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

A

ABSOLUTE - Variable in class org.biomage.Measurement.Measurement.Type

ABSTRACT - Static variable in class org.biomage.tools.generate_er.CreateMageER

the object (table) is abstract

action - Variable in class org.biomage.BioMaterial.Treatment

The event that occurred (e.g.

actionMeasurement - Variable in class org.biomage.BioMaterial.Treatment

Measures events like duration, centrifuge speed, etc.

addToAdjustments(int, ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation

Method to add ZoneDefect at position to Adjustments_list

addToAdjustments(int, ZoneDefect) - Method in interface org.biomage.Interface.HasAdjustments

Method to add ZoneDefect at position to Adjustments_list

addToAdjustments(ZoneDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation

Method to add ZoneDefect to Adjustments_list

addToAdjustments(ZoneDefect) - Method in interface org.biomage.Interface.HasAdjustments

Method to add ZoneDefect to Adjustments_list

addToAnalysisResults(BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssayDataCluster to AnalysisResults_list

addToAnalysisResults(BioAssayDataCluster) - Method in interface org.biomage.Interface.HasAnalysisResults

Method to add BioAssayDataCluster to AnalysisResults_list

addToAnalysisResults(int, BioAssayDataCluster) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssayDataCluster at position to AnalysisResults_list

addToAnalysisResults(int, BioAssayDataCluster) - Method in interface org.biomage.Interface.HasAnalysisResults

Method to add BioAssayDataCluster at position to AnalysisResults_list

addToAnnotations(int, OntologyEntry) - Method in class org.biomage.Description.Description

Method to add OntologyEntry at position to Annotations_list

addToAnnotations(int, OntologyEntry) - Method in interface org.biomage.Interface.HasAnnotations

Method to add OntologyEntry at position to Annotations_list

addToAnnotations(OntologyEntry) - Method in class org.biomage.Description.Description

Method to add OntologyEntry to Annotations_list

addToAnnotations(OntologyEntry) - Method in interface org.biomage.Interface.HasAnnotations

Method to add OntologyEntry to Annotations_list

addToArray_list(Array) - Method in class org.biomage.Array.Array_package

Method to add Array to Array_list

addToArray_list(int, Array) - Method in class org.biomage.Array.Array_package

Method to add Array at position to Array_list

addToArrayDesign_list(ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add ArrayDesign to ArrayDesign_list

addToArrayDesign_list(int, ArrayDesign) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add ArrayDesign at position to ArrayDesign_list

addToArrayGroup_list(ArrayGroup) - Method in class org.biomage.Array.Array_package

Method to add ArrayGroup to ArrayGroup_list

addToArrayGroup_list(int, ArrayGroup) - Method in class org.biomage.Array.Array_package

Method to add ArrayGroup at position to ArrayGroup_list

addToArrayManufacture_list(ArrayManufacture) - Method in class org.biomage.Array.Array_package

Method to add ArrayManufacture to ArrayManufacture_list

addToArrayManufacture_list(int, ArrayManufacture) - Method in class org.biomage.Array.Array_package

Method to add ArrayManufacture at position to ArrayManufacture_list

addToArrayManufactureDeviations(ArrayManufactureDeviation) - Method in class org.biomage.Array.Array

Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list

addToArrayManufactureDeviations(ArrayManufactureDeviation) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations

Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list

addToArrayManufactureDeviations(int, ArrayManufactureDeviation) - Method in class org.biomage.Array.Array

Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list

addToArrayManufactureDeviations(int, ArrayManufactureDeviation) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations

Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list

addToArrayManufacturers(Contact) - Method in class org.biomage.Array.ArrayManufacture

Method to add Contact to ArrayManufacturers_list

addToArrayManufacturers(Contact) - Method in interface org.biomage.Interface.HasArrayManufacturers

Method to add Contact to ArrayManufacturers_list

addToArrayManufacturers(int, Contact) - Method in class org.biomage.Array.ArrayManufacture

Method to add Contact at position to ArrayManufacturers_list

addToArrayManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasArrayManufacturers

Method to add Contact at position to ArrayManufacturers_list

addToArrays(Array) - Method in class org.biomage.Array.ArrayManufacture

Method to add Array to Arrays_list

addToArrays(Array) - Method in class org.biomage.Array.ArrayGroup

Method to add Array to Arrays_list

addToArrays(Array) - Method in interface org.biomage.Interface.HasArrays

Method to add Array to Arrays_list

addToArrays(int, Array) - Method in class org.biomage.Array.ArrayManufacture

Method to add Array at position to Arrays_list

addToArrays(int, Array) - Method in class org.biomage.Array.ArrayGroup

Method to add Array at position to Arrays_list

addToArrays(int, Array) - Method in interface org.biomage.Interface.HasArrays

Method to add Array at position to Arrays_list

addToAuditTrail(Audit) - Method in class org.biomage.Common.Describable

Method to add Audit to AuditTrail_list

addToAuditTrail(Audit) - Method in interface org.biomage.Interface.HasAuditTrail

Method to add Audit to AuditTrail_list

addToAuditTrail(int, Audit) - Method in class org.biomage.Common.Describable

Method to add Audit at position to AuditTrail_list

addToAuditTrail(int, Audit) - Method in interface org.biomage.Interface.HasAuditTrail

Method to add Audit at position to AuditTrail_list

addToBibliographicReferences(BibliographicReference) - Method in class org.biomage.Description.Description

Method to add BibliographicReference to BibliographicReferences_list

addToBibliographicReferences(BibliographicReference) - Method in interface org.biomage.Interface.HasBibliographicReferences

Method to add BibliographicReference to BibliographicReferences_list

addToBibliographicReferences(int, BibliographicReference) - Method in class org.biomage.Description.Description

Method to add BibliographicReference at position to BibliographicReferences_list

addToBibliographicReferences(int, BibliographicReference) - Method in interface org.biomage.Interface.HasBibliographicReferences

Method to add BibliographicReference at position to BibliographicReferences_list

addToBioAssay_list(BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package

Method to add BioAssay to BioAssay_list

addToBioAssay_list(int, BioAssay) - Method in class org.biomage.BioAssay.BioAssay_package

Method to add BioAssay at position to BioAssay_list

addToBioAssayData_list(BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayData to BioAssayData_list

addToBioAssayData_list(int, BioAssayData) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayData at position to BioAssayData_list

addToBioAssayData(BioAssayData) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssayData to BioAssayData_list

addToBioAssayData(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayData

Method to add BioAssayData to BioAssayData_list

addToBioAssayData(int, BioAssayData) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssayData at position to BioAssayData_list

addToBioAssayData(int, BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayData

Method to add BioAssayData at position to BioAssayData_list

addToBioAssayDataCluster_list(BioAssayDataCluster) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package

Method to add BioAssayDataCluster to BioAssayDataCluster_list

addToBioAssayDataCluster_list(int, BioAssayDataCluster) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package

Method to add BioAssayDataCluster at position to BioAssayDataCluster_list

addToBioAssayDataSources(BioAssayData) - Method in class org.biomage.BioAssayData.Transformation

Method to add BioAssayData to BioAssayDataSources_list

addToBioAssayDataSources(BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayDataSources

Method to add BioAssayData to BioAssayDataSources_list

addToBioAssayDataSources(int, BioAssayData) - Method in class org.biomage.BioAssayData.Transformation

Method to add BioAssayData at position to BioAssayDataSources_list

addToBioAssayDataSources(int, BioAssayData) - Method in interface org.biomage.Interface.HasBioAssayDataSources

Method to add BioAssayData at position to BioAssayDataSources_list

addToBioAssayDimension_list(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayDimension to BioAssayDimension_list

addToBioAssayDimension_list(int, BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayDimension at position to BioAssayDimension_list

addToBioAssayFactorValues(FactorValue) - Method in class org.biomage.BioAssay.BioAssay

Method to add FactorValue to BioAssayFactorValues_list

addToBioAssayFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasBioAssayFactorValues

Method to add FactorValue to BioAssayFactorValues_list

addToBioAssayFactorValues(int, FactorValue) - Method in class org.biomage.BioAssay.BioAssay

