Uses of Class
org.biomage.Description.OntologyEntry

Packages that use OntologyEntry
gov.nih.nci.caarray.services.arraydesign   
gov.nih.nci.caarray.services.biomaterial   
gov.nih.nci.caarray.services.experiment   
gov.nih.nci.caarray.services.mageloader   
gov.nih.nci.caarray.services.protocol   
gov.nih.nci.caarray.services.util   
gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers   
gov.nih.nci.caarray.services.util.dataconverter.test   
gov.nih.nci.caarray.services.vocab   
org.biomage.Array   
org.biomage.ArrayDesign   
org.biomage.AuditAndSecurity   
org.biomage.BioAssay   
org.biomage.BioMaterial   
org.biomage.BioSequence   
org.biomage.BQS   
org.biomage.Description   
org.biomage.Description.Ontology   
org.biomage.DesignElement   
org.biomage.Experiment   
org.biomage.HigherLevelAnalysis   
org.biomage.Interface   
org.biomage.Protocol   
org.biomage.QuantitationType   
org.biomage.tools.helpers   
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.arraydesign
 

Methods in gov.nih.nci.caarray.services.arraydesign that return OntologyEntry
 OntologyEntry DbArrayDesignDataSource.getOntologyEntry(java.lang.String category, java.lang.String value)
           
 OntologyEntry ArrayDesignDataSource.getOntologyEntry(java.lang.String category, java.lang.String value)
          Returns the entry corresponding to the data given or null if not found.
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.biomaterial
 

Methods in gov.nih.nci.caarray.services.biomaterial that return OntologyEntry
 OntologyEntry[] BioMaterialManagerDB.getCharacteristicsFromSourceBioSourcesOf(long bioMaterialId, java.lang.Class objectClass)
          Retrieves a list of distinct characteristics of the source BioSource's that are used to produce the specified product BioSample or LabeledExtract.
static OntologyEntry[] BioMaterialUtils.toOntologyEntries(VocabData[] characteristics)
           
 

Methods in gov.nih.nci.caarray.services.biomaterial with parameters of type OntologyEntry
static VocabData[] BioMaterialUtils.toVocabData(OntologyEntry[] characteristics)
           
 void BioMaterialManagerDB.updateBioMaterialCharacteristics(long bioMaterialId, java.lang.Class bioMaterialClass, OntologyEntry[] characteristics)
          Save the specified BioMaterial with the specified characteristics.
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.experiment
 

Methods in gov.nih.nci.caarray.services.experiment that return OntologyEntry
 OntologyEntry ExperimentManagerDB.getAdditionalQualifier(long id)
           
 

Methods in gov.nih.nci.caarray.services.experiment with parameters of type OntologyEntry
 long ExperimentManagerDB.addAdditionalQualifier(long experimentId, OntologyEntry qualifier)
           
static void ExperimentUtils.copy(AdditionalQualifierData source, OntologyEntry target)
           
static void ExperimentUtils.copy(OntologyEntry source, AdditionalQualifierData target)
           
 void ExperimentManagerDB.updateAdditionalQualifier(OntologyEntry qualifier)
           
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.mageloader
 

Methods in gov.nih.nci.caarray.services.mageloader that return OntologyEntry
 OntologyEntry MAGEMLImportManagerDB.matchOntologyEntry(OntologyEntry entry)
           
 

Methods in gov.nih.nci.caarray.services.mageloader with parameters of type OntologyEntry
 OntologyEntry MAGEMLImportManagerDB.matchOntologyEntry(OntologyEntry entry)
           
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.protocol
 

Methods in gov.nih.nci.caarray.services.protocol that return OntologyEntry
 OntologyEntry[] ProtocolManagerDB.getProtocolTypes()
          Get available protocol types.
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.util
 

Methods in gov.nih.nci.caarray.services.util that return OntologyEntry
static OntologyEntry DBUtils.matchOntologyEntry(OntologyEntry entry, org.apache.ojb.broker.PersistenceBroker broker)
           
 

Methods in gov.nih.nci.caarray.services.util with parameters of type OntologyEntry
static OntologyEntry DBUtils.matchOntologyEntry(OntologyEntry entry, org.apache.ojb.broker.PersistenceBroker broker)
           
