterGroupSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(OrganizationSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(PersonSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(UserSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(GroupSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
 
toOJBCriteria(ExperimentSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a ExperimentSearchCriteria to an OJB Criteria
toOJBCriteria(BioMaterialSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a BioMaterialSearchCriteria to an OJB Criteria
toOJBCriteria(ArraySearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a ArraySearchCriteria to an OJB Criteria
toOJBCriteria(MAGEMLFileUploadSearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a MAGEMLFileUploadSearchCriteria to an OJB Criteria
toOJBCriteria(FileUploadHistorySearchCriteria) - Static method in class gov.nih.nci.caarray.services.util.SearchCriteriaConverter
Convert a MAGEMLFileUploadSearchCriteria to an OJB Criteria
toOntologyEntries(VocabData[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
top - Variable in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
topElementNames - Static variable in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: The top level class.
topLevelBioAssays - Variable in class org.biomage.Experiment.ExperimentDesign
The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)
topLevelBioMaterials - Variable in class org.biomage.BioMaterial.BioMaterial
This association is one way from BioMaterial to it top most parent biomaterial.
toString() - Method in class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.contact.PersonData
 
toString() - Method in class gov.nih.nci.caarray.common.data.contact.PersonDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadEntryData
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileType
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean
 
toString() - Method in class gov.nih.nci.caarray.common.data.measurement.MeasurementData
 
toString() - Method in class gov.nih.nci.caarray.common.data.protocol.HardwareDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc
 
toString() - Method in class gov.nih.nci.caarray.common.data.util.BaseSearchCriteria
 
toString() - Method in class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
toString() - Method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
 
toString() - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration
 
toString() - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration
 
toString() - Method in class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionResult
 
toString() - Method in class gov.nih.nci.caarray.services.fileparse.gpr.GenePixDesignElement
 
toString() - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.SequenceInputFile
 
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry
Returns the string representation of this object.
toString() - Method in class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean
 
toString() - Method in class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadResults
 
toString() - Method in class gov.nih.nci.caarray.services.security.CaArrayPrincipal
Return a string representation of this CaArrayPrincipal.
toString() - Method in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
 
toString() - Method in class gov.nih.nci.caarray.services.util.cache.ObjectCacheEHCacheImpl
 
toString() - Method in class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles
print a list of selectedFileMap contents: Name,
toString() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpUploadFile
Modify the file name to include its data type for display purpose only.
toString() - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Returns the (client-side) file name for this file.
toString() - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition
 
toString() - Method in class org.biomage.AuditAndSecurity.Audit.Action
 
toString() - Method in class org.biomage.BioAssayData.BioDataCube.Order
 
toString() - Method in class org.biomage.BioSequence.SeqFeature.Basis
 
toString() - Method in class org.biomage.Common.Extendable
 
toString() - Method in class org.biomage.Common.Identifiable
 
toString() - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.MassUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.Measurement.KindCV
 
toString() - Method in class org.biomage.Measurement.Measurement.Type
 
toString() - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
toString() - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
toString() - Method in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
Description: Writes the name of the association role, capitulized.
toString() - Method in class org.biomage.tools.helpers.MGEDOntologyEntry
 
toUnit(UnitData) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.UnitDataFieldMapper
 
toUnitNameCV(String, Class) - Static method in class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion
Convert the String value of the specified strUnitNameCV to the appropriate UnitNameCV based on the object type of the specified Unit subclass.
toUnitNameCVString(Object) - Static method in class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion
 
toVocabData(OntologyEntry[]) - Static method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialUtils
 
TransactionException - Exception in gov.nih.nci.caarray.services.util.transaction
Used to indicate a problem in the transaction handling system.
TransactionException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.util.transaction.TransactionException
 
TransactionHandler - Class in gov.nih.nci.caarray.services.util.db
This class allows for a common way to perform transaction operations for either a locally accessed database or J2EE DataSource.
TransactionHandler() - Constructor for class gov.nih.nci.caarray.services.util.db.TransactionHandler
 
TransactionHandler - Interface in gov.nih.nci.caarray.services.util.transaction
Wraps transaction behavior.
transform(Vector) - Method in interface org.biomage.tools.generate_classes.CreateMageClasses.CreateClassTransformer
 
transform(Vector) - Method in class org.biomage.tools.generate_dtd.TransformBioAssayData
Description: Transform the BioAssayData class for producing modified DTD for its associations and attributes.
transform(Vector) - Method in interface org.biomage.tools.generate_dtd.WriteDTDFile.CreateClassTransformer
 
transform(Vector) - Method in class org.biomage.tools.generate_java.TransformBioAssayData
Description: Transform the BioAssayData class for producing modified DTD for its associations and attributes.
Transformation - Class in org.biomage.BioAssayData
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays.
Transformation() - Constructor for class org.biomage.BioAssayData.Transformation
Default constructor.
Transformation(Attributes) - Constructor for class org.biomage.BioAssayData.Transformation
Attribute constructor.
TransformBioAssayData - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for transforming the class list passed in.
TransformBioAssayData() - Constructor for class org.biomage.tools.generate_dtd.TransformBioAssayData
 
TransformBioAssayData - Class in org.biomage.tools.generate_java
Description: Class that is resposible for transforming the class list passed in.
TransformBioAssayData() - Constructor for class org.biomage.tools.generate_java.TransformBioAssayData
 
transformer - Variable in class org.biomage.tools.generate_classes.CreateMageClasses
Description: A class that implements the transformation interface.
transformer - Variable in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: A class that implements the transformation interface.
translateQuantitationTypes(Object[], QuantitationType) - Static method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
translateQuantitationTypes(Object, QuantitationType) - Static method in class gov.nih.nci.caarray.services.util.netcdf.NonNumericQuantitationTypesService
 
treatBioMaterial(TreatmentData, BioMaterialData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
treatBioMaterial(TreatmentData[], BioMaterialData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
treatBioMaterial(TreatmentData, BioMaterialData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Applies the specified treatment to produce the specified output biomaterial.
treatBioMaterial(TreatmentData[], BioMaterialData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Applies the specified series of treatments to produce the specified output biomaterial.
Treatment - Class in org.biomage.BioMaterial
The process by which a biomaterial is created (from source biomaterials).
Treatment() - Constructor for class org.biomage.BioMaterial.Treatment
Default constructor.
Treatment(Attributes) - Constructor for class org.biomage.BioMaterial.Treatment
Attribute constructor.
TREATMENT_EVENTS - Static variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialConstants
 
TreatmentActionOne - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentActionOne() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionOne
 
TreatmentActionThree - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentActionThree() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionThree
 
TreatmentActionTwo - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentActionTwo() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentActionTwo
 
TreatmentAssembler - Class in gov.nih.nci.caarray.services.util.dataconverter.assembler
 
TreatmentAssembler() - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.assembler.TreatmentAssembler
 
TreatmentData - Class in gov.nih.nci.caarray.common.data.biomaterial
 
TreatmentData() - Constructor for class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData
 
TreatmentEvent - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentEvent() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent
 
TreatmentFormOne - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentFormOne() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
 
TreatmentFormThree - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentFormThree() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
TreatmentFormTwo - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentFormTwo() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
TreatmentModifyForm - Class in gov.nih.nci.caarray.ui.biomaterial
 
TreatmentModifyForm() - Constructor for class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
treatments - Variable in class org.biomage.BioMaterial.BioMaterial
This association is one way from BioMaterial to Treatment.
treatments_ - Variable in class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView
 
trim() - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm
 
trim() - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm
 
trim() - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm
 
TRUE - Static variable in class org.biomage.tools.generate_er.CreateMageER
the foreign key causes a cascade action
ttestGetVocabularys() - Method in class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
 