Method to add FactorValue at position to BioAssayFactorValues_list

addToBioAssayFactorValues(int, FactorValue) - Method in interface org.biomage.Interface.HasBioAssayFactorValues

Method to add FactorValue at position to BioAssayFactorValues_list

addToBioAssayMap_list(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayMap to BioAssayMap_list

addToBioAssayMap_list(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add BioAssayMap at position to BioAssayMap_list

addToBioAssayMaps(BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping

Method to add BioAssayMap to BioAssayMaps_list

addToBioAssayMaps(BioAssayMap) - Method in interface org.biomage.Interface.HasBioAssayMaps

Method to add BioAssayMap to BioAssayMaps_list

addToBioAssayMaps(int, BioAssayMap) - Method in class org.biomage.BioAssayData.BioAssayMapping

Method to add BioAssayMap at position to BioAssayMaps_list

addToBioAssayMaps(int, BioAssayMap) - Method in interface org.biomage.Interface.HasBioAssayMaps

Method to add BioAssayMap at position to BioAssayMaps_list

addToBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension

Method to add BioAssay to BioAssays_list

addToBioAssays(BioAssay) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssay to BioAssays_list

addToBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasBioAssays

Method to add BioAssay to BioAssays_list

addToBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDimension

Method to add BioAssay at position to BioAssays_list

addToBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.Experiment

Method to add BioAssay at position to BioAssays_list

addToBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasBioAssays

Method to add BioAssay at position to BioAssays_list

addToBioAssayTreatments(BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Method to add BioAssayTreatment to BioAssayTreatments_list

addToBioAssayTreatments(BioAssayTreatment) - Method in interface org.biomage.Interface.HasBioAssayTreatments

Method to add BioAssayTreatment to BioAssayTreatments_list

addToBioAssayTreatments(int, BioAssayTreatment) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Method to add BioAssayTreatment at position to BioAssayTreatments_list

addToBioAssayTreatments(int, BioAssayTreatment) - Method in interface org.biomage.Interface.HasBioAssayTreatments

Method to add BioAssayTreatment at position to BioAssayTreatments_list

addToBioAssayTupleData(BioAssayDatum) - Method in class org.biomage.BioAssayData.BioDataTuples

Method to add BioAssayDatum to BioAssayTupleData_list

addToBioAssayTupleData(BioAssayDatum) - Method in interface org.biomage.Interface.HasBioAssayTupleData

Method to add BioAssayDatum to BioAssayTupleData_list

addToBioAssayTupleData(int, BioAssayDatum) - Method in class org.biomage.BioAssayData.BioDataTuples

Method to add BioAssayDatum at position to BioAssayTupleData_list

addToBioAssayTupleData(int, BioAssayDatum) - Method in interface org.biomage.Interface.HasBioAssayTupleData

Method to add BioAssayDatum at position to BioAssayTupleData_list

addToBiologicalCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add BioSequence to BiologicalCharacteristics_list

addToBiologicalCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics

Method to add BioSequence to BiologicalCharacteristics_list

addToBiologicalCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add BioSequence at position to BiologicalCharacteristics_list

addToBiologicalCharacteristics(int, BioSequence) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics

Method to add BioSequence at position to BiologicalCharacteristics_list

addToBioMaterial_list(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial_package

Method to add BioMaterial to BioMaterial_list

addToBioMaterial_list(int, BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterial_package

Method to add BioMaterial at position to BioMaterial_list

addToBioSequence_list(BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package

Method to add BioSequence to BioSequence_list

addToBioSequence_list(int, BioSequence) - Method in class org.biomage.BioSequence.BioSequence_package

Method to add BioSequence at position to BioSequence_list

addToChannel_list(Channel) - Method in class org.biomage.BioAssay.BioAssay_package

Method to add Channel to Channel_list

addToChannel_list(int, Channel) - Method in class org.biomage.BioAssay.BioAssay_package

Method to add Channel at position to Channel_list

addToChannels(Channel) - Method in class org.biomage.BioAssay.Image

Method to add Channel to Channels_list

addToChannels(Channel) - Method in class org.biomage.BioAssay.BioAssay

Method to add Channel to Channels_list

addToChannels(Channel) - Method in interface org.biomage.Interface.HasChannels

Method to add Channel to Channels_list

addToChannels(int, Channel) - Method in class org.biomage.BioAssay.Image

Method to add Channel at position to Channels_list

addToChannels(int, Channel) - Method in class org.biomage.BioAssay.BioAssay

Method to add Channel at position to Channels_list

addToChannels(int, Channel) - Method in interface org.biomage.Interface.HasChannels

Method to add Channel at position to Channels_list

addToCharacteristics(int, OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add OntologyEntry at position to Characteristics_list

addToCharacteristics(int, OntologyEntry) - Method in interface org.biomage.Interface.HasCharacteristics

Method to add OntologyEntry at position to Characteristics_list

addToCharacteristics(OntologyEntry) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add OntologyEntry to Characteristics_list

addToCharacteristics(OntologyEntry) - Method in interface org.biomage.Interface.HasCharacteristics

Method to add OntologyEntry to Characteristics_list

addToComponentCompounds(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Compound

Method to add CompoundMeasurement to ComponentCompounds_list

addToComponentCompounds(CompoundMeasurement) - Method in interface org.biomage.Interface.HasComponentCompounds

Method to add CompoundMeasurement to ComponentCompounds_list

addToComponentCompounds(int, CompoundMeasurement) - Method in class org.biomage.BioMaterial.Compound

Method to add CompoundMeasurement at position to ComponentCompounds_list

addToComponentCompounds(int, CompoundMeasurement) - Method in interface org.biomage.Interface.HasComponentCompounds

Method to add CompoundMeasurement at position to ComponentCompounds_list

addToCompositeCompositeMap_list(CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add CompositeCompositeMap to CompositeCompositeMap_list

addToCompositeCompositeMap_list(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add CompositeCompositeMap at position to CompositeCompositeMap_list

addToCompositeCompositeMaps(CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add CompositeCompositeMap to CompositeCompositeMaps_list

addToCompositeCompositeMaps(CompositeCompositeMap) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps

Method to add CompositeCompositeMap to CompositeCompositeMaps_list

addToCompositeCompositeMaps(int, CompositeCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

addToCompositeCompositeMaps(int, CompositeCompositeMap) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps

Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

addToCompositeGroup_list(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add CompositeGroup to CompositeGroup_list

addToCompositeGroup_list(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add CompositeGroup at position to CompositeGroup_list

addToCompositeGroups(CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add CompositeGroup to CompositeGroups_list

addToCompositeGroups(CompositeGroup) - Method in interface org.biomage.Interface.HasCompositeGroups

Method to add CompositeGroup to CompositeGroups_list

addToCompositeGroups(int, CompositeGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add CompositeGroup at position to CompositeGroups_list

addToCompositeGroups(int, CompositeGroup) - Method in interface org.biomage.Interface.HasCompositeGroups

Method to add CompositeGroup at position to CompositeGroups_list

addToCompositePositionSources(CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap

Method to add CompositePosition to CompositePositionSources_list

addToCompositePositionSources(CompositePosition) - Method in interface org.biomage.Interface.HasCompositePositionSources

Method to add CompositePosition to CompositePositionSources_list

addToCompositePositionSources(int, CompositePosition) - Method in class org.biomage.DesignElement.CompositeCompositeMap

Method to add CompositePosition at position to CompositePositionSources_list

addToCompositePositionSources(int, CompositePosition) - Method in interface org.biomage.Interface.HasCompositePositionSources

Method to add CompositePosition at position to CompositePositionSources_list

addToCompositeSequence_list(CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add CompositeSequence to CompositeSequence_list

addToCompositeSequence_list(int, CompositeSequence) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add CompositeSequence at position to CompositeSequence_list

addToCompositeSequences(CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup

Method to add CompositeSequence to CompositeSequences_list

addToCompositeSequences(CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension

Method to add CompositeSequence to CompositeSequences_list

addToCompositeSequences(CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequences

Method to add CompositeSequence to CompositeSequences_list

addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.ArrayDesign.CompositeGroup

Method to add CompositeSequence at position to CompositeSequences_list

addToCompositeSequences(int, CompositeSequence) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension

Method to add CompositeSequence at position to CompositeSequences_list

addToCompositeSequences(int, CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequences

Method to add CompositeSequence at position to CompositeSequences_list

addToCompound_list(Compound) - Method in class org.biomage.BioMaterial.BioMaterial_package

Method to add Compound to Compound_list

addToCompound_list(int, Compound) - Method in class org.biomage.BioMaterial.BioMaterial_package

Method to add Compound at position to Compound_list

addToCompoundMeasurements(CompoundMeasurement) - Method in class org.biomage.BioMaterial.Treatment

Method to add CompoundMeasurement to CompoundMeasurements_list

addToCompoundMeasurements(CompoundMeasurement) - Method in interface org.biomage.Interface.HasCompoundMeasurements

Method to add CompoundMeasurement to CompoundMeasurements_list

addToCompoundMeasurements(int, CompoundMeasurement) - Method in class org.biomage.BioMaterial.Treatment

Method to add CompoundMeasurement at position to CompoundMeasurements_list

addToCompoundMeasurements(int, CompoundMeasurement) - Method in interface org.biomage.Interface.HasCompoundMeasurements

Method to add CompoundMeasurement at position to CompoundMeasurements_list

addToConfidenceIndicators(ConfidenceIndicator) - Method in interface org.biomage.Interface.HasConfidenceIndicators

Method to add ConfidenceIndicator to ConfidenceIndicators_list

addToConfidenceIndicators(ConfidenceIndicator) - Method in class org.biomage.QuantitationType.QuantitationType

Method to add ConfidenceIndicator to ConfidenceIndicators_list

addToConfidenceIndicators(int, ConfidenceIndicator) - Method in interface org.biomage.Interface.HasConfidenceIndicators

Method to add ConfidenceIndicator at position to ConfidenceIndicators_list

addToConfidenceIndicators(int, ConfidenceIndicator) - Method in class org.biomage.QuantitationType.QuantitationType

Method to add ConfidenceIndicator at position to ConfidenceIndicators_list

addToContact_list(Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add Contact to Contact_list

addToContact_list(int, Contact) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add Contact at position to Contact_list

addToContacts(Contact) - Method in class org.biomage.Description.Database

Method to add Contact to Contacts_list

addToContacts(Contact) - Method in interface org.biomage.Interface.HasContacts

Method to add Contact to Contacts_list

addToContacts(int, Contact) - Method in class org.biomage.Description.Database

Method to add Contact at position to Contacts_list

addToContacts(int, Contact) - Method in interface org.biomage.Interface.HasContacts

Method to add Contact at position to Contacts_list

addToContainedFeatures(Feature) - Method in class org.biomage.BioAssayData.FeatureDimension

Method to add Feature to ContainedFeatures_list

addToContainedFeatures(Feature) - Method in interface org.biomage.Interface.HasContainedFeatures

Method to add Feature to ContainedFeatures_list

addToContainedFeatures(int, Feature) - Method in class org.biomage.BioAssayData.FeatureDimension

Method to add Feature at position to ContainedFeatures_list

addToContainedFeatures(int, Feature) - Method in interface org.biomage.Interface.HasContainedFeatures

Method to add Feature at position to ContainedFeatures_list

addToControlFeatures(Feature) - Method in class org.biomage.DesignElement.Feature

Method to add Feature to ControlFeatures_list

addToControlFeatures(Feature) - Method in interface org.biomage.Interface.HasControlFeatures

Method to add Feature to ControlFeatures_list

addToControlFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature

Method to add Feature at position to ControlFeatures_list

addToControlFeatures(int, Feature) - Method in interface org.biomage.Interface.HasControlFeatures

Method to add Feature at position to ControlFeatures_list

addToControlledFeatures(Feature) - Method in class org.biomage.DesignElement.Feature

Method to add Feature to ControlledFeatures_list

addToControlledFeatures(Feature) - Method in interface org.biomage.Interface.HasControlledFeatures

Method to add Feature to ControlledFeatures_list

addToControlledFeatures(int, Feature) - Method in class org.biomage.DesignElement.Feature

Method to add Feature at position to ControlledFeatures_list

addToControlledFeatures(int, Feature) - Method in interface org.biomage.Interface.HasControlledFeatures

Method to add Feature at position to ControlledFeatures_list

addToDatabase_list(Database) - Method in class org.biomage.Description.Description_package

Method to add Database to Database_list

addToDatabase_list(int, Database) - Method in class org.biomage.Description.Description_package

Method to add Database at position to Database_list

addToDatabaseReferences(DatabaseEntry) - Method in class org.biomage.Description.Description

Method to add DatabaseEntry to DatabaseReferences_list

addToDatabaseReferences(DatabaseEntry) - Method in interface org.biomage.Interface.HasDatabaseReferences

Method to add DatabaseEntry to DatabaseReferences_list

addToDatabaseReferences(int, DatabaseEntry) - Method in class org.biomage.Description.Description

Method to add DatabaseEntry at position to DatabaseReferences_list

addToDatabaseReferences(int, DatabaseEntry) - Method in interface org.biomage.Interface.HasDatabaseReferences

Method to add DatabaseEntry at position to DatabaseReferences_list

addToDerivedBioAssayData(DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay

Method to add DerivedBioAssayData to DerivedBioAssayData_list

addToDerivedBioAssayData(DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayData

Method to add DerivedBioAssayData to DerivedBioAssayData_list

addToDerivedBioAssayData(int, DerivedBioAssayData) - Method in class org.biomage.BioAssay.DerivedBioAssay

Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

addToDerivedBioAssayData(int, DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayData

Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

addToDescriptions(Description) - Method in class org.biomage.Common.Describable

Method to add Description to Descriptions_list

addToDescriptions(Description) - Method in interface org.biomage.Interface.HasDescriptions

Method to add Description to Descriptions_list

addToDescriptions(int, Description) - Method in class org.biomage.Common.Describable

Method to add Description at position to Descriptions_list

addToDescriptions(int, Description) - Method in interface org.biomage.Interface.HasDescriptions

Method to add Description at position to Descriptions_list

addToDesignElementDimension_list(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add DesignElementDimension to DesignElementDimension_list

addToDesignElementDimension_list(int, DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add DesignElementDimension at position to DesignElementDimension_list

addToDesignElementMaps(DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping

Method to add DesignElementMap to DesignElementMaps_list

addToDesignElementMaps(DesignElementMap) - Method in interface org.biomage.Interface.HasDesignElementMaps

Method to add DesignElementMap to DesignElementMaps_list

addToDesignElementMaps(int, DesignElementMap) - Method in class org.biomage.BioAssayData.DesignElementMapping

Method to add DesignElementMap at position to DesignElementMaps_list

addToDesignElementMaps(int, DesignElementMap) - Method in interface org.biomage.Interface.HasDesignElementMaps

Method to add DesignElementMap at position to DesignElementMaps_list

addToDesignProviders(Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add Contact to DesignProviders_list

addToDesignProviders(Contact) - Method in interface org.biomage.Interface.HasDesignProviders

Method to add Contact to DesignProviders_list

addToDesignProviders(int, Contact) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add Contact at position to DesignProviders_list

addToDesignProviders(int, Contact) - Method in interface org.biomage.Interface.HasDesignProviders

Method to add Contact at position to DesignProviders_list

addToExperiment_list(Experiment) - Method in class org.biomage.Experiment.Experiment_package

Method to add Experiment to Experiment_list

addToExperiment_list(int, Experiment) - Method in class org.biomage.Experiment.Experiment_package

Method to add Experiment at position to Experiment_list

addToExperimentalFactors(ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add ExperimentalFactor to ExperimentalFactors_list

addToExperimentalFactors(ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactors

Method to add ExperimentalFactor to ExperimentalFactors_list

addToExperimentalFactors(int, ExperimentalFactor) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add ExperimentalFactor at position to ExperimentalFactors_list

addToExperimentalFactors(int, ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactors

Method to add ExperimentalFactor at position to ExperimentalFactors_list

addToFactorValues(FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor

Method to add FactorValue to FactorValues_list

addToFactorValues(FactorValue) - Method in interface org.biomage.Interface.HasFactorValues

Method to add FactorValue to FactorValues_list

addToFactorValues(int, FactorValue) - Method in class org.biomage.Experiment.ExperimentalFactor