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers
 

Methods in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers that return OntologyEntry
static OntologyEntry VocabDataFieldMapper.getOntologyEntry(java.lang.Object bean, java.lang.String fieldName, java.util.List annotations)
           
static OntologyEntry VocabDataFieldMapper.getOntologyEntryByCategory(java.lang.String category, java.util.List annotations)
          Get from the specified list of OntologyEntrys the element whose category matches the specified category.
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.util.dataconverter.test
 

Methods in gov.nih.nci.caarray.services.util.dataconverter.test with parameters of type OntologyEntry
static void TestExperimentConversion.compare(OntologyEntry entry, AdditionalQualifierData data)
           
static void TestVocabConversion.compare(OntologyEntry entry, VocabData vocabData)
           
 

Uses of OntologyEntry in gov.nih.nci.caarray.services.vocab
 

Methods in gov.nih.nci.caarray.services.vocab that return OntologyEntry
 OntologyEntry[] VocabManagerDB.getOntologies(long parentVocabId)
           
 OntologyEntry[] VocabManagerDB.getOntologies(VocabSearchCriteria criteria)
           
 OntologyEntry VocabManagerDB.getOntology(long id)
           
 OntologyEntry VocabManagerDB.getOntology(java.lang.String category, java.lang.String value)
           
 OntologyEntry VocabManagerDB.getOntologyEntryOrNull(java.lang.String category, java.lang.String value)
          Returns the requested OntologyEntry or null if not found.
 OntologyEntry[] VocabManagerDB.getProtocolTypes(long actionId)
          Retrieves the list of protocol types that are mapped to the specified action.
static OntologyEntry[] VocabUtils.getVisibleEntries(javax.ejb.SessionContext ctx, OntologyEntry[] entries)
           
 

Methods in gov.nih.nci.caarray.services.vocab with parameters of type OntologyEntry
 long VocabManagerDB.addOntology(OntologyEntry entry)
           
 long VocabManagerDB.addOntology(OntologyEntry entry, long parentOntologyEntryId)
           
static void VocabUtils.copy(OntologyEntry entry, VocabData vocab)
           
static void VocabUtils.copy(OntologyEntry entry, VocabDesc vocabDesc)
           
static void VocabUtils.copy(VocabData vocab, OntologyEntry entry)
           
static OntologyEntry[] VocabUtils.getVisibleEntries(javax.ejb.SessionContext ctx, OntologyEntry[] entries)
           
 void VocabManagerDB.updateOntology(OntologyEntry entry)
           
 

Uses of OntologyEntry in org.biomage.Array
 

Fields in org.biomage.Array declared as OntologyEntry
protected  OntologyEntry ZoneDefect.defectType
          Indicates the type of defect (e.g.
protected  OntologyEntry FeatureDefect.defectType
          Indicates the type of defect (e.g.
protected  OntologyEntry Fiducial.fiducialType
          A descriptive string that indicates the type of a fiducial (e.g.
protected  OntologyEntry ArrayGroup.substrateType
          Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.
 

Methods in org.biomage.Array that return OntologyEntry
 OntologyEntry ZoneDefect.getDefectType()
          Get method for defectType
 OntologyEntry FeatureDefect.getDefectType()
          Get method for defectType
 OntologyEntry Fiducial.getFiducialType()
          Get method for fiducialType
 OntologyEntry ArrayGroup.getSubstrateType()
          Get method for substrateType
 

Methods in org.biomage.Array with parameters of type OntologyEntry
 void ZoneDefect.setDefectType(OntologyEntry defectType)
          Set method for defectType
 void FeatureDefect.setDefectType(OntologyEntry defectType)
          Set method for defectType
 void Fiducial.setFiducialType(OntologyEntry fiducialType)
          Set method for fiducialType
 void ArrayGroup.setSubstrateType(OntologyEntry substrateType)
          Set method for substrateType
 

Uses of OntologyEntry in org.biomage.ArrayDesign
 

Fields in org.biomage.ArrayDesign declared as OntologyEntry
protected  OntologyEntry FeatureGroup.featureShape
          The expected shape of the feature on the array: circular, oval, square, etc.
protected  OntologyEntry DesignElementGroup.species
          The organism from which the biosequences of this group are from.
protected  OntologyEntry PhysicalArrayDesign.surfaceType
          The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
protected  OntologyEntry FeatureGroup.technologyType
          The technology type of this design.
 

