Serialized Form


Package gov.nih.nci.caarray.common.data.array

Class gov.nih.nci.caarray.common.data.array.ArrayData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

manufacturingProtocolApplication_

ProtocolApplicationData manufacturingProtocolApplication_

Class gov.nih.nci.caarray.common.data.array.ArrayGroupData extends java.lang.Object implements Serializable

Serialized Fields

desc_

ArrayGroupDesc desc_

arrays_

ArrayData[] arrays_

numArrays_

int numArrays_

arrayGroupBarCode_

java.lang.String arrayGroupBarCode_

substrateType_

VocabData substrateType_

arrayGroupSpacingX_

float arrayGroupSpacingX_

arrayGroupSpacingY_

float arrayGroupSpacingY_

arrayWidth_

float arrayWidth_

arrayLength_

float arrayLength_

arrayOrientationMark_

java.lang.String arrayOrientationMark_

arrayOrientationMarkPosition_

java.lang.String arrayOrientationMarkPosition_

arrayGroupDescription_

java.lang.String arrayGroupDescription_

visibility_

long visibility_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.array.ArrayGroupDesc extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

groupName_

java.lang.String groupName_

manufactureDate_

java.util.Date manufactureDate_

arrayDesign_

ArrayDesignData arrayDesign_

arrayManufacturers_

java.util.ArrayList<E> arrayManufacturers_

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

arrayNameArrayDesignName

java.lang.String arrayNameArrayDesignName

Class gov.nih.nci.caarray.common.data.array.ArraySearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

arrayDesignId_

long arrayDesignId_

freeText_

java.lang.String freeText_

substrateType_

VocabData substrateType_

manufacturingProtocolId_

long manufacturingProtocolId_

manufacturerId_

long manufacturerId_

startManufactureDate_

java.util.Date startManufactureDate_

endManufactureDate_

java.util.Date endManufactureDate_

groupName_

java.lang.String groupName_

visibility_

ProtectionGroupData visibility_

Package gov.nih.nci.caarray.common.data.arraydesign

Class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignData extends java.lang.Object implements Serializable

Serialized Fields

desc_

ArrayDesignDesc desc_

reporterFileType_

java.lang.String reporterFileType_

reporterFileLocation_

java.lang.String reporterFileLocation_

additionalReporterFileLocation_

java.lang.String additionalReporterFileLocation_

version_

java.lang.String version_

surfaceType_

VocabData surfaceType_

substrateType_

VocabData substrateType_

technologyType_

VocabData technologyType_

attachmentType_

VocabData attachmentType_

strandType_

VocabData strandType_

species_

VocabData species_

description_

java.lang.String description_

numberOfFeatures_

int numberOfFeatures_

providedByAffymetrix_

boolean providedByAffymetrix_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignDesc extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

identifier_

java.lang.String identifier_

name_

java.lang.String name_

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

Class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

arrayDesignId_

long arrayDesignId_

identifier_

java.lang.String identifier_

attachmentType_

VocabData attachmentType_

freeText_

java.lang.String freeText_

name_

java.lang.String name_

speciesType_

VocabData speciesType_

strandType_

VocabData strandType_

substrateType_

VocabData substrateType_

surfaceType_

VocabData surfaceType_

technologyType_

VocabData technologyType_

visibility_

ProtectionGroupData visibility_

providerId_

long providerId_

Class gov.nih.nci.caarray.common.data.arraydesign.ArrayDesignView extends ArrayDesignData implements Serializable

Serialized Fields

designProviderRoles_

java.util.ArrayList<E> designProviderRoles_

protocolApplications_

java.util.ArrayList<E> protocolApplications_

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupData extends java.lang.Object implements Serializable

Serialized Fields

desc_

CompositeGroupDesc desc_

compositeSequences_

java.util.Vector<E> compositeSequences_

Class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

name_

java.lang.String name_

id_

long id_

species_

VocabData species_

visibilitys_

long[] visibilitys_

Class gov.nih.nci.caarray.common.data.arraydesign.CompositeGroupSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

name_

java.lang.String name_

compositegroupid_

long compositegroupid_

species_

VocabData species_

visibility_

ProtectionGroupData visibility_

Class gov.nih.nci.caarray.common.data.arraydesign.DesignProviderRoleData extends java.lang.Object implements Serializable

Serialized Fields

role_

VocabData role_

contact_

ContactData contact_

Class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupData extends java.lang.Object implements Serializable

Serialized Fields

desc_

FeatureGroupDesc desc_

Class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

id_

long id_

name_

java.lang.String name_

species_

VocabData species_

technologyType_

VocabData technologyType_

featureShape_

VocabData featureShape_

distanceUnit_

java.lang.String distanceUnit_

featureWidth_

double featureWidth_

featureLength_

double featureLength_

featureHeight_

double featureHeight_

visibilitys_

long[] visibilitys_

Class gov.nih.nci.caarray.common.data.arraydesign.FeatureGroupSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

manufacturer_

OrganizationDesc manufacturer_

featuregroupid_

long featuregroupid_

name_

java.lang.String name_

species_

VocabData species_

technologyType_

VocabData technologyType_

featureShape_

VocabData featureShape_

distanceUnit_

java.lang.String distanceUnit_

featureWidth_

double featureWidth_

featureLength_

double featureLength_

featureHeight_

double featureHeight_

visibility_

ProtectionGroupData visibility_

Class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupData extends java.lang.Object implements Serializable

Serialized Fields

desc_

ReporterGroupDesc desc_

Class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

name_

java.lang.String name_

species_

VocabData species_

id_

long id_

visibilitys_

long[] visibilitys_

Class gov.nih.nci.caarray.common.data.arraydesign.ReporterGroupSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

name_

java.lang.String name_

species_

VocabData species_

reportergroupid_

long reportergroupid_

visibility_

ProtectionGroupData visibility_

Package gov.nih.nci.caarray.common.data.biomaterial

Class gov.nih.nci.caarray.common.data.biomaterial.ActionProtocolTypeMapData extends java.lang.Object implements Serializable

Serialized Fields

action_

VocabData action_

protocolTypes_

java.util.ArrayList<E> protocolTypes_

Class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialData extends java.lang.Object implements Serializable

Serialized Fields

desc_

BioMaterialDesc desc_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialDesc extends java.lang.Object implements Serializable

Serialized Fields

protectionGroups_

ProtectionGroupData[] protectionGroups_

id_

long id_

name_

java.lang.String name_

description_

java.lang.String description_

materialType_

VocabData materialType_

species_

VocabData species_

parents_

java.util.ArrayList<E> parents_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

biomaterialId

long biomaterialId

materialType_

VocabData materialType_

species_

VocabData species_

sampleType_

VocabData sampleType_

provider_

VocabData provider_

biosourceType_

VocabData biosourceType_

freeText_

java.lang.String freeText_

bioMaterialName_

java.lang.String bioMaterialName_

visibility_

ProtectionGroupData visibility_

parentBioSampleId_

long parentBioSampleId_

parentBioSourceId_

long parentBioSourceId_

ignoreCopy

boolean ignoreCopy

Class gov.nih.nci.caarray.common.data.biomaterial.BioMaterialView extends BioMaterialData implements Serializable

Serialized Fields

treatments_

java.util.ArrayList<E> treatments_

characteristics_

java.util.ArrayList<E> characteristics_

Class gov.nih.nci.caarray.common.data.biomaterial.BioSampleData extends BioMaterialData implements Serializable

Class gov.nih.nci.caarray.common.data.biomaterial.BioSampleDesc extends BioMaterialDesc implements Serializable

Serialized Fields

bioSampleType_

VocabData bioSampleType_

Class gov.nih.nci.caarray.common.data.biomaterial.BioSampleView extends BioMaterialView implements Serializable

Serialized Fields

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.biomaterial.BioSourceData extends BioMaterialData implements Serializable

Serialized Fields

provider

ContactData provider

Class gov.nih.nci.caarray.common.data.biomaterial.BioSourceDesc extends BioMaterialDesc implements Serializable

Serialized Fields

bioSourceType_

VocabData bioSourceType_

Class gov.nih.nci.caarray.common.data.biomaterial.BioSourceView extends BioMaterialView implements Serializable

Serialized Fields

provider_

ContactData provider_

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.biomaterial.CompoundMeasurementData extends java.lang.Object implements Serializable

Serialized Fields

compound_

VocabData compound_

measurement_

MeasurementData measurement_

Class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractData extends BioMaterialData implements Serializable

Serialized Fields

label_

VocabData label_

Class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractDesc extends BioMaterialDesc implements Serializable

Class gov.nih.nci.caarray.common.data.biomaterial.LabeledExtractView extends BioMaterialView implements Serializable

Serialized Fields

label_

VocabData label_

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.biomaterial.SplitBioSampleData extends BioSampleData implements Serializable

Serialized Fields

measurement_

MeasurementData measurement_

Class gov.nih.nci.caarray.common.data.biomaterial.TreatmentData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

treatmentType_

VocabData treatmentType_

treatmentOrder_

java.lang.Integer treatmentOrder_

measurement_

MeasurementData measurement_

protocolApplication_

ProtocolApplicationData protocolApplication_

compoundMeasurements_

java.util.ArrayList<E> compoundMeasurements_

treatmentAction_

java.lang.String treatmentAction_

Package gov.nih.nci.caarray.common.data.contact

Class gov.nih.nci.caarray.common.data.contact.ContactData extends java.lang.Object implements Serializable

Serialized Fields

phone_

java.lang.String phone_

tollFreePhone_

java.lang.String tollFreePhone_

fax_

java.lang.String fax_

Class gov.nih.nci.caarray.common.data.contact.OrganizationData extends ContactData implements Serializable

Serialized Fields

desc_

OrganizationDesc desc_

email_

java.lang.String email_

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.contact.OrganizationDesc extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

name_

java.lang.String name_

address_

java.lang.String address_

URI_

java.lang.String URI_

Class gov.nih.nci.caarray.common.data.contact.OrganizationSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

organizationName_

java.lang.String organizationName_

Class gov.nih.nci.caarray.common.data.contact.PersonData extends ContactData implements Serializable

Serialized Fields

address_

java.lang.String address_

desc_

PersonDesc desc_

organization_

OrganizationData organization_

URI_

java.lang.String URI_

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.common.data.contact.PersonDesc extends java.lang.Object implements Serializable

Serialized Fields

email_

java.lang.String email_

firstName_

java.lang.String firstName_

id_

long id_

lastName_

java.lang.String lastName_

midInitials_

java.lang.String midInitials_

Class gov.nih.nci.caarray.common.data.contact.PersonSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

firstName_

java.lang.String firstName_

lastName_

java.lang.String lastName_

organizationName_

java.lang.String organizationName_

Package gov.nih.nci.caarray.common.data.designelement

Class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceData extends java.lang.Object implements Serializable

Serialized Fields

desc_

CompositeSequenceDesc desc_

Class gov.nih.nci.caarray.common.data.designelement.CompositeSequenceDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

name_

java.lang.String name_

id_

long id_

Package gov.nih.nci.caarray.common.data.experiment

Class gov.nih.nci.caarray.common.data.experiment.AdditionalDataProcessingData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

location_

java.lang.String location_

protocolApplication_

ProtocolApplicationData protocolApplication_

experiment_

ExperimentDesc experiment_

Class gov.nih.nci.caarray.common.data.experiment.AdditionalQualifierData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

name_

java.lang.String name_

value_

java.lang.String value_

source_

java.lang.String source_

Class gov.nih.nci.caarray.common.data.experiment.AdditionalUploadedFileData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

description_

java.lang.String description_

location_

java.lang.String location_

experiment_

ExperimentDesc experiment_

Class gov.nih.nci.caarray.common.data.experiment.ExperimentalFactorData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

type_

VocabData type_

name_

java.lang.String name_

scale_

VocabData scale_

factorValues_

java.util.ArrayList<E> factorValues_

Class gov.nih.nci.caarray.common.data.experiment.ExperimentData extends java.lang.Object implements Serializable

Serialized Fields

desc_

ExperimentDesc desc_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.experiment.ExperimentDesc extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

securedElementId_

java.lang.String securedElementId_

identifier_

java.lang.String identifier_

name_

java.lang.String name_

description_

java.lang.String description_

completionDate_

java.util.Date completionDate_

species_

VocabData species_

types_

java.util.ArrayList<E> types_

experimentProviderRoles_

java.util.ArrayList<E> experimentProviderRoles_

numberOfHybridizations_

int numberOfHybridizations_

protectionGroups_

ProtectionGroupData[] protectionGroups_

Class gov.nih.nci.caarray.common.data.experiment.ExperimentFtpData extends java.lang.Object implements Serializable

Serialized Fields

archive_value

java.lang.String archive_value

sobject

java.lang.String sobject

sokey

java.lang.String sokey

serverURL

java.lang.String serverURL

destination

java.lang.String destination

endJumptoUrl

java.lang.String endJumptoUrl

files

java.lang.String files

actionCommand

java.lang.String actionCommand

Class gov.nih.nci.caarray.common.data.experiment.ExperimentProviderRoleData extends java.lang.Object implements Serializable

Serialized Fields

role_

VocabData role_

contact_

ContactData contact_

Class gov.nih.nci.caarray.common.data.experiment.ExperimentSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

id_

long id_

identifier_

java.lang.String identifier_

experimentName_

java.lang.String experimentName_

experimentType_

VocabData experimentType_

contact_

long contact_

species_

VocabData species_

freeText_

java.lang.String freeText_

visibility_

ProtectionGroupData visibility_

Class gov.nih.nci.caarray.common.data.experiment.ExperimentShortDesc extends ExperimentDesc implements Serializable

Class gov.nih.nci.caarray.common.data.experiment.ExperimentView extends ExperimentData implements Serializable

Serialized Fields

publications_

java.util.ArrayList<E> publications_

experimentalFactors_

java.util.ArrayList<E> experimentalFactors_

additionalQualifiers_

java.util.ArrayList<E> additionalQualifiers_

qualityControl_

QualityControlData qualityControl_

hybridizationFileUploads_

java.util.ArrayList<E> hybridizationFileUploads_

additionalUploadedFiles_

java.util.ArrayList<E> additionalUploadedFiles_

additionalDataProcessings_

java.util.ArrayList<E> additionalDataProcessings_

Class gov.nih.nci.caarray.common.data.experiment.FactorValueData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

value_

java.lang.String value_

name_

java.lang.String name_

Class gov.nih.nci.caarray.common.data.experiment.HybridizationFileUploadData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_
Deprecated. 

array_

ArrayData array_
Deprecated. 

arrayDesign

ArrayDesignDesc arrayDesign
Deprecated. 

experiment_

ExperimentDesc experiment_
Deprecated. 

arrayBatchName_

java.lang.String arrayBatchName_
Deprecated. 

arrayIdentifier_

java.lang.String arrayIdentifier_
Deprecated. 

hybridizationProtocolApplication_

ProtocolApplicationData hybridizationProtocolApplication_
Deprecated. 

imageAcquisitionProtocolApplication_

ProtocolApplicationData imageAcquisitionProtocolApplication_
Deprecated. 

featureExtractionProtocolApplication_

ProtocolApplicationData featureExtractionProtocolApplication_
Deprecated. 

uploadGroupName_

java.lang.String uploadGroupName_
Deprecated. 

numberOfChannels_

java.lang.Integer numberOfChannels_
Deprecated. 

factorValues_

java.util.ArrayList<E> factorValues_
Deprecated. 

extract_

LabeledExtractDesc extract_
Deprecated. 

spikedControl_

LabeledExtractDesc spikedControl_
Deprecated. 

celFileLocation_

java.lang.String celFileLocation_
Deprecated. 

expFileLocation_

java.lang.String expFileLocation_
Deprecated. 

txtFileLocation_

java.lang.String txtFileLocation_
Deprecated. 

chpFileLocation_

java.lang.String chpFileLocation_
Deprecated. 

channelTwoFactorValues_

java.util.ArrayList<E> channelTwoFactorValues_
Deprecated. 

channelTwoExtract_

LabeledExtractDesc channelTwoExtract_
Deprecated. 

channelTwoSpikedControl_

LabeledExtractDesc channelTwoSpikedControl_
Deprecated. 

gprFileLocation_

java.lang.String gprFileLocation_
Deprecated. 

gpsFileLocation_

java.lang.String gpsFileLocation_
Deprecated. 

gprFromSpotFileLocation_

java.lang.String gprFromSpotFileLocation_
Deprecated. 

hybridizationMappingType_

int hybridizationMappingType_
Deprecated. 

Class gov.nih.nci.caarray.common.data.experiment.PublicationData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

publication_

java.lang.String publication_

pubMedId_

java.lang.String pubMedId_

pubMedLink_

java.lang.String pubMedLink_

title_

java.lang.String title_

publisher_

java.lang.String publisher_

editor_

java.lang.String editor_

year_

java.util.Date year_

volume_

java.lang.String volume_

issue_

java.lang.String issue_

pages_

java.lang.String pages_

URI_

java.lang.String URI_

authors_

java.lang.String authors_

Class gov.nih.nci.caarray.common.data.experiment.QualityControlData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

description_

java.lang.String description_

types_

VocabData[] types_

Package gov.nih.nci.caarray.common.data.fileupload2

Class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileParsingEntryData extends FileParsingEntryData implements Serializable

Class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadEntryData extends FileUploadEntryData implements Serializable

Serialized Fields

fileParsingEntry_

ArrayDesignFileParsingEntryData fileParsingEntry_

Class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignFileUploadGroupData extends FileUploadGroupData implements Serializable

Serialized Fields

arrayDesign_

ArrayDesignDesc arrayDesign_

fileUploadEntries_

java.util.ArrayList<E> fileUploadEntries_

Class gov.nih.nci.caarray.common.data.fileupload2.ArrayDesignUploadedFileData extends java.lang.Object implements Serializable

Serialized Fields

uploadedFileData

UploadedFileData uploadedFileData

arrayDesignId

long arrayDesignId

fileEntryId

long fileEntryId

fileParsingEntryId

long fileParsingEntryId

fileGroupId

long fileGroupId

Class gov.nih.nci.caarray.common.data.fileupload2.CAArrayDesignFileUploadEntryData extends java.lang.Object implements Serializable

Serialized Fields

arrayDesignId

long arrayDesignId

fileEntryId

long fileEntryId

fileParsingEntryId

long fileParsingEntryId

fileGroupId

long fileGroupId

Class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadEntryData extends java.lang.Object implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

id

long id

fileTypeId

java.lang.String fileTypeId

fileName

java.lang.String fileName

uploadDate

java.util.Date uploadDate

caArrayDesignFileEntryData

CAArrayDesignFileUploadEntryData caArrayDesignFileEntryData

caFileUploadHistoryData

CAFileUploadHistoryData caFileUploadHistoryData

caMagemlFileEntryData

CAMagemlFileUploadEntryData caMagemlFileEntryData

status

java.lang.String status

statusDate

java.util.Date statusDate

validatorCode

java.lang.String validatorCode

userId

java.lang.String userId

originalFileName

java.lang.String originalFileName

Class gov.nih.nci.caarray.common.data.fileupload2.CAFileUploadHistoryData extends java.lang.Object implements Serializable

Serialized Fields

id

long id

fileEntryId

long fileEntryId

status

java.lang.String status

statusDate

java.util.Date statusDate

description

java.lang.String description

Class gov.nih.nci.caarray.common.data.fileupload2.CAMagemlFileUploadEntryData extends java.lang.Object implements Serializable

Serialized Fields

fileEntryId

long fileEntryId

fileParsingEntryId

long fileParsingEntryId

contactId

long contactId

magellFileGroupId

long magellFileGroupId

name

java.lang.String name

version

java.lang.String version

description

java.lang.String description

contentType

java.lang.String contentType

msgToCurator

java.lang.String msgToCurator

Class gov.nih.nci.caarray.common.data.fileupload2.FileParsingEntryData extends SerializableFileUploadDataBean implements Serializable

Serialized Fields

parsingStartDate_

java.util.Date parsingStartDate_

parsingEndDate_

java.util.Date parsingEndDate_

parsingSucceeded_

java.lang.String parsingSucceeded_

failureDescription_

java.lang.String failureDescription_

Class gov.nih.nci.caarray.common.data.fileupload2.FileType extends java.lang.Object implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

id

java.lang.String id

creatingSoftware

java.lang.String creatingSoftware

creatingSoftwareVersion

java.lang.String creatingSoftwareVersion

fileExtension

java.lang.String fileExtension

fileZipExtension

java.lang.String fileZipExtension

fileCategory

java.lang.String fileCategory

required

java.lang.Boolean required

Class gov.nih.nci.caarray.common.data.fileupload2.FileTypeMap extends java.lang.Object implements Serializable

Serialized Fields

fileTypeMappings_

java.util.LinkedHashMap<K,V> fileTypeMappings_

Class gov.nih.nci.caarray.common.data.fileupload2.FileUploadEntryData extends SerializableFileUploadDataBean implements Serializable

serialVersionUID: -1999989794623791411L

Serialized Fields

fileType_

FileType fileType_

fileName_

java.lang.String fileName_

status_

java.lang.String status_

statusDate_

java.util.Date statusDate_

validatorCode_

java.lang.String validatorCode_

userId_

java.lang.String userId_

originalFileName_

java.lang.String originalFileName_

Class gov.nih.nci.caarray.common.data.fileupload2.FileUploadGroupData extends SerializableFileUploadDataBean implements Serializable

Serialized Fields

parsingStartDate_

java.util.Date parsingStartDate_

parsingEndDate_

java.util.Date parsingEndDate_

parsingSucceeded_

java.lang.String parsingSucceeded_

acceptableFileTypes_

java.util.ArrayList<E> acceptableFileTypes_

Class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistoryData extends SerializableFileUploadDataBean implements Serializable

Serialized Fields

fileUploadEntry_

FileUploadEntryData fileUploadEntry_

status_

java.lang.String status_

statusDate_

java.util.Date statusDate_

description_

java.lang.String description_

Class gov.nih.nci.caarray.common.data.fileupload2.FileUploadHistorySearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

fileUploadEntry_

long fileUploadEntry_

Class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileParsingEntryData extends FileParsingEntryData implements Serializable

Class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileType extends FileType implements Serializable

Class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntryData extends FileUploadEntryData implements Serializable

Serialized Fields

fileParsingEntry_

HybridizationFileParsingEntryData fileParsingEntry_

experiment_

ExperimentDesc experiment_

arrayGroup_

ArrayGroupData arrayGroup_

channelOneExtract_

LabeledExtractDesc channelOneExtract_

channelOneSpikedControl_

LabeledExtractDesc channelOneSpikedControl_

channelTwoExtract_

LabeledExtractDesc channelTwoExtract_

channelTwoSpikedControl_

LabeledExtractDesc channelTwoSpikedControl_

featureExtractionProtocolApplication_

ProtocolApplicationData featureExtractionProtocolApplication_

hybridizationProtocolApplication_

ProtocolApplicationData hybridizationProtocolApplication_

imageAcquisitionProtocolApplication_

ProtocolApplicationData imageAcquisitionProtocolApplication_

channelOneFactorValues_

java.util.ArrayList<E> channelOneFactorValues_

channelTwoFactorValues_

java.util.ArrayList<E> channelTwoFactorValues_

Class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadEntrySummaryData extends SerializableFileUploadDataBean implements Serializable

Serialized Fields

fileType_

HybridizationFileType fileType_

fileName_

java.lang.String fileName_

parsingStartDate_

java.util.Date parsingStartDate_

parsingEndDate_

java.util.Date parsingEndDate_

statusDate_

java.util.Date statusDate_

originalFileName_

java.lang.String originalFileName_

userId_

java.lang.String userId_

validatorCode_

java.lang.String validatorCode_

parsingSucceeded_

java.lang.String parsingSucceeded_

failureDescription

java.lang.String failureDescription

Class gov.nih.nci.caarray.common.data.fileupload2.HybridizationFileUploadGroupData extends FileUploadGroupData implements Serializable

Serialized Fields

file2FileTypeMap_

java.util.LinkedHashMap<K,V> file2FileTypeMap_

experiment_

ExperimentDesc experiment_

arrayGroup_

ArrayGroupData arrayGroup_

channelOneExtract_

LabeledExtractDesc channelOneExtract_

channelOneSpikedControl_

LabeledExtractDesc channelOneSpikedControl_

channelTwoExtract_

LabeledExtractDesc channelTwoExtract_

channelTwoSpikedControl_

LabeledExtractDesc channelTwoSpikedControl_

featureExtractionProtocolApplication_

ProtocolApplicationData featureExtractionProtocolApplication_

hybridizationProtocolApplication_

ProtocolApplicationData hybridizationProtocolApplication_

imageAcquisitionProtocolApplication_

ProtocolApplicationData imageAcquisitionProtocolApplication_

channelOneFactorValues_

java.util.ArrayList<E> channelOneFactorValues_

channelTwoFactorValues_

java.util.ArrayList<E> channelTwoFactorValues_

fileUploadEntries_

java.util.ArrayList<E> fileUploadEntries_

Class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadEntryData extends FileUploadEntryData implements Serializable