Method to add FactorValue at position to FactorValues_list

addToFactorValues(int, FactorValue) - Method in interface org.biomage.Interface.HasFactorValues

Method to add FactorValue at position to FactorValues_list

addToFailTypes(int, OntologyEntry) - Method in class org.biomage.DesignElement.Reporter

Method to add OntologyEntry at position to FailTypes_list

addToFailTypes(int, OntologyEntry) - Method in interface org.biomage.Interface.HasFailTypes

Method to add OntologyEntry at position to FailTypes_list

addToFailTypes(OntologyEntry) - Method in class org.biomage.DesignElement.Reporter

Method to add OntologyEntry to FailTypes_list

addToFailTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasFailTypes

Method to add OntologyEntry to FailTypes_list

addToFeatureDefects(FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation

Method to add FeatureDefect to FeatureDefects_list

addToFeatureDefects(FeatureDefect) - Method in interface org.biomage.Interface.HasFeatureDefects

Method to add FeatureDefect to FeatureDefects_list

addToFeatureDefects(int, FeatureDefect) - Method in class org.biomage.Array.ArrayManufactureDeviation

Method to add FeatureDefect at position to FeatureDefects_list

addToFeatureDefects(int, FeatureDefect) - Method in interface org.biomage.Interface.HasFeatureDefects

Method to add FeatureDefect at position to FeatureDefects_list

addToFeatureGroups(FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add FeatureGroup to FeatureGroups_list

addToFeatureGroups(FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroups

Method to add FeatureGroup to FeatureGroups_list

addToFeatureGroups(int, FeatureGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add FeatureGroup at position to FeatureGroups_list

addToFeatureGroups(int, FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroups

Method to add FeatureGroup at position to FeatureGroups_list

addToFeatureInformationSources(FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap

Method to add FeatureInformation to FeatureInformationSources_list

addToFeatureInformationSources(FeatureInformation) - Method in interface org.biomage.Interface.HasFeatureInformationSources

Method to add FeatureInformation to FeatureInformationSources_list

addToFeatureInformationSources(int, FeatureInformation) - Method in class org.biomage.DesignElement.FeatureReporterMap

Method to add FeatureInformation at position to FeatureInformationSources_list

addToFeatureInformationSources(int, FeatureInformation) - Method in interface org.biomage.Interface.HasFeatureInformationSources

Method to add FeatureInformation at position to FeatureInformationSources_list

addToFeatureLIMSs(int, ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture

Method to add ManufactureLIMS at position to FeatureLIMSs_list

addToFeatureLIMSs(int, ManufactureLIMS) - Method in interface org.biomage.Interface.HasFeatureLIMSs

Method to add ManufactureLIMS at position to FeatureLIMSs_list

addToFeatureLIMSs(ManufactureLIMS) - Method in class org.biomage.Array.ArrayManufacture

Method to add ManufactureLIMS to FeatureLIMSs_list

addToFeatureLIMSs(ManufactureLIMS) - Method in interface org.biomage.Interface.HasFeatureLIMSs

Method to add ManufactureLIMS to FeatureLIMSs_list

addToFeatureReporterMap_list(FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add FeatureReporterMap to FeatureReporterMap_list

addToFeatureReporterMap_list(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add FeatureReporterMap at position to FeatureReporterMap_list

addToFeatureReporterMaps(FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter

Method to add FeatureReporterMap to FeatureReporterMaps_list

addToFeatureReporterMaps(FeatureReporterMap) - Method in interface org.biomage.Interface.HasFeatureReporterMaps

Method to add FeatureReporterMap to FeatureReporterMaps_list

addToFeatureReporterMaps(int, FeatureReporterMap) - Method in class org.biomage.DesignElement.Reporter

Method to add FeatureReporterMap at position to FeatureReporterMaps_list

addToFeatureReporterMaps(int, FeatureReporterMap) - Method in interface org.biomage.Interface.HasFeatureReporterMaps

Method to add FeatureReporterMap at position to FeatureReporterMaps_list

addToFeatures(Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup

Method to add Feature to Features_list

addToFeatures(Feature) - Method in interface org.biomage.Interface.HasFeatures

Method to add Feature to Features_list

addToFeatures(int, Feature) - Method in class org.biomage.ArrayDesign.FeatureGroup

Method to add Feature at position to Features_list

addToFeatures(int, Feature) - Method in interface org.biomage.Interface.HasFeatures

Method to add Feature at position to Features_list

addToFiducials(Fiducial) - Method in class org.biomage.Array.ArrayGroup

Method to add Fiducial to Fiducials_list

addToFiducials(Fiducial) - Method in interface org.biomage.Interface.HasFiducials

Method to add Fiducial to Fiducials_list

addToFiducials(int, Fiducial) - Method in class org.biomage.Array.ArrayGroup

Method to add Fiducial at position to Fiducials_list

addToFiducials(int, Fiducial) - Method in interface org.biomage.Interface.HasFiducials

Method to add Fiducial at position to Fiducials_list

addToHardware_list(Hardware) - Method in class org.biomage.Protocol.Protocol_package

Method to add Hardware to Hardware_list

addToHardware_list(int, Hardware) - Method in class org.biomage.Protocol.Protocol_package

Method to add Hardware at position to Hardware_list

addToHardwareApplications(HardwareApplication) - Method in interface org.biomage.Interface.HasHardwareApplications

Method to add HardwareApplication to HardwareApplications_list

addToHardwareApplications(HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add HardwareApplication to HardwareApplications_list

addToHardwareApplications(int, HardwareApplication) - Method in interface org.biomage.Interface.HasHardwareApplications

Method to add HardwareApplication at position to HardwareApplications_list

addToHardwareApplications(int, HardwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add HardwareApplication at position to HardwareApplications_list

addToHardwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasHardwareManufacturers

Method to add Contact to HardwareManufacturers_list

addToHardwareManufacturers(Contact) - Method in class org.biomage.Protocol.Hardware

Method to add Contact to HardwareManufacturers_list

addToHardwareManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasHardwareManufacturers

Method to add Contact at position to HardwareManufacturers_list

addToHardwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Hardware

Method to add Contact at position to HardwareManufacturers_list

addToHardwares(Hardware) - Method in interface org.biomage.Interface.HasHardwares

Method to add Hardware to Hardwares_list

addToHardwares(Hardware) - Method in class org.biomage.Protocol.Protocol

Method to add Hardware to Hardwares_list

addToHardwares(int, Hardware) - Method in interface org.biomage.Interface.HasHardwares

Method to add Hardware at position to Hardwares_list

addToHardwares(int, Hardware) - Method in class org.biomage.Protocol.Protocol

Method to add Hardware at position to Hardwares_list

addToImages(Image) - Method in class org.biomage.BioAssay.ImageAcquisition

Method to add Image to Images_list

addToImages(Image) - Method in interface org.biomage.Interface.HasImages

Method to add Image to Images_list

addToImages(int, Image) - Method in class org.biomage.BioAssay.ImageAcquisition

Method to add Image at position to Images_list

addToImages(int, Image) - Method in interface org.biomage.Interface.HasImages

Method to add Image at position to Images_list

addToImmobilizedCharacteristics(BioSequence) - Method in class org.biomage.DesignElement.Reporter

Method to add BioSequence to ImmobilizedCharacteristics_list

addToImmobilizedCharacteristics(BioSequence) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics

Method to add BioSequence to ImmobilizedCharacteristics_list

addToImmobilizedCharacteristics(int, BioSequence) - Method in class org.biomage.DesignElement.Reporter

Method to add BioSequence at position to ImmobilizedCharacteristics_list

addToImmobilizedCharacteristics(int, BioSequence) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics

Method to add BioSequence at position to ImmobilizedCharacteristics_list

addToLabels(Compound) - Method in class org.biomage.BioAssay.Channel

Method to add Compound to Labels_list

addToLabels(Compound) - Method in class org.biomage.BioMaterial.LabeledExtract

Method to add Compound to Labels_list

addToLabels(Compound) - Method in interface org.biomage.Interface.HasLabels

Method to add Compound to Labels_list

addToLabels(int, Compound) - Method in class org.biomage.BioAssay.Channel

Method to add Compound at position to Labels_list

addToLabels(int, Compound) - Method in class org.biomage.BioMaterial.LabeledExtract