Methods in org.biomage.ArrayDesign that return OntologyEntry
 OntologyEntry FeatureGroup.getFeatureShape()
          Get method for featureShape
 OntologyEntry DesignElementGroup.getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 OntologyEntry DesignProviderRole.getRole()
           
 OntologyEntry DesignElementGroup.getSpecies()
          Get method for species
 OntologyEntry PhysicalArrayDesign.getSurfaceType()
          Get method for surfaceType
 OntologyEntry FeatureGroup.getTechnologyType()
          Get method for technologyType
 

Methods in org.biomage.ArrayDesign with parameters of type OntologyEntry
 void DesignElementGroup.addToTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void DesignElementGroup.addToTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 void DesignElementGroup.removeFromTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void FeatureGroup.setFeatureShape(OntologyEntry featureShape)
          Set method for featureShape
 void DesignProviderRole.setRole(OntologyEntry entry)
           
 void DesignElementGroup.setSpecies(OntologyEntry species)
          Set method for species
 void PhysicalArrayDesign.setSurfaceType(OntologyEntry surfaceType)
          Set method for surfaceType
 void FeatureGroup.setTechnologyType(OntologyEntry technologyType)
          Set method for technologyType
 

Uses of OntologyEntry in org.biomage.AuditAndSecurity
 

Methods in org.biomage.AuditAndSecurity that return OntologyEntry
 OntologyEntry Contact.getFromRoles(int position)
          Method to get OntologyEntry from Roles_list
 

Methods in org.biomage.AuditAndSecurity with parameters of type OntologyEntry
 void Contact.addToRoles(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Roles_list
 void Contact.addToRoles(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Roles_list
 void Contact.removeFromRoles(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Roles_list
 

Uses of OntologyEntry in org.biomage.BioAssay
 

Fields in org.biomage.BioAssay declared as OntologyEntry
protected  OntologyEntry Image.format
          The file format of the image typically a TIF or a JPEG.
protected  OntologyEntry DerivedBioAssay.type
          The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
 

Methods in org.biomage.BioAssay that return OntologyEntry
 OntologyEntry Image.getFormat()
          Get method for format
 OntologyEntry DerivedBioAssay.getType()
          Get method for type
 

Methods in org.biomage.BioAssay with parameters of type OntologyEntry
 void Image.setFormat(OntologyEntry format)
          Set method for format
 void DerivedBioAssay.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.BioMaterial
 

Fields in org.biomage.BioMaterial declared as OntologyEntry
protected  OntologyEntry Treatment.action
          The event that occurred (e.g.
protected  OntologyEntry BioMaterial.materialType
          The type of material used, i.e.
protected  OntologyEntry BioSample.type
          The Type attribute describes the role the BioSample holds in the treatment hierarchy.
 

Methods in org.biomage.BioMaterial that return OntologyEntry
 OntologyEntry Treatment.getAction()
          Get method for action
 OntologyEntry ActionProtocolTypeMap.getAction()
           
 OntologyEntry BioMaterial.getFromCharacteristics(int position)
          Method to get OntologyEntry from Characteristics_list
 OntologyEntry Compound.getFromCompoundIndices(int position)
          Method to get OntologyEntry from CompoundIndices_list
 OntologyEntry BioMaterial.getMaterialType()
          Get method for materialType
 OntologyEntry BioSample.getType()
          Get method for type
 

Methods in org.biomage.BioMaterial with parameters of type OntologyEntry
 void BioMaterial.addToCharacteristics(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Characteristics_list
 void BioMaterial.addToCharacteristics(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Characteristics_list
 void Compound.addToCompoundIndices(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to CompoundIndices_list
 void Compound.addToCompoundIndices(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to CompoundIndices_list
 void BioMaterial.removeFromCharacteristics(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Characteristics_list
 void Compound.removeFromCompoundIndices(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from CompoundIndices_list
 void Treatment.setAction(OntologyEntry action)
          Set method for action
 void ActionProtocolTypeMap.setAction(OntologyEntry entry)
           
 void BioMaterial.setMaterialType(OntologyEntry materialType)
          Set method for materialType
 void BioSample.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.BioSequence
 

Fields in org.biomage.BioSequence declared as OntologyEntry
protected  OntologyEntry BioSequence.polymerType
          A choice of protein, RNA, or DNA.
protected  OntologyEntry BioSequence.species
          The organism from which this sequence was obtained.
protected  OntologyEntry BioSequence.type
          The type of biosequence, i.e.
 