Serialized Fields

name_

java.lang.String name_

version_

java.lang.String version_

description_

java.lang.String description_

contentType_

java.lang.String contentType_

contact_

PersonData contact_

msgToCurator_

java.lang.String msgToCurator_

Class gov.nih.nci.caarray.common.data.fileupload2.MAGEMLFileUploadSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

name_

java.lang.String name_

version_

java.lang.String version_

description_

java.lang.String description_

contentType_

java.lang.String contentType_

contact_

long contact_

msgToCurator_

java.lang.String msgToCurator_

userId_

java.lang.String userId_

Class gov.nih.nci.caarray.common.data.fileupload2.SerializableFileUploadDataBean extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

Class gov.nih.nci.caarray.common.data.fileupload2.UploadedFileData extends java.lang.Object implements Serializable

Serialized Fields

id

long id

fileTypeId

java.lang.String fileTypeId

fileName

java.lang.String fileName

status

java.lang.String status

statusDate

java.util.Date statusDate

validatorCode

java.lang.String validatorCode

userId

java.lang.String userId

originalFileName

java.lang.String originalFileName

Package gov.nih.nci.caarray.common.data.measurement

Class gov.nih.nci.caarray.common.data.measurement.MeasurementData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

value_

java.lang.String value_

unit_

UnitData unit_

Class gov.nih.nci.caarray.common.data.measurement.UnitData extends java.lang.Object implements Serializable

Serialized Fields

type_

VocabData type_

name_

VocabData name_

Package gov.nih.nci.caarray.common.data.protocol

Class gov.nih.nci.caarray.common.data.protocol.HardwareApplicationData extends ParameterizableApplicationData implements Serializable

Serialized Fields

hardware_

HardwareData hardware_

serialNumber_

java.lang.String serialNumber_

Class gov.nih.nci.caarray.common.data.protocol.HardwareData extends java.lang.Object implements Serializable

Serialized Fields

desc_

HardwareDesc desc_

URI_

java.lang.String URI_

parameters_

java.util.ArrayList<E> parameters_

softwares_

java.util.ArrayList<E> softwares_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.protocol.HardwareDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

id_

long id_

visibilitys_

long[] visibilitys_

make_

java.lang.String make_

name_

java.lang.String name_

manufacturer_

OrganizationData manufacturer_

model_

java.lang.String model_

type_

VocabData type_

Class gov.nih.nci.caarray.common.data.protocol.HardwareSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

hardwareId_

long hardwareId_

model_

java.lang.String model_

make_

java.lang.String make_

name_

java.lang.String name_

manufacturerId_

long manufacturerId_

type_

VocabData type_

freeText_

java.lang.String freeText_

visibility_

ProtectionGroupData visibility_

Class gov.nih.nci.caarray.common.data.protocol.ParameterData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

name_

java.lang.String name_

defaultValue_

MeasurementData defaultValue_

dataType_

VocabData dataType_

Class gov.nih.nci.caarray.common.data.protocol.ParameterizableApplicationData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

parameterValues_

java.util.ArrayList<E> parameterValues_

Class gov.nih.nci.caarray.common.data.protocol.ParameterValueData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

parameter_

ParameterData parameter_

value_

java.lang.String value_

Class gov.nih.nci.caarray.common.data.protocol.ProtocolApplicationData extends ParameterizableApplicationData implements Serializable

Serialized Fields

protocol_

ProtocolData protocol_

performer_

PersonData performer_

activityDate_

java.util.Date activityDate_

softwareApplications_

java.util.ArrayList<E> softwareApplications_

hardwareApplications_

java.util.ArrayList<E> hardwareApplications_

activityDateAsString_

java.lang.String activityDateAsString_

Class gov.nih.nci.caarray.common.data.protocol.ProtocolData extends java.lang.Object implements Serializable

Serialized Fields

desc_

ProtocolDesc desc_

identifier_

java.lang.String identifier_

description_

java.lang.String description_

hardwares_

java.util.Vector<E> hardwares_

softwares_

java.util.Vector<E> softwares_

parameters_

java.util.Vector<E> parameters_

URI_

java.lang.String URI_

mageIdentifier

java.lang.String mageIdentifier

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.protocol.ProtocolDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

name_

java.lang.String name_

visibilitys_

long[] visibilitys_

id_

long id_

type_

VocabData type_

Class gov.nih.nci.caarray.common.data.protocol.ProtocolSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

name_

java.lang.String name_

protocolId_

long protocolId_

type_

VocabData type_

softwareManufacturerId_

long softwareManufacturerId_

hardwareManufacturerId_

long hardwareManufacturerId_

visibility_

ProtectionGroupData visibility_

Class gov.nih.nci.caarray.common.data.protocol.SoftwareApplicationData extends ParameterizableApplicationData implements Serializable

Serialized Fields

software_

SoftwareData software_

releaseDate_

java.util.Date releaseDate_

version_

java.lang.String version_

releaseDateAsString_

java.lang.String releaseDateAsString_

Class gov.nih.nci.caarray.common.data.protocol.SoftwareData extends java.lang.Object implements Serializable

Serialized Fields

description_

java.lang.String description_

parameters_

java.util.ArrayList<E> parameters_

desc_

SoftwareDesc desc_

URI_

java.lang.String URI_

hardware_

HardwareDesc hardware_

softwares_

java.util.ArrayList<E> softwares_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.protocol.SoftwareDesc extends java.lang.Object implements Serializable

Serialized Fields

securedElement_

SecuredElementData securedElement_

protectionGroups_

ProtectionGroupData[] protectionGroups_

manufacturer_

OrganizationData manufacturer_

name_

java.lang.String name_

id_

long id_

type_

VocabData type_

visibilitys_

long[] visibilitys_

Class gov.nih.nci.caarray.common.data.protocol.SoftwareSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

manufacturer_

java.lang.String manufacturer_

manufacturerId_

long manufacturerId_

name_

java.lang.String name_

releaseDate_

java.util.Date releaseDate_

softwareId_

long softwareId_

type_

VocabData type_

visibility_

ProtectionGroupData visibility_

Package gov.nih.nci.caarray.common.data.security

Class gov.nih.nci.caarray.common.data.security.ProtectionGroupData extends java.lang.Object implements Serializable

Serialized Fields

name_

java.lang.String name_

description_

java.lang.String description_

protectionGroupId_

long protectionGroupId_

Class gov.nih.nci.caarray.common.data.security.Role extends java.lang.Object implements Serializable

Serialized Fields

roleId

long roleId

roleName

java.lang.String roleName

roleDesc

java.lang.String roleDesc

applicationId

long applicationId

Class gov.nih.nci.caarray.common.data.security.RoleAssignmentData extends java.lang.Object implements Serializable

Serialized Fields

role_

RoleData role_

protectionGroups_

java.util.Vector<E> protectionGroups_

Class gov.nih.nci.caarray.common.data.security.RoleData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

name_

java.lang.String name_

Class gov.nih.nci.caarray.common.data.security.SecuredElementData extends java.lang.Object implements Serializable

Serialized Fields

objectId_

java.lang.String objectId_

name_

java.lang.String name_

description_

java.lang.String description_

ownerUserName_

java.lang.String ownerUserName_

protectionGroups_

ProtectionGroupData[] protectionGroups_

Class gov.nih.nci.caarray.common.data.security.UserData extends java.lang.Object implements Serializable

Serialized Fields

desc_

UserDesc desc_

title_

java.lang.String title_

phoneNumber_

java.lang.String phoneNumber_

email_

java.lang.String email_

organization_

java.lang.String organization_

dept_

java.lang.String dept_

location_

java.lang.String location_

Class gov.nih.nci.caarray.common.data.security.UserDesc extends java.lang.Object implements Serializable

Serialized Fields

loginName_

java.lang.String loginName_

lastName_

java.lang.String lastName_

firstName_

java.lang.String firstName_

Class gov.nih.nci.caarray.common.data.security.UserRoleData extends java.lang.Object implements Serializable

Serialized Fields

userName_

java.lang.String userName_

roles_

java.util.Vector<E> roles_

Package gov.nih.nci.caarray.common.data.useradmin

Class gov.nih.nci.caarray.common.data.useradmin.AdminData extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.common.data.useradmin.GroupData extends AdminData implements Serializable

Serialized Fields

id

long id

groupName

java.lang.String groupName

description

java.lang.String description

largeElementCountFlag

java.lang.String largeElementCountFlag

updateDate

long updateDate

protectionGroupTypeId

long protectionGroupTypeId

users

java.util.Vector<E> users

role

java.lang.String role

Class gov.nih.nci.caarray.common.data.useradmin.GroupSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

groupName

java.lang.String groupName

Class gov.nih.nci.caarray.common.data.useradmin.UserData extends AdminData implements Serializable

Serialized Fields

id

java.lang.Long id

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

title

java.lang.String title

emailAddress

java.lang.String emailAddress

institutionName

java.lang.String institutionName

department

java.lang.String department

location

java.lang.String location

updateDate

java.lang.Long updateDate

startDate

java.lang.Long startDate

endDate

java.lang.Long endDate

isAdminUser

boolean isAdminUser

shouldBeAdminUser

boolean shouldBeAdminUser

role

java.lang.String role

status

java.lang.String status

userRoles

java.util.Vector<E> userRoles

allGroups

java.util.Collection<E> allGroups

groups

java.util.Vector<E> groups

phoneNumber

java.lang.String phoneNumber

password

java.lang.String password

userGroupData

java.util.Vector<E> userGroupData

Class gov.nih.nci.caarray.common.data.useradmin.UserGroupData extends GroupData implements Serializable

Serialized Fields

id

long id

groupName

java.lang.String groupName

currentSelection

long currentSelection

role

java.lang.String role

Class gov.nih.nci.caarray.common.data.useradmin.UserRoleData extends AdminData implements Serializable

Serialized Fields

id

java.lang.Long id

updateDate

java.lang.Long updateDate

roleId

java.lang.Long roleId

protectionGroupId

java.lang.Long protectionGroupId

userId

java.lang.Long userId

protectionElementId

java.lang.Long protectionElementId

protectionTypeId

java.lang.Long protectionTypeId

startDate

java.lang.Long startDate

endDate

java.lang.Long endDate

group

GroupData group

user

UserData user

Class gov.nih.nci.caarray.common.data.useradmin.UserSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

institutionName

java.lang.String institutionName

emailAddress

java.lang.String emailAddress

roleSelection

int roleSelection

statusSelection

int statusSelection

Package gov.nih.nci.caarray.common.data.util

Class gov.nih.nci.caarray.common.data.util.BaseSearchCriteria extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.common.data.util.FileData extends java.lang.Object implements Serializable

Serialized Fields

creationDate_

java.util.Date creationDate_

pathName_

java.lang.String pathName_

size_

long size_

Package gov.nih.nci.caarray.common.data.vocab

Class gov.nih.nci.caarray.common.data.vocab.AgeData extends VocabData implements Serializable

Serialized Fields

age_

java.lang.Integer age_

measurement_

VocabData measurement_

max_

java.lang.Integer max_

maxMeasurement_

VocabData maxMeasurement_

min_

java.lang.Integer min_

minMeasurement_

VocabData minMeasurement_

initialTimePoint_

VocabData initialTimePoint_

Class gov.nih.nci.caarray.common.data.vocab.BiometricsData extends VocabData implements Serializable

Serialized Fields

weight_

java.lang.Float weight_

weightMeasurement_

VocabData weightMeasurement_

height_

java.lang.Float height_

heightMeasurement_

VocabData heightMeasurement_

Class gov.nih.nci.caarray.common.data.vocab.ChromosomalAberrationData extends VocabData implements Serializable

Serialized Fields

types_

java.util.ArrayList<E> types_

Class gov.nih.nci.caarray.common.data.vocab.DatabaseData extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

category_

java.lang.String category_

name_

java.lang.String name_

version_

java.lang.String version_

userDefined_

boolean userDefined_

Class gov.nih.nci.caarray.common.data.vocab.VocabCategory extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.common.data.vocab.VocabData extends java.lang.Object implements Serializable

Serialized Fields

database_

DatabaseData database_

desc_

VocabDesc desc_

description_

java.lang.String description_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.common.data.vocab.VocabDesc extends java.lang.Object implements Serializable

Serialized Fields

id_

long id_

name_

java.lang.String name_

category_

java.lang.String category_

accessionNumber_

java.lang.String accessionNumber_

databaseReference_

java.lang.String databaseReference_

URI_

java.lang.String URI_

securedElement_

SecuredElementData securedElement_

Class gov.nih.nci.caarray.common.data.vocab.VocabSearchCriteria extends BaseSearchCriteria implements Serializable

Serialized Fields

name_

java.lang.String name_

databaseReference_

java.lang.String databaseReference_

accessionNumber_

java.lang.String accessionNumber_

category_

java.lang.String category_

includeAllSubCategories_

boolean includeAllSubCategories_

vocabId_

long vocabId_

userName_

java.lang.String userName_

Package gov.nih.nci.caarray.common.exception

Class gov.nih.nci.caarray.common.exception.GeneralException extends java.lang.Exception implements Serializable

Serialized Fields

errorCode_

java.lang.String errorCode_
The errorCode corresponds to the String message in the resource bundle

Class gov.nih.nci.caarray.common.exception.ImportException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.array.ejb

Class gov.nih.nci.caarray.services.array.ejb.ArrayManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.arraydesign

Class gov.nih.nci.caarray.services.arraydesign.ArrayDesignDataSourceException extends java.lang.Exception implements Serializable

serialVersionUID: 5984882405977838443L

Class gov.nih.nci.caarray.services.arraydesign.ArrayDesignRetrievalException extends java.lang.Exception implements Serializable

serialVersionUID: 2164143692840119460L


Package gov.nih.nci.caarray.services.arraydesign.ejb

Class gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.arraydesign.loader

Class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignFileParsingJob extends java.lang.Object implements Serializable

serialVersionUID: 2297586445975630752L

Serialized Fields

caFileEntry

CAFileUploadEntry caFileEntry

username

java.lang.String username

Class gov.nih.nci.caarray.services.arraydesign.loader.ArrayDesignSaveException extends java.lang.Exception implements Serializable

serialVersionUID: 1L


Package gov.nih.nci.caarray.services.arraydesign.loader.affymetrix

Class gov.nih.nci.caarray.services.arraydesign.loader.affymetrix.CdfFileNotFoundException extends java.lang.Exception implements Serializable

serialVersionUID: 5786747394362872165L


Package gov.nih.nci.caarray.services.arraydesign.loader.agilent

Class gov.nih.nci.caarray.services.arraydesign.loader.agilent.AgilentTxtFormatException extends java.lang.Exception implements Serializable

serialVersionUID: 1003370171931726185L


Package gov.nih.nci.caarray.services.arraydesign.loader.genepix

Class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGalFormatException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.arraydesign.loader.genepix.GenepixGprFormatException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.arraydesign.loader.handler

Class gov.nih.nci.caarray.services.arraydesign.loader.handler.ArrayDesignFileParsingException extends java.lang.Exception implements Serializable

serialVersionUID: -3391277380299151472L


Package gov.nih.nci.caarray.services.arraydesign.loader.illumina

Class gov.nih.nci.caarray.services.arraydesign.loader.illumina.IlluminaCsvFormatException extends java.lang.Exception implements Serializable

serialVersionUID: -4582752762679694994L


Package gov.nih.nci.caarray.services.arraydesign.loader.imagene

Class gov.nih.nci.caarray.services.arraydesign.loader.imagene.ImageneTxtFormatException extends java.lang.Exception implements Serializable

serialVersionUID: 1003370171931726185L


Package gov.nih.nci.caarray.services.arraydesign.loader.ucsf

Class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGalFormatException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.arraydesign.loader.ucsf.UcsfGprFormatException extends java.lang.Exception implements Serializable

serialVersionUID: -8781404315438435762L


Package gov.nih.nci.caarray.services.bioassaydata

Class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataInfo extends java.lang.Object implements Serializable

serialVersionUID: 5440280342450437500L

Serialized Fields

bioAssay

BioAssay bioAssay

bioAssayData

BioAssayData bioAssayData

dataFile

java.io.File dataFile

sourceType

SourceType sourceType

array

Array array

username

java.lang.String username

newBioDataCube

boolean newBioDataCube

experiment

Experiment experiment

Class gov.nih.nci.caarray.services.bioassaydata.BioAssayDataLoaderException extends java.lang.Exception implements Serializable

serialVersionUID: -2213097078438126860L

Class gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceException extends java.lang.Exception implements Serializable

serialVersionUID: -6753131552372664841L


Package gov.nih.nci.caarray.services.bioassaydata.reader

Class gov.nih.nci.caarray.services.bioassaydata.reader.DataFileParseException extends java.lang.Exception implements Serializable

serialVersionUID: -538846822195287478L


Package gov.nih.nci.caarray.services.biomaterial.ejb

Class gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.contact.ejb

Class gov.nih.nci.caarray.services.contact.ejb.ContactManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.exception

Class gov.nih.nci.caarray.services.exception.AccessDeniedException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.ConfigurationException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.CreateObjectException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.CreateSecuredElementException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.DBException extends java.lang.Exception implements Serializable

Serialized Fields

sourceException

java.lang.Throwable sourceException
The cause of this Exception.

Class gov.nih.nci.caarray.services.exception.InheritedAccessDeniedException extends AccessDeniedException implements Serializable

Class gov.nih.nci.caarray.services.exception.InsertObjectException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.MissingSecuredElementIdException extends AccessDeniedException implements Serializable

Class gov.nih.nci.caarray.services.exception.ObjectInUseException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.ObjectNotExistException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.ParseException extends java.lang.Exception implements Serializable

Serialized Fields

sourceException

java.lang.Throwable sourceException
The cause of this Exception.

Class gov.nih.nci.caarray.services.exception.SecurityException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.exception.ServiceLookupException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.experiment.ejb

Class gov.nih.nci.caarray.services.experiment.ejb.ExperimentCleaningConfiguration extends java.lang.Object implements Serializable

serialVersionUID: -887818599562541L

Serialized Fields

idsToExperimentsForDeletion

java.util.Map<K,V> idsToExperimentsForDeletion

idsToHybridizationDeletionConfigurations

java.util.Map<K,V> idsToHybridizationDeletionConfigurations

username

java.lang.String username

password

java.lang.String password

authConf

java.lang.String authConf

hostname

java.lang.String hostname

port

int port

Class gov.nih.nci.caarray.services.experiment.ejb.ExperimentDeletionResult extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB extends AbstractSessionBean implements Serializable

Class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionConfiguration extends java.lang.Object implements Serializable

serialVersionUID: 6843872786525969757L

Serialized Fields

experimentId

long experimentId

filenamesToDatas

java.util.Map<K,V> filenamesToDatas

experimentData

ExperimentData experimentData

Class gov.nih.nci.caarray.services.experiment.ejb.HybridizationDeletionResult extends java.lang.Object implements Serializable

serialVersionUID: -971484719512285103L

Serialized Fields

messages

java.util.List<E> messages

Package gov.nih.nci.caarray.services.fileparse.mdb

Class gov.nih.nci.caarray.services.fileparse.mdb.ArrayDesignUploadManagerMDB extends java.lang.Object implements Serializable

Serialized Fields

ejbContext

javax.ejb.MessageDrivenContext ejbContext

jndiContext

javax.naming.InitialContext jndiContext

Class gov.nih.nci.caarray.services.fileparse.mdb.FileUploadManagerMDB extends java.lang.Object implements Serializable

Serialized Fields

ejbContext

javax.ejb.MessageDrivenContext ejbContext

jndiContext

javax.naming.InitialContext jndiContext

Package gov.nih.nci.caarray.services.fileparse2.mdb

Class gov.nih.nci.caarray.services.fileparse2.mdb.ArrayDesignFileParserMDB extends java.lang.Object implements Serializable

Serialized Fields

mdbCtx_

javax.ejb.MessageDrivenContext mdbCtx_

jndiContext

javax.naming.InitialContext jndiContext

Class gov.nih.nci.caarray.services.fileparse2.mdb.HybridizationFileParserMDB extends java.lang.Object implements Serializable

Serialized Fields

mdbCtx_

javax.ejb.MessageDrivenContext mdbCtx_

jndiContext

javax.naming.InitialContext jndiContext

Package gov.nih.nci.caarray.services.fileparse2.parsers

Class gov.nih.nci.caarray.services.fileparse2.parsers.LocalDynaBeanImpl extends org.apache.commons.beanutils.BasicDynaBean implements Serializable


Package gov.nih.nci.caarray.services.fileupload

Class gov.nih.nci.caarray.services.fileupload.ArrayDesignValues extends java.lang.Object implements Serializable

Serialized Fields

arrayDesignDesc_

ArrayDesignDesc arrayDesignDesc_

uploadFile_

UploadFile uploadFile_

protectionGroups_

ProtectionGroupData[] protectionGroups_

owner_

java.lang.String owner_

Class gov.nih.nci.caarray.services.fileupload.UploadFile extends java.lang.Object implements Serializable

Serialized Fields

bioAssayId

java.lang.Long bioAssayId

fileName

java.lang.String fileName

fileType

UploadFileTypes.MICROARRAY_FILE_TYPE fileType

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.AFFY_CEL_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.AFFY_CHP_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GAL_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GPR_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_GPS_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.GENEPIX_SPOT_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MAGEML_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.MICROARRAY_FILE_TYPE extends java.lang.Object implements Serializable

Serialized Fields

softwareName

java.lang.String softwareName

Class gov.nih.nci.caarray.services.fileupload.UploadFileTypes.OTHER_TYPE_CLASS extends UploadFileTypes.MICROARRAY_FILE_TYPE implements Serializable

Class gov.nih.nci.caarray.services.fileupload.UploadFileValues extends java.lang.Object implements Serializable

Serialized Fields

experimentId_

java.lang.Long experimentId_

bioAssayFiles_

java.util.HashMap<K,V> bioAssayFiles_

nonBioAssayFiles_

java.util.ArrayList<E> nonBioAssayFiles_

owner_

java.lang.String owner_

protectionGroups_

ProtectionGroupData[] protectionGroups_

tempDirectory_

java.lang.String tempDirectory_

Package gov.nih.nci.caarray.services.fileupload2

Class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileParsingEntry extends FileParsingEntry implements Serializable

Class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadEntry extends FileUploadEntry implements Serializable

Serialized Fields

fileUploadEntry

FileUploadEntry fileUploadEntry

arrayDesign

PhysicalArrayDesign arrayDesign

fileParsingEntry

ArrayDesignFileParsingEntry fileParsingEntry

Class gov.nih.nci.caarray.services.fileupload2.ArrayDesignFileUploadGroup extends FileUploadGroup implements Serializable

Serialized Fields

fileUploadEntries

java.util.List<E> fileUploadEntries

Class gov.nih.nci.caarray.services.fileupload2.CAArrayDesignFileUploadEntry extends java.lang.Object implements Serializable

Serialized Fields

arrayDesignId

java.lang.Long arrayDesignId

fileEntryId

java.lang.Long fileEntryId

fileParsingEntryId

java.lang.Long fileParsingEntryId

fileGroupId

java.lang.Long fileGroupId

fileParsingEntry

ArrayDesignFileParsingEntry fileParsingEntry

Class gov.nih.nci.caarray.services.fileupload2.CAFileUploadEntry extends java.lang.Object implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

id

java.lang.Long id

fileTypeId

java.lang.String fileTypeId

fileName

java.lang.String fileName

caArrayDesignFileEntry

CAArrayDesignFileUploadEntry caArrayDesignFileEntry

caFileUploadHistory

CAFileUploadHistory caFileUploadHistory

caMagemlFileEntry

CAMagemlFileUploadEntry caMagemlFileEntry

status

java.lang.String status

statusDate

java.util.Date statusDate

validatorCode

java.lang.String validatorCode

userId

java.lang.String userId

originalFileName

java.lang.String originalFileName

Class gov.nih.nci.caarray.services.fileupload2.CAFileUploadHistory extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Long id

fileEntryId

java.lang.Long fileEntryId

status

java.lang.String status

statusDate

java.util.Date statusDate

description

java.lang.String description

Class gov.nih.nci.caarray.services.fileupload2.CAMagemlFileUploadEntry extends java.lang.Object implements Serializable