Method to add Compound at position to Labels_list

addToLabels(int, Compound) - Method in interface org.biomage.Interface.HasLabels

Method to add Compound at position to Labels_list

addToMeasuredBioAssayData(int, MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay

Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list

addToMeasuredBioAssayData(int, MeasuredBioAssayData) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData

Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list

addToMeasuredBioAssayData(MeasuredBioAssayData) - Method in class org.biomage.BioAssay.MeasuredBioAssay

Method to add MeasuredBioAssayData to MeasuredBioAssayData_list

addToMeasuredBioAssayData(MeasuredBioAssayData) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData

Method to add MeasuredBioAssayData to MeasuredBioAssayData_list

addToMembers(Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup

Method to add Contact to Members_list

addToMembers(Contact) - Method in interface org.biomage.Interface.HasMembers

Method to add Contact to Members_list

addToMembers(int, Contact) - Method in class org.biomage.AuditAndSecurity.SecurityGroup

Method to add Contact at position to Members_list

addToMembers(int, Contact) - Method in interface org.biomage.Interface.HasMembers

Method to add Contact at position to Members_list

addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition

Method to add MismatchInformation at position to MismatchInformation_list

addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation

Method to add MismatchInformation at position to MismatchInformation_list

addToMismatchInformation(int, MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition

Method to add MismatchInformation at position to MismatchInformation_list

addToMismatchInformation(int, MismatchInformation) - Method in interface org.biomage.Interface.HasMismatchInformation

Method to add MismatchInformation at position to MismatchInformation_list

addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.ReporterPosition

Method to add MismatchInformation to MismatchInformation_list

addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.FeatureInformation

Method to add MismatchInformation to MismatchInformation_list

addToMismatchInformation(MismatchInformation) - Method in class org.biomage.DesignElement.CompositePosition

Method to add MismatchInformation to MismatchInformation_list

addToMismatchInformation(MismatchInformation) - Method in interface org.biomage.Interface.HasMismatchInformation

Method to add MismatchInformation to MismatchInformation_list

addToNodeContents(int, NodeContents) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add NodeContents at position to NodeContents_list

addToNodeContents(int, NodeContents) - Method in interface org.biomage.Interface.HasNodeContents

Method to add NodeContents at position to NodeContents_list

addToNodeContents(NodeContents) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add NodeContents to NodeContents_list

addToNodeContents(NodeContents) - Method in interface org.biomage.Interface.HasNodeContents

Method to add NodeContents to NodeContents_list

addToNodes(int, Node) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add Node at position to Nodes_list

addToNodes(int, Node) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Method to add Node at position to Nodes_list

addToNodes(int, Node) - Method in interface org.biomage.Interface.HasNodes

Method to add Node at position to Nodes_list

addToNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add Node to Nodes_list

addToNodes(Node) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Method to add Node to Nodes_list

addToNodes(Node) - Method in interface org.biomage.Interface.HasNodes

Method to add Node to Nodes_list

addToNodeValue(int, NodeValue) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add NodeValue at position to NodeValue_list

addToNodeValue(int, NodeValue) - Method in interface org.biomage.Interface.HasNodeValue

Method to add NodeValue at position to NodeValue_list

addToNodeValue(NodeValue) - Method in class org.biomage.HigherLevelAnalysis.Node

Method to add NodeValue to NodeValue_list

addToNodeValue(NodeValue) - Method in interface org.biomage.Interface.HasNodeValue

Method to add NodeValue to NodeValue_list

addToOntologyEntries(int, OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence

Method to add OntologyEntry at position to OntologyEntries_list

addToOntologyEntries(int, OntologyEntry) - Method in interface org.biomage.Interface.HasOntologyEntries

Method to add OntologyEntry at position to OntologyEntries_list

addToOntologyEntries(OntologyEntry) - Method in class org.biomage.BioSequence.BioSequence

Method to add OntologyEntry to OntologyEntries_list

addToOntologyEntries(OntologyEntry) - Method in interface org.biomage.Interface.HasOntologyEntries

Method to add OntologyEntry to OntologyEntries_list

addToParameters(int, OntologyEntry) - Method in class org.biomage.BQS.BibliographicReference

Method to add OntologyEntry at position to Parameters_list

addToParameters(int, OntologyEntry) - Method in interface org.biomage.Interface.HasParameters

Method to add OntologyEntry at position to Parameters_list

addToParameters(OntologyEntry) - Method in class org.biomage.BQS.BibliographicReference

Method to add OntologyEntry to Parameters_list

addToParameters(OntologyEntry) - Method in interface org.biomage.Interface.HasParameters

Method to add OntologyEntry to Parameters_list

addToParameterTypes(int, Parameter) - Method in interface org.biomage.Interface.HasParameterTypes

Method to add Parameter at position to ParameterTypes_list

addToParameterTypes(int, Parameter) - Method in class org.biomage.Protocol.Parameterizable

Method to add Parameter at position to ParameterTypes_list

addToParameterTypes(Parameter) - Method in interface org.biomage.Interface.HasParameterTypes

Method to add Parameter to ParameterTypes_list

addToParameterTypes(Parameter) - Method in class org.biomage.Protocol.Parameterizable

Method to add Parameter to ParameterTypes_list

addToParameterValues(int, ParameterValue) - Method in interface org.biomage.Interface.HasParameterValues

Method to add ParameterValue at position to ParameterValues_list

addToParameterValues(int, ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication

Method to add ParameterValue at position to ParameterValues_list

addToParameterValues(ParameterValue) - Method in interface org.biomage.Interface.HasParameterValues

Method to add ParameterValue to ParameterValues_list

addToParameterValues(ParameterValue) - Method in class org.biomage.Protocol.ParameterizableApplication

Method to add ParameterValue to ParameterValues_list

addToPerformers(int, Person) - Method in interface org.biomage.Interface.HasPerformers

Method to add Person at position to Performers_list

addToPerformers(int, Person) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add Person at position to Performers_list

addToPerformers(Person) - Method in interface org.biomage.Interface.HasPerformers

Method to add Person to Performers_list

addToPerformers(Person) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add Person to Performers_list

addToPhysicalBioAssayData(Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Method to add Image to PhysicalBioAssayData_list

addToPhysicalBioAssayData(Image) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData

Method to add Image to PhysicalBioAssayData_list

addToPhysicalBioAssayData(int, Image) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Method to add Image at position to PhysicalBioAssayData_list

addToPhysicalBioAssayData(int, Image) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData

Method to add Image at position to PhysicalBioAssayData_list

addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.NameValueType

Method to add NameValueType at position to PropertySets_list

addToPropertySets(int, NameValueType) - Method in class org.biomage.Common.Extendable

Method to add NameValueType at position to PropertySets_list

addToPropertySets(int, NameValueType) - Method in interface org.biomage.Interface.HasPropertySets

Method to add NameValueType at position to PropertySets_list

addToPropertySets(NameValueType) - Method in class org.biomage.Common.NameValueType

Method to add NameValueType to PropertySets_list

addToPropertySets(NameValueType) - Method in class org.biomage.Common.Extendable

Method to add NameValueType to PropertySets_list

addToPropertySets(NameValueType) - Method in interface org.biomage.Interface.HasPropertySets

Method to add NameValueType to PropertySets_list

addToProtocol_list(int, Protocol) - Method in class org.biomage.Protocol.Protocol_package

Method to add Protocol at position to Protocol_list

addToProtocol_list(Protocol) - Method in class org.biomage.Protocol.Protocol_package

Method to add Protocol to Protocol_list

addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture

Method to add ProtocolApplication at position to ProtocolApplications_list

addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add ProtocolApplication at position to ProtocolApplications_list

addToProtocolApplications(int, ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent

Method to add ProtocolApplication at position to ProtocolApplications_list

addToProtocolApplications(int, ProtocolApplication) - Method in interface org.biomage.Interface.HasProtocolApplications

Method to add ProtocolApplication at position to ProtocolApplications_list

addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.Array.ArrayManufacture

Method to add ProtocolApplication to ProtocolApplications_list

addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add ProtocolApplication to ProtocolApplications_list

addToProtocolApplications(ProtocolApplication) - Method in class org.biomage.BioEvent.BioEvent