Methods in org.biomage.BioSequence that return OntologyEntry
 OntologyEntry BioSequence.getFromOntologyEntries(int position)
          Method to get OntologyEntry from OntologyEntries_list
 OntologyEntry BioSequence.getPolymerType()
          Get method for polymerType
 OntologyEntry BioSequence.getSpecies()
          Get method for species
 OntologyEntry BioSequence.getType()
          Get method for type
 

Methods in org.biomage.BioSequence with parameters of type OntologyEntry
 void BioSequence.addToOntologyEntries(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to OntologyEntries_list
 void BioSequence.addToOntologyEntries(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to OntologyEntries_list
 void BioSequence.removeFromOntologyEntries(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from OntologyEntries_list
 void BioSequence.setPolymerType(OntologyEntry polymerType)
          Set method for polymerType
 void BioSequence.setSpecies(OntologyEntry species)
          Set method for species
 void BioSequence.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.BQS
 

Methods in org.biomage.BQS that return OntologyEntry
 OntologyEntry BibliographicReference.getFromParameters(int position)
          Method to get OntologyEntry from Parameters_list
 

Methods in org.biomage.BQS with parameters of type OntologyEntry
 void BibliographicReference.addToParameters(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Parameters_list
 void BibliographicReference.addToParameters(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Parameters_list
 void BibliographicReference.removeFromParameters(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Parameters_list
 

Uses of OntologyEntry in org.biomage.Description
 

Fields in org.biomage.Description declared as OntologyEntry
protected  OntologyEntry DatabaseEntry.type
          The type of record (e.g.
 

Methods in org.biomage.Description that return OntologyEntry
 OntologyEntry Description.getFromAnnotations(int position)
          Method to get OntologyEntry from Annotations_list
 OntologyEntry OntologyEntry.getFromAssociations(int position)
          Method to get OntologyEntry from Associations_list
 OntologyEntry DatabaseEntry.getType()
          Get method for type
 

Methods in org.biomage.Description with parameters of type OntologyEntry
 void Description.addToAnnotations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Annotations_list
 void Description.addToAnnotations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Annotations_list
 void OntologyEntry.addToAssociations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Associations_list
 void OntologyEntry.addToAssociations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Associations_list
 void Description.removeFromAnnotations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Annotations_list
 void OntologyEntry.removeFromAssociations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Associations_list
 void DatabaseEntry.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.Description.Ontology
 

Subclasses of OntologyEntry in org.biomage.Description.Ontology
 class Age
           
 class Biometrics
           
 class ChromosomalAberration
           
 

Methods in org.biomage.Description.Ontology that return OntologyEntry
protected static OntologyEntry BioMaterialCharacteristic.createMGEDMeasurementRestriction(java.lang.String restriction, OntologyEntry value, OntologyEntry unit)
           
 OntologyEntry Age.getAgeValue()
           
abstract  OntologyEntry BioMaterialCharacteristic.getFromAssociations(int position)
          Method to get OntologyEntry from Associations_list
 OntologyEntry Biometrics.getHeight()
           
 OntologyEntry Biometrics.getHeightMeasurement()
           
 OntologyEntry Age.getInitialTimePoint()
           
 OntologyEntry Age.getMaxMeasurement()
           
 OntologyEntry Age.getMaxValue()
           
 OntologyEntry Age.getMeasurement()
           
 OntologyEntry Age.getMinMeasurement()
           
 OntologyEntry Age.getMinValue()
           
 OntologyEntry Biometrics.getWeight()
           
 OntologyEntry Biometrics.getWeightMeasurement()
           
 