Serialized Fields

fileEntryId

java.lang.Long fileEntryId

fileParsingEntryId

java.lang.Long fileParsingEntryId

contactId

java.lang.Long contactId

magellFileGroupId

java.lang.Long magellFileGroupId

name

java.lang.String name

version

java.lang.String version

description

java.lang.String description

contentType

java.lang.String contentType

msgToCurator

java.lang.String msgToCurator

Class gov.nih.nci.caarray.services.fileupload2.FileParsingEntry extends SerializableFileUploadBean implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

parsingStartDate

java.util.Date parsingStartDate

parsingEndDate

java.util.Date parsingEndDate

parsingSucceeded

java.lang.String parsingSucceeded

failureDescription

java.lang.String failureDescription

Class gov.nih.nci.caarray.services.fileupload2.FileUploadEntry extends SerializableFileUploadBean implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

fileType

FileType fileType

fileName

java.lang.String fileName

status

java.lang.String status

statusDate

java.util.Date statusDate

validatorCode

java.lang.String validatorCode

userId

java.lang.String userId

originalFileName

java.lang.String originalFileName

Class gov.nih.nci.caarray.services.fileupload2.FileUploadGroup extends SerializableFileUploadBean implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

parsingStartDate

java.util.Date parsingStartDate

parsingEndDate

java.util.Date parsingEndDate

parsingSucceeded

java.lang.String parsingSucceeded

Class gov.nih.nci.caarray.services.fileupload2.FileUploadHistory extends SerializableFileUploadBean implements Serializable

Serialized Fields

fileUploadEntry

FileUploadEntry fileUploadEntry

status

java.lang.String status

statusDate

java.util.Date statusDate

description

java.lang.String description

Class gov.nih.nci.caarray.services.fileupload2.HybridizationFileParsingEntry extends FileParsingEntry implements Serializable

Class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadEntry extends FileUploadEntry implements Serializable

Serialized Fields

fileUploadEntry

FileUploadEntry fileUploadEntry

fileParsingEntry

HybridizationFileParsingEntry fileParsingEntry

experiment

Experiment experiment

channelOneExtract

LabeledExtract channelOneExtract

channelOneSpikedControl

LabeledExtract channelOneSpikedControl

channelTwoExtract

LabeledExtract channelTwoExtract

channelTwoSpikedControl

LabeledExtract channelTwoSpikedControl

channelOneFactorValues

java.util.List<E> channelOneFactorValues

channelTwoFactorValues

java.util.List<E> channelTwoFactorValues

measuredBioAssay

MeasuredBioAssay measuredBioAssay

derivedBioAssay

DerivedBioAssay derivedBioAssay

Class gov.nih.nci.caarray.services.fileupload2.HybridizationFileUploadGroup extends FileUploadGroup implements Serializable

Serialized Fields

fileUploadEntries

java.util.List<E> fileUploadEntries

Class gov.nih.nci.caarray.services.fileupload2.MAGEMLFileUploadEntry extends FileUploadEntry implements Serializable

Serialized Fields

fileUploadEntry

FileUploadEntry fileUploadEntry

name

java.lang.String name

version

java.lang.String version

description

java.lang.String description

contentType

java.lang.String contentType

msgToCurator

java.lang.String msgToCurator

contact

Person contact

Class gov.nih.nci.caarray.services.fileupload2.SerializableFileUploadBean extends java.lang.Object implements Serializable

Serialized Fields

id

long id

Package gov.nih.nci.caarray.services.fileupload2.ejb

Class gov.nih.nci.caarray.services.fileupload2.ejb.FileUploadManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.fileupload2.mdb

Class gov.nih.nci.caarray.services.fileupload2.mdb.FileUploadHandlerMDB extends java.lang.Object implements Serializable

serialVersionUID: 3632908452772996870L

Serialized Fields

messageDrivenContext

javax.ejb.MessageDrivenContext messageDrivenContext

Package gov.nih.nci.caarray.services.hybridization

Class gov.nih.nci.caarray.services.hybridization.EntrySaveException extends java.lang.Exception implements Serializable

serialVersionUID: -6910414834644372520L

Class gov.nih.nci.caarray.services.hybridization.HybridizationDataJob extends java.lang.Object implements Serializable

serialVersionUID: -9051098553615891425L

Serialized Fields

fileUploadEntries

HybridizationFileUploadEntry[] fileUploadEntries

username

java.lang.String username

Package gov.nih.nci.caarray.services.hybridization.ejb

Class gov.nih.nci.caarray.services.hybridization.ejb.DataFileAssessment extends java.lang.Object implements Serializable

serialVersionUID: -75923324000366449L

Serialized Fields

dataFile

java.io.File dataFile

problems

java.util.List<E> problems

warnings

java.util.List<E> warnings

canRepair

boolean canRepair

needsRepair

boolean needsRepair

canReload

boolean canReload

Class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadConfiguration extends java.lang.Object implements Serializable

Serialized Fields

username

java.lang.String username

password

java.lang.String password

authConf

java.lang.String authConf

hostname

java.lang.String hostname

port

int port

fileTypes

java.util.List<E> fileTypes

statuses

java.util.List<E> statuses

repair

boolean repair

reload

boolean reload

minutesToRun

int minutesToRun

maxFilesToProcess

int maxFilesToProcess

experimentIds

java.util.List<E> experimentIds

arrayDesignNames

java.util.List<E> arrayDesignNames

transactionTimeoutMinutes

int transactionTimeoutMinutes

Class gov.nih.nci.caarray.services.hybridization.ejb.DataFileReloadResults extends java.lang.Object implements Serializable

serialVersionUID: -827591905547974310L

Serialized Fields

successful

boolean successful

dataFile

java.io.File dataFile

errorMessage

java.lang.String errorMessage

Class gov.nih.nci.caarray.services.hybridization.ejb.DataFileRepairResults extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.hybridization.ejb.FileUploadEntryLookupException extends java.lang.Exception implements Serializable

Class gov.nih.nci.caarray.services.hybridization.ejb.HybridizationFileHandlerEJB extends AbstractSessionBean implements Serializable

serialVersionUID: 5665773104514322885L


Package gov.nih.nci.caarray.services.mageml

Class gov.nih.nci.caarray.services.mageml.MAGEMLFileValues extends java.lang.Object implements Serializable

Serialized Fields

objectId_

java.lang.Long objectId_

objectType_

java.lang.Integer objectType_

pathName_

java.lang.String pathName_

zip_

boolean zip_

Package gov.nih.nci.caarray.services.mageml.ejb

Class gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.mageml.mdb

Class gov.nih.nci.caarray.services.mageml.mdb.MAGEMLGeneratorMDB extends java.lang.Object implements Serializable

Serialized Fields

ejbContext

javax.ejb.MessageDrivenContext ejbContext

jndiContext

javax.naming.InitialContext jndiContext

Package gov.nih.nci.caarray.services.protocol.ejb

Class gov.nih.nci.caarray.services.protocol.ejb.HardwareManagerEJB extends AbstractSessionBean implements Serializable

Class gov.nih.nci.caarray.services.protocol.ejb.ProtocolManagerEJB extends AbstractSessionBean implements Serializable

Class gov.nih.nci.caarray.services.protocol.ejb.SoftwareManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.security

Class gov.nih.nci.caarray.services.security.CaArrayPrincipal extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name
 

Package gov.nih.nci.caarray.services.security.db

Class gov.nih.nci.caarray.services.security.db.PoolException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.security.ejb

Class gov.nih.nci.caarray.services.security.ejb.CaSecurityManagerEJB extends AbstractSessionBean implements Serializable

Class gov.nih.nci.caarray.services.security.ejb.SecurityManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.security.mageom.mdb

Class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementIdUpdaterMDB extends java.lang.Object implements Serializable

Serialized Fields

maxAttempts_

long maxAttempts_

waitTime_

long waitTime_

updater_

SecuredElementIdUpdater updater_

orphanHandler_

SecuredElementOrphanHandler orphanHandler_

Class gov.nih.nci.caarray.services.security.mageom.mdb.SecuredElementUpdateMessage extends java.lang.Object implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

_className

java.lang.String _className
The class name of the newly inserted SecuredElement


_id

java.lang.String _id
The id of the newly inserted SecuredElement


_attempts

int _attempts
Number of times this message has been queued.


_waitTime

long _waitTime
The time this message waited befor being requeued.


Package gov.nih.nci.caarray.services.test

Class gov.nih.nci.caarray.services.test.TestException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.test.ejb

Class gov.nih.nci.caarray.services.test.ejb.TestManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.useradmin.ejb

Class gov.nih.nci.caarray.services.useradmin.ejb.AdminManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.services.util

Class gov.nih.nci.caarray.services.util.BaseSecuredElement extends java.lang.Object implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

securedElementId

java.lang.String securedElementId

isEditable

boolean isEditable

securedElementClassName

java.lang.String securedElementClassName

id

java.lang.Object id

Package gov.nih.nci.caarray.services.util.cache

Class gov.nih.nci.caarray.services.util.cache.RuntimeCacheException extends org.apache.ojb.broker.OJBRuntimeException implements Serializable


Package gov.nih.nci.caarray.services.util.dataconverter.assembler

Class gov.nih.nci.caarray.services.util.dataconverter.assembler.AssemblerNotAvailableException extends java.lang.RuntimeException implements Serializable


Package gov.nih.nci.caarray.services.util.db

Class gov.nih.nci.caarray.services.util.db.PersistenceBrokerManagerInitializationException extends java.lang.RuntimeException implements Serializable


Package gov.nih.nci.caarray.services.util.file

Class gov.nih.nci.caarray.services.util.file.DownloadFile extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

Class gov.nih.nci.caarray.services.util.file.ProcessBatchFileDownload extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

Class gov.nih.nci.caarray.services.util.file.ProcessFetchFileList extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

Class gov.nih.nci.caarray.services.util.file.ProcessFileUpload extends javax.servlet.http.HttpServlet implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

Package gov.nih.nci.caarray.services.util.fileuploadapplet

Class gov.nih.nci.caarray.services.util.fileuploadapplet.SelectedFiles extends java.lang.Object implements Serializable

Serialized Fields

selectedFileNameMap_

java.util.TreeMap<K,V> selectedFileNameMap_
TreeMap with key = fileName, value = PlatformFile


Package gov.nih.nci.caarray.services.util.httpfileuploadapplet

Class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet extends javax.swing.JApplet implements Serializable

Serialized Fields

pattern

java.lang.String[] pattern

INSTRUCTION

java.lang.String INSTRUCTION

SUMMARY

java.lang.String SUMMARY

SUCCESS

java.lang.String SUCCESS

FAILURE

java.lang.String FAILURE

TIMEBYTES

java.lang.String TIMEBYTES

chooseLst

java.awt.List chooseLst

selectedLst

java.awt.List selectedLst

dataBt

javax.swing.JButton dataBt

otherBt

javax.swing.JButton otherBt

removeBt

javax.swing.JButton removeBt

removeAllBt

javax.swing.JButton removeAllBt

uploadBt

javax.swing.JButton uploadBt

stopBt

javax.swing.JButton stopBt

helpBt

javax.swing.JButton helpBt

doneBt

javax.swing.JButton doneBt

selectAllBt

javax.swing.JButton selectAllBt

deSelectAllBt

javax.swing.JButton deSelectAllBt

progressBar

javax.swing.JProgressBar progressBar

driveLabel

javax.swing.JLabel driveLabel

selectedFiles

javax.swing.JLabel selectedFiles

uploadFileName

javax.swing.JLabel uploadFileName

currentDir

java.io.File currentDir

files

java.lang.String[] files

dateFormatter

java.text.DateFormat dateFormatter

cDirLabel

javax.swing.JLabel cDirLabel

directoryDisplayLabel

javax.swing.JLabel directoryDisplayLabel

driveChoice

java.awt.Choice driveChoice

selectedFileVec

java.util.Vector<E> selectedFileVec

uFile

HttpUploadFile uFile

up

HttpUploadParameters up

thread

HttpFileUploadThread thread

timer

javax.swing.Timer timer

resultWindow

HttpFileUploadApplet.ResultFrame resultWindow

helpWindow

HttpFileUploadApplet.HelpFrame helpWindow

extensions

java.lang.String[] extensions

module

java.lang.String module

isSingleFile

boolean isSingleFile

Class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.HelpFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

close

javax.swing.JButton close

helpLabel

javax.swing.JLabel helpLabel

helpText

javax.swing.JTextArea helpText

helpPane

javax.swing.JScrollPane helpPane

contentPane

java.awt.Container contentPane

Class gov.nih.nci.caarray.services.util.httpfileuploadapplet.HttpFileUploadApplet.ResultFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

close

javax.swing.JButton close

successLabel

javax.swing.JLabel successLabel

failLabel

javax.swing.JLabel failLabel

timeLabel

javax.swing.JLabel timeLabel

successText

javax.swing.JTextArea successText

failText

javax.swing.JTextArea failText

timeText

javax.swing.JTextArea timeText

successPane

javax.swing.JScrollPane successPane

failPane

javax.swing.JScrollPane failPane

contentPane

java.awt.Container contentPane

Class gov.nih.nci.caarray.services.util.httpfileuploadapplet.ProcessDuplicatedFileName extends javax.swing.JDialog implements Serializable

Serialized Fields

contentPane

javax.swing.JPanel contentPane

duplicatedFileList

java.awt.List duplicatedFileList

overwriteBt

javax.swing.JButton overwriteBt

message

javax.swing.JLabel message

cancelBt

javax.swing.JButton cancelBt

directory

java.lang.String directory

noteLb

javax.swing.JLabel noteLb

jLabel1

javax.swing.JLabel jLabel1

emptyLb

javax.swing.JLabel emptyLb

selectAllBt

javax.swing.JButton selectAllBt

gridBagLayout1

java.awt.GridBagLayout gridBagLayout1

cList

java.util.ArrayList<E> cList

Package gov.nih.nci.caarray.services.util.jms

Class gov.nih.nci.caarray.services.util.jms.DefaultJMSMessageCollection extends java.util.ArrayList implements Serializable

Class gov.nih.nci.caarray.services.util.jms.MessageData extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.Long id

waitTime

java.lang.Long waitTime

queueName

java.lang.String queueName

data

byte[] data

hostIP

java.lang.String hostIP

Package gov.nih.nci.caarray.services.util.netcdf

Class gov.nih.nci.caarray.services.util.netcdf.NETCDFException extends java.lang.Exception implements Serializable


Package gov.nih.nci.caarray.services.util.ojb

Class gov.nih.nci.caarray.services.util.ojb.QueryCustomizerExcludingObjectsMarkedAsDeleted extends org.apache.ojb.broker.accesslayer.QueryCustomizerDefaultImpl implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.RowReaderBioSequence extends org.apache.ojb.broker.accesslayer.RowReaderDefaultImpl implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.RowReaderUnit extends org.apache.ojb.broker.accesslayer.RowReaderDefaultImpl implements Serializable


Package gov.nih.nci.caarray.services.util.ojb.conversions

Class gov.nih.nci.caarray.services.util.ojb.conversions.Action2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.Basis2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.Boolean2IntFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.KindCV2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.Long2LongObjectFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.Order2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.OrientationMarkPosition2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.SourceType2StringFieldConversion extends java.lang.Object implements Serializable

serialVersionUID: 8346405256667832336L

Class gov.nih.nci.caarray.services.util.ojb.conversions.Type2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.UnitNameCV2StringFieldConversion extends java.lang.Object implements Serializable

Class gov.nih.nci.caarray.services.util.ojb.conversions.Value2StringFieldConversion extends java.lang.Object implements Serializable


Package gov.nih.nci.caarray.services.util.parse

Class gov.nih.nci.caarray.services.util.parse.LocalDynaBeanImpl extends org.apache.commons.beanutils.BasicDynaBean implements Serializable


Package gov.nih.nci.caarray.services.util.transaction

Class gov.nih.nci.caarray.services.util.transaction.TransactionException extends java.lang.Exception implements Serializable

serialVersionUID: 191544618098222917L


Package gov.nih.nci.caarray.services.vocab.ejb

Class gov.nih.nci.caarray.services.vocab.ejb.VocabManagerEJB extends AbstractSessionBean implements Serializable


Package gov.nih.nci.caarray.ui.arraydesign

Class gov.nih.nci.caarray.ui.arraydesign.ArrayAddUpdateForm extends ArrayBaseForm implements Serializable

Serialized Fields

action

java.lang.String action

Class gov.nih.nci.caarray.ui.arraydesign.ArrayBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

arrayId

long arrayId

manufactureDate

java.lang.String manufactureDate

arrayName

java.lang.String arrayName

barcode

java.lang.String barcode

arrayDesignId

long arrayDesignId

arrayDesigns

java.util.Collection<E> arrayDesigns

substrateType

long substrateType

substrateTypes

java.util.Collection<E> substrateTypes

manufacturers

java.util.Collection<E> manufacturers

selectedManufacturers

java.lang.String[] selectedManufacturers

width

java.lang.String width

length

java.lang.String length

orientationMark

java.lang.String orientationMark

orientationMarkPosition

java.lang.String orientationMarkPosition

orientationMarkPositions

java.util.Collection<E> orientationMarkPositions

visibilitys

java.util.Collection<E> visibilitys

selectedVisibilitys

java.lang.String[] selectedVisibilitys

description

java.lang.String description

protocols

java.util.Collection<E> protocols

protocolId

long protocolId

reason

java.lang.String reason

fileId

long fileId

expId

long expId

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.arraydesign.ArrayCopyForm extends ArrayBaseForm implements Serializable

Serialized Fields

arrayDesignName

java.lang.String arrayDesignName

substrateTypeName

java.lang.String substrateTypeName

manufacturerName

java.lang.String manufacturerName

numberCopies

long numberCopies

mode

java.lang.String mode

Class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignAddUpdateForm extends ArrayDesignBaseForm implements Serializable

Serialized Fields

selectedVisibilityNames

java.lang.String[] selectedVisibilityNames

selectedVisibilityIds

java.lang.String[] selectedVisibilityIds

providerId

long providerId

providerType

long providerType

providers_

java.util.Collection<E> providers_

providersOrgs_

java.util.Collection<E> providersOrgs_

roleId

long roleId

roles

java.util.Collection<E> roles

protocolId

long protocolId

protocols

java.util.Collection<E> protocols

mode_

java.lang.String mode_

uploadFile

boolean uploadFile

Class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

arrayDesignId

long arrayDesignId

attachmentTypeId_

long attachmentTypeId_
Attachment Type ID


attachmentTypeName_

java.lang.String attachmentTypeName_

attachmentTypes_

java.util.Collection<E> attachmentTypes_
Attachment Types


description_

java.lang.String description_

uploadTypeId

int uploadTypeId

uploadTypes_

java.util.Collection<E> uploadTypes_

reporterTypeId_

int reporterTypeId_

reporterTypes_

java.util.Collection<E> reporterTypes_

fileAdditional_

CustomFormFile fileAdditional_

fileGAL_

CustomFormFile fileGAL_
Full path to Definition File


fileMAGE_

CustomFormFile fileMAGE_
Full path to Annotation File


identifier_

java.lang.String identifier_

name_

java.lang.String name_
Array Design Name


selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

speciesTypeId_

long speciesTypeId_
Species Type ID


speciesTypes_

java.util.Collection<E> speciesTypes_
Species Types


strandTypeId_

long strandTypeId_
Strand Type ID


strandTypes_

java.util.Collection<E> strandTypes_
Strand Types


substrateTypeId_

long substrateTypeId_
Substrate Type ID


substrateTypes_

java.util.Collection<E> substrateTypes_
SubStrate Types


surfaceTypeId_

long surfaceTypeId_
surface Type ID


surfaceTypes_

java.util.Collection<E> surfaceTypes_
Surface Types


technologyTypeId_

long technologyTypeId_
Technology Type ID


technologyTypes_

java.util.Collection<E> technologyTypes_
Technology Types


version_

java.lang.String version_
Array Version


visibilitys_

java.util.Collection<E> visibilitys_

speciesTypeName_

java.lang.String speciesTypeName_

strandTypeName_

java.lang.String strandTypeName_

substrateTypeName_

java.lang.String substrateTypeName_

surfaceTypeName_

java.lang.String surfaceTypeName_

technologyTypeName_

java.lang.String technologyTypeName_

Class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignDetailForm extends ArrayDesignBaseForm implements Serializable

Serialized Fields

mode_

java.lang.String mode_

numberOfFeatures_

int numberOfFeatures_

protocolApplicationId_

long protocolApplicationId_

protocolApplication_

ProtocolApplicationData protocolApplication_

protocolApplications_

ProtocolApplicationData[] protocolApplications_

providerId_

long providerId_

providers_

DesignProviderRoleData[] providers_

reporterFileLocation_

java.lang.String reporterFileLocation_

additionalReporterFileLocation_

java.lang.String additionalReporterFileLocation_

galFileLocation_

java.lang.String galFileLocation_

mageFileLocation_

java.lang.String mageFileLocation_

reporterTypeId_

int reporterTypeId_

reporterTypeName_

java.lang.String reporterTypeName_

reporterTypes_

java.util.Collection<E> reporterTypes_

uploadTypeId_

int uploadTypeId_

uploadTypeName_

java.lang.String uploadTypeName_

uploadTypes_

java.util.Collection<E> uploadTypes_

providedByAffymetrix

boolean providedByAffymetrix

arrayDesignFile

ArrayDesignUploadedFileData arrayDesignFile

uploadFile

boolean uploadFile

arrayDesignFileToken

java.lang.String arrayDesignFileToken

mageIdentifier

java.lang.String mageIdentifier

isEditable

boolean isEditable

arrayDesignFileUploadEntryData

ArrayDesignFileUploadEntryData arrayDesignFileUploadEntryData

Class gov.nih.nci.caarray.ui.arraydesign.ArrayDesignSearchForm extends ArrayDesignBaseForm implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_
free search text


searchResults_

java.util.Collection<E> searchResults_

visibilityId_

long visibilityId_

providerId

long providerId

providers_

java.util.Collection<E> providers_

providersOrgs_

java.util.Collection<E> providersOrgs_

mode

java.lang.String mode

Class gov.nih.nci.caarray.ui.arraydesign.ArrayDetailForm extends ArrayBaseForm implements Serializable

Serialized Fields

arrayDesignName

java.lang.String arrayDesignName

substrateTypeName

java.lang.String substrateTypeName

manufacturerName

java.lang.String manufacturerName

orientationMarkPositionName

java.lang.String orientationMarkPositionName

protocolApplications_

ProtocolApplicationData[] protocolApplications_

Class gov.nih.nci.caarray.ui.arraydesign.ArraySearchForm extends ArrayBaseForm implements Serializable