TUMOR_GRADING - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
tumorGrading_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
TUMORGRADING_JSP_PREFIX - Static variable in class gov.nih.nci.caarray.ui.ontology.OntologyConstants
 
tumorGradingId_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
tumorGradings_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
TX_MODE_LOCAL - Static variable in class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManager
 
TXT_FILE - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
type - Variable in class org.biomage.BioAssay.DerivedBioAssay
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
type - Variable in class org.biomage.BioMaterial.BioSample
The Type attribute describes the role the BioSample holds in the treatment hierarchy.
type - Variable in class org.biomage.BioSequence.BioSequence
The type of biosequence, i.e.
type - Variable in class org.biomage.Description.DatabaseEntry
The type of record (e.g.
type - Variable in class org.biomage.HigherLevelAnalysis.NodeValue
The type of value, distance, etc.
type - Variable in class org.biomage.Protocol.Hardware
The type of a piece of Hardware.
type - Variable in class org.biomage.Protocol.Protocol
The type of a Protocol, a user should provide/use a recommended vocabulary.
type - Variable in class org.biomage.Protocol.Software
The type of a piece of Software.
Type2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Type2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Type2StringFieldConversion
 
typeAggregate - Variable in class org.biomage.tools.generate_classes.CreateFile.AssociationAttrInformation
 
typeAggregated(Element) - Method in class org.biomage.tools.generate_classes.CreateClassFile
Description: returns the type of aggregation.
typeAssociationEndAggregate(Element) - Static method in class org.biomage.tools.generate_classes.XMIParseHelpers
Description: Returns whether the association end is aggregate.
typeOwned - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: The information on whether this class's lifetime is owned by some other class.
typeOwned() - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Returns how the class is owned.
typeOwned(int) - Method in class org.biomage.tools.generate_classes.CreateFile
Description: Sets how the class is owned.
typeRole - Variable in class org.biomage.tools.generate_classes.CreateFile.RoleInformation
 
types - Variable in class org.biomage.ArrayDesign.DesignElementGroup
The specific type of a feature, reporter, or composite.
types - Variable in class org.biomage.Experiment.ExperimentDesign
Classification of an experiment.

U

UcsfGalArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.ucsf
Loads array design annotation from a GenePix GAL file.
UcsfGalFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.ucsf
Indicates a badly formatted GAL file.
UcsfGprArrayDesignLoader - Class in gov.nih.nci.caarray.services.arraydesign.loader.ucsf
Loads array design annotation from a GenePix GPR file (used as a last resort if data files are not associated with a complete array design).
UcsfGprFormatException - Exception in gov.nih.nci.caarray.services.arraydesign.loader.ucsf
Indicates a formatting error in a UCSF Spot converted GPR file.
UcsfGprFormatException() - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprFormatException
 
UcsfGprFormatException(String) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprFormatException
 
UcsfGprFormatException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprFormatException
 
UcsfGprFormatException(Throwable) - Constructor for exception gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprFormatException
 
UCSFSpotFileHeaderParser - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign
 
UCSFSpotFileHeaderParser(DataSetMapper) - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.UCSFSpotFileHeaderParser
 
UCSFSpotGprReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Provides functionality to read GenePix GPR files.
UCSFSpotZoneMatcher - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers
This ZoneMatcher is to look up Zone for a UCSF .spt file.
UCSFSpotZoneMatcher() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.UCSFSpotZoneMatcher
 
ug - Variable in class org.biomage.Measurement.MassUnit.UnitNameCV
 
UIConstants - Class in gov.nih.nci.caarray.ui
 
UIMessageConstants - Class in gov.nih.nci.caarray.common.exception
 
ul - Variable in class org.biomage.Measurement.VolumeUnit.UnitNameCV
 
uM - Variable in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
 
um - Variable in class org.biomage.Measurement.DistanceUnit.UnitNameCV
 
UML_CLASS - Static variable in class org.biomage.tools.generate_classes.CreateFile
 
UML_MODEL - Static variable in class org.biomage.tools.generate_classes.CreateFile
Description: Enumeration to represent the different model elements.
UML_PACKAGE - Static variable in class org.biomage.tools.generate_classes.CreateFile
 
umol - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV
 
UNAUTHENTICATED_USER - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
underconstruction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupSearchAction
 
underconstruction(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
unEscapeXMLSensitiveCharacters(String) - Static method in class org.biomage.tools.helpers.StringManipHelpers
 
Unique - Class in org.biomage.tools.generate_er
 
Unique() - Constructor for class org.biomage.tools.generate_er.Unique
Description: Constructor for the Unique object.
Unique(Vector) - Constructor for class org.biomage.tools.generate_er.Unique
Description: Constructor for the Unique object.
UNIT - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
unit - Variable in class org.biomage.Measurement.Measurement
The Unit associated with the Measurement.
Unit - Class in org.biomage.Measurement
The unit is a strict enumeration of types.
Unit() - Constructor for class org.biomage.Measurement.Unit
Default constructor.
Unit(Attributes) - Constructor for class org.biomage.Measurement.Unit
Attribute constructor.
UnitData - Class in gov.nih.nci.caarray.common.data.measurement
 
UnitData() - Constructor for class gov.nih.nci.caarray.common.data.measurement.UnitData
 
UnitDataFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
UnitDataFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.UnitDataFieldMapper
 
UnitNameCV2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
UnitNameCV2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion
 
unknown - Variable in class org.biomage.BioSequence.SeqFeature.Basis
 
unlink(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
unlink(Object, String) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
 
unresolvedRefList - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler
 
unZip(String, String) - Static method in class gov.nih.nci.caarray.services.util.file.FileZipper
unzip a file relative to the specified directory
unzip(File, File) - Static method in class gov.nih.nci.caarray.services.util.file.ZipUtil
Unzips the first file in the zip file provided to the destination provided.
unzip(InputStream, File) - Static method in class gov.nih.nci.caarray.services.util.file.ZipUtil
Unzips the first file in the zip strean provided to the destination provided.
unZip(String, String) - Static method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
unzip ze file relative to the specified directory
unZip(String, String, UploadFile[]) - Static method in class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
unzip ze file relative to the specified directory
up() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
A convenience method to display the contents of the parent directory
up() - Method in class gov.nih.nci.caarray.ui.experiment.UploadApplet
A convenience method to display the contents of the parent directory
update(String) - Static method in class gov.nih.nci.caarray.services.security.db.SecurityDSConnectionUtil
 
update(String, String) - Method in class gov.nih.nci.caarray.services.security.mageom.DefaultSecuredElementIdUpdater
 
update(String, String) - Method in interface gov.nih.nci.caarray.services.security.mageom.SecuredElementIdUpdater
Updates the securedElementId member of child objects given the parent object identity.
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
update(Object[], Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
update(Class[], List, Object, boolean) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
update(List, List, Object, boolean) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerFactory
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.BibliographicReferenceAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.DefaultAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.ExperimentAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.HybridizationFileUploadEntryAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.MeasuredBioAssayAssembler
 
update(List, Object, boolean) - Method in class gov.nih.nci.caarray.services.util.dataconverter.assembler.TreatmentAssembler
 
update(Object[], Object, boolean) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
Update the specified target object with data provided by the specified array of source objects.
update(Object, Object, boolean) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
 
update(Object[], Object) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
 
update(Object, Object) - Static method in class gov.nih.nci.caarray.services.util.dataconverter.DataConverter
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.LabelAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
update(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
updateAdditionalQualifier(long, AdditionalQualifierData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateAdditionalQualifier(long, AdditionalQualifierData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateAdditionalQualifier(OntologyEntry) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateArrayDesign(ArrayDesignData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
updateArrayDesign(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
updateArrayDesign(ArrayDesignData) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
updateArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateArrayDesignFileUploadEntry(ArrayDesignFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateArrayDesignFileUploadEntry(ArrayDesignFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateArrayDesignFileUploadGroup(ArrayDesignFileUploadGroupData) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateArrayDesignFileUploadGroup(ArrayDesignFileUploadGroupData) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateArrayDesignVisibility(ArrayDesignData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayDesignManagerDelegate
 