Methods in org.biomage.Description.Ontology with parameters of type OntologyEntry
abstract  void BioMaterialCharacteristic.addToAssociations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Associations_list
abstract  void BioMaterialCharacteristic.addToAssociations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Associations_list
 void ChromosomalAberration.addToTypes(OntologyEntry type)
           
protected static OntologyEntry BioMaterialCharacteristic.createMGEDMeasurementRestriction(java.lang.String restriction, OntologyEntry value, OntologyEntry unit)
           
abstract  void BioMaterialCharacteristic.removeFromAssociations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Associations_list
 void ChromosomalAberration.removeFromTypes(OntologyEntry type)
           
 void Age.setAgeValue(OntologyEntry entry)
           
 void Biometrics.setHeight(OntologyEntry entry)
           
 void Biometrics.setHeightMeasurement(OntologyEntry entry)
           
 void Age.setInitialTimePoint(OntologyEntry entry)
           
 void Age.setMaxMeasurement(OntologyEntry entry)
           
 void Age.setMaxValue(OntologyEntry entry)
           
 void Age.setMeasurement(OntologyEntry entry)
           
 void Age.setMinMeasurement(OntologyEntry entry)
           
 void Age.setMinValue(OntologyEntry entry)
           
 void Biometrics.setWeight(OntologyEntry entry)
           
 void Biometrics.setWeightMeasurement(OntologyEntry entry)
           
 

Uses of OntologyEntry in org.biomage.DesignElement
 

Fields in org.biomage.DesignElement declared as OntologyEntry
protected  OntologyEntry DesignElement.controlType
          If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
protected  OntologyEntry Reporter.warningType
          Similar to failType but indicates a warning rather than a failure.
 

Methods in org.biomage.DesignElement that return OntologyEntry
 OntologyEntry DesignElement.getControlType()
          Get method for controlType
 OntologyEntry Reporter.getFromFailTypes(int position)
          Method to get OntologyEntry from FailTypes_list
 OntologyEntry Reporter.getWarningType()
          Get method for warningType
 

Methods in org.biomage.DesignElement with parameters of type OntologyEntry
 void Reporter.addToFailTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to FailTypes_list
 void Reporter.addToFailTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to FailTypes_list
 void Reporter.removeFromFailTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from FailTypes_list
 void DesignElement.setControlType(OntologyEntry controlType)
          Set method for controlType
 void Reporter.setWarningType(OntologyEntry warningType)
          Set method for warningType
 

Uses of OntologyEntry in org.biomage.Experiment
 

Fields in org.biomage.Experiment declared as OntologyEntry
protected  OntologyEntry ExperimentalFactor.category
          The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols).
protected  OntologyEntry FactorValue.value
          Allows a more complex value to be specified for a FactorValue than a simple Measurement.
 

Methods in org.biomage.Experiment that return OntologyEntry
 OntologyEntry ExperimentalFactor.getCategory()
          Get method for category
 OntologyEntry ExperimentalFactor.getFromAnnotations(int position)
          Method to get OntologyEntry from Annotations_list
 OntologyEntry ExperimentDesign.getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 OntologyEntry ExperimentProviderRole.getRole()
           
 OntologyEntry FactorValue.getValue()
          Get method for value
 

Methods in org.biomage.Experiment with parameters of type OntologyEntry
 void ExperimentalFactor.addToAnnotations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Annotations_list
 void ExperimentalFactor.addToAnnotations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Annotations_list
 void ExperimentDesign.addToTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void ExperimentDesign.addToTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 void ExperimentalFactor.removeFromAnnotations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Annotations_list
 void ExperimentDesign.removeFromTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void ExperimentalFactor.setCategory(OntologyEntry category)
          Set method for category
 void ExperimentProviderRole.setRole(OntologyEntry entry)
           
 void FactorValue.setValue(OntologyEntry value)
          Set method for value
 

Uses of OntologyEntry in org.biomage.HigherLevelAnalysis
 

Fields in org.biomage.HigherLevelAnalysis declared as OntologyEntry
protected  OntologyEntry NodeValue.dataType
          The data type of the any element.
protected  OntologyEntry NodeValue.scale
          The scale (linear, log10, ln, etc.) of the value.
protected  OntologyEntry NodeValue.type
          The type of value, distance, etc.
 