Serialized Fields

searchResults

java.util.Collection<E> searchResults

manufacturerId

long manufacturerId

visibilityId

long visibilityId

manufactureDateStart

java.lang.String manufactureDateStart

manufactureDateEnd

java.lang.String manufactureDateEnd

Package gov.nih.nci.caarray.ui.biomaterial

Class gov.nih.nci.caarray.ui.biomaterial.BiomaterialBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

back_

java.lang.String back_

mode_

java.lang.String mode_

biomaterialId_

long biomaterialId_

materialTypeId_

long materialTypeId_

materialTypeName_

java.lang.String materialTypeName_

materialTypes_

java.util.Collection<E> materialTypes_

taxonType_

long taxonType_

taxonTypes_

java.util.Collection<E> taxonTypes_

visibilitys_

java.util.Collection<E> visibilitys_

charList_

java.util.Collection<E> charList_

biomaterialCharacteristics_

VocabData[] biomaterialCharacteristics_

ageTypes_

java.lang.String[] ageTypes_

ageUnits_

java.util.Collection<E> ageUnits_

age_

int age_

ageUnitName_

java.lang.String ageUnitName_

ageUnitId_

long ageUnitId_

ageMax_

int ageMax_

ageMaxUnitName_

java.lang.String ageMaxUnitName_

ageMaxUnitId_

long ageMaxUnitId_

ageMin_

int ageMin_

ageMinUnitName_

java.lang.String ageMinUnitName_

ageMinUnitId_

long ageMinUnitId_

allele_

java.lang.String allele_

initialTimePoints_

java.util.Collection<E> initialTimePoints_

initialTimePointName_

java.lang.String initialTimePointName_

initialTimePointId_

long initialTimePointId_

bedding_

java.lang.String bedding_

clinicalHistory_

java.lang.String clinicalHistory_

familyHistory_

java.lang.String familyHistory_

generation_

java.lang.String generation_

geographicLocation_

java.lang.String geographicLocation_

host_

java.lang.String host_

pathogenTest_

java.lang.String pathogenTest_

environmentalHistoryDesign_

java.lang.String environmentalHistoryDesign_

atmosphere_

java.lang.String atmosphere_

barrierFacility_

java.lang.String barrierFacility_

humidity_

java.lang.String humidity_

light_

java.lang.String light_

nutrients_

java.lang.String nutrients_

populationDensity_

java.lang.String populationDensity_

temperature_

java.lang.String temperature_

water_

java.lang.String water_

biometricWeightUnits_

java.util.Collection<E> biometricWeightUnits_

biometricWeight_

float biometricWeight_

biometricWeightUnitName_

java.lang.String biometricWeightUnitName_

biometricWeightUnitId_

long biometricWeightUnitId_

biometricHeightUnits_

java.util.Collection<E> biometricHeightUnits_

biometricHeight_

float biometricHeight_

biometricHeightUnitName_

java.lang.String biometricHeightUnitName_

biometricHeightUnitId_

long biometricHeightUnitId_

cellLine_

java.lang.String cellLine_

cellLineId_

long cellLineId_

cellLines_

java.util.Collection<E> cellLines_

cellType_

java.lang.String cellType_

cellTypeId_

long cellTypeId_

cellTypes_

java.util.Collection<E> cellTypes_

chromosomalAberrationTypeId_

long chromosomalAberrationTypeId_

chromosomalAberrationTypes_

java.util.Collection<E> chromosomalAberrationTypes_

chromosomalAberrations_

java.util.Collection<E> chromosomalAberrations_

chromosomalAberrationDescription_

java.lang.String chromosomalAberrationDescription_

clinicalTest_

java.lang.String clinicalTest_

clinicalTreatment_

java.lang.String clinicalTreatment_

developmentalStage_

java.lang.String developmentalStage_

developmentalStageId_

long developmentalStageId_

developmentalStages_

java.util.Collection<E> developmentalStages_

diseaseLocation_

java.lang.String diseaseLocation_

diseaseLocationId_

long diseaseLocationId_

diseaseLocations_

java.util.Collection<E> diseaseLocations_

diseaseStage_

java.lang.String diseaseStage_

diseaseStageId

long[] diseaseStageId

diseaseStages_

java.util.Collection<E> diseaseStages_

diseaseState

java.lang.String diseaseState

diseaseStateId

long diseaseStateId

diseaseStates

java.util.Collection<E> diseaseStates

geneticModificationId_

long geneticModificationId_

geneticModificationName_

java.lang.String geneticModificationName_

geneticModifications_

java.util.Collection<E> geneticModifications_

geneticModificationDescription_

java.lang.String geneticModificationDescription_

genotype_

java.lang.String genotype_

histology_

java.lang.String histology_

individual_

java.lang.String individual_

organismPart_

java.lang.String organismPart_

organismPartId_

long organismPartId_

organismParts_

java.util.Collection<E> organismParts_

organismStatus_

java.lang.String organismStatus_

organismStatusId_

long organismStatusId_

organismStatuses_

java.util.Collection<E> organismStatuses_

ploidy_

java.lang.String ploidy_

ploidyId_

long ploidyId_

ploidys_

java.util.Collection<E> ploidys_

phenotype_

java.lang.String phenotype_

sex_

java.lang.String sex_

sexId_

long sexId_

sexTypes_

java.util.Collection<E> sexTypes_

media_

java.lang.String media_

mediaId_

long mediaId_

mediaTypes_

java.util.Collection<E> mediaTypes_

strainOrLine_

java.lang.String strainOrLine_

strainOrLineId_

long strainOrLineId_

strainOrLines_

java.util.Collection<E> strainOrLines_

tumorGrading_

java.lang.String tumorGrading_

tumorGradingId_

long tumorGradingId_

tumorGradings_

java.util.Collection<E> tumorGradings_

targetedCellType_

java.lang.String targetedCellType_

targetedCellTypeId_

long targetedCellTypeId_

targetedCellTypes_

java.util.Collection<E> targetedCellTypes_

selectedCharacteristics_

java.util.ArrayList<E> selectedCharacteristics_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.biomaterial.BiomaterialCharacteristicsForm extends BiomaterialBaseForm implements Serializable

Serialized Fields

allCharacteristics_

java.util.Collection<E> allCharacteristics_

object_

java.lang.String object_

returnFwd_

java.lang.String returnFwd_

error_

java.lang.String error_

ageOrRange_

java.lang.String ageOrRange_

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

Class gov.nih.nci.caarray.ui.biomaterial.BiosourceAddUpdateForm extends BiosourceBaseForm implements Serializable

Serialized Fields

description_

java.lang.String description_

selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

newTypeName_

java.lang.String newTypeName_

newTaxonTypeName_

java.lang.String newTaxonTypeName_

newMaterialTypeName_

java.lang.String newMaterialTypeName_

isCancel_

java.lang.String isCancel_

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

Class gov.nih.nci.caarray.ui.biomaterial.BiosourceBaseForm extends BiomaterialBaseForm implements Serializable

Serialized Fields

biosourceName

java.lang.String biosourceName

biosourceType

long biosourceType

biosourceTypes

java.util.Collection<E> biosourceTypes

provider

long provider

providers

java.util.Collection<E> providers

selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

visibilitys_

java.util.Collection<E> visibilitys_

Class gov.nih.nci.caarray.ui.biomaterial.BiosourceDetailForm extends BiosourceBaseForm implements Serializable

Serialized Fields

description

java.lang.String description

visibility

java.util.Collection<E> visibility

materialTypeName

java.lang.String materialTypeName

taxonName

java.lang.String taxonName

providerName

java.lang.String providerName

biosourceTypeName

java.lang.String biosourceTypeName

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.ui.biomaterial.BiosourceSearchForm extends BiosourceBaseForm implements Serializable

Serialized Fields

freeText

java.lang.String freeText

visibilityId

long visibilityId

searchResults_

java.util.Collection<E> searchResults_

Class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractBaseForm extends BiosourceBaseForm implements Serializable

Serialized Fields

labeledExtractName_

java.lang.String labeledExtractName_

labeledExtractID_

long labeledExtractID_

error_

java.lang.String error_

biosampleId_

long biosampleId_

biosamples_

java.util.Collection<E> biosamples_

label_

long label_

labels_

java.util.Collection<E> labels_

amount_

java.lang.String amount_

amountUnit_

long amountUnit_

units_

java.util.Collection<E> units_

newLabel_

java.lang.String newLabel_

errors_

java.lang.String errors_

protocolApplication_

ProtocolApplicationData protocolApplication_

reason

java.lang.String reason

fileId

long fileId

expId

long expId

description

java.lang.String description

parents

java.util.Collection<E> parents

labelName_

java.lang.String labelName_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractDetailForm extends LabeledExtractBaseForm implements Serializable

Serialized Fields

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.ui.biomaterial.LabeledExtractSearchForm extends LabeledExtractBaseForm implements Serializable

Serialized Fields

visibilityId

long visibilityId

freeText

java.lang.String freeText

sampleId

long sampleId

searchResults_

java.util.Collection<E> searchResults_

Class gov.nih.nci.caarray.ui.biomaterial.PoolForm extends BiosourceBaseForm implements Serializable

Serialized Fields

outputName

java.lang.String outputName

outputDesc

java.lang.String outputDesc

biomaterials

java.util.Collection<E> biomaterials

selectedBiomaterials

java.lang.String[] selectedBiomaterials

mode

java.lang.String mode

measurementValue

java.lang.String measurementValue

measurementUnits

java.util.Collection<E> measurementUnits

measurementUnit

long measurementUnit

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

measurementUnitType

long measurementUnitType

Class gov.nih.nci.caarray.ui.biomaterial.SampleBaseForm extends BiomaterialBaseForm implements Serializable

Serialized Fields

sampleName

java.lang.String sampleName

sampleType

long sampleType

sampleTypes

java.util.Collection<E> sampleTypes

sourceBiomaterials

java.util.Collection<E> sourceBiomaterials

Class gov.nih.nci.caarray.ui.biomaterial.SampleDetailForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

treatmentAction

java.lang.String treatmentAction

biomaterialId

long biomaterialId

creationDescription

java.lang.String creationDescription

description

java.lang.String description

id

long id

parentBiomaterials

java.util.Collection<E> parentBiomaterials

sampleName

java.lang.String sampleName

sampleType

long sampleType

sampleTypeName

java.lang.String sampleTypeName

sampleTypes

java.util.Collection<E> sampleTypes

sourceBiomaterials

java.util.Collection<E> sourceBiomaterials

treatmentEvents

java.util.ArrayList<E> treatmentEvents

compoundMData

CompoundMeasurementData[] compoundMData

biomaterialCharacteristics

VocabData[] biomaterialCharacteristics

treatmentNumber

int treatmentNumber

back

java.lang.String back

treatmentEventId

long treatmentEventId

mode

java.lang.String mode

individualTreatmentId

java.lang.String individualTreatmentId

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

requestAction

java.lang.String requestAction

mageIdentifier

java.lang.String mageIdentifier

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.biomaterial.SampleSearchForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

sampleName

java.lang.String sampleName

speciesTypeId

long speciesTypeId

speciesTypes

java.util.Collection<E> speciesTypes

materialTypeId

long materialTypeId

materialTypes

java.util.Collection<E> materialTypes

biosourceId

long biosourceId

biosources

java.util.Collection<E> biosources

visibilityId

long visibilityId

visibilitys

java.util.Collection<E> visibilitys

searchResults_

java.util.Collection<E> searchResults_

Class gov.nih.nci.caarray.ui.biomaterial.SampleUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

biomaterialCharacteristics

VocabData[] biomaterialCharacteristics

description

java.lang.String description

creationDescription

java.lang.String creationDescription

selectedVisibilities

java.util.Collection<E> selectedVisibilities

sourceBiomaterialId

long sourceBiomaterialId

sourceBiomaterialName

java.lang.String sourceBiomaterialName

resultingBiomaterialTypeId

long resultingBiomaterialTypeId

biomaterialId

long biomaterialId

resultingName

java.lang.String resultingName

resultingBiomaterialTypeName

java.lang.String resultingBiomaterialTypeName

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

measurementUnits

java.util.Collection<E> measurementUnits

treatments

TreatmentEvent[] treatments

parentBiomaterials

java.util.Collection<E> parentBiomaterials

treatmentTypes

java.util.Collection<E> treatmentTypes

treatmentAction

java.lang.String treatmentAction

mode

java.lang.String mode

treatmentEvents

java.util.ArrayList<E> treatmentEvents

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

Class gov.nih.nci.caarray.ui.biomaterial.SplitForm extends BiosourceBaseForm implements Serializable

Serialized Fields

biomaterials

java.util.Collection<E> biomaterials

selectedBiomaterial

long selectedBiomaterial

selectedBiomaterialName

java.lang.String selectedBiomaterialName

numberSamples

long numberSamples

splitAction

java.lang.String splitAction

outputName1

java.lang.String outputName1

outputDesc1

java.lang.String outputDesc1

outputName2

java.lang.String outputName2

outputDesc2

java.lang.String outputDesc2

mode

java.lang.String mode

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

measurementValue1

java.lang.String measurementValue1

measurementUnits1

java.util.Collection<E> measurementUnits1

measurementUnit1

long measurementUnit1

measurementUnitType1

long measurementUnitType1

measurementValue2

java.lang.String measurementValue2

measurementUnits2

java.util.Collection<E> measurementUnits2

measurementUnit2

long measurementUnit2

measurementUnitType2

long measurementUnitType2

Class gov.nih.nci.caarray.ui.biomaterial.TreatmentEvent extends java.lang.Object implements Serializable

Serialized Fields

creationDescription

java.lang.String creationDescription

measurementValue

java.lang.String measurementValue

treatmentType

long treatmentType

treatmentTypeName

java.lang.String treatmentTypeName

measurementType

long measurementType

measurementTypeName

java.lang.String measurementTypeName

measurementUnit

long measurementUnit

measurementUnitName

java.lang.String measurementUnitName

treatmentOrder

long treatmentOrder

protocolApplication

ProtocolApplicationData protocolApplication

protocolVisibility

java.util.Collection<E> protocolVisibility

deleteLabel

java.lang.String deleteLabel

treatmentAction

java.lang.String treatmentAction

compoundMData

CompoundMeasurementData[] compoundMData

Class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormOne extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

sourceBiomaterialId

long sourceBiomaterialId

sourceBiomaterialName

java.lang.String sourceBiomaterialName

resultingDescription

java.lang.String resultingDescription

resultingName

java.lang.String resultingName

resultingBiomaterialType

long resultingBiomaterialType

resultingBiomaterialTypeName

java.lang.String resultingBiomaterialTypeName

treatmentAction

java.lang.String treatmentAction

mode

java.lang.String mode

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

measurementUnits

java.util.Collection<E> measurementUnits

treatments

TreatmentEvent[] treatments

treatmentTypes

java.util.Collection<E> treatmentTypes

newMaterialTypeName

java.lang.String newMaterialTypeName

treatmentType

long treatmentType

treatmentOrder

long treatmentOrder

measurementValue

java.lang.String measurementValue

measurementUnitType

long measurementUnitType

measurementUnit

long measurementUnit

protocols

java.util.Collection<E> protocols

treatmentTypeName

java.lang.String treatmentTypeName

Class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormThree extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

biomaterials

java.util.Collection<E> biomaterials

creationDescription

java.lang.String creationDescription

mode

java.lang.String mode

resultingBiomaterialType

long resultingBiomaterialType

resultingBiomaterialTypeName

java.lang.String resultingBiomaterialTypeName

resultingDescription

java.lang.String resultingDescription

resultingName

java.lang.String resultingName

sourceBiomaterialId

long sourceBiomaterialId

sourceBiomaterialName

java.lang.String sourceBiomaterialName

treatmentAction

java.lang.String treatmentAction

treatmentEvents

java.util.ArrayList<E> treatmentEvents

treatmentTypeName

java.lang.String treatmentTypeName

treatmentOrder

int treatmentOrder

submitted

java.lang.String submitted

Class gov.nih.nci.caarray.ui.biomaterial.TreatmentFormTwo extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

biomaterials

java.util.Collection<E> biomaterials

compoundID_

long compoundID_

creationDescription

java.lang.String creationDescription

compounds

java.util.Collection<E> compounds

materialTypes

java.util.Collection<E> materialTypes

measurementUnit

long measurementUnit

compoundmeasurementUnit

long compoundmeasurementUnit

measurementUnits

java.util.Collection<E> measurementUnits

compoundmeasurementUnits

java.util.Collection<E> compoundmeasurementUnits

measurementUnitType

long measurementUnitType

compoundmeasurementUnitType

long compoundmeasurementUnitType

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

compoundmeasurementUnitTypes

java.util.Collection<E> compoundmeasurementUnitTypes

otherUnitType

int otherUnitType

otherCompoundUnitType

int otherCompoundUnitType

otherUnitTypeName

java.lang.String otherUnitTypeName

otherCompoundUnitTypeName

java.lang.String otherCompoundUnitTypeName

otherUnit

java.lang.String otherUnit

otherCompoundUnit

java.lang.String otherCompoundUnit

measurementValue

java.lang.String measurementValue

compoundmeasurementValue

java.lang.String compoundmeasurementValue

mode

java.lang.String mode

protocolApplication

ProtocolApplicationData protocolApplication

protocolVisibility

java.util.Collection<E> protocolVisibility

resultingBiomaterialType

long resultingBiomaterialType

resultingBiomaterialTypeName

java.lang.String resultingBiomaterialTypeName

resultingDescription

java.lang.String resultingDescription

resultingName

java.lang.String resultingName

sourceBiomaterialId

long sourceBiomaterialId

sourceBiomaterialName

java.lang.String sourceBiomaterialName

treatmentAction

java.lang.String treatmentAction

treatmentEvents

java.util.ArrayList<E> treatmentEvents

treatmentOrder

int treatmentOrder

treatmentType

long treatmentType

treatmentTypeName

java.lang.String treatmentTypeName

treatmentTypes

java.util.Collection<E> treatmentTypes

log_

org.apache.commons.logging.Log log_

protocolId

long protocolId

valid

boolean valid

compoundOrder

int compoundOrder

eventOrder

int eventOrder

deleteAction

java.lang.String deleteAction

compoundMeasurements

java.util.Collection<E> compoundMeasurements

Class gov.nih.nci.caarray.ui.biomaterial.TreatmentModifyForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

compounds

java.util.Collection<E> compounds

measurementUnits

java.util.Collection<E> measurementUnits

measurementUnitTypes

java.util.Collection<E> measurementUnitTypes

compoundmeasurementUnits

java.util.Collection<E> compoundmeasurementUnits

treatmentEvents

java.util.ArrayList<E> treatmentEvents

treatmentTypes

java.util.Collection<E> treatmentTypes

compoundMeasurements

java.util.List<E> compoundMeasurements

protocolApplication

ProtocolApplicationData protocolApplication

measurementUnit

long measurementUnit

compoundmeasurementUnit

long compoundmeasurementUnit

measurementUnitType

long measurementUnitType

compoundmeasurementUnitType

long compoundmeasurementUnitType

compoundData

CompoundMeasurementData compoundData

compoundModifyUnits

java.util.Collection<E> compoundModifyUnits

otherCompoundModifyUnitTypeName

java.lang.String otherCompoundModifyUnitTypeName

otherCompoundModifyUnit

java.lang.String otherCompoundModifyUnit

modifyUnit

long modifyUnit

modifyUnitType

long modifyUnitType

modifyUnitValue

java.lang.String modifyUnitValue

otherUnitTypeName

java.lang.String otherUnitTypeName

otherCompoundUnitTypeName

java.lang.String otherCompoundUnitTypeName

otherUnit

java.lang.String otherUnit

otherCompoundUnit

java.lang.String otherCompoundUnit

measurementValue

java.lang.String measurementValue

compoundmeasurementValue

java.lang.String compoundmeasurementValue

mode

java.lang.String mode

compoundId

long compoundId

sourceBiomaterialId

long sourceBiomaterialId

treatmentId

long treatmentId

treatmentOrder

int treatmentOrder

treatmentType

long treatmentType

treatmentTypeName

java.lang.String treatmentTypeName

compoundOrder

int compoundOrder

eventOrder

int eventOrder

protocolId

long protocolId

sourceBiomaterialName

java.lang.String sourceBiomaterialName

resultingName

java.lang.String resultingName

resultingBiomaterialTypeName

java.lang.String resultingBiomaterialTypeName

resultingDescription

java.lang.String resultingDescription

action

java.lang.String action

isNew

boolean isNew

reason

java.lang.String reason

fileId

long fileId

expId

long expId

labelId

long labelId

Package gov.nih.nci.caarray.ui.contact

Class gov.nih.nci.caarray.ui.contact.OrganizationAddUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

name

java.lang.String name

middleInitials

java.lang.String middleInitials

address

java.lang.String address

city

java.lang.String city

state

java.lang.String state

zip

java.lang.String zip

country

java.lang.String country

phoneNumber

java.lang.String phoneNumber

faxNumber

java.lang.String faxNumber

email

java.lang.String email

url

java.lang.String url

affiliation

long affiliation

back

java.lang.String back

mode

java.lang.String mode

orgAddress

java.lang.String orgAddress

Class gov.nih.nci.caarray.ui.contact.OrganizationDetailForm extends PersonDetailForm implements Serializable

Class gov.nih.nci.caarray.ui.contact.OrganizationSearchForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

results

java.util.Collection<E> results

nameSearch

java.lang.String nameSearch

Class gov.nih.nci.caarray.ui.contact.PeopleSearchForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

results

java.util.Collection<E> results

firstNameSearch

java.lang.String firstNameSearch

lastNameSearch

java.lang.String lastNameSearch

Class gov.nih.nci.caarray.ui.contact.PersonAddUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

address

java.lang.String address

affiliationId

long affiliationId

affiliations

java.util.Collection<E> affiliations

email

java.lang.String email

faxNumber

java.lang.String faxNumber

firstName

java.lang.String firstName

id

long id

lastName

java.lang.String lastName

middleInitial

java.lang.String middleInitial

phoneNumber

java.lang.String phoneNumber

url

java.lang.String url

back

java.lang.String back

mode

java.lang.String mode

Class gov.nih.nci.caarray.ui.contact.PersonDetailForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

firstName

java.lang.String firstName

lastName

java.lang.String lastName

name

java.lang.String name

middleInitials

java.lang.String middleInitials

address

java.lang.String address

city

java.lang.String city

state

java.lang.String state

zip

java.lang.String zip

country

java.lang.String country

phoneNumber

java.lang.String phoneNumber

faxNumber

java.lang.String faxNumber

email

java.lang.String email

url

java.lang.String url

affiliation

long affiliation

affiliationName

java.lang.String affiliationName

firstNameSearch

java.lang.String firstNameSearch

lastNameSearch

java.lang.String lastNameSearch

mageIdentifier

java.lang.String mageIdentifier

Package gov.nih.nci.caarray.ui.core

Class gov.nih.nci.caarray.ui.core.BaseForm extends org.apache.struts.action.ActionForm implements Serializable

Class gov.nih.nci.caarray.ui.core.HttpFileUploadAppletParams extends java.lang.Object implements Serializable

Serialized Fields

uploadURL

java.lang.String uploadURL
The destination url to which the uploading files will be sent and saved.


notifyURL

java.lang.String notifyURL
The destination url to which server is notified for the next step process.


defaultURL

java.lang.String defaultURL
The default url to go when user presses the done button to end the uploading process.


id

java.lang.String id
The String variable that holds the key to the hybridization annotation data for this upload operation,that is stored in a static cache on the server side.


archiveValue

java.lang.String archiveValue
The String variable holding the value for HttpFileUploadpplet archive jar file path. default to nothing.


sid

java.lang.String sid
The session id for session identification.


module

java.lang.String module
The string token to indicate where the applet is invoked, so set the applet to perform required function.


tunnelURL

java.lang.String tunnelURL
The URL from which the existing file names are fetched to the applet to ensure the same file names are handled. Works together with the module token.


permissibleFileExtension

java.lang.String permissibleFileExtension
The concatenated file extension permissible to the module.

Class gov.nih.nci.caarray.ui.core.HttpFileUploadSessionData extends java.lang.Object implements Serializable

Serialized Fields

fileData

HybridizationFileUploadGroupData fileData
The data object that gathers all the hybridization annotation data through many jsp pages.


caFileEntryData

CAFileUploadEntryData caFileEntryData

timeStamp

java.lang.String timeStamp

fileList

java.util.List<E> fileList
The container object that is the place for all meta data for the uploaded files. Valid data type: HttpUploadedFileData.


isStopped

boolean isStopped
The boolean flag. Set to true when user requests a stop action. Otherwise it is false. Default value is false.

Class gov.nih.nci.caarray.ui.core.HttpUploadedFileData extends java.lang.Object implements Serializable

Serialized Fields

type

java.lang.String type
The type means Data or Other user set at the time files are selected.


filePath

java.lang.String filePath
The absolute file path of the uploaded file on the client machine, before it was zipped.


fileName

java.lang.String fileName
The zip file name for the uploaded file, based on zip file naming convention for the application such as hybData_gpr.zip from hybData.gpr.


userId

java.lang.String userId
The sumbitters userId for the uploaded file,.


originalFileName

java.lang.String originalFileName
The original file name for the uploaded file, hybData.gpr.


validatorCode

java.lang.String validatorCode
The validatorCode validation for the for the uploaded file.


fileExtension

java.lang.String fileExtension
The original file's extension that is preserved in the zipped file file name.


id

java.lang.String id
It is actually the key to access cached data about this upload operation.