Method to add ProtocolApplication to ProtocolApplications_list

addToProtocolApplications(ProtocolApplication) - Method in interface org.biomage.Interface.HasProtocolApplications

Method to add ProtocolApplication to ProtocolApplications_list

addToProviders(Contact) - Method in class org.biomage.Experiment.Experiment

Method to add Contact to Providers_list

addToProviders(Contact) - Method in interface org.biomage.Interface.HasProviders

Method to add Contact to Providers_list

addToProviders(int, Contact) - Method in class org.biomage.Experiment.Experiment

Method to add Contact at position to Providers_list

addToProviders(int, Contact) - Method in interface org.biomage.Interface.HasProviders

Method to add Contact at position to Providers_list

addToQualityControlStatistics(int, NameValueType) - Method in class org.biomage.Array.ArrayManufacture

Method to add NameValueType at position to QualityControlStatistics_list

addToQualityControlStatistics(int, NameValueType) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add NameValueType at position to QualityControlStatistics_list

addToQualityControlStatistics(int, NameValueType) - Method in interface org.biomage.Interface.HasQualityControlStatistics

Method to add NameValueType at position to QualityControlStatistics_list

addToQualityControlStatistics(NameValueType) - Method in class org.biomage.Array.ArrayManufacture

Method to add NameValueType to QualityControlStatistics_list

addToQualityControlStatistics(NameValueType) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add NameValueType to QualityControlStatistics_list

addToQualityControlStatistics(NameValueType) - Method in interface org.biomage.Interface.HasQualityControlStatistics

Method to add NameValueType to QualityControlStatistics_list

addToQuantitationType_list(int, QuantitationType) - Method in class org.biomage.QuantitationType.QuantitationType_package

Method to add QuantitationType at position to QuantitationType_list

addToQuantitationType_list(QuantitationType) - Method in class org.biomage.QuantitationType.QuantitationType_package

Method to add QuantitationType to QuantitationType_list

addToQuantitationTypeDimension_list(int, QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list

addToQuantitationTypeDimension_list(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add QuantitationTypeDimension to QuantitationTypeDimension_list

addToQuantitationTypeMap_list(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add QuantitationTypeMap at position to QuantitationTypeMap_list

addToQuantitationTypeMap_list(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.BioAssayData_package

Method to add QuantitationTypeMap to QuantitationTypeMap_list

addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping

Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list

addToQuantitationTypeMaps(int, QuantitationTypeMap) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps

Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list

addToQuantitationTypeMaps(QuantitationTypeMap) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping

Method to add QuantitationTypeMap to QuantitationTypeMaps_list

addToQuantitationTypeMaps(QuantitationTypeMap) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps

Method to add QuantitationTypeMap to QuantitationTypeMaps_list

addToQuantitationTypes(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension

Method to add QuantitationType at position to QuantitationTypes_list

addToQuantitationTypes(int, QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationTypes

Method to add QuantitationType at position to QuantitationTypes_list

addToQuantitationTypes(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension

Method to add QuantitationType to QuantitationTypes_list

addToQuantitationTypes(QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationTypes

Method to add QuantitationType to QuantitationTypes_list

addToReadGroups(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security

Method to add SecurityGroup at position to ReadGroups_list

addToReadGroups(int, SecurityGroup) - Method in interface org.biomage.Interface.HasReadGroups

Method to add SecurityGroup at position to ReadGroups_list

addToReadGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security

Method to add SecurityGroup to ReadGroups_list

addToReadGroups(SecurityGroup) - Method in interface org.biomage.Interface.HasReadGroups

Method to add SecurityGroup to ReadGroups_list

addToRegions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature

Method to add SeqFeatureLocation at position to Regions_list

addToRegions(int, SeqFeatureLocation) - Method in interface org.biomage.Interface.HasRegions

Method to add SeqFeatureLocation at position to Regions_list

addToRegions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeature

Method to add SeqFeatureLocation to Regions_list

addToRegions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasRegions

Method to add SeqFeatureLocation to Regions_list

addToReporter_list(int, Reporter) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add Reporter at position to Reporter_list

addToReporter_list(Reporter) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add Reporter to Reporter_list

addToReporterCompositeMap_list(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add ReporterCompositeMap at position to ReporterCompositeMap_list

addToReporterCompositeMap_list(ReporterCompositeMap) - Method in class org.biomage.DesignElement.DesignElement_package

Method to add ReporterCompositeMap to ReporterCompositeMap_list

addToReporterCompositeMaps(int, ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

addToReporterCompositeMaps(int, ReporterCompositeMap) - Method in interface org.biomage.Interface.HasReporterCompositeMaps

Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

addToReporterCompositeMaps(ReporterCompositeMap) - Method in class org.biomage.DesignElement.CompositeSequence

Method to add ReporterCompositeMap to ReporterCompositeMaps_list

addToReporterCompositeMaps(ReporterCompositeMap) - Method in interface org.biomage.Interface.HasReporterCompositeMaps

Method to add ReporterCompositeMap to ReporterCompositeMaps_list

addToReporterGroup_list(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add ReporterGroup at position to ReporterGroup_list

addToReporterGroup_list(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Method to add ReporterGroup to ReporterGroup_list

addToReporterGroups(int, ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add ReporterGroup at position to ReporterGroups_list

addToReporterGroups(int, ReporterGroup) - Method in interface org.biomage.Interface.HasReporterGroups

Method to add ReporterGroup at position to ReporterGroups_list

addToReporterGroups(ReporterGroup) - Method in class org.biomage.ArrayDesign.ArrayDesign

Method to add ReporterGroup to ReporterGroups_list

addToReporterGroups(ReporterGroup) - Method in interface org.biomage.Interface.HasReporterGroups

Method to add ReporterGroup to ReporterGroups_list

addToReporterPositionSources(int, ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap

Method to add ReporterPosition at position to ReporterPositionSources_list

addToReporterPositionSources(int, ReporterPosition) - Method in interface org.biomage.Interface.HasReporterPositionSources

Method to add ReporterPosition at position to ReporterPositionSources_list

addToReporterPositionSources(ReporterPosition) - Method in class org.biomage.DesignElement.ReporterCompositeMap

Method to add ReporterPosition to ReporterPositionSources_list

addToReporterPositionSources(ReporterPosition) - Method in interface org.biomage.Interface.HasReporterPositionSources

Method to add ReporterPosition to ReporterPositionSources_list

addToReporters(int, Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup

Method to add Reporter at position to Reporters_list

addToReporters(int, Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension

Method to add Reporter at position to Reporters_list

addToReporters(int, Reporter) - Method in interface org.biomage.Interface.HasReporters

Method to add Reporter at position to Reporters_list

addToReporters(Reporter) - Method in class org.biomage.ArrayDesign.ReporterGroup

Method to add Reporter to Reporters_list

addToReporters(Reporter) - Method in class org.biomage.BioAssayData.ReporterDimension

Method to add Reporter to Reporters_list

addToReporters(Reporter) - Method in interface org.biomage.Interface.HasReporters

Method to add Reporter to Reporters_list

addToRoles(int, OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact

Method to add OntologyEntry at position to Roles_list

addToRoles(int, OntologyEntry) - Method in interface org.biomage.Interface.HasRoles

Method to add OntologyEntry at position to Roles_list

addToRoles(OntologyEntry) - Method in class org.biomage.AuditAndSecurity.Contact

Method to add OntologyEntry to Roles_list

addToRoles(OntologyEntry) - Method in interface org.biomage.Interface.HasRoles

Method to add OntologyEntry to Roles_list

addToSecurity_list(int, Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add Security at position to Security_list

addToSecurity_list(Security) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add Security to Security_list

addToSecurityGroup_list(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add SecurityGroup at position to SecurityGroup_list

addToSecurityGroup_list(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Method to add SecurityGroup to SecurityGroup_list

addToSeqFeatures(int, SeqFeature) - Method in class org.biomage.BioSequence.BioSequence

Method to add SeqFeature at position to SeqFeatures_list

addToSeqFeatures(int, SeqFeature) - Method in interface org.biomage.Interface.HasSeqFeatures