Methods in org.biomage.HigherLevelAnalysis that return OntologyEntry
 OntologyEntry NodeValue.getDataType()
          Get method for dataType
 OntologyEntry NodeValue.getScale()
          Get method for scale
 OntologyEntry NodeValue.getType()
          Get method for type
 

Methods in org.biomage.HigherLevelAnalysis with parameters of type OntologyEntry
 void NodeValue.setDataType(OntologyEntry dataType)
          Set method for dataType
 void NodeValue.setScale(OntologyEntry scale)
          Set method for scale
 void NodeValue.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.Interface
 

Methods in org.biomage.Interface that return OntologyEntry
 OntologyEntry HasAction.getAction()
          Get method for action
 OntologyEntry HasCategory.getCategory()
          Get method for category
 OntologyEntry HasControlType.getControlType()
          Get method for controlType
 OntologyEntry HasDataType.getDataType()
          Get method for dataType
 OntologyEntry HasDefectType.getDefectType()
          Get method for defectType
 OntologyEntry HasFeatureShape.getFeatureShape()
          Get method for featureShape
 OntologyEntry HasFiducialType.getFiducialType()
          Get method for fiducialType
 OntologyEntry HasFormat.getFormat()
          Get method for format
 OntologyEntry HasAnnotations.getFromAnnotations(int position)
          Method to get OntologyEntry from Annotations_list
 OntologyEntry HasAssociations.getFromAssociations(int position)
          Method to get OntologyEntry from Associations_list
 OntologyEntry HasCharacteristics.getFromCharacteristics(int position)
          Method to get OntologyEntry from Characteristics_list
 OntologyEntry HasCompoundIndices.getFromCompoundIndices(int position)
          Method to get OntologyEntry from CompoundIndices_list
 OntologyEntry HasFailTypes.getFromFailTypes(int position)
          Method to get OntologyEntry from FailTypes_list
 OntologyEntry HasOntologyEntries.getFromOntologyEntries(int position)
          Method to get OntologyEntry from OntologyEntries_list
 OntologyEntry HasParameters.getFromParameters(int position)
          Method to get OntologyEntry from Parameters_list
 OntologyEntry HasRoles.getFromRoles(int position)
          Method to get OntologyEntry from Roles_list
 OntologyEntry HasTypes.getFromTypes(int position)
          Method to get OntologyEntry from Types_list
 OntologyEntry HasMaterialType.getMaterialType()
          Get method for materialType
 OntologyEntry HasPolymerType.getPolymerType()
          Get method for polymerType
 OntologyEntry HasScale.getScale()
          Get method for scale
 OntologyEntry HasSpecies.getSpecies()
          Get method for species
 OntologyEntry HasSubstrateType.getSubstrateType()
          Get method for substrateType
 OntologyEntry HasSurfaceType.getSurfaceType()
          Get method for surfaceType
 OntologyEntry HasTechnologyType.getTechnologyType()
          Get method for technologyType
 OntologyEntry HasType.getType()
          Get method for type
 OntologyEntry HasValue.getValue()
          Get method for value
 OntologyEntry HasWarningType.getWarningType()
          Get method for warningType
 