updateArrayDesignVisibility(ArrayDesignData) - Method in class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
 
updateArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.common.delegate.ArrayManagerDelegate
 
updateArrayGroup(ArrayGroup) - Method in class gov.nih.nci.caarray.services.array.ArrayManagerDB
 
updateArrayGroup(ArrayGroupData) - Method in class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB
 
updateBar(int) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet
 
updateBibliographicReference(BibliographicReference) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateBioMaterialCharacteristics(long, VocabData[]) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
updateBioMaterialCharacteristics(long, Class, OntologyEntry[]) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Save the specified BioMaterial with the specified characteristics.
updateBioMaterialCharacteristics(long, VocabData[]) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Performs the following: Update the characteristics with the new data if they exist (ID > 0) and are currently associated with the specified BioMaterial.
updateBioSample(BioSampleData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
updateBioSample(BioSample) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
updateBioSample(BioSampleData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Updates BioSample
updateBioSource(BioSourceData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
updateBioSource(BioSource) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
Update a BioSource
updateBioSource(BioSourceData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Updates BioSource
UpdateBioSourceCharacteristicsTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
UpdateBioSourceCharacteristicsTest(String) - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.UpdateBioSourceCharacteristicsTest
 
updateCharacteristicsList(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsAction
 
updateCompositeGroup(CompositeGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.CompositeGroupManagerDB
Updates an existing CompositeGroup and cascade-updates the associated compositeSequences.
updateContactInformation(ExperimentData) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentContactAction
 
updateElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB
updateProtectionGroups for a securedElement/Object
updateElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB
updateProtectionGroups for a securedElement/Object
updateEntryInList(long, HttpServletRequest, Class<? extends BioMaterialDesc>) - Static method in class gov.nih.nci.caarray.ui.biomaterial.BioMaterialUIUtils
 
updateExperiment(ExperimentData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateExperiment(ExperimentData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateExperiment(Experiment) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateExperimentalFactor(long, ExperimentalFactorData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateExperimentalFactor(long, ExperimentalFactorData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateExperimentalFactor(ExperimentalFactor) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateExperimentalFactors(long, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateExperimentalFactors(long, ExperimentalFactorData[]) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateFeatureGroup(FeatureGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.FeatureGroupManagerDB
Updates an existing FeatureGroup and cascade-updates the associated features.
updateGeneralInformation(ExperimentData) - Method in class gov.nih.nci.caarray.ui.experiment.ModifyExperimentGeneralInfoAction
 
updateGroup(GroupData) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
updateGroup(GroupData) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
updateGroup(GroupData) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Updates an existing caArray Group in the persistence store with the specified data.
updateHardware(HardwareData) - Method in class gov.nih.nci.caarray.common.delegate.HardwareManagerDelegate
 
updateHardware(HardwareData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB
 
updateHardware(Hardware) - Method in class gov.nih.nci.caarray.services.protocol.HardwareManagerDB
Update an existing hardware.
updateHybridizationFileParsingEntry(HybridizationFileParsingEntry) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateHybridizationFileUpload(HybridizationFileUploadData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateHybridizationFileUpload(HybridizationFileUploadData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup
updateHybridizationFileUpload(HybridizationFileUpload) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateHybridizationFileUploadEntry(HybridizationFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateHybridizationFileUploadEntry(HybridizationFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateHybridizationFileUploadEntry(HybridizationFileUploadEntry, boolean, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateHybridizationFileUploadEntryFactorValues(long, long[], long[]) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateHybridizationFileUploadEntryFactorValues(long, long[], long[]) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateHybridizationFileUploadEntryFactorValues(long, long[], long[]) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateHybridizationFileUploadGroup(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateHybridizationFileUploadGroup(HybridizationFileUploadGroupData) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateHybridizationFileUploadGroup(HybridizationFileUploadGroup) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateHybridizationFileUploadGroup(HybridizationFileUploadGroup, boolean) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateLabeledExtract(TreatmentData, LabeledExtractData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
updateLabeledExtract(LabeledExtract) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
updateLabeledExtract(TreatmentData, LabeledExtractData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Updates LabeledExtract
updateMAGEMLFileUploadEntry(MAGEMLFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.common.delegate.FileUploadManagerDelegate
 
updateMAGEMLFileUploadEntry(MAGEMLFileUploadEntryData, String) - Method in class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB
 
updateMAGEMLFileUploadEntry(MAGEMLFileUploadEntry, String) - Method in class gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB
 
updateObject(Object) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Updates an object.
updateObject(Object, boolean) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
 
updateObject(Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.mageloader.MAGEMLImportManagerDB
Updates an object.
updateObject(Object, PersistenceBroker) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Updates an object.
updateObject(Object) - Method in class gov.nih.nci.caarray.services.util.db.ManagerDB
Updates an object.
updateOntology(OntologyEntry) - Method in class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
updateOrganization(OrganizationData) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
updateOrganization(Organization) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
updateOrganization(OrganizationData) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Updates an existing organization in the persistence store with the specified data.
updatePerson(PersonData) - Method in class gov.nih.nci.caarray.common.delegate.ContactManagerDelegate
 
updatePerson(Person) - Method in class gov.nih.nci.caarray.services.contact.ContactManagerDB
 
updatePerson(PersonData) - Method in class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB
Updates an existing person in the persistence store with the specified data.
updateProtectionElem(long, String, String, String, String, String) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Update a protection element.
updateProtectionGroups(ProtectionGroupData[], String) - Static method in class gov.nih.nci.caarray.services.util.EJBUtils
 
updateProtocol(ProtocolData) - Method in class gov.nih.nci.caarray.common.delegate.ProtocolManagerDelegate
 
updateProtocol(ProtocolData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB
 
updateProtocol(Protocol) - Method in class gov.nih.nci.caarray.services.protocol.ProtocolManagerDB
Updates a Protocol.
updateProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateProtocolApplication(ProtocolApplicationData) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updatePublication(long, PublicationData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updatePublication(long, PublicationData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateQualityControl(long, QualityControlData) - Method in class gov.nih.nci.caarray.common.delegate.ExperimentManagerDelegate
 
updateQualityControl(long, QualityControlData) - Method in class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
 
updateQualityControl(Description) - Method in class gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
 
updateReporterGroup(ReporterGroup) - Method in class gov.nih.nci.caarray.services.arraydesign.ReporterGroupManagerDB
Updates an existing ReporterGroup and cascade-updates the associated reporters.
updateSecuredElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.CaSecurityManagerDelegate
update the protectionGroups associated with a Secured Element
updateSecuredElementProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.common.delegate.SecurityManagerDelegate
update the protectionGroups associated with a Secured Element
updateSecuredElemProtectionGroups(String, ProtectionGroupData[]) - Method in class gov.nih.nci.caarray.services.security.SecurityAdminService
Update ProtectionGroups associated with a protection element to AS_PROTECTION_GROUP_ELEMENT table.
updateSoftware(SoftwareData) - Method in class gov.nih.nci.caarray.common.delegate.SoftwareManagerDelegate
 
updateSoftware(SoftwareData) - Method in class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB
 
updateSoftware(Software) - Method in class gov.nih.nci.caarray.services.protocol.SoftwareManagerDB
Update an existing software.
updateTopLevelOnly(PhysicalArrayDesign) - Method in class gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
 
updateTreatment(TreatmentData) - Method in class gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate
 
updateTreatment(Treatment, boolean) - Method in class gov.nih.nci.caarray.services.biomaterial.BioMaterialManagerDB
 
updateTreatment(TreatmentData) - Method in class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
Updates Treatment
UpdateTreatmentTest - Class in gov.nih.nci.caarray.services.biomaterial.test
 