Method to add SeqFeature at position to SeqFeatures_list

addToSeqFeatures(SeqFeature) - Method in class org.biomage.BioSequence.BioSequence

Method to add SeqFeature to SeqFeatures_list

addToSeqFeatures(SeqFeature) - Method in interface org.biomage.Interface.HasSeqFeatures

Method to add SeqFeature to SeqFeatures_list

addToSequenceDatabases(DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence

Method to add DatabaseEntry to SequenceDatabases_list

addToSequenceDatabases(DatabaseEntry) - Method in interface org.biomage.Interface.HasSequenceDatabases

Method to add DatabaseEntry to SequenceDatabases_list

addToSequenceDatabases(int, DatabaseEntry) - Method in class org.biomage.BioSequence.BioSequence

Method to add DatabaseEntry at position to SequenceDatabases_list

addToSequenceDatabases(int, DatabaseEntry) - Method in interface org.biomage.Interface.HasSequenceDatabases

Method to add DatabaseEntry at position to SequenceDatabases_list

addToSoftware_list(int, Software) - Method in class org.biomage.Protocol.Protocol_package

Method to add Software at position to Software_list

addToSoftware_list(Software) - Method in class org.biomage.Protocol.Protocol_package

Method to add Software to Software_list

addToSoftwareApplications(int, SoftwareApplication) - Method in interface org.biomage.Interface.HasSoftwareApplications

Method to add SoftwareApplication at position to SoftwareApplications_list

addToSoftwareApplications(int, SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add SoftwareApplication at position to SoftwareApplications_list

addToSoftwareApplications(SoftwareApplication) - Method in interface org.biomage.Interface.HasSoftwareApplications

Method to add SoftwareApplication to SoftwareApplications_list

addToSoftwareApplications(SoftwareApplication) - Method in class org.biomage.Protocol.ProtocolApplication

Method to add SoftwareApplication to SoftwareApplications_list

addToSoftwareManufacturers(Contact) - Method in interface org.biomage.Interface.HasSoftwareManufacturers

Method to add Contact to SoftwareManufacturers_list

addToSoftwareManufacturers(Contact) - Method in class org.biomage.Protocol.Software

Method to add Contact to SoftwareManufacturers_list

addToSoftwareManufacturers(int, Contact) - Method in interface org.biomage.Interface.HasSoftwareManufacturers

Method to add Contact at position to SoftwareManufacturers_list

addToSoftwareManufacturers(int, Contact) - Method in class org.biomage.Protocol.Software

Method to add Contact at position to SoftwareManufacturers_list

addToSoftwares(int, Software) - Method in interface org.biomage.Interface.HasSoftwares

Method to add Software at position to Softwares_list

addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Software

Method to add Software at position to Softwares_list

addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Protocol

Method to add Software at position to Softwares_list

addToSoftwares(int, Software) - Method in class org.biomage.Protocol.Hardware

Method to add Software at position to Softwares_list

addToSoftwares(Software) - Method in interface org.biomage.Interface.HasSoftwares

Method to add Software to Softwares_list

addToSoftwares(Software) - Method in class org.biomage.Protocol.Software

Method to add Software to Softwares_list

addToSoftwares(Software) - Method in class org.biomage.Protocol.Protocol

Method to add Software to Softwares_list

addToSoftwares(Software) - Method in class org.biomage.Protocol.Hardware

Method to add Software to Softwares_list

addToSourceBioAssays(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap

Method to add BioAssay to SourceBioAssays_list

addToSourceBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasSourceBioAssays

Method to add BioAssay to SourceBioAssays_list

addToSourceBioAssays(int, BioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap

Method to add BioAssay at position to SourceBioAssays_list

addToSourceBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasSourceBioAssays

Method to add BioAssay at position to SourceBioAssays_list

addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation

Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in class org.biomage.BioMaterial.Treatment

Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

addToSourceBioMaterialMeasurements(BioMaterialMeasurement) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in class org.biomage.BioAssay.BioAssayCreation

Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in class org.biomage.BioMaterial.Treatment

Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

addToSourceBioMaterialMeasurements(int, BioMaterialMeasurement) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

addToSourcesQuantitationType(int, QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap

Method to add QuantitationType at position to SourcesQuantitationType_list

addToSourcesQuantitationType(int, QuantitationType) - Method in interface org.biomage.Interface.HasSourcesQuantitationType

Method to add QuantitationType at position to SourcesQuantitationType_list

addToSourcesQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.QuantitationTypeMap

Method to add QuantitationType to SourcesQuantitationType_list

addToSourcesQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasSourcesQuantitationType

Method to add QuantitationType to SourcesQuantitationType_list

addToSubregions(int, SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation

Method to add SeqFeatureLocation at position to Subregions_list

addToSubregions(int, SeqFeatureLocation) - Method in interface org.biomage.Interface.HasSubregions

Method to add SeqFeatureLocation at position to Subregions_list

addToSubregions(SeqFeatureLocation) - Method in class org.biomage.BioSequence.SeqFeatureLocation

Method to add SeqFeatureLocation to Subregions_list

addToSubregions(SeqFeatureLocation) - Method in interface org.biomage.Interface.HasSubregions

Method to add SeqFeatureLocation to Subregions_list

addToSummaryStatistics(int, NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData

Method to add NameValueType at position to SummaryStatistics_list

addToSummaryStatistics(int, NameValueType) - Method in interface org.biomage.Interface.HasSummaryStatistics

Method to add NameValueType at position to SummaryStatistics_list

addToSummaryStatistics(NameValueType) - Method in class org.biomage.BioAssayData.BioAssayData

Method to add NameValueType to SummaryStatistics_list

addToSummaryStatistics(NameValueType) - Method in interface org.biomage.Interface.HasSummaryStatistics

Method to add NameValueType to SummaryStatistics_list

addToTopLevelBioAssays(BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add BioAssay to TopLevelBioAssays_list

addToTopLevelBioAssays(BioAssay) - Method in interface org.biomage.Interface.HasTopLevelBioAssays

Method to add BioAssay to TopLevelBioAssays_list

addToTopLevelBioAssays(int, BioAssay) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add BioAssay at position to TopLevelBioAssays_list

addToTopLevelBioAssays(int, BioAssay) - Method in interface org.biomage.Interface.HasTopLevelBioAssays

Method to add BioAssay at position to TopLevelBioAssays_list

addToTreatments(int, Treatment) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add Treatment at position to Treatments_list

addToTreatments(int, Treatment) - Method in interface org.biomage.Interface.HasTreatments

Method to add Treatment at position to Treatments_list

addToTreatments(Treatment) - Method in class org.biomage.BioMaterial.BioMaterial

Method to add Treatment to Treatments_list

addToTreatments(Treatment) - Method in interface org.biomage.Interface.HasTreatments

Method to add Treatment to Treatments_list

addToTypes(int, OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup

Method to add OntologyEntry at position to Types_list

addToTypes(int, OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add OntologyEntry at position to Types_list

addToTypes(int, OntologyEntry) - Method in interface org.biomage.Interface.HasTypes

Method to add OntologyEntry at position to Types_list

addToTypes(OntologyEntry) - Method in class org.biomage.ArrayDesign.DesignElementGroup

Method to add OntologyEntry to Types_list

addToTypes(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentDesign

Method to add OntologyEntry to Types_list

addToTypes(OntologyEntry) - Method in interface org.biomage.Interface.HasTypes

Method to add OntologyEntry to Types_list

addToWriteGroups(int, SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security

Method to add SecurityGroup at position to WriteGroups_list

addToWriteGroups(int, SecurityGroup) - Method in interface org.biomage.Interface.HasWriteGroups

Method to add SecurityGroup at position to WriteGroups_list

addToWriteGroups(SecurityGroup) - Method in class org.biomage.AuditAndSecurity.Security

Method to add SecurityGroup to WriteGroups_list

addToWriteGroups(SecurityGroup) - Method in interface org.biomage.Interface.HasWriteGroups

Method to add SecurityGroup to WriteGroups_list

addToZoneGroups(int, ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign

Method to add ZoneGroup at position to ZoneGroups_list

addToZoneGroups(int, ZoneGroup) - Method in interface org.biomage.Interface.HasZoneGroups