Methods in org.biomage.Interface with parameters of type OntologyEntry
 void HasAnnotations.addToAnnotations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Annotations_list
 void HasAnnotations.addToAnnotations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Annotations_list
 void HasAssociations.addToAssociations(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Associations_list
 void HasAssociations.addToAssociations(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Associations_list
 void HasCharacteristics.addToCharacteristics(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Characteristics_list
 void HasCharacteristics.addToCharacteristics(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Characteristics_list
 void HasCompoundIndices.addToCompoundIndices(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to CompoundIndices_list
 void HasCompoundIndices.addToCompoundIndices(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to CompoundIndices_list
 void HasFailTypes.addToFailTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to FailTypes_list
 void HasFailTypes.addToFailTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to FailTypes_list
 void HasOntologyEntries.addToOntologyEntries(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to OntologyEntries_list
 void HasOntologyEntries.addToOntologyEntries(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to OntologyEntries_list
 void HasParameters.addToParameters(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Parameters_list
 void HasParameters.addToParameters(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Parameters_list
 void HasRoles.addToRoles(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Roles_list
 void HasRoles.addToRoles(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Roles_list
 void HasTypes.addToTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to Types_list
 void HasTypes.addToTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to Types_list
 void HasAnnotations.removeFromAnnotations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Annotations_list
 void HasAssociations.removeFromAssociations(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Associations_list
 void HasCharacteristics.removeFromCharacteristics(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Characteristics_list
 void HasCompoundIndices.removeFromCompoundIndices(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from CompoundIndices_list
 void HasFailTypes.removeFromFailTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from FailTypes_list
 void HasOntologyEntries.removeFromOntologyEntries(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from OntologyEntries_list
 void HasParameters.removeFromParameters(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Parameters_list
 void HasRoles.removeFromRoles(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Roles_list
 void HasTypes.removeFromTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from Types_list
 void HasAction.setAction(OntologyEntry action)
          Set method for action
 void HasCategory.setCategory(OntologyEntry category)
          Set method for category
 void HasControlType.setControlType(OntologyEntry controlType)
          Set method for controlType
 void HasDataType.setDataType(OntologyEntry dataType)
          Set method for dataType
 void HasDefectType.setDefectType(OntologyEntry defectType)
          Set method for defectType
 void HasFeatureShape.setFeatureShape(OntologyEntry featureShape)
          Set method for featureShape
 void HasFiducialType.setFiducialType(OntologyEntry fiducialType)
          Set method for fiducialType
 void HasFormat.setFormat(OntologyEntry format)
          Set method for format
 void HasMaterialType.setMaterialType(OntologyEntry materialType)
          Set method for materialType
 void HasPolymerType.setPolymerType(OntologyEntry polymerType)
          Set method for polymerType
 void HasScale.setScale(OntologyEntry scale)
          Set method for scale
 void HasSpecies.setSpecies(OntologyEntry species)
          Set method for species
 void HasSubstrateType.setSubstrateType(OntologyEntry substrateType)
          Set method for substrateType
 void HasSurfaceType.setSurfaceType(OntologyEntry surfaceType)
          Set method for surfaceType
 void HasTechnologyType.setTechnologyType(OntologyEntry technologyType)
          Set method for technologyType
 void HasType.setType(OntologyEntry type)
          Set method for type
 void HasValue.setValue(OntologyEntry value)
          Set method for value
 void HasWarningType.setWarningType(OntologyEntry warningType)
          Set method for warningType
 

Uses of OntologyEntry in org.biomage.Protocol
 

Fields in org.biomage.Protocol declared as OntologyEntry
protected  OntologyEntry Parameter.dataType
          The type of data generated by the parameter i.e.
protected  OntologyEntry Software.type
          The type of a piece of Software.
protected  OntologyEntry Protocol.type
          The type of a Protocol, a user should provide/use a recommended vocabulary.
protected  OntologyEntry Hardware.type
          The type of a piece of Hardware.
 

Methods in org.biomage.Protocol that return OntologyEntry
 OntologyEntry Parameter.getDataType()
          Get method for dataType
 OntologyEntry Software.getType()
          Get method for type
 OntologyEntry Protocol.getType()
          Get method for type
 OntologyEntry Hardware.getType()
          Get method for type
 

Methods in org.biomage.Protocol with parameters of type OntologyEntry
 void Parameter.setDataType(OntologyEntry dataType)
          Set method for dataType
 void Software.setType(OntologyEntry type)
          Set method for type
 void Protocol.setType(OntologyEntry type)
          Set method for type
 void Hardware.setType(OntologyEntry type)
          Set method for type
 

Uses of OntologyEntry in org.biomage.QuantitationType
 

Fields in org.biomage.QuantitationType declared as OntologyEntry
protected  OntologyEntry QuantitationType.dataType
          The specific type for the quantitations.
protected  OntologyEntry QuantitationType.scale
          Indication of how to interpret the value.
 

Methods in org.biomage.QuantitationType that return OntologyEntry
 OntologyEntry QuantitationType.getDataType()
          Get method for dataType
 OntologyEntry QuantitationType.getScale()
          Get method for scale
 

Methods in org.biomage.QuantitationType with parameters of type OntologyEntry
 void QuantitationType.setDataType(OntologyEntry dataType)
          Set method for dataType
 void QuantitationType.setScale(OntologyEntry scale)
          Set method for scale
 

Uses of OntologyEntry in org.biomage.tools.helpers
 

Subclasses of OntologyEntry in org.biomage.tools.helpers
 class MGEDOntologyClassEntry
           
 class MGEDOntologyEntry
           
 class MGEDOntologyPropertyEntry