UpdateTreatmentTest() - Constructor for class gov.nih.nci.caarray.services.biomaterial.test.UpdateTreatmentTest
 
updateUser(UserData) - Method in class gov.nih.nci.caarray.common.delegate.AdminManagerDelegate
 
updateUser(UserData) - Method in class gov.nih.nci.caarray.services.useradmin.AdminManagerDB
 
updateUser(UserData) - Method in class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB
Updates an existing caArray user in the persistence store with the specified data.
updateVisibility(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignUpdateAction
 
updateVocabulary(VocabData) - Method in class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
updateVocabulary(VocabData) - Method in class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
upload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentAdditionalUploadFileAction
 
upload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentDataProcessingAction
 
upload(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.experiment.PerformExperimentImportMageMLAction
 
UPLOAD_TYPE_AFFYMETRIX_CDF - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_AFFYMETRIX_CDF_DB - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_AFFYMETRIX_CDF_DISPLAY - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_GAL - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_GAL_DB - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_GAL_DISPLAY - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_ILLUMINA - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_ILLUMINA_DB - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_ILLUMINA_DISPLAY - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_MAGEML - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_MAGEML_DB - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_MAGEML_DISPLAY - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_UCSF_SPOT_GAL - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_UCSF_SPOT_GAL_DB - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UPLOAD_TYPE_UCSF_SPOT_GAL_DISPLAY - Static variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignConstants
 
UploadApplet - Class in gov.nih.nci.caarray.ui.experiment
 
UploadApplet() - Constructor for class gov.nih.nci.caarray.ui.experiment.UploadApplet
Construct the frame
uploadArrayDesign(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddAction
 
UploadedFileData - Class in gov.nih.nci.caarray.common.data.fileupload2
This class contains information about the a file for download by the web client.
UploadedFileData() - Constructor for class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData
 
UploadFile - Class in gov.nih.nci.caarray.services.fileupload
A value object that contains file names and it's types
UploadFile(String, UploadFileTypes.MICROARRAY_FILE_TYPE) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFile
 
UploadFile(Long, String, UploadFileTypes.MICROARRAY_FILE_TYPE) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFile
 
uploadFilesViaHttpClient() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Implementation of the file upload using Apatche's HttpClient framework.
uploadFilesViaSocket() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
The imploemetation of file upload using java.net.Socket.
uploadFilesViaURLConnection() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
The method using URLConnection to upload files.
UploadFileTypes - Class in gov.nih.nci.caarray.services.fileupload
A set of static classes to define microarray file types
UploadFileTypes() - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes
 
UploadFileTypes.AFFY_CEL_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.AFFY_CEL_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.AFFY_CEL_TYPE_CLASS
 
UploadFileTypes.AFFY_CHP_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.AFFY_CHP_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.AFFY_CHP_TYPE_CLASS
 
UploadFileTypes.GENEPIX_GAL_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.GENEPIX_GAL_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GAL_TYPE_CLASS
 
UploadFileTypes.GENEPIX_GPR_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.GENEPIX_GPR_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GPR_TYPE_CLASS
 
UploadFileTypes.GENEPIX_GPS_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.GENEPIX_GPS_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GPS_TYPE_CLASS
 
UploadFileTypes.GENEPIX_SPOT_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.GENEPIX_SPOT_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_SPOT_TYPE_CLASS
 
UploadFileTypes.MAGEML_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.MAGEML_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MAGEML_TYPE_CLASS
 
UploadFileTypes.MICROARRAY_FILE_TYPE - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.MICROARRAY_FILE_TYPE(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MICROARRAY_FILE_TYPE
 
UploadFileTypes.OTHER_TYPE_CLASS - Class in gov.nih.nci.caarray.services.fileupload
 
UploadFileTypes.OTHER_TYPE_CLASS(String) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.OTHER_TYPE_CLASS
 
UploadFileValues - Class in gov.nih.nci.caarray.services.fileupload
A value object to communicate with the FileUploader MDB contains lists of files associated with the experiment
UploadFileValues() - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
UploadFileValues(Long) - Constructor for class gov.nih.nci.caarray.services.fileupload.UploadFileValues
 
UploadTypeData - Class in gov.nih.nci.caarray.ui.arraydesign
 
UploadTypeData(int, String, String) - Constructor for class gov.nih.nci.caarray.ui.arraydesign.UploadTypeData
 
uploadTypeId - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm
 
URI - Variable in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
 
URI_ - Variable in class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm
 
us - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
UseCase - Interface in gov.nih.nci.caarray.services.fileparse.test.usecases
Interface for application use cases.
UseCase - Interface in gov.nih.nci.caarray.services.security.test.usecases
Interface for application use cases.
UseCase - Interface in gov.nih.nci.caarray.services.test.usecases
Interface for application use cases.
UseCase - Interface in gov.nih.nci.caarray.services.util.netcdf.test.usecases
Interface for application use cases.
User - Class in org.biomage.AuditAndSecurity
A user for which the attributes are self describing.
User() - Constructor for class org.biomage.AuditAndSecurity.User
 
User(Attributes) - Constructor for class org.biomage.AuditAndSecurity.User
 
USER_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
USER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
USER_ROLE_ADMIN - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
USER_ROLE_BOTH - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
USER_ROLE_USER - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
USER_STATUS_ACTIVE - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
USER_STATUS_BOTH - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
USER_STATUS_DISABLED - Static variable in class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 
UserAddUpdateAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateAction
 
UserAddUpdateForm - Class in gov.nih.nci.caarray.ui.useradmin
 
UserAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
UserAdminAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserAdminAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserAdminAction
 
UserData - Class in gov.nih.nci.caarray.common.data.security
 
UserData() - Constructor for class gov.nih.nci.caarray.common.data.security.UserData
 
UserData - Class in gov.nih.nci.caarray.common.data.useradmin
 
UserData() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.UserData
 
UserDesc - Class in gov.nih.nci.caarray.common.data.security
 
UserDesc() - Constructor for class gov.nih.nci.caarray.common.data.security.UserDesc
 
UserDetailAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserDetailAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserDetailAction
 
UserDetailForm - Class in gov.nih.nci.caarray.ui.useradmin
 
UserDetailForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserDetailForm
 
UserGroupAddUpdateAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserGroupAddUpdateAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateAction
 
UserGroupAddUpdateForm - Class in gov.nih.nci.caarray.ui.useradmin
 
UserGroupAddUpdateForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm
 
UserGroupData - Class in gov.nih.nci.caarray.common.data.useradmin
 
UserGroupData() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.UserGroupData
 
UserInfo - Class in gov.nih.nci.caarray.services.util
 
UserInfo(Subject, String) - Constructor for class gov.nih.nci.caarray.services.util.UserInfo
 
UserInfo - Class in gov.nih.nci.caarray.ui.core
 
UserInfo(Subject, String) - Constructor for class gov.nih.nci.caarray.ui.core.UserInfo
 
UserManagementAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserManagementAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserManagementAction
 
UserRoleData - Class in gov.nih.nci.caarray.common.data.security
 
UserRoleData() - Constructor for class gov.nih.nci.caarray.common.data.security.UserRoleData
 
UserRoleData - Class in gov.nih.nci.caarray.common.data.useradmin
 
UserRoleData() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.UserRoleData
 
UserSearchAction - Class in gov.nih.nci.caarray.ui.useradmin
 
UserSearchAction() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserSearchAction
 