Method to add ZoneGroup at position to ZoneGroups_list

addToZoneGroups(ZoneGroup) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign

Method to add ZoneGroup to ZoneGroups_list

addToZoneGroups(ZoneGroup) - Method in interface org.biomage.Interface.HasZoneGroups

Method to add ZoneGroup to ZoneGroups_list

addToZoneLocations(int, Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup

Method to add Zone at position to ZoneLocations_list

addToZoneLocations(int, Zone) - Method in interface org.biomage.Interface.HasZoneLocations

Method to add Zone at position to ZoneLocations_list

addToZoneLocations(Zone) - Method in class org.biomage.ArrayDesign.ZoneGroup

Method to add Zone to ZoneLocations_list

addToZoneLocations(Zone) - Method in interface org.biomage.Interface.HasZoneLocations

Method to add Zone to ZoneLocations_list

adjustments - Variable in class org.biomage.Array.ArrayManufactureDeviation

Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.

affiliation - Variable in class org.biomage.AuditAndSecurity.Person

The organization a person belongs to.

aLine - Static variable in class org.biomage.tools.generate_er.CreateMageER

a line for seperation

alphabetLinkingTabelName(String, String) - Method in class org.biomage.tools.generate_er.CreateMageER

Description: compare two strings and link them alphabetically if string1 < string2: negative number

AMOL - Variable in class org.biomage.Measurement.QuantityUnit.UnitNameCV

analysisResults - Variable in class org.biomage.Experiment.Experiment

The results of analyzing the data, typically with a clustering algorithm.

annotations - Variable in class org.biomage.Description.Description

Allows specification of ontology entries related to the instance being described.

array - Variable in class org.biomage.BioAssay.BioAssayCreation

The array used in the BioAssayCreation event.

Array - class org.biomage.Array.Array.

The physical substrate along with its features and their annotation

array_list - Variable in class org.biomage.Array.Array_package

The physical substrate along with its features and their annotation

array_package - Variable in class org.biomage.Common.MAGEJava

Describes the process of creating arrays from array designs.

Array_package - class org.biomage.Array.Array_package.

Describes the process of creating arrays from array designs.

Array_package.Array_list - class org.biomage.Array.Array_package.Array_list.

Inner list class for holding multiple entries for attribute array.

Array_package.Array_list() - Constructor for class org.biomage.Array.Array_package.Array_list

Array_package.ArrayGroup_list - class org.biomage.Array.Array_package.ArrayGroup_list.

Inner list class for holding multiple entries for attribute arrayGroup.

Array_package.ArrayGroup_list() - Constructor for class org.biomage.Array.Array_package.ArrayGroup_list

Array_package.ArrayManufacture_list - class org.biomage.Array.Array_package.ArrayManufacture_list.

Inner list class for holding multiple entries for attribute arrayManufacture.

Array_package.ArrayManufacture_list() - Constructor for class org.biomage.Array.Array_package.ArrayManufacture_list

Array_package() - Constructor for class org.biomage.Array.Array_package

Default constructor.

Array_package(Attributes) - Constructor for class org.biomage.Array.Array_package

Attribute constructor.

Array() - Constructor for class org.biomage.Array.Array

Default constructor.

Array(Attributes) - Constructor for class org.biomage.Array.Array

Attribute constructor.

arrayDesign - Variable in class org.biomage.Array.Array

The association of a physical array with its array design.

ArrayDesign - class org.biomage.ArrayDesign.ArrayDesign.

Describes the design of an gene expression layout.

arrayDesign_list - Variable in class org.biomage.ArrayDesign.ArrayDesign_package

Describes the design of an gene expression layout.

arrayDesign_package - Variable in class org.biomage.Common.MAGEJava

Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.

ArrayDesign_package - class org.biomage.ArrayDesign.ArrayDesign_package.

Describes a microarray design that can be printed and then, in the case of gene expression, hybridized.

ArrayDesign_package.ArrayDesign_list - class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list.

Inner list class for holding multiple entries for attribute arrayDesign.

ArrayDesign_package.ArrayDesign_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list

ArrayDesign_package.CompositeGroup_list - class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list.

Inner list class for holding multiple entries for attribute compositeGroup.

ArrayDesign_package.CompositeGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list

ArrayDesign_package.ReporterGroup_list - class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list.

Inner list class for holding multiple entries for attribute reporterGroup.

ArrayDesign_package.ReporterGroup_list() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list

ArrayDesign_package() - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package

Default constructor.

ArrayDesign_package(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign_package

Attribute constructor.

ArrayDesign() - Constructor for class org.biomage.ArrayDesign.ArrayDesign

Default constructor.

ArrayDesign(Attributes) - Constructor for class org.biomage.ArrayDesign.ArrayDesign

Attribute constructor.

arrayGroup - Variable in class org.biomage.Array.Array

Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.

ArrayGroup - class org.biomage.Array.ArrayGroup.

An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.

arrayGroup_list - Variable in class org.biomage.Array.Array_package

An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.

ArrayGroup.OrientationMarkPosition - class org.biomage.Array.ArrayGroup.OrientationMarkPosition.

Inner class for the enumeration values that the attribute orientationMarkPosition can assume.

ArrayGroup() - Constructor for class org.biomage.Array.ArrayGroup

Default constructor.

ArrayGroup(Attributes) - Constructor for class org.biomage.Array.ArrayGroup

Attribute constructor.

ArrayManufacture - class org.biomage.Array.ArrayManufacture.

Describes the process by which arrays are produced.

arrayManufacture_list - Variable in class org.biomage.Array.Array_package

Describes the process by which arrays are produced.

ArrayManufacture() - Constructor for class org.biomage.Array.ArrayManufacture

Default constructor.

ArrayManufacture(Attributes) - Constructor for class org.biomage.Array.ArrayManufacture

Attribute constructor.

ArrayManufactureDeviation - class org.biomage.Array.ArrayManufactureDeviation.

Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g.

ArrayManufactureDeviation() - Constructor for class org.biomage.Array.ArrayManufactureDeviation

Default constructor.

ArrayManufactureDeviation(Attributes) - Constructor for class org.biomage.Array.ArrayManufactureDeviation

Attribute constructor.

arrayManufactureDeviations - Variable in class org.biomage.Array.Array

Association to classes to describe deviations from the ArrayDesign.

arrayManufacturers - Variable in class org.biomage.Array.ArrayManufacture

The person or organization to contact for information concerning the ArrayManufacture.

arrays - Variable in class org.biomage.Array.ArrayManufacture

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

arrays - Variable in class org.biomage.Array.ArrayGroup

Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.

AssociationColumn - class org.biomage.tools.generate_er.AssociationColumn.

AssociationColumn() - Constructor for class org.biomage.tools.generate_er.AssociationColumn

Description: Constructor for the AssociationColumn object.

associationStack - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler

associationType - Variable in class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef

Audit - class org.biomage.AuditAndSecurity.Audit.

Tracks information on the contact that creates or modifies an object.

Audit.Action - class org.biomage.AuditAndSecurity.Audit.Action.

Inner class for the enumeration values that the attribute action can assume.

Audit() - Constructor for class org.biomage.AuditAndSecurity.Audit

Default constructor.

Audit(Attributes) - Constructor for class org.biomage.AuditAndSecurity.Audit

Attribute constructor.

auditAndSecurity_package - Variable in class org.biomage.Common.MAGEJava

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

AuditAndSecurity_package - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.

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

AuditAndSecurity_package.Contact_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list.

Inner list class for holding multiple entries for attribute contact.

AuditAndSecurity_package.Contact_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list

AuditAndSecurity_package.Security_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list.

Inner list class for holding multiple entries for attribute security.

AuditAndSecurity_package.Security_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list

AuditAndSecurity_package.SecurityGroup_list - class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list.

Inner list class for holding multiple entries for attribute securityGroup.

AuditAndSecurity_package.SecurityGroup_list() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list

AuditAndSecurity_package() - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Default constructor.

AuditAndSecurity_package(Attributes) - Constructor for class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Attribute constructor.

auditTrail - Variable in class org.biomage.Common.Describable

A list of Audit instances that track changes to the instance of Describable.