Package gov.nih.nci.caarray.ui.experiment

Class gov.nih.nci.caarray.ui.experiment.ExperimentBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

experimentTypeID_

long[] experimentTypeID_

experimentSearchTypeID_

long experimentSearchTypeID_

experimentTypes_

java.util.Collection<E> experimentTypes_

visibility_

java.lang.String[] visibility_

visibilities_

java.util.Collection<E> visibilities_

principalInvestigator_

java.lang.String principalInvestigator_

investigators_

java.util.Collection<E> investigators_

species_

long species_

speciesLists_

java.util.Collection<E> speciesLists_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.experiment.ExperimentDetailForm extends ExperimentBaseForm implements Serializable

Serialized Fields

hybridizationGroupName

java.lang.String hybridizationGroupName

log_

org.apache.commons.logging.Log log_

ID_

long ID_

expId

java.lang.String expId

method

java.lang.String method

experimentTitle_

java.lang.String experimentTitle_

experimentCompleteDate_

java.lang.String experimentCompleteDate_

otherExperimentType_

java.lang.String otherExperimentType_

description_

java.lang.String description_

contactor_

java.lang.String contactor_

numberOfFactor_

java.lang.String numberOfFactor_

factorTypes_

java.util.Collection<E> factorTypes_

factorNames_

java.lang.String[] factorNames_

fTypes_

java.lang.String[] fTypes_

scaleTypes_

java.util.Collection<E> scaleTypes_

scales_

java.lang.String[] scales_

levels_

java.lang.String[] levels_

experimentType_

java.lang.String[] experimentType_

visibility_

java.lang.String[] visibility_

investigatorID_

long investigatorID_

contactID_

long contactID_

experimentFactorData_

java.util.Collection<E> experimentFactorData_

factorValue_

java.lang.String[] factorValue_

factorID

long factorID

factorValueID

long factorValueID

factorName_

java.lang.String factorName_

experimentFactorTypeID_

long experimentFactorTypeID_

experimentFactorScaleID_

long experimentFactorScaleID_

pubMedID_

java.lang.String pubMedID_

pubMedLink_

java.lang.String pubMedLink_

publicationTitle_

java.lang.String publicationTitle_

publicationAuthor_

java.lang.String publicationAuthor_

publication_

java.lang.String publication_

publisher_

java.lang.String publisher_

publicationEditor_

java.lang.String publicationEditor_

publishYear_

java.lang.String publishYear_

publicationVolume_

java.lang.String publicationVolume_

publicationIssue_

java.lang.String publicationIssue_

publicationPage_

java.lang.String publicationPage_

publicationURI_

java.lang.String publicationURI_

publicationData_

java.util.Collection<E> publicationData_

publicationDataID_

long publicationDataID_

buttonName_

java.lang.String buttonName_

qualityControlData_

QualityControlData qualityControlData_

qualityControlTypeList_

java.util.Collection<E> qualityControlTypeList_

qualityControlDescription_

java.lang.String qualityControlDescription_

selectedQualityControlType_

java.lang.String[] selectedQualityControlType_

additionalQualifierData_

java.util.Collection<E> additionalQualifierData_

additionalQualifierName_

java.lang.String additionalQualifierName_

additionalQualifierSource_

java.lang.String additionalQualifierSource_

additionalQualifierValue_

java.lang.String additionalQualifierValue_

additionalQualifierDataID_

long additionalQualifierDataID_

additionalDataProcessData_

java.util.Collection<E> additionalDataProcessData_

additionalUploadedFileData_

java.util.Collection<E> additionalUploadedFileData_

additionalUploadFile_

CustomFormFile additionalUploadFile_

additionalUploadFileDesc_

java.lang.String additionalUploadFileDesc_

additionalDataProcessingFile_

CustomFormFile additionalDataProcessingFile_

applyProtocolID_

long applyProtocolID_

applyProtocol_

java.util.Collection<E> applyProtocol_

selectedVisibilityNames_

java.lang.String[] selectedVisibilityNames_

hybridizationData_

java.util.Collection<E> hybridizationData_

arrayDesign_

java.util.Collection<E> arrayDesign_

manufacture_

java.util.Collection<E> manufacture_

manufactureID_

long manufactureID_

numberOfHybridization_

int numberOfHybridization_

arrayDesignID_

long arrayDesignID_

hybridizationProtocols_

java.util.Collection<E> hybridizationProtocols_

hybridizationProtocolID_

long hybridizationProtocolID_

imageProtocols_

java.util.Collection<E> imageProtocols_

imageProtocolID_

long imageProtocolID_

imageProtocolData_

ProtocolData imageProtocolData_

featureProtocols_

java.util.Collection<E> featureProtocols_

featureProtocolID_

long featureProtocolID_

hybridizationProtocolData_

ProtocolData hybridizationProtocolData_

hybridizationActivityDate_

java.lang.String hybridizationActivityDate_

hybridizationParameters_

java.lang.String[] hybridizationParameters_

imageActivateDate_

java.lang.String imageActivateDate_

imageParameters_

java.lang.String[] imageParameters_

featureProtocolData_

ProtocolData featureProtocolData_

performerID_

long performerID_

performers_

java.util.Collection<E> performers_

featureParameters_

java.lang.String[] featureParameters_

featureActivateDate_

java.lang.String featureActivateDate_

arrayDesignName_

java.lang.String arrayDesignName_

numberOfChannels_

int numberOfChannels_

hybridizationProtocolName_

java.lang.String hybridizationProtocolName_

imageProtocolName_

java.lang.String imageProtocolName_

featureProtocolName_

java.lang.String featureProtocolName_

arrayBatch_

java.lang.String[] arrayBatch_

arrayIdentifier_

long[] arrayIdentifier_

arrayIdentifiers_

java.util.Collection<E> arrayIdentifiers_

extract_

java.util.Collection<E> extract_

extractID_

long[] extractID_

spikedControls_

java.util.Collection<E> spikedControls_

spikedControlID_

long[] spikedControlID_

hybridizationFactors_

java.util.Collection<E> hybridizationFactors_

hybridizationFactorValues_

java.lang.String[] hybridizationFactorValues_

additionalDataApplyProtocolData_

ProtocolData additionalDataApplyProtocolData_

dataProcessURI_

java.lang.String dataProcessURI_

dataProcessProtocolDescription_

java.lang.String dataProcessProtocolDescription_

dataProcessSoftwareReleaseDate_

java.lang.String[] dataProcessSoftwareReleaseDate_

dataProcessSoftwareVersion_

java.lang.String[] dataProcessSoftwareVersion_

dataProcessSoftwareParameters_

java.lang.String[] dataProcessSoftwareParameters_

magemlFileLocation_

java.lang.String magemlFileLocation_

hybridizationProtocol

ProtocolApplicationData[] hybridizationProtocol

featureProtocol

ProtocolApplicationData[] featureProtocol

imageProtocol

ProtocolApplicationData[] imageProtocol

fileMAGEML_

CustomFormFile fileMAGEML_

hybridizations

Hybridization[] hybridizations

dataProcessProtocolParameters_

java.lang.String[] dataProcessProtocolParameters_

dataProcessHardwareSerialNumber_

java.lang.String[] dataProcessHardwareSerialNumber_

dataProcessHardwareParameters_

java.lang.String[] dataProcessHardwareParameters_

dataProcessProtocolPerformers_

java.util.Collection<E> dataProcessProtocolPerformers_

protocolPerformerID_

long protocolPerformerID_

protocolActivityDate_

java.lang.String protocolActivityDate_

additionalDataProcessDownloadPath_

java.lang.String additionalDataProcessDownloadPath_

isFactorEmpty

java.lang.String isFactorEmpty

curatorMessage_

java.lang.String curatorMessage_

isCancel

java.lang.String isCancel

additionalFileUploadCancel

java.lang.String additionalFileUploadCancel

validate

java.lang.String validate

publicationCancel

java.lang.String publicationCancel

previous

java.lang.String previous

experimentMAGEMLData_

FileData experimentMAGEMLData_

identifier_

java.lang.String identifier_

batchFileName

java.lang.String batchFileName

dArrayDesign

long dArrayDesign

dFactorNameID

long dFactorNameID

dFactorValueID

long dFactorValueID

batchFileResults

java.util.Collection<E> batchFileResults

chp_file_exist

java.lang.String chp_file_exist

cel_file_exist

java.lang.String cel_file_exist

exp_file_exist

java.lang.String exp_file_exist

txt_file_exist

java.lang.String txt_file_exist

gpr_file_exist

java.lang.String gpr_file_exist

gps_file_exist

java.lang.String gps_file_exist

other_file_exist

java.lang.String other_file_exist

fileType

java.lang.String fileType

from

java.lang.String from

isExperimentOwnedByCurrentUser

boolean isExperimentOwnedByCurrentUser

Class gov.nih.nci.caarray.ui.experiment.ExperimentFileDownloadServlet extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: -6826827990796989631L

Class gov.nih.nci.caarray.ui.experiment.ExperimentSearchForm extends ExperimentBaseForm implements Serializable

Serialized Fields

ID_

long ID_

experimentName_

java.lang.String experimentName_

freeText_

java.lang.String freeText_

mode_

java.lang.String mode_

searchResults_

java.util.Collection<E> searchResults_

visibility_

long visibility_

identifier_

java.lang.String identifier_

Class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

id_

long id_

expId

java.lang.String expId

method

java.lang.String method

mode

java.lang.String mode

experimentTitle_

java.lang.String experimentTitle_

experimentCompleteDate_

java.lang.String experimentCompleteDate_

description_

java.lang.String description_

experimentType_

java.lang.String experimentType_

visibility_

java.lang.String visibility_

identifier_

java.lang.String identifier_

fileGroupId

java.lang.String fileGroupId

arrayBatchName

java.lang.String arrayBatchName

fileName

java.lang.String fileName

originalFileName

java.lang.String originalFileName

arrayDesignName

java.lang.String arrayDesignName

numberOfChannels

java.lang.String numberOfChannels

hybridizationProtocolName

java.lang.String hybridizationProtocolName

imageProtocolName

java.lang.String imageProtocolName

featureProtocolName

java.lang.String featureProtocolName

arrayIdentifier

java.lang.String arrayIdentifier

arrayIdentifierId

long arrayIdentifierId

channelOne

LabeledExtractDesc channelOne

channelOneSpike

LabeledExtractDesc channelOneSpike

channelTwo

LabeledExtractDesc channelTwo

channelTwoSpike

LabeledExtractDesc channelTwoSpike

channelId

long channelId

factorLevelChOne

FactorDropDownData[] factorLevelChOne

factorLevelChTwo

FactorDropDownData[] factorLevelChTwo

factorForChannelOne

long[] factorForChannelOne

factorForChannelTwo

long[] factorForChannelTwo

fileList

java.util.Collection<E> fileList

annotationId

int annotationId

multipleIds

java.lang.String[] multipleIds

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.experiment.HybridizationAnnotationMiniForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

id_

long id_

expId

java.lang.String expId

method

java.lang.String method

fileGroupId

java.lang.String fileGroupId

factorForChannelOne

long[] factorForChannelOne

factorForChannelTwo

long[] factorForChannelTwo

Class gov.nih.nci.caarray.ui.experiment.HybridizationDetailForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

method

java.lang.String method

id

java.lang.String id

hybridizationId

java.lang.String hybridizationId

hybridizationGroupName

java.lang.String hybridizationGroupName

arrayDesignName

java.lang.String arrayDesignName

numberOfChannels

java.lang.String numberOfChannels

numberOfHybridization

java.lang.String numberOfHybridization

hybridizationProtocolName

java.lang.String hybridizationProtocolName

imageProtocolName

java.lang.String imageProtocolName

featureProtocolName

java.lang.String featureProtocolName

validate

java.lang.String validate

hybridizations

Hybridization[] hybridizations

arrayIdentifier

long[] arrayIdentifier

arrayIdentifiers

java.util.Collection<E> arrayIdentifiers

Class gov.nih.nci.caarray.ui.experiment.HybridizationFileUploadForm extends ExperimentBaseForm implements Serializable

Serialized Fields

arrayGroupTemplateName

java.lang.String arrayGroupTemplateName

log

org.apache.commons.logging.Log log

ID

long ID

method

java.lang.String method

arrayDesign

java.util.Collection<E> arrayDesign

fileMappingType

java.util.Collection<E> fileMappingType

arrayDesignID

long arrayDesignID

hybridizationProtocolID

long hybridizationProtocolID

imageProtocolID

long imageProtocolID

featureProtocolID

long featureProtocolID

hybridizationProtocols

java.util.Collection<E> hybridizationProtocols

imageProtocols

java.util.Collection<E> imageProtocols

featureProtocols

java.util.Collection<E> featureProtocols

hybridizationProtocolData

ProtocolData hybridizationProtocolData

imageProtocolData

ProtocolData imageProtocolData

featureProtocolData

ProtocolData featureProtocolData

performers

java.util.Collection<E> performers

numberOfChannels

int numberOfChannels

arrayDesignName

java.lang.String arrayDesignName

hybridizationProtocolName

java.lang.String hybridizationProtocolName

imageProtocolName

java.lang.String imageProtocolName

featureProtocolName

java.lang.String featureProtocolName

arrayBatch

java.lang.String arrayBatch

arrayIdentifier

long arrayIdentifier

arrayIdentifiers

java.util.Collection<E> arrayIdentifiers

extractID

long extractID

extractIDCh2

long extractIDCh2

spikedControlID

long spikedControlID

spikedControlIDCh2

long spikedControlIDCh2

hybridizationProtocol

ProtocolApplicationData[] hybridizationProtocol

featureProtocol

ProtocolApplicationData[] featureProtocol

imageProtocol

ProtocolApplicationData[] imageProtocol

hybridization

Hybridization hybridization

fileType

int fileType

fileTypeName

java.lang.String fileTypeName

Class gov.nih.nci.caarray.ui.experiment.UploadApplet extends javax.swing.JFrame implements Serializable

Serialized Fields

contentPane

javax.swing.JPanel contentPane

chooseLst

java.awt.List chooseLst

selectedLst

java.awt.List selectedLst

dataBt

javax.swing.JButton dataBt

otherBt

javax.swing.JButton otherBt

removeBt

javax.swing.JButton removeBt

removeAllBt

javax.swing.JButton removeAllBt

uploadBt

javax.swing.JButton uploadBt

selectAllBt

javax.swing.JButton selectAllBt

deSelectAllBt

javax.swing.JButton deSelectAllBt

progressBar

javax.swing.JProgressBar progressBar

driveLabel

javax.swing.JLabel driveLabel

selectedFiles

javax.swing.JLabel selectedFiles

uploadFileName

javax.swing.JLabel uploadFileName

currentDir

java.io.File currentDir

files

java.lang.String[] files

dateFormatter

java.text.DateFormat dateFormatter

cDirLabel

javax.swing.JLabel cDirLabel

directoryDisplayLabel

javax.swing.JLabel directoryDisplayLabel

driveChoice

java.awt.Choice driveChoice

selectedFileVec

java.util.Vector<E> selectedFileVec

uFile

gov.nih.nci.caarray.ui.experiment.UploadFile uFile

Package gov.nih.nci.caarray.ui.experiment.data

Class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadAppletParams extends java.lang.Object implements Serializable

Serialized Fields

uploadURL

java.lang.String uploadURL
The destination url to which the uploading files will be sent and saved.


notifyURL

java.lang.String notifyURL
The destination url to which server is notified for the next step process.


defaultURL

java.lang.String defaultURL
The default url to go when user presses the done button to end the uploading process.


id

java.lang.String id
The String variable that holds the key to the hybridization annotation data for this upload operation,that is stored in a static cache on the server side.


archiveValue

java.lang.String archiveValue
The String variable holding the value for HttpFileUploadpplet archive jar file path. default to nothing.


sid

java.lang.String sid
The session id for session identification.


module

java.lang.String module
The string token to indicate where the applet is invoked, so set the applet to perform required function.


tunnelURL

java.lang.String tunnelURL
The URL from which the existing file names are fetched to the applet to ensure the same file names are handled. Works together with the module token.


permissibleFileExtension

java.lang.String permissibleFileExtension
The concatenated file extension permissible to the module.

Class gov.nih.nci.caarray.ui.experiment.data.HttpFileUploadCache extends java.lang.Object implements Serializable

Serialized Fields

fileData

HybridizationFileUploadGroupData fileData
The data object that gathers all the hybridization annotation data through many jsp pages.


fileArrayDesignData

ArrayDesignFileUploadGroupData fileArrayDesignData

fileList

java.util.List<E> fileList
The container object that is the place for all meta data for the uploaded files. Valid data type: HttpUploadedFileData.


isStopped

boolean isStopped
The boolean flag. Set to true when user requests a stop action. Otherwise it is false. Default value is false.

Class gov.nih.nci.caarray.ui.experiment.data.HttpUploadedFileData extends java.lang.Object implements Serializable

Serialized Fields

type

java.lang.String type
The type means Data or Other user set at the time files are selected.


filePath

java.lang.String filePath
The absolute file path of the uploaded file on the client machine, before it was zipped.


fileName

java.lang.String fileName
The zip file name for the uploaded file, based on zip file naming convention for the application such as hybData_gpr.zip from hybData.gpr.


userId

java.lang.String userId
The sumbitters userId for the uploaded file,.


originalFileName

java.lang.String originalFileName
The original file name for the uploaded file, hybData.gpr.


validatorCode

java.lang.String validatorCode
The validatorCode validation for the for the uploaded file.


fileExtension

java.lang.String fileExtension
The original file's extension that is preserved in the zipped file file name.


id

java.lang.String id
It is actually the key to access cached data about this upload operation.


Package gov.nih.nci.caarray.ui.login

Class gov.nih.nci.caarray.ui.login.LoginForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

userName

java.lang.String userName

password

java.lang.String password

Class gov.nih.nci.caarray.ui.login.RegisterForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

affiliation

java.lang.String affiliation

firstName

java.lang.String firstName

middleInitial

java.lang.String middleInitial

lastName

java.lang.String lastName

address1

java.lang.String address1

address2

java.lang.String address2

city

java.lang.String city

state

java.lang.String state

zip

java.lang.String zip

country

java.lang.String country

phone

java.lang.String phone

email

java.lang.String email

Package gov.nih.nci.caarray.ui.ontology

Class gov.nih.nci.caarray.ui.ontology.OntologyActionForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

accessionNumber

java.lang.String accessionNumber

back

java.lang.String back

databaseId

long databaseId

databaseName

java.lang.String databaseName

databases

DatabaseData[] databases

databaseVersion

java.lang.String databaseVersion

description

java.lang.String description

error

java.lang.String error

id

long id

log_

org.apache.commons.logging.Log log_

mode

java.lang.String mode

name

java.lang.String name

searchResults

java.util.Collection<E> searchResults

URI

java.lang.String URI

nameAndDatabase

java.lang.String nameAndDatabase

Class gov.nih.nci.caarray.ui.ontology.OntologyStrainLineActionForm extends OntologyActionForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

cultivarOrEcotype

java.lang.String cultivarOrEcotype

Package gov.nih.nci.caarray.ui.protocol

Class gov.nih.nci.caarray.ui.protocol.HardwareAddUpdateForm extends HardwareBaseForm implements Serializable

Serialized Fields

visibilitys_

java.util.Collection<E> visibilitys_

selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

back

java.lang.String back

newTypeName_

java.lang.String newTypeName_

URI_

java.lang.String URI_

Class gov.nih.nci.caarray.ui.protocol.HardwareBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

mode_

java.lang.String mode_

hardwareId_

long hardwareId_

hardwareTypeId_

long hardwareTypeId_

hardwareTypeName_

java.lang.String hardwareTypeName_

hardwareTypes_

java.util.Collection<E> hardwareTypes_

hardwareModel_

java.lang.String hardwareModel_

hardwareName_

java.lang.String hardwareName_

hardwareMake_

java.lang.String hardwareMake_

hardwareManufacturerId_

long hardwareManufacturerId_

hardwareManufacturerName_

java.lang.String hardwareManufacturerName_

hardwareManufacturers_

java.util.Collection<E> hardwareManufacturers_

isEditable

boolean isEditable

error_

java.lang.String error_

Class gov.nih.nci.caarray.ui.protocol.HardwareDetailForm extends HardwareBaseForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

id

long id

visibility

java.util.Collection<E> visibility

parameters

java.util.Collection<E> parameters

back

java.lang.String back

URI_

java.lang.String URI_

newSoftwareId

long newSoftwareId

allSoftware

java.util.Collection<E> allSoftware

associatedSoftware

SoftwareDesc[] associatedSoftware

Class gov.nih.nci.caarray.ui.protocol.HardwareSearchForm extends HardwareBaseForm implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

visibilityId_

long visibilityId_

visibilityName_

java.lang.String visibilityName_

visibilitys_

java.util.Collection<E> visibilitys_

searchResults_

java.util.Collection<E> searchResults_

Class gov.nih.nci.caarray.ui.protocol.ParameterAddForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

back

java.lang.String back

dataType_

java.lang.String dataType_

dataTypeId_

long dataTypeId_

dataTypes_

java.util.Collection<E> dataTypes_

defaultValue

java.lang.String defaultValue

name

java.lang.String name

object

java.lang.String object

objectId

long objectId

parameterId

long parameterId

unitNames_

java.util.Collection<E> unitNames_

unitNameId_

long unitNameId_

unitOtherId_

long unitOtherId_

unitTypeOther_

java.lang.String unitTypeOther_

unitNameOther_

java.lang.String unitNameOther_

unitTypes_

java.util.Collection<E> unitTypes_

unitTypeId_

long unitTypeId_

mode_

java.lang.String mode_

Class gov.nih.nci.caarray.ui.protocol.ProtocolActionMappingsForm extends ProtocolBaseForm implements Serializable

Class gov.nih.nci.caarray.ui.protocol.ProtocolAddUpdateForm extends ProtocolBaseForm implements Serializable

Serialized Fields

id

long id

description

java.lang.String description

selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

visibilitys_

java.util.Collection<E> visibilitys_

back

java.lang.String back

newTypeName_

java.lang.String newTypeName_

Class gov.nih.nci.caarray.ui.protocol.ProtocolApplicationForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

cancelURI

java.lang.String cancelURI

id

long id

cancel

java.lang.String cancel

parameters_

java.util.Collection<E> parameters_

parameterValues_

java.lang.String[] parameterValues_

performerId_

long performerId_

performers_

java.util.Collection<E> performers_

activityDate_

java.lang.String activityDate_

description_

java.lang.String description_

protocolType_

java.lang.String protocolType_

protocolId_

long protocolId_

protocols_

java.util.Collection<E> protocols_

protocolsApp_

ProtocolApplicationData[] protocolsApp_

mode_

java.lang.String mode_

applyMode_

java.lang.String applyMode_

button

java.lang.String button

reason

java.lang.String reason

fileId

long fileId

expId

long expId

originalProtocolsApp

ProtocolApplicationData originalProtocolsApp

originalProtocolId

long originalProtocolId

Class gov.nih.nci.caarray.ui.protocol.ProtocolBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

mode_

java.lang.String mode_

isEditable

boolean isEditable

protocolId_

long protocolId_

name_

java.lang.String name_

protocolTypeId_

long protocolTypeId_

protocolTypeName_

java.lang.String protocolTypeName_

protocolTypes_

java.util.Collection<E> protocolTypes_

error_

java.lang.String error_

description_

java.lang.String description_

URI_

java.lang.String URI_

Class gov.nih.nci.caarray.ui.protocol.ProtocolDetailForm extends ProtocolBaseForm implements Serializable

Serialized Fields

id

long id

description

java.lang.String description

visibility_

java.util.Collection<E> visibility_

parameters

java.util.Collection<E> parameters

back_

java.lang.String back_

hardware

java.util.Collection<E> hardware

software

java.util.Collection<E> software

allHardware

java.util.Collection<E> allHardware

allSoftware

java.util.Collection<E> allSoftware

newHardwareId

long newHardwareId

newSoftwareId

long newSoftwareId

mageIdentifier

java.lang.String mageIdentifier

Class gov.nih.nci.caarray.ui.protocol.ProtocolSearchForm extends ProtocolBaseForm implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

visibilityId_

long visibilityId_

visibilityName_

java.lang.String visibilityName_

visibilitys_

java.util.Collection<E> visibilitys_

searchResults_

java.util.Collection<E> searchResults_

Class gov.nih.nci.caarray.ui.protocol.SoftwareAddUpdateForm extends SoftwareBaseForm implements Serializable

Serialized Fields

visibilitys_

java.util.Collection<E> visibilitys_

selectedVisibilitys_

java.lang.String[] selectedVisibilitys_

back

java.lang.String back

newTypeName_

java.lang.String newTypeName_

URI_

java.lang.String URI_

Class gov.nih.nci.caarray.ui.protocol.SoftwareBaseForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

mode_

java.lang.String mode_

softwareId_

long softwareId_

name_

java.lang.String name_

softwareTypeId_

long softwareTypeId_

softwareTypeName_

java.lang.String softwareTypeName_

softwareTypes_

java.util.Collection<E> softwareTypes_

releaseDate_

java.lang.String releaseDate_

softwareManufacturerId_

long softwareManufacturerId_

softwareManufacturerName_

java.lang.String softwareManufacturerName_

softwareManufacturers_

java.util.Collection<E> softwareManufacturers_

error_

java.lang.String error_

isEditable

boolean isEditable

Class gov.nih.nci.caarray.ui.protocol.SoftwareDetailForm extends SoftwareBaseForm implements Serializable

Serialized Fields

log_

org.apache.commons.logging.Log log_

id

long id

visibility

java.util.Collection<E> visibility

parameters

java.util.Collection<E> parameters

back

java.lang.String back

URI_

java.lang.String URI_

hardwareID

long hardwareID

subSoftwareID

long subSoftwareID

allHardware

java.util.Collection<E> allHardware

allSoftware

java.util.Collection<E> allSoftware

associatedSoftware

java.util.Collection<E> associatedSoftware

associatedHardware

HardwareDesc associatedHardware

Class gov.nih.nci.caarray.ui.protocol.SoftwareSearchForm extends SoftwareBaseForm implements Serializable

Serialized Fields

freeText_

java.lang.String freeText_

visibilityId_

long visibilityId_

visibilityName_

java.lang.String visibilityName_

visibilitys_

java.util.Collection<E> visibilitys_

searchResults_

java.util.Collection<E> searchResults_

Package gov.nih.nci.caarray.ui.useradmin

Class gov.nih.nci.caarray.ui.useradmin.GroupAddUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

groupName

java.lang.String groupName

description

java.lang.String description

largeElementCountFlag

java.lang.String largeElementCountFlag

updateDate

long updateDate

protectionGroupTypeId

long protectionGroupTypeId

back

java.lang.String back

mode

java.lang.String mode

Class gov.nih.nci.caarray.ui.useradmin.GroupDetailForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

groupName

java.lang.String groupName

description

java.lang.String description

largeElementCountFlag

java.lang.String largeElementCountFlag

updateDate

long updateDate

protectionGroupTypeId

long protectionGroupTypeId

Class gov.nih.nci.caarray.ui.useradmin.GroupSearchForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

results

java.util.Collection<E> results

groupNameSearch

java.lang.String groupNameSearch

Class gov.nih.nci.caarray.ui.useradmin.UserAddUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

title

java.lang.String title

emailAddress

java.lang.String emailAddress

institutionName

java.lang.String institutionName

department

java.lang.String department

location

java.lang.String location

updateDate

java.lang.String updateDate

startDate

java.lang.String startDate

endDate

java.lang.String endDate

status

java.lang.String status

back

java.lang.String back

mode

java.lang.String mode

isAdminUser

boolean isAdminUser

phoneNumber

java.lang.String phoneNumber

pwd

java.lang.String pwd

confirmPassword

java.lang.String confirmPassword

userRoles

java.util.Vector<E> userRoles

Class gov.nih.nci.caarray.ui.useradmin.UserDetailForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

title

java.lang.String title

emailAddress

java.lang.String emailAddress

institutionName

java.lang.String institutionName

department

java.lang.String department

location

java.lang.String location

updateDate

java.lang.String updateDate

startDate

java.lang.String startDate

endDate

java.lang.String endDate

status

java.lang.String status

isAdminUser

boolean isAdminUser

role

java.lang.String role

userRoles

java.util.Vector<E> userRoles

groups

java.util.Collection<E> groups

phoneNumber

java.lang.String phoneNumber

password

java.lang.String password

Class gov.nih.nci.caarray.ui.useradmin.UserGroupAddUpdateForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

id

long id

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

groups

java.util.Vector<E> groups

assignedGroups

java.util.Vector<E> assignedGroups

groupIds

java.lang.String[] groupIds

Class gov.nih.nci.caarray.ui.useradmin.UserSearchForm extends org.apache.struts.action.ActionForm implements Serializable

Serialized Fields

results

java.util.Collection<E> results

firstNameSearch

java.lang.String firstNameSearch

lastNameSearch

java.lang.String lastNameSearch

loginNameSearch

java.lang.String loginNameSearch

institutionSearch

java.lang.String institutionSearch

emailSearch

java.lang.String emailSearch

userRoleSelection

int userRoleSelection

userRoleCollection

java.util.Vector<E> userRoleCollection

userStatusSelection

int userStatusSelection

userStatusCollection

java.util.Vector<E> userStatusCollection

Package org.biomage.Array

Class org.biomage.Array.Array extends Identifiable implements Serializable

Serialized Fields

arrayIdentifier

java.lang.String arrayIdentifier
An identifying string, e.g. a barcode.


arrayXOrigin

java.lang.Float arrayXOrigin
This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.


arrayYOrigin

java.lang.Float arrayYOrigin
This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.


originRelativeTo

java.lang.String originRelativeTo
What the array origin is relative to, e.g. upper left corner, fiducial, etc.


arrayDesign

ArrayDesign arrayDesign
The association of a physical array with its array design.


information

ArrayManufacture information
Association between the manufactured array and the information on that manufacture.


arrayGroup

ArrayGroup 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.


arrayManufactureDeviations

java.util.List<E> arrayManufactureDeviations
Association to classes to describe deviations from the ArrayDesign.