UserSearchCriteria - Class in gov.nih.nci.caarray.common.data.useradmin
 
UserSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria
 
UserSearchForm - Class in gov.nih.nci.caarray.ui.useradmin
 
UserSearchForm() - Constructor for class gov.nih.nci.caarray.ui.useradmin.UserSearchForm
 

V

V - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
validate(SequenceInputFile, boolean) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
Validates the file if it's the right one before proceeding further.
validate(SequenceInputFile, boolean) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.MicroarrayTextFileHeaderParser
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm
This validation method checks the required fields for a new Treatment submission or update
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne
This validation method checks the required fields for a new Treatment submission or update
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm
 
VALIDATE - Static variable in class gov.nih.nci.caarray.ui.experiment.data.ExperimentUIConstants
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.login.LoginForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.login.RegisterForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyActionForm
This validation method checks the required fields for an ontology submission or update
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm
 
validate(HardwareAddUpdateForm) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateAction
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.protocol.ParameterAddForm
 
validate(ProtocolAddUpdateForm) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateAction
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm
 
validate(SoftwareAddUpdateForm) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateAction
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm
 
validate(ActionMapping, HttpServletRequest) - Method in class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm
 
validateEntry() - Method in class org.biomage.tools.apps.annot.PagePanel
Description: verifies all entries.
validateEntry() - Method in class org.biomage.tools.apps.annot.pages.ArrayPage
Description: checks if the page is ready to convert
validateEntry() - Method in class org.biomage.tools.apps.annot.pages.Contact
Description: verifies all entries.
validateFile(File, String) - Static method in class gov.nih.nci.caarray.services.util.file.FileValidator
 
validateHybridization(Hybridization[], ActionErrors) - Static method in class gov.nih.nci.caarray.ui.experiment.data.ExperimentValidationUtil
 
VALIDATION - Static variable in class org.biomage.tools.generate_er.CreateMageER
table type is validation
validChecker - Variable in class org.biomage.tools.apps.annot.pages.ArrayPage
 
validURI(String) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
 
value - Variable in class org.biomage.Experiment.FactorValue
Allows a more complex value to be specified for a FactorValue than a simple Measurement.
Value2StringFieldConversion - Class in gov.nih.nci.caarray.services.util.ojb.conversions
 
Value2StringFieldConversion() - Constructor for class gov.nih.nci.caarray.services.util.ojb.conversions.Value2StringFieldConversion
 
VALUE_DELIMITER - Static variable in class gov.nih.nci.caarray.services.fileparse2.hybridization.SimpleDesignElement
 
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.arraydesign.ArrayDesignType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataColumnDescriptor
Returns the enum constant of this type with the specified name.
valueOf(DataTableDescriptor, String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataColumnDescriptor
 
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataTableDescriptor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataTypeEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.ScaleEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.services.contact.OrganizationDescriptor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biomage.BioAssayData.SourceType
Returns the enum constant of this type with the specified name.
values() - Static method in enum gov.nih.nci.caarray.services.arraydesign.ArrayDesignType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataColumnDescriptor
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataTableDescriptor
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.DataTypeEnum
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.QuantitationTypeDescriptor
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.bioassaydata.descriptor.ScaleEnum
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum gov.nih.nci.caarray.services.contact.OrganizationDescriptor
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biomage.BioAssayData.SourceType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Method in class org.biomage.tools.xmlutils.MultiHashMap
values() - Method in class org.biomage.tools.xmlutils.MultiHashtable
valuesSets() - Method in class org.biomage.tools.xmlutils.MultiHashMap
 
valuesSets() - Method in class org.biomage.tools.xmlutils.MultiHashtable
 
valuesSets() - Method in interface org.biomage.tools.xmlutils.MultiMap
 
varit(String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
vectorize(String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
 
verbose - Static variable in class org.biomage.tools.helpers.StringOutputHelpers
Description: The verboseness level.
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.FloatValidator
 
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.IntValidator
 
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.MandatoryFloat
 
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.MandatoryInt
 
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.MandatoryText
 
verify(JComponent) - Method in class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
 
VIEW - Static variable in class org.biomage.tools.generate_er.CreateMageER
table type is view
visibility - Variable in class org.biomage.tools.generate_classes.CreateFile
Description: Visibility of the class.
VISIBILITY_NOT_SELECTED - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
VISIBILITY_SELECTED - Static variable in class gov.nih.nci.caarray.ui.UIConstants
 
VisibilityComparator - Class in gov.nih.nci.caarray.ui.core
 
VisibilityComparator() - Constructor for class gov.nih.nci.caarray.ui.core.VisibilityComparator
 
VisibilityData - Class in gov.nih.nci.caarray.common.data.security
 
VisibilityData() - Constructor for class gov.nih.nci.caarray.common.data.security.VisibilityData
 
visibilitys_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
VocabCategory - Class in gov.nih.nci.caarray.common.data.vocab
 
VocabCategory() - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
VocabData - Class in gov.nih.nci.caarray.common.data.vocab
 
VocabData() - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabData
 
VocabData(long) - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabData
 
VocabData(String, String) - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabData
 
VocabDataFieldMapper - Class in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 
VocabDataFieldMapper(ClassMapper, SimpleField, SimpleField) - Constructor for class gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers.VocabDataFieldMapper
 
VocabDesc - Class in gov.nih.nci.caarray.common.data.vocab
 
VocabDesc() - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
VocabDesc(String) - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
VocabDesc(String, String) - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabDesc
 
VocabManagerAddTest - Class in gov.nih.nci.caarray.services.vocab.test
 
VocabManagerAddTest(String) - Constructor for class gov.nih.nci.caarray.services.vocab.test.VocabManagerAddTest
Constructor for VocabManagerDelegateTest.
VocabManagerDB - Class in gov.nih.nci.caarray.services.vocab
 
VocabManagerDB() - Constructor for class gov.nih.nci.caarray.services.vocab.VocabManagerDB
 
VocabManagerDelegate - Class in gov.nih.nci.caarray.common.delegate
 
VocabManagerDelegate() - Constructor for class gov.nih.nci.caarray.common.delegate.VocabManagerDelegate
 
VocabManagerDeleteTest - Class in gov.nih.nci.caarray.services.vocab.test
 
VocabManagerDeleteTest(String) - Constructor for class gov.nih.nci.caarray.services.vocab.test.VocabManagerDeleteTest
Constructor for VocabManagerDelegateTest.
VocabManagerEJB - Class in gov.nih.nci.caarray.services.vocab.ejb
VocabManagerEJB
VocabManagerEJB() - Constructor for class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB
 
VocabManagerGetTest - Class in gov.nih.nci.caarray.services.vocab.test
 
VocabManagerGetTest(String) - Constructor for class gov.nih.nci.caarray.services.vocab.test.VocabManagerGetTest
Constructor for VocabManagerDelegateTest.
VocabManagerUpdateTest - Class in gov.nih.nci.caarray.services.vocab.test
 
VocabManagerUpdateTest(String) - Constructor for class gov.nih.nci.caarray.services.vocab.test.VocabManagerUpdateTest
Constructor for VocabManagerDelegateTest.
VocabSearchCriteria - Class in gov.nih.nci.caarray.common.data.vocab
 
VocabSearchCriteria() - Constructor for class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria
 
VOCABULARY_MANAGER_ROLE - Static variable in class gov.nih.nci.caarray.services.util.SecurityConstants
 
VocabUtils - Class in gov.nih.nci.caarray.services.vocab
 
VocabUtils() - Constructor for class gov.nih.nci.caarray.services.vocab.VocabUtils
 
volume - Variable in class org.biomage.Measurement.Measurement.KindCV
 
VolumeUnit - Class in org.biomage.Measurement
Volume
VolumeUnit() - Constructor for class org.biomage.Measurement.VolumeUnit
Default constructor.
VolumeUnit(Attributes) - Constructor for class org.biomage.Measurement.VolumeUnit
Attribute constructor.
VolumeUnit.UnitNameCV - Class in org.biomage.Measurement
Inner class for the enumeration values that the attribute unitNameCV can assume.

W

W - Static variable in class org.biomage.tools.apps.annot.GuiSet
 
warningType - Variable in class org.biomage.DesignElement.Reporter
Similar to failType but indicates a warning rather than a failure.
water_ - Variable in class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm
 
WATER_NR - Static variable in class gov.nih.nci.caarray.common.data.vocab.VocabCategory
 
wc - Variable in class gov.nih.nci.caarray.ui.test.BaseHttpUnitTest
 
weeks - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 
WHITE_SPACE_DELIMITED - Static variable in interface gov.nih.nci.caarray.services.util.file.LineSplitter
 
WhiteSpaceDelimitedTxtReader - Class in gov.nih.nci.caarray.services.bioassaydata.reader
Reader for tab-delimited txt files imported via caAMEL.
width - Variable in class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm
 
wrapString(String, int, int) - Static method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Takes the input string and breaks it into appropriate sized pieces.
wrapString(String, int, int) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the input string and breaks it into appropriate sized pieces.
write(Object[]) - Method in class gov.nih.nci.caarray.services.fileparse2.parsers.DelimitedFileWriter
Write a single record/row which values are written in the same order as they are in the specified array.
write(File) - Method in class gov.nih.nci.caarray.ui.core.CustomCommonsFormFile
Delegates to the org.apache.commons.fileupload.FileItem of the Apache Commons FileUpload framework.
write(File) - Method in interface gov.nih.nci.caarray.ui.core.CustomFormFile
A convenience method to write an uploaded item to disk.
writeAbstractInfo(CreateFile, Table) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: set the if the the class (table) is abstract
writeAssnAttrDecl(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the association declarations out to the file.
writeAssnAttrMethods(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the association declarations out to the file.
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorBodyWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.IncludeWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.RemoveFromWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeAssoc(CreateFile, CreateFile.AssociationAttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.TemplateWriter
 
writeAssocComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
writeAssocComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
writeAssocComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeAssociationInfo(CreateFile, Table, FileWriter) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: set an association's name, scope, and data type.
writeAssociations(Writer) - Method in class org.biomage.Array.Array
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.Array_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.FeatureDefect
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.Fiducial
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.PositionDelta
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Array.ZoneDefect
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.Zone
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Person
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.Security
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssay
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.Channel
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.Hybridization
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.Image
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioAssayTuple
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DataExternal
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DataInternal
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.Datum
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.DesignElementTuple
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioAssayData.Transformation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioEvent.Map
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.BioMaterial
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.BioMaterial_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.BioSample
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.BioSource
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.Compound
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.CompoundMeasurement
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.LabeledExtract
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioMaterial.Treatment
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BQS.BibliographicReference
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.BQS.BQS_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Common.Describable
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Common.Extendable
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Common.Identifiable
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Common.MAGEJava
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Common.NameValueType
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.Database
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.DatabaseEntry
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.Description
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.Description_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.ExternalReference
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Description.OntologyEntry
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositePosition
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.DesignElement
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.Feature
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.Position
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.Reporter
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Experiment.Experiment
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Experiment.Experiment_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Experiment.FactorValue
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.HigherLevelAnalysis.Node
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.ConcentrationUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.DistanceUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.MassUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.Measurement
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.Measurement_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.QuantityUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.TemperatureUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.TimeUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.Unit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Measurement.VolumeUnit
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Hardware
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.HardwareApplication
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Parameter
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Parameterizable
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.ParameterValue
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Protocol
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Protocol_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.Software
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.ConfidenceIndicator
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.DerivedSignal
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.Error
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.ExpectedValue
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.Failed
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.MeasuredSignal
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.PresentAbsent
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.PValue
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.QuantitationType
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.QuantitationType_package
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.Ratio
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
writeAssociations This method is responsible for assembling the association data into XML.
writeAssociations(Writer) - Method in class org.biomage.QuantitationType.StandardQuantitationType
writeAssociations This method is responsible for assembling the association data into XML.
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ClassDeclWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
writeAttr(CreateFile, CreateFile.AttrInformation, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeAttr(FileWriter, CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaClassFile.WriteDataAttrInformation
Description: Writes itself to the file.
writeAttr(FileWriter, CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: Writes the attribute declaration to the file.
writeAttr(FileWriter, CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAttrInformation
Description: Writes itself to the file.
writeAttrComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.DataMemberWriter
 
writeAttrComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.GetAndSetWriter
 
writeAttrComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeAttrDecl(FileWriter, Vector, CreateJavaFile.WriteAttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the attribute declarations out to the file.
writeAttributeConstructor(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the attribute constructor out to the file.
writeAttributes(Writer) - Method in class org.biomage.Array.Array
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.Array_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.FeatureDefect
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.Fiducial
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.PositionDelta
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Array.ZoneDefect
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.Zone
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Person
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.Security
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssay
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.Channel
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.Hybridization
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.Image
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioAssayTuple
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DataExternal
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DataInternal
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.Datum
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.DesignElementTuple
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioAssayData.Transformation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioEvent.Map
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.BioMaterial
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.BioMaterial_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.BioSample
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.BioSource
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.Compound
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.CompoundMeasurement
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.LabeledExtract
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioMaterial.Treatment
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BQS.BibliographicReference
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.BQS.BQS_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Common.Describable
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Common.Extendable
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Common.Identifiable
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Common.MAGEJava
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Common.NameValueType
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.Database
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.DatabaseEntry
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.Description
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.Description_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.ExternalReference
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Description.OntologyEntry
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositePosition
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.DesignElement
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.Feature
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.Position
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.Reporter
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Experiment.Experiment
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Experiment.Experiment_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Experiment.FactorValue
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.HigherLevelAnalysis.Node
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.ConcentrationUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.DistanceUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.MassUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.Measurement
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.Measurement_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.QuantityUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.TemperatureUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.TimeUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.Unit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Measurement.VolumeUnit
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Hardware
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.HardwareApplication
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Parameter
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Parameterizable
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.ParameterValue
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Protocol
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Protocol_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.Software
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.ConfidenceIndicator
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.DerivedSignal
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.Error
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.ExpectedValue
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.Failed
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.MeasuredSignal
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.PresentAbsent
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.PValue
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.QuantitationType
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.QuantitationType_package
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.Ratio
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttributes(Writer) - Method in class org.biomage.QuantitationType.StandardQuantitationType
writeAttributes This method is responsible for assembling the attribute data into XML.
writeAttrInfo(CreateFile, Table) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: set an attribute's name, scope, and data type.
writeAttrMethods(FileWriter, Vector, CreateJavaFile.WriteAttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the attribute declarations out to the file.
writeAttrs(FileWriter, Vector, String) - Method in class org.biomage.tools.generate_doc.CreateDocFile
Description: Constructor for the Doc file generator.
writeBase(CreateFile, String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.AssignmentWriter
 
writeBase(CreateFile, String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ConstructorWriter
 
writeBase(CreateFile, String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.ImportWriter
 
writeBase(CreateFile, String, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeBaseClassName(CreateFile, Table) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: set the base class name for the class
writeBaseComment(CreateFile) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile.specificWriter
 