Class org.biomage.Array.Array_package extends java.lang.Object implements Serializable

Serialized Fields

arrayGroup_list

Array_package.ArrayGroup_list arrayGroup_list
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.


array_list

Array_package.Array_list array_list
The physical substrate along with its features and their annotation


arrayManufacture_list

Array_package.ArrayManufacture_list arrayManufacture_list
Describes the process by which arrays are produced.

Class org.biomage.Array.Array_package.Array_list extends java.util.Vector implements Serializable

Class org.biomage.Array.Array_package.ArrayGroup_list extends java.util.Vector implements Serializable

Class org.biomage.Array.Array_package.ArrayManufacture_list extends java.util.Vector implements Serializable

Class org.biomage.Array.ArrayGroup extends Identifiable implements Serializable

Serialized Fields

barcode

java.lang.String barcode
Identifier for the ArrayGroup.


arraySpacingX

java.lang.Float arraySpacingX
If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.


arraySpacingY

java.lang.Float arraySpacingY
If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.


numArrays

java.lang.Integer numArrays
This attribute defines the number of arrays on a chip or a slide.


orientationMark

java.lang.String orientationMark
For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.


orientationMarkPosition

ArrayGroup.OrientationMarkPosition orientationMarkPosition
One of top, bottom, left or right.


width

java.lang.Float width
The width of the platform


length

java.lang.Float length
The length of the platform.


fiducials

java.util.List<E> fiducials
Association to the marks on the Array for alignment for the scanner.


arrays

java.util.List<E> arrays
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.


substrateType

OntologyEntry substrateType
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.


distanceUnit

DistanceUnit distanceUnit
The unit of the measurement attributes.

Class org.biomage.Array.ArrayGroup.OrientationMarkPosition extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

top

int top

bottom

int bottom

left

int left

right

int right

VALID_POSITIONS

java.util.ArrayList<E> VALID_POSITIONS

Class org.biomage.Array.ArrayManufacture extends Identifiable implements Serializable

Serialized Fields

manufacturingDate

java.util.Date manufacturingDate
The date the arrays were manufactured


tolerance

java.lang.Float tolerance
The allowable error of a feature printed to its intended position.


arrays

java.util.List<E> arrays
Association between the manufactured array and the information on that manufacture.


arrayManufacturers

java.util.List<E> arrayManufacturers
The person or organization to contact for information concerning the ArrayManufacture.


qualityControlStatistics

java.util.List<E> qualityControlStatistics
Information on the quality of the ArrayManufacture.


featureLIMSs

java.util.List<E> featureLIMSs
Information on the manufacture of the features.


protocolApplications

java.util.List<E> protocolApplications
The protocols followed in the manufacturing of the arrays.

Class org.biomage.Array.ArrayManufactureDeviation extends Extendable implements Serializable

Serialized Fields

adjustments

java.util.List<E> adjustments
Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.


featureDefects

java.util.List<E> featureDefects
Description on features who are manufactured in a different location than specified in the ArrayDesign.

Class org.biomage.Array.FeatureDefect extends Extendable implements Serializable

Serialized Fields

defectType

OntologyEntry defectType
Indicates the type of defect (e.g. a missing feature or a moved feature).


positionDelta

PositionDelta positionDelta
How the feature deviates in position from the ArrayDesign.


feature

Feature feature
The feature that was manufactured defectively.

Class org.biomage.Array.Fiducial extends Describable implements Serializable

Serialized Fields

fiducialType

OntologyEntry fiducialType
A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).


distanceUnit

DistanceUnit distanceUnit
The units the fiducial is measured in.


position

Position position
The position, relative to the upper left corner, of the fiducial

Class org.biomage.Array.ManufactureLIMS extends Describable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

quality

java.lang.String quality
A brief description of the quality of the array manufacture process.


feature

Feature feature
The feature whose LIMS information is being described.


bioMaterial

BioMaterial bioMaterial
The BioMaterial used for the feature.


identifierLIMS

DatabaseEntry identifierLIMS
Association to a LIMS data source for further information on the manufacturing process.

Class org.biomage.Array.ManufactureLIMSBiomaterial extends ManufactureLIMS implements Serializable

Serialized Fields

bioMaterialPlateIdentifier

java.lang.String bioMaterialPlateIdentifier
The plate from which a biomaterial was obtained.


bioMaterialPlateRow

java.lang.String bioMaterialPlateRow
The plate row from which a biomaterial was obtained. Specified by a letter.


bioMaterialPlateCol

java.lang.String bioMaterialPlateCol
The plate column from which a biomaterial was obtained. Specified by a number.

Class org.biomage.Array.PositionDelta extends Extendable implements Serializable

Serialized Fields

deltaX

java.lang.Float deltaX
Deviation from the y coordinate of this feature's position.


deltaY

java.lang.Float deltaY
Deviation from the y coordinate of this feature's position.


distanceUnit

DistanceUnit distanceUnit
The unit for the attributes.

Class org.biomage.Array.ZoneDefect extends Extendable implements Serializable

Serialized Fields

defectType

OntologyEntry defectType
Indicates the type of defect (e.g. a missing zone or a moved zone).


positionDelta

PositionDelta positionDelta
How the zone deviates in position from the ArrayDesign.


zone

Zone zone
Reference to the Zone that was misprinted.


Package org.biomage.ArrayDesign

Class org.biomage.ArrayDesign.ArrayDesign extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

reporterFileLocation

java.lang.String reporterFileLocation

reporterFileType

java.lang.String reporterFileType

additionalReporterFileLocation

java.lang.String additionalReporterFileLocation

deleted

boolean deleted

version

java.lang.String version
The version of this design.


numberOfFeatures

java.lang.Integer numberOfFeatures
The number of features for this array


protocolApplications

java.util.List<E> protocolApplications
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.


featureGroups

java.util.List<E> featureGroups
The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.


reporterGroups

java.util.List<E> reporterGroups
The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.


compositeGroups

java.util.List<E> compositeGroups
The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.


designProviderRoles

java.util.List<E> designProviderRoles
The providers of the ArrayDesign that have a role which describes how he/she contributes the ArrayDesign, e.g. investigator, primary contact, etc.

Class org.biomage.ArrayDesign.ArrayDesign_package extends java.lang.Object implements Serializable

Serialized Fields

reporterGroup_list

ArrayDesign_package.ReporterGroup_list reporterGroup_list
Allows specification of the type of Reporter Design Element.


compositeGroup_list

ArrayDesign_package.CompositeGroup_list compositeGroup_list
Allows specification of the type of Composite Design Element.


arrayDesign_list

ArrayDesign_package.ArrayDesign_list arrayDesign_list
Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

Class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list extends java.util.Vector implements Serializable

Class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list extends java.util.Vector implements Serializable

Class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list extends java.util.Vector implements Serializable

Class org.biomage.ArrayDesign.CompositeGroup extends DesignElementGroup implements Serializable

Serialized Fields

compositeSequences

java.util.List<E> compositeSequences
The compositeSequences that belong to this group.

Class org.biomage.ArrayDesign.DesignElementGroup extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

types

java.util.List<E> types
The specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.


species

OntologyEntry species
The organism from which the biosequences of this group are from.

Class org.biomage.ArrayDesign.DesignProviderRole extends java.lang.Object implements Serializable

Serialized Fields

contact

Contact contact

role

OntologyEntry role

Class org.biomage.ArrayDesign.FeatureGroup extends DesignElementGroup implements Serializable

Serialized Fields

featureWidth

java.lang.Float featureWidth
The width of the feature.


featureLength

java.lang.Float featureLength
The length of the feature.


featureHeight

java.lang.Float featureHeight
The height of the feature.


technologyType

OntologyEntry technologyType
The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography.


featureShape

OntologyEntry featureShape
The expected shape of the feature on the array: circular, oval, square, etc.


distanceUnit

DistanceUnit distanceUnit
The unit for the feature measures.


features

java.util.List<E> features
The features that belong to this group.

Class org.biomage.ArrayDesign.PhysicalArrayDesign extends ArrayDesign implements Serializable

Serialized Fields

surfaceType

OntologyEntry surfaceType
The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.


zoneGroups

java.util.List<E> zoneGroups
In the case where the array design is specified by one or more zones, allows specifying where those zones are located.

Class org.biomage.ArrayDesign.ReporterGroup extends DesignElementGroup implements Serializable

Serialized Fields

reporters

java.util.List<E> reporters
The reporters that belong to this group.

Class org.biomage.ArrayDesign.Zone extends Identifiable implements Serializable

Serialized Fields

row

java.lang.Integer row
row position in the ZoneGroup


column

java.lang.Integer column
column position in the ZoneGroup.


upperLeftX

java.lang.Float upperLeftX
Boundary vertical upper left position relative to (0,0).


upperLeftY

java.lang.Float upperLeftY
Boundary horizontal upper left position relative to (0,0).


lowerRightX

java.lang.Float lowerRightX
Boundary vertical lower right position relative to (0,0).


lowerRightY

java.lang.Float lowerRightY
Boundary horizontal lower right position relative to (0,0).


distanceUnit

DistanceUnit distanceUnit
Unit for the Zone attributes.

Class org.biomage.ArrayDesign.ZoneGroup extends Extendable implements Serializable

Serialized Fields

spacingsBetweenZonesX

java.lang.Float spacingsBetweenZonesX
Spacing between zones, if applicable.


spacingsBetweenZonesY

java.lang.Float spacingsBetweenZonesY
Spacing between zones, if applicable.


zonesPerX

java.lang.Integer zonesPerX
The number of zones on the x-axis.


zonesPerY

java.lang.Integer zonesPerY
The number of zones on the y-axis.


distanceUnit

DistanceUnit distanceUnit
Unit for the ZoneGroup attributes.


zoneLayout

ZoneLayout zoneLayout
Describes the rectangular layout of features in the array design.


zoneLocations

java.util.List<E> zoneLocations
Describes the location of different zones within the array design.

Class org.biomage.ArrayDesign.ZoneLayout extends Extendable implements Serializable

Serialized Fields

numFeaturesPerRow

java.lang.Integer numFeaturesPerRow
The number of features from left to right.


numFeaturesPerCol

java.lang.Integer numFeaturesPerCol
The number of features from top to bottom of the grid.


spacingBetweenRows

java.lang.Float spacingBetweenRows
Spacing between the rows.


spacingBetweenCols

java.lang.Float spacingBetweenCols
Spacing between the columns.


distanceUnit

DistanceUnit distanceUnit
Unit of the ZoneLayout attributes.


Package org.biomage.AuditAndSecurity

Class org.biomage.AuditAndSecurity.Audit extends Describable implements Serializable

Serialized Fields

date

java.util.Date date
The date of a change.


action

Audit.Action action
Indicates whether an action is a creation or a modification.


performer

Contact performer
The contact for creating or changing the instance referred to by the Audit.

Class org.biomage.AuditAndSecurity.Audit.Action extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

creation

int creation

modification

int modification

Class org.biomage.AuditAndSecurity.AuditAndSecurity_package extends java.lang.Object implements Serializable

Serialized Fields

contact_list

AuditAndSecurity_package.Contact_list contact_list
A contact is either a person or an organization.


securityGroup_list

AuditAndSecurity_package.SecurityGroup_list securityGroup_list
Groups contacts together based on their security privileges.


security_list

AuditAndSecurity_package.Security_list security_list
Permission information for an object as to ownership, write and read permissions.

Class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list extends java.util.Vector implements Serializable

Class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list extends java.util.Vector implements Serializable

Class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list extends java.util.Vector implements Serializable

Class org.biomage.AuditAndSecurity.Contact extends Identifiable implements Serializable

Serialized Fields

URI

java.lang.String URI

address

java.lang.String address

phone

java.lang.String phone

tollFreePhone

java.lang.String tollFreePhone

email

java.lang.String email

fax

java.lang.String fax

roles

java.util.List<E> roles
The roles (lab equipment sales, contractor, etc.) the contact fills.

Class org.biomage.AuditAndSecurity.Organization extends Contact implements Serializable

Serialized Fields

parent

Organization parent
The containing organization (the university or business which a lab belongs to, etc.)

Class org.biomage.AuditAndSecurity.Person extends Contact implements Serializable

Serialized Fields

lastName

java.lang.String lastName

firstName

java.lang.String firstName

midInitials

java.lang.String midInitials

affiliation

Organization affiliation
The organization a person belongs to.

Class org.biomage.AuditAndSecurity.Security extends Identifiable implements Serializable

Serialized Fields

owner

java.util.List<E> owner
The owner of the security rights.


securityGroups

java.util.List<E> securityGroups
Specifies which security groups have permission to view the associated object.

Class org.biomage.AuditAndSecurity.SecurityGroup extends Identifiable implements Serializable

Serialized Fields

members

java.util.List<E> members
The members of the Security Group.

Class org.biomage.AuditAndSecurity.User extends Contact implements Serializable

Serialized Fields

loginName

java.lang.String loginName

firstName

java.lang.String firstName

lastName

java.lang.String lastName

emailAddress

java.lang.String emailAddress

institutionName

java.lang.String institutionName

Package org.biomage.BioAssay

Class org.biomage.BioAssay.BioAssay extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

channels

java.util.List<E> channels
Channels can be non-null for all subclasses. For instance, collapsing across replicate features will create a DerivedBioAssay that will potentially reference channels.


bioAssayFactorValues

java.util.List<E> bioAssayFactorValues
The values that this BioAssay is associated with for the experiment.


deleted

boolean deleted
caARRAY-specific marker for a DELETED BioAssay. tranp.

Class org.biomage.BioAssay.BioAssay_package extends java.lang.Object implements Serializable

Serialized Fields

channel_list

BioAssay_package.Channel_list channel_list
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.


bioAssay_list

BioAssay_package.BioAssay_list bioAssay_list
An abstract class which represents both physical and computational groupings of arrays and biomaterials.

Class org.biomage.BioAssay.BioAssay_package.BioAssay_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssay.BioAssay_package.Channel_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssay.BioAssayCreation extends BioEvent implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

sourceBioMaterialMeasurements

java.util.List<E> sourceBioMaterialMeasurements
The BioSample and its amount used in the BioAssayCreation event.


array

Array array
The array used in the BioAssayCreation event.


physicalBioAssayTarget

PhysicalBioAssay physicalBioAssayTarget
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.

Class org.biomage.BioAssay.BioAssayTreatment extends BioEvent implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

physicalBioAssay

PhysicalBioAssay physicalBioAssay
The set of treatments undergone by this PhysicalBioAssay.


target

PhysicalBioAssay target
The PhysicalBioAssay that was treated.

Class org.biomage.BioAssay.Channel extends Identifiable implements Serializable

Serialized Fields

labels

java.util.List<E> labels
The compound used to label the extract.

Class org.biomage.BioAssay.DerivedBioAssay extends BioAssay implements Serializable

Serialized Fields

type

OntologyEntry type
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.


derivedBioAssayData

java.util.List<E> derivedBioAssayData
The data associated with the DerivedBioAssay.


derivedBioAssayMap

java.util.List<E> derivedBioAssayMap
The DerivedBioAssay that is produced by the sources of the BioAssayMap.

Class org.biomage.BioAssay.FeatureExtraction extends BioEvent implements Serializable

Serialized Fields

physicalBioAssaySource

PhysicalBioAssay physicalBioAssaySource
The PhysicalBioAssay used in the FeatureExtraction event.


measuredBioAssayTarget

MeasuredBioAssay measuredBioAssayTarget
The association between the MeasuredBioAssay and the FeatureExtraction Event.

Class org.biomage.BioAssay.Hybridization extends BioAssayCreation implements Serializable

Class org.biomage.BioAssay.Image extends Identifiable implements Serializable

Serialized Fields

URI

java.lang.String URI
The file location in which an image may be found.


channels

java.util.List<E> channels
The channels captured in this image.


format

OntologyEntry format
The file format of the image typically a TIF or a JPEG.

Class org.biomage.BioAssay.ImageAcquisition extends BioAssayTreatment implements Serializable

Serialized Fields

images

java.util.List<E> images
The images produced by the ImageAcquisition event.

Class org.biomage.BioAssay.MeasuredBioAssay extends BioAssay implements Serializable

Serialized Fields

featureExtraction

FeatureExtraction featureExtraction
The association between the MeasuredBioAssay and the FeatureExtraction Event.


measuredBioAssayData

java.util.List<E> measuredBioAssayData
The data associated with the MeasuredBioAssay.

Class org.biomage.BioAssay.PhysicalBioAssay extends BioAssay implements Serializable

Serialized Fields

physicalBioAssayData

java.util.List<E> physicalBioAssayData
The Images associated with this PhysicalBioAssay by ImageAcquisition.


bioAssayCreation

BioAssayCreation bioAssayCreation
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.


bioAssayTreatments

java.util.List<E> bioAssayTreatments
The set of treatments undergone by this PhysicalBioAssay.


Package org.biomage.BioAssayData

Class org.biomage.BioAssayData.BioAssayData extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

summaryStatistics

java.util.List<E> summaryStatistics
Statistics on the Quality of the BioAssayData.


bioAssayDimension

BioAssayDimension bioAssayDimension
The BioAssays of the BioAssayData.


designElementDimension

DesignElementDimension designElementDimension
The DesignElements of the BioAssayData.


quantitationTypeDimension

QuantitationTypeDimension quantitationTypeDimension
The QuantitationTypes of the BioAssayData.


bioDataValues

BioDataValues bioDataValues
The data values of the BioAssayData.

Class org.biomage.BioAssayData.BioAssayData_package extends java.lang.Object implements Serializable

Serialized Fields

bioAssayDimension_list

BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
An ordered list of bioAssays.


designElementDimension_list

BioAssayData_package.DesignElementDimension_list designElementDimension_list
An ordered list of designElements. It will be realized as one of its three subclasses.


quantitationTypeDimension_list

BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
An ordered list of quantitationTypes.


bioAssayMap_list

BioAssayData_package.BioAssayMap_list bioAssayMap_list
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.


quantitationTypeMap_list

BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.


bioAssayData_list

BioAssayData_package.BioAssayData_list bioAssayData_list
Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.

Class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list extends java.util.Vector implements Serializable

Class org.biomage.BioAssayData.BioAssayDimension extends Identifiable implements Serializable

Serialized Fields

bioAssays

java.util.List<E> bioAssays
The BioAssays for this Dimension

Class org.biomage.BioAssayData.BioAssayMap extends Map implements Serializable

Serialized Fields

bioAssayMapTarget

DerivedBioAssay bioAssayMapTarget
The DerivedBioAssay that is produced by the sources of the BioAssayMap.


sourceBioAssays

java.util.List<E> sourceBioAssays
The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

Class org.biomage.BioAssayData.BioAssayMapping extends Extendable implements Serializable

Serialized Fields

bioAssayMaps

java.util.List<E> bioAssayMaps
The maps for the BioAssays.

Class org.biomage.BioAssayData.BioAssayTuple extends Extendable implements Serializable

Serialized Fields

bioAssay

BioAssay bioAssay
The BioAssay associated with the value of the BioAssayDatum.


designElementTuples

HasDesignElementTuples.DesignElementTuples_list designElementTuples
DesignElement with the QuantitationTypes and their values for this BioAssay

Class org.biomage.BioAssayData.BioDataCube extends BioDataValues implements Serializable

Serialized Fields

order

BioDataCube.Order order
The order to expect the dimension. The enumeration uses the first letter of the three dimensions to represent the six possible orderings.


dataInternal

DataInternal dataInternal
Transformed class to associate white spaced delimited data to the BioAssayDataCube


dataExternal

DataExternal dataExternal
Transformed class to associate external data to the BioAssayDataCube


sourceType

SourceType sourceType
Indicates the type of data file (or DataInternal) where the cube originated. Note that this is a caArray extension to the MAGE model.

Class org.biomage.BioAssayData.BioDataCube.Order extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

BDQ

int BDQ

BQD

int BQD

DBQ

int DBQ

DQB

int DQB

QBD

int QBD

QDB

int QDB

Class org.biomage.BioAssayData.BioDataTuples extends BioDataValues implements Serializable

Serialized Fields

bioAssayTuples

HasBioAssayTupleData.BioAssayTuples_list bioAssayTuples
Each BioAssayTuple contains the the Data for a BioAssay.

Class org.biomage.BioAssayData.BioDataValues extends Extendable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

Class org.biomage.BioAssayData.CompositeSequenceDimension extends DesignElementDimension implements Serializable

Serialized Fields

compositeSequences

java.util.List<E> compositeSequences
The CompositeSequences for this Dimension.

Class org.biomage.BioAssayData.DataExternal extends Extendable implements Serializable

Serialized Fields

dataFormat

java.lang.String dataFormat
The format of the external file, whitespace delimited, tab delimited, netcdf, etc...


dataFormatInfoURI

java.lang.String dataFormatInfoURI
Location for documentation on the data format


filenameURI

java.lang.String filenameURI
The name and location of the file containing the external data

Class org.biomage.BioAssayData.DataInternal extends Extendable implements Serializable

Serialized Fields

pcData

PCData pcData
The tab delimited data.

Class org.biomage.BioAssayData.Datum extends Extendable implements Serializable

Serialized Fields

value

java.lang.Object value
Value for the BioAssay, DesignElement and QuantitationType specified by the parent tuple elements.

Class org.biomage.BioAssayData.DerivedBioAssayData extends BioAssayData implements Serializable

Serialized Fields

producerTransformation

Transformation producerTransformation
The association between the DerivedBioAssayData and the Transformation event that produced it.

Class org.biomage.BioAssayData.DesignElementDimension extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

Class org.biomage.BioAssayData.DesignElementMap extends Map implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

Class org.biomage.BioAssayData.DesignElementMapping extends Extendable implements Serializable

Serialized Fields

designElementMaps

java.util.List<E> designElementMaps
The maps for the DesignElements.