writeBigHeaders(String, String, File, Vector, String, String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Writes all the header files into a standard include so that we can access them in mass.
writeBinaryStream(File, HttpServletResponse) - Static method in class gov.nih.nci.caarray.ui.core.ActionUtils
Writes the specified file as a binary stream to the response object to force the client browser to open the Save As dialog for download.
writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Method to write out entities.
writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
Description: Method to write out the body.
writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDMageElement
Description: Method to write out the body.
writeBody(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
Description: Method to write out the body.
writeClassDecl(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the class declaration out to the file.
writeCommentBody(FileWriter, Vector, String, String) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Writes out the body of a comment.
writeCPPClassDecl(CreateFile, FileWriter) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Writes the CPP class declaration out to the Header file.
writeCPPClassFiles(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageClasses
Description: For each object on the Vector, will call writeJavaFile().
writeCPPComment(CreateFile, FileWriter, String, int, String, boolean, boolean) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Takes the comment, formats it for C++ and outputs it.
writeCPPComment(FileWriter, String, int, String, boolean, boolean) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the comment, formats it for C++ and outputs it.
writeCPPCommon(CreateFile, FileWriter) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Writes the common methods, common to all the CPP class Header files.
writeDataAttrDecl(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaClassFile
Description: Writes the data declarations out to the file.
writeDataAttrDecl(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the data declarations out to the file.
writeDataAttrMethods(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the data declarations out to the file.
writeDefaultConstructor(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the default constructor out to the file.
writeDocFile(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Writes the documentation out to the specified file..
WriteDTDClassElement - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for generating the DTD entities, if base class, and element and attribute if not abstract for the CreateClassFile passed into the c'tor.
WriteDTDClassElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Constructor for classes for the DTD file generator.
writeDTDComment(FileWriter, String, String, boolean, boolean) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the comment, formats it for JavaDoc and outputs it.
WriteDTDElement - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
WriteDTDElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDElement
Description: Constructor for the DTD file generator.
writeDTDFile(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Writes the header to the DTD header then creates a WriteDTDFile to write the rest of the file.
WriteDTDFile - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
WriteDTDFile(Vector, String, String, File, String, Element) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDFile
Description: Constructor for the DTD file generator.
WriteDTDFile.CreateClassTransformer - Interface in org.biomage.tools.generate_dtd
Description: An interface implemented by classes that take a class list and transform the members by either changing the relationships or adding or subtracting classes.
WriteDTDFile.PackageDependencies - Class in org.biomage.tools.generate_dtd
Description: An inner class to hold the inter and intra package dependencies.
WriteDTDFile.PackageDependencies() - Constructor for class org.biomage.tools.generate_dtd.WriteDTDFile.PackageDependencies
 
WriteDTDMageElement - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
WriteDTDMageElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDMageElement
Description: Constructor for the DTD file generator.
WriteDTDPackageElement - Class in org.biomage.tools.generate_dtd
Description: Class that is resposible for generating a DTD file for the classes represented by the list of class nodes passed into the constructor.
WriteDTDPackageElement(CreateFile) - Constructor for class org.biomage.tools.generate_dtd.WriteDTDPackageElement
Description: Constructor for the DTD file generator.
writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDClassElement
Description: Method to write out entities.
writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDElement
Description: Method to write out entities.
writeEntities(FileWriter) - Method in class org.biomage.tools.generate_dtd.WriteDTDPackageElement
Description: Method to write out entities.
writeERFiles(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageClasses
Description: For each object on the Vector, will call writeJavaFile().
writeExceptionClass(String, String, File, File, String) - Method in class org.biomage.tools.generate_cpp.CreateCPPFile
Description: Writes the exception class template out to a file.
writeExceptionClass(String, File, File) - Static method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the exception class template out to a file.
writeFile() - Method in class gov.nih.nci.caarray.services.util.parse.DelimitedExporter
Method writeFile for non streaming.
writeFileDocs(FileWriter, CreateFile) - Method in class org.biomage.tools.generate_doc.CreateDocFile
Description: Work horse method that takes a CreateFile and writes out the documentation for it.
writeGetAndSet(FileWriter, CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: Writes the attribute set and get methods.
writeGetAndSet(FileWriter, CreateFile.AttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAttrInformation
Description: Writes the attribute set and get methods.
writeHeader(FileWriter, CreateClassFile.DataTypeAttrInformation) - Method in class org.biomage.tools.generate_doc.CreateDocFile
Description: Simple method to distinguish between true attribute from the other subclasses.
writeHeader(FileWriter, CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_doc.CreateDocFile
Description: Simple method to distinguish between true attribute from the other subclasses.
writeHeader(FileWriter, File) - Method in class org.biomage.tools.generate_dtd.WriteDTDFile
Description: Writes the header information out to the file.
writeHeader(FileWriter, File) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Writes the header information out to the file.
writeImports(FileWriter, String) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the import list to the file.
writeJavaClassFiles(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageClasses
Description: For each object on the Vector, will call writeJavaFile().
writeJavaClassFiles(Vector, String, String, File, File) - Method in class org.biomage.tools.generate_java.CreateJavaClasses
Description: For each object on the Vector, will call CreateJavaFile.writeJavaClassFile().
writeJavaComment(FileWriter, String, int, String, boolean, boolean) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: Takes the comment, formats it for JavaDoc and outputs it.
writeListClass(FileWriter, CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: Writes out an inner class based on the attribute name.
writeListPassThroughs(FileWriter, CreateFile.AssociationAttrInformation) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: Writes methods for adding, getting and removing individual elements from the named vector.
WriteMAGEER(Map, FileWriter, FileWriter) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: traverse the map and write out the MAGEER.xml
writeMAGEML(File, String, boolean, boolean) - Method in class gov.nih.nci.caarray.services.util.mage.MAGEWriter
 
writeMAGEML(Writer) - Method in class org.biomage.Array.Array
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.Array_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayManufacture
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ArrayManufactureDeviation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.FeatureDefect
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.Fiducial
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ManufactureLIMS
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.PositionDelta
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Array.ZoneDefect
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ArrayDesign_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.CompositeGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.DesignElementGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.FeatureGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ReporterGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.Zone
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ZoneGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.ArrayDesign.ZoneLayout
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Audit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Contact
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Organization
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Person
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.Security
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.AuditAndSecurity.SecurityGroup
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssay
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssay_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssayCreation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.BioAssayTreatment
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Channel
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.DerivedBioAssay
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.FeatureExtraction
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Hybridization
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.Image
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.ImageAcquisition
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.MeasuredBioAssay
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssay.PhysicalBioAssay
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayData
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayData_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayMapping
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioAssayTuple
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataCube
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataTuples
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.BioDataValues
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DataExternal
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DataInternal
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.Datum
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DerivedBioAssayData
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementMapping
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.DesignElementTuple
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.FeatureDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.MeasuredBioAssayData
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.QuantitationTypeTuple
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.ReporterDimension
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioAssayData.Transformation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.BioEvent
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.BioEvent_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioEvent.Map
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.BioMaterial
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.BioMaterial_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.BioSample
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.BioSource
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.Compound
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.CompoundMeasurement
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.LabeledExtract
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioMaterial.Treatment
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.BioSequence
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.BioSequence_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SeqFeature
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SeqFeatureLocation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BioSequence.SequencePosition
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BQS.BibliographicReference
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.BQS.BQS_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Common.Describable
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Common.Extendable
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Common.Identifiable
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Common.MAGEJava
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Common.NameValueType
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.Database
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.DatabaseEntry
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.Description
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.Description_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.ExternalReference
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Description.OntologyEntry
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositeCompositeMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositePosition
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.CompositeSequence
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.DesignElement
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.DesignElement_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Feature
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureInformation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureLocation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.FeatureReporterMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.MismatchInformation
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Position
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.Reporter
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.ReporterCompositeMap
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.DesignElement.ReporterPosition
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Experiment.Experiment
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Experiment.Experiment_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Experiment.ExperimentalFactor
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Experiment.ExperimentDesign
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Experiment.FactorValue
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.HigherLevelAnalysis.Node
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeContents
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.HigherLevelAnalysis.NodeValue
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.ConcentrationUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.DistanceUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.MassUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.Measurement
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.Measurement_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.QuantityUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.TemperatureUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.TimeUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.Unit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Measurement.VolumeUnit
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Hardware
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.HardwareApplication
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Parameter
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Parameterizable
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.ParameterizableApplication
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.ParameterValue
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Protocol
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Protocol_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.ProtocolApplication
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.Software
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.Protocol.SoftwareApplication
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.ConfidenceIndicator
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.DerivedSignal
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.Error
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.ExpectedValue
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.Failed
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.MeasuredSignal
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.PresentAbsent
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.PValue
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.QuantitationType
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.QuantitationType_package
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.Ratio
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.SpecializedQuantitationType
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in class org.biomage.QuantitationType.StandardQuantitationType
writeMAGEML This method is responsible for assembling the attribute and association data into XML.
writeMAGEML(Writer) - Method in interface org.biomage.tools.xmlutils.PCData
 
writeMAGEML(Writer) - Method in class org.biomage.tools.xmlutils.PCDataImpl
 
writeMethod(FileWriter, CreateFile.AssociationAttrInformation, String, boolean, boolean, boolean, String, String) - Method in class org.biomage.tools.generate_java.CreateJavaFile.WriteAssociationAttrInformation
Description: Writes out a method.
writeMethods(FileWriter, Vector) - Method in class org.biomage.tools.generate_doc.CreateDocFile
Description: Constructor for the Doc file generator.
writeModelToClassMap(FileWriter, String) - Method in class org.biomage.tools.generate_java.CreateJavaMAGEFile
Description: It is not clear from the XML where to find the class when instantiating objects.
writeNETCDFFile() - Method in class gov.nih.nci.caarray.services.mageloader.MAGECubeBuilder
Writes out the netCDF file!
writeNETcdfFile(String) - Method in class gov.nih.nci.caarray.services.util.netcdf.NETCDFCreator
Writes the bioassays in the cube out to a netcdf file(s)
WriteOneTable(Table, FileWriter) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: write one table to the output file
writeOutput(String, int) - Static method in class org.biomage.tools.helpers.StringOutputHelpers
Description: The verboseness level.
writePlatform(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageClasses
Description: Picks the specified platform and calls the class that creates that platform.
writePlatform(Vector) - Method in class org.biomage.tools.generate_classes.CreateMageDTDClasses
Description: Picks the specified platform and calls the class that creates that platform.
writeRecord(PagePanel, PageRecord) - Method in interface org.biomage.tools.apps.annot.data.DataLoader
 
writeTableName(CreateFile, Table) - Method in class org.biomage.tools.generate_er.CreateMageER
Description: set the table name and create primary key column and set the primary key into the table
writeXMLWriterMethods(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaFile
Description: Writes the methods for generating XML from the object data.
writeXMLWriterMethods(FileWriter) - Method in class org.biomage.tools.generate_java.CreateJavaMAGEFile
Description: Writes the methods for generating XML from the object data.
wrotesome - Variable in class org.biomage.tools.generate_cpp.CreateCPPFile.EquivalenceWriter
 

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XMIParseHelpers - Class in org.biomage.tools.generate_classes
 
XMIParseHelpers() - Constructor for class org.biomage.tools.generate_classes.XMIParseHelpers
 
XMIParseHelpers.IDREFException - Exception in org.biomage.tools.generate_classes
Description: Thrown when a lookup fails and the top element has an IDREF attribute.
XMIParseHelpers.IDREFException(String) - Constructor for exception org.biomage.tools.generate_classes.XMIParseHelpers.IDREFException
 
XMIParseHelpers.IDREFException() - Constructor for exception org.biomage.tools.generate_classes.XMIParseHelpers.IDREFException
 
XMLConvertInputVerifier - Class in org.biomage.tools.apps.annot.validator
 
XMLConvertInputVerifier() - Constructor for class org.biomage.tools.apps.annot.validator.XMLConvertInputVerifier
Description: Default constructor.

Y

years - Variable in class org.biomage.Measurement.TimeUnit.UnitNameCV
 

Z

zipFile(HttpUploadFile) - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
This method puts a single file into a zip format.
zipFiles() - Method in class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploader
Zip files into zip file one at a time.
Zipper - Class in gov.nih.nci.caarray.services.util.fileuploadapplet
This object creates a zip file conaining the set of files within a SelectedFiles object.
Zipper() - Constructor for class gov.nih.nci.caarray.services.util.fileuploadapplet.Zipper
no-arg constructor
ZipUtil - Class in gov.nih.nci.caarray.services.util.file
 
ZipUtil() - Constructor for class gov.nih.nci.caarray.services.util.file.ZipUtil
 
zone - Variable in class org.biomage.Array.ZoneDefect
Reference to the Zone that was misprinted.
Zone - Class in org.biomage.ArrayDesign
Specifies the location of a zone on an array.
Zone() - Constructor for class org.biomage.ArrayDesign.Zone
Default constructor.
Zone(Attributes) - Constructor for class org.biomage.ArrayDesign.Zone
Attribute constructor.
zone - Variable in class org.biomage.DesignElement.Feature
A reference to the zone this feature is in.
ZoneDefect - Class in org.biomage.Array
Stores the defect information for a zone.
ZoneDefect() - Constructor for class org.biomage.Array.ZoneDefect
Default constructor.
ZoneDefect(Attributes) - Constructor for class org.biomage.Array.ZoneDefect
Attribute constructor.
ZoneGroup - Class in org.biomage.ArrayDesign
Specifies a repeating area on an array.
ZoneGroup() - Constructor for class org.biomage.ArrayDesign.ZoneGroup
Default constructor.
ZoneGroup(Attributes) - Constructor for class org.biomage.ArrayDesign.ZoneGroup
Attribute constructor.
ZoneGroupManagerDB - Class in gov.nih.nci.caarray.services.arraydesign
 
ZoneGroupManagerDB() - Constructor for class gov.nih.nci.caarray.services.arraydesign.ZoneGroupManagerDB
Default Constructor
zoneGroups - Variable in class org.biomage.ArrayDesign.PhysicalArrayDesign
In the case where the array design is specified by one or more zones, allows specifying where those zones are located.
zoneLayout - Variable in class org.biomage.ArrayDesign.ZoneGroup
Describes the rectangular layout of features in the array design.
ZoneLayout - Class in org.biomage.ArrayDesign
Specifies the layout of features in a rectangular grid.
ZoneLayout() - Constructor for class org.biomage.ArrayDesign.ZoneLayout
Default constructor.
ZoneLayout(Attributes) - Constructor for class org.biomage.ArrayDesign.ZoneLayout
Attribute constructor.
ZoneLocationZoneMatcher - Class in gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers
 
ZoneLocationZoneMatcher() - Constructor for class gov.nih.nci.caarray.services.fileparse2.arraydesign.zonematchers.ZoneLocationZoneMatcher
 
ZoneMatcher - Interface in gov.nih.nci.caarray.services.fileparse2.arraydesign
This interface allows for custom looking up the zone for a feature row in an array list.

_

_attempts - Variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
Number of times this message has been queued.
_className - Variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
The class name of the newly inserted SecuredElement
_id - Variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
The id of the newly inserted SecuredElement
_testProps - Variable in class gov.nih.nci.caarray.services.test.BaseInContainerTest
 
_tx - Variable in class gov.nih.nci.caarray.services.test.BaseInContainerTest
 
_waitTime - Variable in class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage
The time this message waited befor being requeued.

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