Class org.biomage.BioAssayData.DesignElementTuple extends Extendable implements Serializable

Serialized Fields

designElement

DesignElement designElement
The DesignElement associated with the value of the BioAssayDatum.


quantitationTypeTuples

HasQuantitationTypeTuples.QuantitationTypeTuples_list quantitationTypeTuples
A QuantitationType and the value associated with it

Class org.biomage.BioAssayData.FeatureDimension extends DesignElementDimension implements Serializable

Serialized Fields

containedFeatures

java.util.List<E> containedFeatures
The features for this dimension.

Class org.biomage.BioAssayData.MeasuredBioAssayData extends BioAssayData implements Serializable

Class org.biomage.BioAssayData.QuantitationTypeDimension extends Identifiable implements Serializable

Serialized Fields

quantitationTypes

java.util.List<E> quantitationTypes
The QuantitationTypes for this Dimension.

Class org.biomage.BioAssayData.QuantitationTypeMap extends Map implements Serializable

Serialized Fields

targetQuantitationType

QuantitationType targetQuantitationType
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.


sourcesQuantitationType

java.util.List<E> sourcesQuantitationType
The QuantitationType sources for values for the transformation.

Class org.biomage.BioAssayData.QuantitationTypeMapping extends Extendable implements Serializable

Serialized Fields

quantitationTypeMaps

java.util.List<E> quantitationTypeMaps
The maps for the QuantitationTypes.

Class org.biomage.BioAssayData.QuantitationTypeTuple extends Extendable implements Serializable

Serialized Fields

quantitationType

QuantitationType quantitationType
The QuantitationType associated with the value of the BioAssayDatum.


datum

Datum datum
The value to associate with the Quantitation Type.

Class org.biomage.BioAssayData.ReporterDimension extends DesignElementDimension implements Serializable

Serialized Fields

reporters

java.util.List<E> reporters
The reporters for this dimension.

Class org.biomage.BioAssayData.Transformation extends BioEvent implements Serializable

Serialized Fields

bioAssayDataSources

java.util.List<E> bioAssayDataSources
The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.


derivedBioAssayDataTarget

DerivedBioAssayData derivedBioAssayDataTarget
The association between the DerivedBioAssayData and the Transformation event that produced it.


quantitationTypeMapping

QuantitationTypeMapping quantitationTypeMapping
The collection of mappings for the QuantitationTypes.


designElementMapping

DesignElementMapping designElementMapping
The collection of mappings for the DesignElements.


bioAssayMapping

BioAssayMapping bioAssayMapping
The collection of mappings for the BioAssays.


Package org.biomage.BioEvent

Class org.biomage.BioEvent.BioEvent extends Identifiable implements Serializable

Serialized Fields

protocolApplications

java.util.List<E> protocolApplications
The applied protocols to the BioEvent.

Class org.biomage.BioEvent.BioEvent_package extends java.lang.Object implements Serializable

Class org.biomage.BioEvent.Map extends BioEvent implements Serializable


Package org.biomage.BioMaterial

Class org.biomage.BioMaterial.ActionProtocolTypeMap extends java.lang.Object implements Serializable

Serialized Fields

action

OntologyEntry action

protocolTypes

java.util.List<E> protocolTypes

Class org.biomage.BioMaterial.BioMaterial extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

imported

boolean imported
caARRAY internal flag to indicate if this BioMaterial is imported. This should only be set to TRUE by MAGEML importer and not be changed afterwards.


copied

java.lang.Boolean copied
caARRAY internal flag to indicate if this BioMaterial is generated by copy of existing biomaterial. This should only be set to TRUE when adding the biomaterial by copy of Labeledextract/Biomaterial and not be changed afterwards. This would allow to query biomaterial and ignore the ones generated by copy.


qualityControlStatistics

java.util.List<E> qualityControlStatistics
Measures of the quality of the BioMaterial.


characteristics

java.util.List<E> characteristics
Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.


materialType

OntologyEntry materialType
The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.


treatments

java.util.List<E> treatments
This association is one way from BioMaterial to Treatment. From this a BioMaterial can discover the amount and type of BioMaterial that was part of the treatment that produced it.


topLevelBioMaterials

java.util.List<E> topLevelBioMaterials
This association is one way from BioMaterial to it top most parent biomaterial. From this, a biomaterial can discover its topm parent biosource and the associated securedelementID. This relation is added for caArray to efficiently discover the parent bioseource and associated secured element id.

Class org.biomage.BioMaterial.BioMaterial_package extends java.lang.Object implements Serializable

Serialized Fields

compound_list

BioMaterial_package.Compound_list compound_list
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media.


bioMaterial_list

BioMaterial_package.BioMaterial_list bioMaterial_list
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)).

Class org.biomage.BioMaterial.BioMaterial_package.BioMaterial_list extends java.util.Vector implements Serializable

Class org.biomage.BioMaterial.BioMaterial_package.Compound_list extends java.util.Vector implements Serializable

Class org.biomage.BioMaterial.BioMaterialMeasurement extends Extendable implements Serializable

Serialized Fields

bioMaterial

BioMaterial bioMaterial
A source BioMaterial for a treatment.


measurement

Measurement measurement
The amount of the BioMaterial.

Class org.biomage.BioMaterial.BioSample extends BioMaterial implements Serializable

Serialized Fields

type

OntologyEntry type
The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.

Class org.biomage.BioMaterial.BioSource extends BioMaterial implements Serializable

Serialized Fields

sourceContact

java.util.List<E> sourceContact
The BioSource's source is the provider of the biological material (a cell line, strain, etc...). This could be the ATTC (American Tissue Type Collection).

Class org.biomage.BioMaterial.Compound extends Identifiable implements Serializable

Serialized Fields

isSolvent

java.lang.Boolean isSolvent
A Compound may be a special case Solvent.


compoundIndices

java.util.List<E> compoundIndices
Indices into common Compound Indices, such as the Merck Index, for this Compound.


componentCompounds

java.util.List<E> componentCompounds
The Compounds and their amounts used to create this Compound.


externalLIMS

DatabaseEntry externalLIMS
Reference to an entry in an external LIMS data source.

Class org.biomage.BioMaterial.CompoundMeasurement extends Extendable implements Serializable

Serialized Fields

compound

Compound compound
A Compound to be used to create another Compound.


measurement

Measurement measurement
The amount of the Compound.

Class org.biomage.BioMaterial.LabeledExtract extends BioMaterial implements Serializable

Serialized Fields

labels

java.util.List<E> labels
Compound used to label the extract.

Class org.biomage.BioMaterial.Treatment extends BioEvent implements Serializable

Serialized Fields

order

java.lang.Integer order
The chronological order in which a treatment occurred (in relation to other treatments). More than one treatment can have the same chronological order indicating that they happened (or were caused to happen) simultaneously.


action

OntologyEntry action
The event that occurred (e.g. grow, wait, add, etc...). The actions should be a recommended vocabulary


actionMeasurement

Measurement actionMeasurement
Measures events like duration, centrifuge speed, etc.


compoundMeasurements

java.util.List<E> compoundMeasurements
The compounds and their amounts used in the treatment.


sourceBioMaterialMeasurements

java.util.List<E> sourceBioMaterialMeasurements
The BioMaterials and the amounts used in the treatment


Package org.biomage.BioSequence

Class org.biomage.BioSequence.BioSequence extends Identifiable implements Serializable

Serialized Fields

length

java.lang.Integer length
The number of residues in the biosequence.


isApproximateLength

java.lang.Boolean isApproximateLength
If length not positively known will be true


isCircular

java.lang.Boolean isCircular
Indicates if the BioSequence is circular in nature.


sequence

java.lang.String sequence
The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G. The attribute is optional and instead of specified here, can be found through the DatabaseEntry.


sequenceDatabases

java.util.List<E> sequenceDatabases
References an entry in a species database, like GenBank, UniGene, etc.


ontologyEntries

java.util.List<E> ontologyEntries
Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.


polymerType

OntologyEntry polymerType
A choice of protein, RNA, or DNA.


type

OntologyEntry type
The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.


species

OntologyEntry species
The organism from which this sequence was obtained.


seqFeatures

java.util.List<E> seqFeatures
Association to annotations for subsequences. Corresponds to the GenBank Frame Table.

Class org.biomage.BioSequence.BioSequence_package extends java.lang.Object implements Serializable

Serialized Fields

bioSequence_list

BioSequence_package.BioSequence_list bioSequence_list
A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.

Class org.biomage.BioSequence.BioSequence_package.BioSequence_list extends java.util.Vector implements Serializable

Class org.biomage.BioSequence.SeqFeature extends Describable implements Serializable

Serialized Fields

basis

SeqFeature.Basis basis
How the evidence for a SeqFeature was determined.


regions

java.util.List<E> regions
Association to classes that describe the location with the sequence of the SeqFeature.

Class org.biomage.BioSequence.SeqFeature.Basis extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

experimental

int experimental

computational

int computational

both

int both

unknown

int unknown

NA

int NA

Class org.biomage.BioSequence.SeqFeatureLocation extends Extendable implements Serializable

Serialized Fields

strandType

java.lang.String strandType
Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' direction, is double stranded, etc.


subregions

java.util.List<E> subregions
Regions within the SeqFeature.


coordinate

SequencePosition coordinate
At which base pairs or amino acid this SeqFeature begins and ends.

Class org.biomage.BioSequence.SequencePosition extends Extendable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

start

java.lang.Integer start
The location of the base, for nucleotides, that the SeqFeature starts.


end

java.lang.Integer end
The location of the base, for nucleotides, that the SeqFeature ends.


Package org.biomage.BQS

Class org.biomage.BQS.BibliographicReference extends Describable implements Serializable

Serialized Fields

title

java.lang.String title

authors

java.lang.String authors

publication

java.lang.String publication

publisher

java.lang.String publisher

editor

java.lang.String editor

year

java.util.Date year

volume

java.lang.String volume

issue

java.lang.String issue

pages

java.lang.String pages

URI

java.lang.String URI

parameters

java.util.List<E> parameters
Criteria that can be used to look up the reference in a repository.


accessions

java.util.List<E> accessions
References in publications, eg Medline and PubMed, for this BibliographicReference.

Class org.biomage.BQS.BQS_package extends java.lang.Object implements Serializable


Package org.biomage.Common

Class org.biomage.Common.Describable extends Extendable implements Serializable

Serialized Fields

descriptions

java.util.List<E> descriptions
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.


auditTrail

java.util.List<E> auditTrail
A list of Audit instances that track changes to the instance of Describable.


security

Security security
Information on the security for the instance of the class.

Class org.biomage.Common.Extendable extends java.lang.Object implements Serializable

Serialized Fields

id

long id

securedElementId

java.lang.String securedElementId

editable

boolean editable

propertySets

java.util.List<E> propertySets
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

Class org.biomage.Common.Identifiable extends Describable implements Serializable

Serialized Fields

identifier

java.lang.String identifier
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.


name

java.lang.String name
The potentially ambiguous common identifier.

Class org.biomage.Common.MAGEException extends java.lang.Exception implements Serializable

Class org.biomage.Common.MAGEJava extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

identifier

java.lang.String identifier

auditAndSecurity_package

AuditAndSecurity_package auditAndSecurity_package
Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.


description_package

Description_package description_package
The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.


measurement_package

Measurement_package measurement_package
The classes of this package provide utility information on the quantities of other classes to each other.


bQS_package

BQS_package bQS_package
Allows a reference to an article, book or other publication to be specified for searching repositories.


bioEvent_package

BioEvent_package bioEvent_package
An abstract class representing an event that takes sources of some type to produce a target of some type. Each of the realized subclasses determines the type of the sources and the target. The association to a protocol application allows specification of how the event was performed.


protocol_package

Protocol_package protocol_package
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. The ProtocolApplication provides values for the replaceable parameters of the Protocol and, through the Description association of Describable, any variation from the Protocol.


bioMaterial_package

BioMaterial_package bioMaterial_package
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. A set of treatments are typically linear in time but can form a Directed Acyclic Graph.


bioSequence_package

BioSequence_package bioSequence_package
Describes a known gene or sequence. BioAssays typically seek to identify what BioSequences are expressed in a BioMaterial after treatments, the expression level measured from the association between the BioMaterial and the Array. The Array's Features typically provide known locations for this association to occur. Most often, the Reporter and CompositeSequence are known and the presence or absence of a particular BioSequence in the BioMaterial is based on whether there as been an association to the DesignElement targeted for it. Some other experiments may not know the DesignElement's target but can discover it with known properties of the BioSequences in the BioMaterial.


designElement_package

DesignElement_package designElement_package
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. The Feature describes an intended location on the Array, the Reporter the Oligo, Clone, PCR Product that is on a Feature and the CompositeSequence which combines Reporters or CompositeSequences into what the child DesignElements are meant to represent biologically, e.g. a Gene, Exon, SpliceVariant, etc.


arrayDesign_package

ArrayDesign_package arrayDesign_package
Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, short (~20-100mer) nucleotide sequences onto the features. Reporters can be grouped together into CompositeSequences, typically representing a gene or one or more splice variants in gene expression experiments. There are then two distinct ways that DesignElements are grouped. The one described in the ArrayDesign package by FeatureGroup, ReporterGroup and CompositeGroup is by technology type, that is, one might want to segregate the controls to a Group and all the non-controls to another. Or if PCR Product and Oligos are both used on an array they would likely be in different groups. The grouping described in the DesignElement package by the mappings relates the Features to the Reporter, the Reporters to CompositeSequence, and at higher levels, CompositeSequences to CompositeSequence.


array_package

Array_package array_package
Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.


bioAssay_package

BioAssay_package bioAssay_package
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. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design of this package and the related BioAssayData package was driven by the following query considerations and the desire to return as little data as necessary to satisfy a query. Often, the first set of queries for experiments below the Experiment level will want to discover the why of an experiment and this is captured in the BioAssay class through its FactorValue, BioEvent and Description associations. This separates it from the data but allows an overview of the experiment hierarchy. The BioAssayData class association to BioDataValues is optional only to allow queries on them to discover the how of the experiment through the association to the transformation and mappings of the three BioAssayData dimensions and the protocols used. Once a researcher, for instance, has narrowed down the experiments of interest then the actual data, represented by the BioDataValues, can be downloaded. Because these data can be in the hundreds of megabytes to gigabytes range, it was considered desirable to be able to return information and annotation on the experiment without the data.


quantitationType_package

QuantitationType_package quantitationType_package
This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue. The subclasses of StandardQuantitationType will be the best fit from FeatureExtraction or Transformation Protocol for the values obtained. Other values can be specified using SpecializedQuantitationType.


bioAssayData_package

BioAssayData_package bioAssayData_package
The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired.


experiment_package

Experiment_package experiment_package
Represents the container for a hierarchical grouping of BioAssays. Can have the end results of Clustering Analysis specified and, through the ExperimentDesign, a description and annotation of the overall design of the experiment and what it was to show.


higherLevelAnalysis_package

HigherLevelAnalysis_package higherLevelAnalysis_package
Describes the results of performing analysis on the result of the BioAssayData from an Experiment.


modelToClass

org.biomage.Common.MAGEJava.ModelNameToClassMap modelToClass
Instantiate the ModelNameToClassMap

Class org.biomage.Common.NameValueType extends java.lang.Object implements Serializable

Serialized Fields

id

long id
caARRAY-specific identifier


name

java.lang.String name
The name of the key.


value

java.lang.String value
The value of the name.


type

java.lang.String type
The type of the key.


propertySets

java.util.List<E> propertySets
Allows nested specification of name/value pairs


Package org.biomage.Description

Class org.biomage.Description.Database extends Identifiable implements Serializable

Serialized Fields

category

java.lang.String category
caARRAY-specific attribute to categorize the appropriate database type that should be used for which ontologies. tranp 08/12/04


userDefined

boolean userDefined
caARRAY-specific attribute to indicate if this database entry represents a public database.


version

java.lang.String version
The version for which a DatabaseReference applies.


URI

java.lang.String URI
The location of the Database.


contacts

java.util.List<E> contacts
Information on the contacts for the database

Class org.biomage.Description.DatabaseEntry extends Extendable implements Serializable

Serialized Fields

accession

java.lang.String accession
The identifier used to look up the record.


accessionVersion

java.lang.String accessionVersion
The appropriate version of the accession (if applicable).


URI

java.lang.String URI
The location of the record.


type

OntologyEntry type
The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD).


database

Database database
Reference to the database where the DataEntry instance can be found.

Class org.biomage.Description.Description extends Describable implements Serializable

Serialized Fields

text

java.lang.String text
The description.


URI

java.lang.String URI
A reference to the location and type of an outside resource.


externalReference

ExternalReference externalReference
Specifies where the described instance was originally obtained from.


annotations

java.util.List<E> annotations
Allows specification of ontology entries related to the instance being described.


databaseReferences

java.util.List<E> databaseReferences
References to entries in databases.


bibliographicReferences

java.util.List<E> bibliographicReferences
References to existing literature.

Class org.biomage.Description.Description_package extends java.lang.Object implements Serializable

Serialized Fields

database_list

Description_package.Database_list database_list
An address to a repository.

Class org.biomage.Description.Description_package.Database_list extends java.util.Vector implements Serializable

Class org.biomage.Description.ExternalReference extends Extendable implements Serializable

Serialized Fields

exportedFromServer

java.lang.String exportedFromServer
The originating server for the object, a network address or common name.


exportedFromDB

java.lang.String exportedFromDB
Name of the database, if applicable, that the object was exported from.


exportID

java.lang.String exportID
The identifier of the object at the originating source.


exportName

java.lang.String exportName
The name of the object at the originating source.

Class org.biomage.Description.OntologyEntry extends BioMaterialCharacteristic implements Serializable

Serialized Fields

category

java.lang.String category
The category to which this entry belongs.


value

java.lang.String value
The value for this entry in this category.


description

java.lang.String description
The description of the meaning for this entry.


ontologyReference

DatabaseEntry ontologyReference
Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference.


associations

java.util.List<E> associations
Allows an instance of an OntologyEntry to be further qualified.


Package org.biomage.Description.Ontology

Class org.biomage.Description.Ontology.Age extends OntologyEntry implements Serializable

Serialized Fields

measurement

OntologyEntry measurement

ageValue

OntologyEntry ageValue

minMeasurement

OntologyEntry minMeasurement

minValue

OntologyEntry minValue

maxMeasurement

OntologyEntry maxMeasurement

maxValue

OntologyEntry maxValue

initialTimePoint

OntologyEntry initialTimePoint

Class org.biomage.Description.Ontology.BioMaterialCharacteristic extends Extendable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

Class org.biomage.Description.Ontology.Biometrics extends OntologyEntry implements Serializable

Serialized Fields

weight

OntologyEntry weight

weightMeasurement

OntologyEntry weightMeasurement

height

OntologyEntry height

heightMeasurement

OntologyEntry heightMeasurement

Class org.biomage.Description.Ontology.ChromosomalAberration extends OntologyEntry implements Serializable

Serialized Fields

types

java.util.List<E> types

Package org.biomage.DesignElement

Class org.biomage.DesignElement.CompositeCompositeMap extends DesignElementMap implements Serializable

Serialized Fields

compositeSequence

CompositeSequence compositeSequence
A map to the compositeSequences that compose this CompositeSequence.


compositePositionSources

java.util.List<E> compositePositionSources
Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.

Class org.biomage.DesignElement.CompositePosition extends SequencePosition implements Serializable

Serialized Fields

composite

CompositeSequence composite
A source CompositeSequence that is part of a target CompositeSequence


mismatchInformation

java.util.List<E> mismatchInformation
Differences in how the contained compositeSequence matches its target compositeSequence's sequence.

Class org.biomage.DesignElement.CompositeSequence extends DesignElement implements Serializable

Serialized Fields

biologicalCharacteristics

java.util.List<E> biologicalCharacteristics
The annotation on the BioSequence this CompositeSequence represents. Typically the sequences will be a Genes, Exons, or SpliceVariants.


reporterCompositeMaps

java.util.List<E> reporterCompositeMaps
A map to the reporters that compose this CompositeSequence.


compositeCompositeMaps

java.util.List<E> compositeCompositeMaps
A map to the compositeSequences that compose this CompositeSequence.

Class org.biomage.DesignElement.DesignElement extends Identifiable implements Serializable

Serialized Fields

controlType

OntologyEntry controlType
If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)

Class org.biomage.DesignElement.DesignElement_package extends java.lang.Object implements Serializable

Serialized Fields

compositeSequence_list

DesignElement_package.CompositeSequence_list compositeSequence_list
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.


reporter_list

DesignElement_package.Reporter_list reporter_list
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. The derived data from the measured data of its Features represents the presence or absence of the biosequence or biosequences it is reporting on in the BioAssay. Reporters are Identifiable and several Features on the same array can be mapped to the same reporter as can Features from a different ArrayDesign. The granularity of the Reporters independence is dependent on the technology and the intent of the ArrayDesign. Oligos using mature technologies can in general be assumed to be safely replicated on many features where as with PCR Products there might be the desire for quality assurence to make reporters one to one with features and use the mappings to CompositeSequences for replication purposes.


compositeCompositeMap_list

DesignElement_package.CompositeCompositeMap_list compositeCompositeMap_list
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.


reporterCompositeMap_list

DesignElement_package.ReporterCompositeMap_list reporterCompositeMap_list
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.


featureReporterMap_list

DesignElement_package.FeatureReporterMap_list featureReporterMap_list
A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter.

Class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list extends java.util.Vector implements Serializable

Class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list extends java.util.Vector implements Serializable

Class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list extends java.util.Vector implements Serializable

Class org.biomage.DesignElement.DesignElement_package.Reporter_list extends java.util.Vector implements Serializable

Class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list extends java.util.Vector implements Serializable

Class org.biomage.DesignElement.Feature extends DesignElement implements Serializable

Serialized Fields

controlFeatures

java.util.List<E> controlFeatures
Associates features with their control features.


controlledFeatures

java.util.List<E> controlledFeatures
Associates features with their control features.


position

Position position
The position of the feature on the array, relative to the top, left corner.


zone

Zone zone
A reference to the zone this feature is in.


featureLocation

FeatureLocation featureLocation
Location of this feature relative to a grid.


featureGroup

FeatureGroup featureGroup
The features that belong to this group.

Class org.biomage.DesignElement.FeatureInformation extends Extendable implements Serializable

Serialized Fields

feature

Feature feature
The feature the FeatureInformation is supplying information for.


mismatchInformation

java.util.List<E> mismatchInformation
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.

Class org.biomage.DesignElement.FeatureLocation extends Extendable implements Serializable

Serialized Fields

row

java.lang.Integer row
row position in the Zone


column

java.lang.Integer column
column position in the Zone.

Class org.biomage.DesignElement.FeatureReporterMap extends DesignElementMap implements Serializable

Serialized Fields

reporter

Reporter reporter
Associates features with their reporter.


featureInformationSources

java.util.List<E> featureInformationSources
Typically, the features on an array that are manufactured with this reporter's BioSequence.

Class org.biomage.DesignElement.MismatchInformation extends Extendable implements Serializable

Serialized Fields

startCoord

java.lang.Integer startCoord
Offset into the sequence that the mismatch occurs.


newSequence

java.lang.String newSequence
The sequence that replaces the specified sequence starting at start_coord.


replacedLength

java.lang.Integer replacedLength
Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence is less than the replacedLength.

Class org.biomage.DesignElement.Position extends Extendable implements Serializable

Serialized Fields

x

java.lang.Float x
The horizontal distance from the upper left corner of the array.


y

java.lang.Float y
The vertical distance from the upper left corner of the array.


distanceUnit

DistanceUnit distanceUnit
The units of the x, y positions.

Class org.biomage.DesignElement.Reporter extends DesignElement implements Serializable

Serialized Fields

immobilizedCharacteristics

java.util.List<E> immobilizedCharacteristics
The sequence annotation on the BioMaterial this reporter represents. Typically the sequences will be an Oligo Sequence, Clone or PCR Primer.


warningType

OntologyEntry warningType
Similar to failType but indicates a warning rather than a failure.


failTypes

java.util.List<E> failTypes
If at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)


featureReporterMaps

java.util.List<E> featureReporterMaps
Associates features with their reporter.

Class org.biomage.DesignElement.ReporterCompositeMap extends DesignElementMap implements Serializable

Serialized Fields

compositeSequence

CompositeSequence compositeSequence
A map to the reporters that compose this CompositeSequence.


reporterPositionSources

java.util.List<E> reporterPositionSources
Association to the reporters that compose this CompositeSequence and where those reporters occur.

Class org.biomage.DesignElement.ReporterPosition extends SequencePosition implements Serializable

Serialized Fields

reporter

Reporter reporter
A reporter that comprises part of a CompositeSequence.


mismatchInformation

java.util.List<E> mismatchInformation
Differences in how the reporter matches its compositeSequence's sequence.


Package org.biomage.Experiment

Class org.biomage.Experiment.AdditionalDataProcessing extends java.lang.Object implements Serializable

Serialized Fields

id

long id

location

java.lang.String location

protocolApplication

ProtocolApplication protocolApplication

experiment

Experiment experiment

Class org.biomage.Experiment.AdditionalUploadedFile extends java.lang.Object implements Serializable

Serialized Fields

id

long id

description

java.lang.String description

location

java.lang.String location

experiment

Experiment experiment

Class org.biomage.Experiment.Experiment extends Identifiable implements Serializable

Serialized Fields

providerRoles

java.util.List<E> providerRoles
The providers of the Experiment that have a role which describes how he/she contributes the experiment, e.g. investigator, primary contact, etc.


analysisResults

java.util.List<E> analysisResults
The results of analyzing the data, typically with a clustering algorithm.


bioAssayData

java.util.List<E> bioAssayData
The collection of BioAssayDatas for this Experiment.


bioAssays

java.util.List<E> bioAssays
The collection of BioAssays for this Experiment.


experimentDesigns

java.util.List<E> experimentDesigns
The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.


deleted

boolean deleted
caARRAY-specific marker if this Experiment is deleted.

Class org.biomage.Experiment.Experiment_package extends java.lang.Object implements Serializable

Serialized Fields

experiment_list

Experiment_package.Experiment_list experiment_list
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.

Class org.biomage.Experiment.Experiment_package.Experiment_list extends java.util.Vector implements Serializable

Class org.biomage.Experiment.ExperimentalFactor extends Identifiable implements Serializable

Serialized Fields

category

OntologyEntry category
The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).


factorValues

java.util.List<E> factorValues
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.


annotations

java.util.List<E> annotations
Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #.

Class org.biomage.Experiment.ExperimentDesign extends Describable implements Serializable

Serialized Fields

types

java.util.List<E> types
Classification of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc.


topLevelBioAssays

java.util.List<E> topLevelBioAssays
The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)


experimentalFactors

java.util.List<E> experimentalFactors
The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays.


qualityControlDescription

Description qualityControlDescription
Description of the quality control aspects of the Experiment.


normalizationDescription

Description normalizationDescription
Description of the normalization strategy of the Experiment.


replicateDescription

Description replicateDescription
Description of the replicate strategy of the Experiment.

Class org.biomage.Experiment.ExperimentProviderRole extends java.lang.Object implements Serializable

Serialized Fields

contact

Contact contact

role

OntologyEntry role

Class org.biomage.Experiment.FactorValue extends Identifiable implements Serializable

Serialized Fields

experimentalFactor

ExperimentalFactor experimentalFactor
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.


measurement

Measurement measurement
The measured value for this factor.


value

OntologyEntry value
Allows a more complex value to be specified for a FactorValue than a simple Measurement.

Class org.biomage.Experiment.HybridizationFileUpload extends java.lang.Object implements Serializable

Serialized Fields

id

long id
Deprecated. 

experiment

Experiment experiment
Deprecated. 

arrayIdentifier

java.lang.String arrayIdentifier
Deprecated. 

arrayBatchName

java.lang.String arrayBatchName
Deprecated. 

celFileLocation

java.lang.String celFileLocation
Deprecated. 

expFileLocation

java.lang.String expFileLocation
Deprecated. 

txtFileLocation

java.lang.String txtFileLocation
Deprecated. 

chpFileLocation

java.lang.String chpFileLocation
Deprecated. 

gprFileLocation

java.lang.String gprFileLocation
Deprecated. 

gpsFileLocation

java.lang.String gpsFileLocation
Deprecated. 

gprFromSpotFileLocation

java.lang.String gprFromSpotFileLocation
Deprecated. 

measuredBioAssay

MeasuredBioAssay measuredBioAssay
Deprecated. 

derivedBioAssay

DerivedBioAssay derivedBioAssay
Deprecated. 

uploadGroupName

java.lang.String uploadGroupName
Deprecated. 

extract

LabeledExtract extract
Deprecated. 

spikedControl

LabeledExtract spikedControl
Deprecated. 

factorValues

java.util.List<E> factorValues
Deprecated. 

channelTwoExtract

LabeledExtract channelTwoExtract
Deprecated. 

channelTwoSpikedControl

LabeledExtract channelTwoSpikedControl
Deprecated. 

channelTwoFactorValues

java.util.List<E> channelTwoFactorValues
Deprecated. 

Package org.biomage.HigherLevelAnalysis

Class org.biomage.HigherLevelAnalysis.BioAssayDataCluster extends Identifiable implements Serializable

Serialized Fields

clusterBioAssayData

BioAssayData clusterBioAssayData
The BioAssayData whose values were used by the cluster algorithm.


nodes

java.util.List<E> nodes
The nodes of the cluster.

Class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package extends java.lang.Object implements Serializable

Serialized Fields

bioAssayDataCluster_list

HigherLevelAnalysis_package.BioAssayDataCluster_list bioAssayDataCluster_list
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

Class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package.BioAssayDataCluster_list extends java.util.Vector implements Serializable

Class org.biomage.HigherLevelAnalysis.Node extends Describable implements Serializable

Serialized Fields

nodes

java.util.List<E> nodes
Nested nodes of the BioAssayDataCluster.


nodeContents

java.util.List<E> nodeContents
The contents of the node, expressed as either a one, two or three dimensional object.


nodeValue

java.util.List<E> nodeValue
Values or measurements for this node that may be produced by the clustering algorithm. Typical are distance values for the nodes.

Class org.biomage.HigherLevelAnalysis.NodeContents extends Describable implements Serializable

Serialized Fields

bioAssayDimension

BioAssayDimension bioAssayDimension
The relevant BioAssays for this NodeContents from the BioAssayData.


designElementDimension

DesignElementDimension designElementDimension
The relevant DesignElements for this NodeContents from the BioAssayData.


quantitationDimension

QuantitationTypeDimension quantitationDimension
The relevant QuantitationTypes for this NodeContents from the BioAssayData.

Class org.biomage.HigherLevelAnalysis.NodeValue extends Extendable implements Serializable

Serialized Fields

name

java.lang.String name
The name for this value.


value

java.lang.Object value
The value for this NodeValue.


type

OntologyEntry type
The type of value, distance, etc.


scale

OntologyEntry scale
The scale (linear, log10, ln, etc.) of the value.


dataType

OntologyEntry dataType
The data type of the any element.


Package org.biomage.Interface

Class org.biomage.Interface.HasAccessions.Accessions_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasAdjustments.Adjustments_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasAnalysisResults.AnalysisResults_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasAnnotations.Annotations_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasArrays.Arrays_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasAssociations.Associations_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasAuditTrail.AuditTrail_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayData.BioAssayData_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssays.BioAssays_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBioAssayTupleData.BioAssayTuples_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasChannels.Channels_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCharacteristics.Characteristics_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompositeGroups.CompositeGroups_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompositeSequences.CompositeSequences_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompoundIndices.CompoundIndices_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasContacts.Contacts_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasControlFeatures.ControlFeatures_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasControlledFeatures.ControlledFeatures_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDerivedBioAssayMap.DerivedBioAssayMap_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDescriptions.Descriptions_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDesignElementMaps.DesignElementMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDesignElementTuples.DesignElementTuples_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasDesignProviders.DesignProviders_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasExperimentalFactors.ExperimentalFactors_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasExperimentDesigns.ExperimentDesigns_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFactorValues.FactorValues_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFailTypes.FailTypes_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatureDefects.FeatureDefects_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatureGroups.FeatureGroups_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatureInformationSources.FeatureInformationSources_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFeatures.Features_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasFiducials.Fiducials_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasHardwareApplications.HardwareApplications_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasHardwareManufacturers.HardwareManufacturers_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasHardwares.Hardwares_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasImages.Images_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasLabels.Labels_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasMembers.Members_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasMismatchInformation.MismatchInformation_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasNodeContents.NodeContents_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasNodes.Nodes_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasNodeValue.NodeValue_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasOntologyEntries.OntologyEntries_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasOwner.Owner_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasParameters.Parameters_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasParameterTypes.ParameterTypes_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasParameterValues.ParameterValues_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasPerformers.Performers_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasPropertySets.PropertySets_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasProviders.Providers_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasQuantitationTypeMaps.QuantitationTypeMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasQuantitationTypes.QuantitationTypes_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasQuantitationTypeTuples.QuantitationTypeTuples_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasRegions.Regions_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasReporterGroups.ReporterGroups_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasReporters.Reporters_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasRoles.Roles_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSecurityGroups.SecurityGroups_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSeqFeatures.SeqFeatures_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSoftwareApplications.SoftwareApplications_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSoftwareManufacturers.SoftwareManufacturers_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSoftwares.Softwares_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSourceContact.SourceContact_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSubregions.Subregions_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasTopBioMaterial.TopLevelBioMaterials_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasTopLevelBioAssays.TopLevelBioAssays_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasTreatments.Treatments_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasTypes.Types_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasZoneGroups.ZoneGroups_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable

Class org.biomage.Interface.HasZoneLocations.ZoneLocations_list extends org.apache.ojb.broker.util.collections.ManageableVector implements Serializable


Package org.biomage.Measurement

Class org.biomage.Measurement.ConcentrationUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

ConcentrationUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.ConcentrationUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

M

int M

mM

int mM

nM

int nM

uM

int uM

pM

int pM

fM

int fM

mg_per_mL

int mg_per_mL

mL_per_L

int mL_per_L

g_per_L

int g_per_L

gram_percent

int gram_percent

percent_vol_per_vol

int percent_vol_per_vol

percent_weight_per_vol

int percent_weight_per_vol

percent_weight_per_weight

int percent_weight_per_weight

other

int other

Class org.biomage.Measurement.DistanceUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

DistanceUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.DistanceUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

nm

int nm

um

int um

mm

int mm

cm

int cm

m

int m

A

int A

other

int other

Class org.biomage.Measurement.MassUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

MassUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.MassUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

kg

int kg

g

int g

mg

int mg

ug

int ug

ng

int ng

pg

int pg

fg

int fg

other

int other

Class org.biomage.Measurement.Measurement extends Extendable implements Serializable

Serialized Fields

type

Measurement.Type type
The type of measurement, for instance if the measurement is five feet, it can be either absolute (five feet tall) or change (five feet further along).


value

java.lang.Object value
The value of the measurement. kindCV (and otherKind) determine with Unit the datatype of value.


kindCV

Measurement.KindCV kindCV
One of the enumeration values to determine the controlled vocabulary of the value.


otherKind

java.lang.String otherKind
Name of the controlled vocabulary if it isn't one of the Unit subclasses.


unit

Unit unit
The Unit associated with the Measurement.

Class org.biomage.Measurement.Measurement_package extends java.lang.Object implements Serializable

Class org.biomage.Measurement.Measurement.KindCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

time

int time

distance

int distance

temperature

int temperature

quantity

int quantity

mass

int mass

volume

int volume

concentration

int concentration

other

int other

Class org.biomage.Measurement.Measurement.Type extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

absolute

int absolute

change

int change

Class org.biomage.Measurement.OtherUnit extends Unit implements Serializable

Class org.biomage.Measurement.QuantityUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

QuantityUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.QuantityUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

mol

int mol

amol

int amol

fmol

int fmol

pmol

int pmol

nmol

int nmol

umol

int umol

molecules

int molecules

other

int other

Class org.biomage.Measurement.TemperatureUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

TemperatureUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.TemperatureUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

degrees_C

int degrees_C

degrees_F

int degrees_F

K

int K

Class org.biomage.Measurement.TimeUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

TimeUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.TimeUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

years

int years

months

int months

weeks

int weeks

days

int days

hours

int hours

minutes

int minutes

seconds

int seconds

us

int us

ms

int ms

other

int other

Class org.biomage.Measurement.Unit extends Extendable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

unitName

java.lang.String unitName
The name of the unit.

Class org.biomage.Measurement.VolumeUnit extends Unit implements Serializable

Serialized Fields

unitNameCV

VolumeUnit.UnitNameCV unitNameCV

Class org.biomage.Measurement.VolumeUnit.UnitNameCV extends java.lang.Object implements Serializable

Serialized Fields

value

int value

name

java.lang.String name

nameToValue

java.util.HashMap<K,V> nameToValue

valueToName

java.util.HashMap<K,V> valueToName

ml

int ml

cc

int cc

dl

int dl

L

int L

ul

int ul

nl

int nl

pl

int pl

fl

int fl

other

int other

Package org.biomage.Protocol

Class org.biomage.Protocol.Hardware extends Parameterizable implements Serializable

Serialized Fields

model

java.lang.String model
The model (number) of a piece of hardware.


make

java.lang.String make
The make of the Hardware (its manufacturer).


type

OntologyEntry type
The type of a piece of Hardware. Examples include: scanner, wash station...


softwares

java.util.List<E> softwares
Associates Hardware and Software together.


hardwareManufacturers

java.util.List<E> hardwareManufacturers
Contact for information on the Hardware.

Class org.biomage.Protocol.HardwareApplication extends ParameterizableApplication implements Serializable

Serialized Fields

serialNumber

java.lang.String serialNumber
Manufacturer's identifier for the Hardware.


hardware

Hardware hardware
The underlying hardware.

Class org.biomage.Protocol.Parameter extends Identifiable implements Serializable

Serialized Fields

defaultValue

Measurement defaultValue
Allows the optional specification of a default values and the unit for the Parameter


dataType

OntologyEntry dataType
The type of data generated by the parameter i.e. Boolean, float, etc...

Class org.biomage.Protocol.Parameterizable extends Identifiable implements Serializable

Serialized Fields

URI

java.lang.String URI
Where an instantiated Parameterizable is located.


parameterTypes

java.util.List<E> parameterTypes
The description of the parameters for the Parameterizable class instance.

Class org.biomage.Protocol.ParameterizableApplication extends Describable implements Serializable

Serialized Fields

parameterValues

java.util.List<E> parameterValues
The parameter values for this Parameterizable Application.

Class org.biomage.Protocol.ParameterValue extends Extendable implements Serializable

Serialized Fields

value

java.lang.Object value
The value of the parameter. Will have the datatype of its associated Parameter.


parameterType

Parameter parameterType
The parameter this value is for.

Class org.biomage.Protocol.Protocol extends Parameterizable implements Serializable

Serialized Fields

text

java.lang.String text
The text description of the Protocol.


title

java.lang.String title
The title of the Protocol


type

OntologyEntry type
The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc...


hardwares

java.util.List<E> hardwares
Hardware used by this protocol.


softwares

java.util.List<E> softwares
Software used by this Protocol.

Class org.biomage.Protocol.Protocol_package extends java.lang.Object implements Serializable

Serialized Fields

hardware_list

Protocol_package.Hardware_list hardware_list
Hardware represents the hardware used. Examples of Hardware include: computers, scanners, wash stations etc...


software_list

Protocol_package.Software_list software_list
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...


protocol_list

Protocol_package.Protocol_list protocol_list
A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.

Class org.biomage.Protocol.Protocol_package.Hardware_list extends java.util.Vector implements Serializable

Class org.biomage.Protocol.Protocol_package.Protocol_list extends java.util.Vector implements Serializable

Class org.biomage.Protocol.Protocol_package.Software_list extends java.util.Vector implements Serializable

Class org.biomage.Protocol.ProtocolApplication extends ParameterizableApplication implements Serializable

Serialized Fields

activityDate

java.util.Date activityDate
When the protocol was applied.


hardwareApplications

java.util.List<E> hardwareApplications
The use of hardware for the application of the protocol.


softwareApplications

java.util.List<E> softwareApplications
The use of software for the application of the protocol.


performers

java.util.List<E> performers
The people who performed the protocol.


protocol

Protocol protocol
The protocol that is being used.

Class org.biomage.Protocol.Software extends Parameterizable implements Serializable

Serialized Fields

type

OntologyEntry type
The type of a piece of Software. Examples include: feature extractor...


hardware

Hardware hardware
Associates Hardware and Software together.


softwares

java.util.List<E> softwares
Software packages this software uses, i.e. operating system, 3rd party software packages, etc.


softwareManufacturers

java.util.List<E> softwareManufacturers
Contact for information on the software.

Class org.biomage.Protocol.SoftwareApplication extends ParameterizableApplication implements Serializable

Serialized Fields

version

java.lang.String version
The version of the software.


releaseDate

java.util.Date releaseDate
When the software was released.


software

Software software
The underlying software.


Package org.biomage.QuantitationType

Class org.biomage.QuantitationType.ConfidenceIndicator extends StandardQuantitationType implements Serializable

Serialized Fields

targetQuantitationType

QuantitationType targetQuantitationType
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.

Class org.biomage.QuantitationType.DerivedSignal extends StandardQuantitationType implements Serializable

Class org.biomage.QuantitationType.Error extends ConfidenceIndicator implements Serializable

Class org.biomage.QuantitationType.ExpectedValue extends ConfidenceIndicator implements Serializable

Class org.biomage.QuantitationType.Failed extends StandardQuantitationType implements Serializable

Class org.biomage.QuantitationType.MeasuredSignal extends StandardQuantitationType implements Serializable

Class org.biomage.QuantitationType.PresentAbsent extends StandardQuantitationType implements Serializable

Class org.biomage.QuantitationType.PValue extends ConfidenceIndicator implements Serializable

Class org.biomage.QuantitationType.QuantitationType extends Identifiable implements Serializable

Serialized Fields

ojbConcreteClass

java.lang.String ojbConcreteClass

isBackground

java.lang.Boolean isBackground
Indicates whether the quantitation has been measured from the background or from the feature itself.


channel

Channel channel
The optional channel associated with the QuantitationType.


scale

OntologyEntry scale
Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}


dataType

OntologyEntry dataType
The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}


confidenceIndicators

java.util.List<E> confidenceIndicators
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.


quantitationTypeMaps

java.util.List<E> quantitationTypeMaps
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.

Class org.biomage.QuantitationType.QuantitationType_package extends java.lang.Object implements Serializable

Serialized Fields

quantitationType_list

QuantitationType_package.QuantitationType_list quantitationType_list
A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).

Class org.biomage.QuantitationType.QuantitationType_package.QuantitationType_list extends java.util.Vector implements Serializable

Class org.biomage.QuantitationType.Ratio extends StandardQuantitationType implements Serializable

Class org.biomage.QuantitationType.SpecializedQuantitationType extends QuantitationType implements Serializable

Class org.biomage.QuantitationType.StandardQuantitationType extends QuantitationType implements Serializable


Package org.biomage.tools.apps.annot

Class org.biomage.tools.apps.annot.MageXMLConverter extends javax.swing.JFrame implements Serializable

Serialized Fields

arrayPage

ArrayPage arrayPage

arrayBtn

javax.swing.JButton arrayBtn

goBtn

javax.swing.JButton goBtn

fileMenu

javax.swing.JMenu fileMenu

pageMenu

javax.swing.JMenu pageMenu

helpMenu

javax.swing.JMenu helpMenu

menuBar

javax.swing.JMenuBar menuBar

aboutMI

javax.swing.JMenuItem aboutMI

arrayMI

javax.swing.JMenuItem arrayMI

exitMI

javax.swing.JMenuItem exitMI

helpMI

javax.swing.JMenuItem helpMI

newMI

javax.swing.JMenuItem newMI

openMI

javax.swing.JMenuItem openMI

saveMI

javax.swing.JMenuItem saveMI

saveAsMI

javax.swing.JMenuItem saveAsMI

topPanel

javax.swing.JPanel topPanel

toolBarPanel

javax.swing.JPanel toolBarPanel

pageSP

javax.swing.JScrollPane pageSP

logSP

javax.swing.JScrollPane logSP

splitPane

javax.swing.JSplitPane splitPane

cmdToolBar

javax.swing.JToolBar cmdToolBar

pageToolBar

javax.swing.JToolBar pageToolBar

toolBarSeperator

javax.swing.JToolBar[] toolBarSeperator

NUM_SEPERATOR

int NUM_SEPERATOR

pageShowed

boolean pageShowed

sizeX

int sizeX

sizeY

int sizeY

Class org.biomage.tools.apps.annot.PagePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

resetBtn

javax.swing.JButton resetBtn

facePanel

javax.swing.JPanel facePanel

guiSet

GuiSet guiSet

Package org.biomage.tools.apps.annot.pages

Class org.biomage.tools.apps.annot.pages.ArrayPage extends PagePanel implements Serializable

Serialized Fields

blankLB

javax.swing.JLabel[] blankLB

urlLB

javax.swing.JLabel urlLB

addrLB

javax.swing.JLabel addrLB

spaceLB

javax.swing.JLabel spaceLB

zSpaceLB

javax.swing.JLabel zSpaceLB

xLB

javax.swing.JLabel xLB

yLB

javax.swing.JLabel yLB

zlRowLB

javax.swing.JLabel zlRowLB

zlColLB

javax.swing.JLabel zlColLB

zNumLB

javax.swing.JLabel zNumLB

zlNumLB

javax.swing.JLabel zlNumLB

arrayDesignPanel

javax.swing.JPanel arrayDesignPanel

manufacturerPanel

javax.swing.JPanel manufacturerPanel

zoneLayoutPanel

javax.swing.JPanel zoneLayoutPanel

zoneGroupPanel

javax.swing.JPanel zoneGroupPanel

urlTF

javax.swing.JTextField urlTF

addrTF

javax.swing.JTextField addrTF

zRowNumTF

javax.swing.JTextField zRowNumTF

zColNumTF

javax.swing.JTextField zColNumTF

zlRowNumTF

javax.swing.JTextField zlRowNumTF

zlColNumTF

javax.swing.JTextField zlColNumTF

rowSpaceTF

javax.swing.JTextField rowSpaceTF

colSpaceTF

javax.swing.JTextField colSpaceTF

zSpaceXTF

javax.swing.JTextField zSpaceXTF

zSpaceYTF

javax.swing.JTextField zSpaceYTF

guiSet

GuiSet guiSet

EMPTY_LABEL

int EMPTY_LABEL

validChecker

XMLConvertInputVerifier validChecker

Class org.biomage.tools.apps.annot.pages.Contact extends PagePanel implements Serializable

Serialized Fields

guiSet

GuiSet guiSet

contactPanel

javax.swing.JPanel contactPanel

personPanel

javax.swing.JPanel personPanel

orgPanel

javax.swing.JPanel orgPanel

contactTypeLB

javax.swing.JLabel contactTypeLB

nameLB

javax.swing.JLabel nameLB

urlLB

javax.swing.JLabel urlLB

addrLB

javax.swing.JLabel addrLB

phoneLB

javax.swing.JLabel phoneLB

tollFreePhoneLB

javax.swing.JLabel tollFreePhoneLB

emailLB

javax.swing.JLabel emailLB

faxLB

javax.swing.JLabel faxLB

firstNameLB

javax.swing.JLabel firstNameLB

lastNameLB

javax.swing.JLabel lastNameLB

midInitialsLB

javax.swing.JLabel midInitialsLB

affiliationLB

javax.swing.JLabel affiliationLB

organizationLB

javax.swing.JLabel organizationLB

nameLI

javax.swing.JList nameLI

urlTF

javax.swing.JTextField urlTF

addrTF

javax.swing.JTextField addrTF

phoneTF

javax.swing.JTextField phoneTF

tollFreePhoneTF

javax.swing.JTextField tollFreePhoneTF

emailTF

javax.swing.JTextField emailTF

faxTF

javax.swing.JTextField faxTF

firstNameTF

javax.swing.JTextField firstNameTF

lastNameTF

javax.swing.JTextField lastNameTF

midInitialsTF

javax.swing.JTextField midInitialsTF

affiliationTF

javax.swing.JTextField affiliationTF

organizationTF

javax.swing.JTextField organizationTF

Package org.biomage.tools.generate_classes

Class org.biomage.tools.generate_classes.XMIParseHelpers.IDREFException extends java.lang.Exception implements Serializable


Package org.biomage.tools.helpers

Class org.biomage.tools.helpers.MGEDOntologyClassEntry extends MGEDOntologyEntry implements Serializable

Serialized Fields

mgedOntologyClass

java.lang.String mgedOntologyClass

isInstantiable

boolean isInstantiable

MOEstack

java.util.ArrayList<E> MOEstack

Class org.biomage.tools.helpers.MGEDOntologyEntry extends OntologyEntry implements Serializable

Serialized Fields

isAssignable

boolean isAssignable

isAssigned

boolean isAssigned

assignableValues

java.util.ArrayList<E> assignableValues

Class org.biomage.tools.helpers.MGEDOntologyEntry.OntologyDatabaseEntry extends DatabaseEntry implements Serializable

Class org.biomage.tools.helpers.MGEDOntologyPropertyEntry extends MGEDOntologyEntry implements Serializable

Serialized Fields

mgedOntologyProperty

java.lang.String mgedOntologyProperty

propType

java.lang.String propType

Package org.biomage.tools.xmlutils

Class org.biomage.tools.xmlutils.MultiHashMap extends java.util.HashMap implements Serializable

Class org.biomage.tools.xmlutils.MultiHashtable extends java.util.Hashtable implements Serializable