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

S

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

scale - Variable in class org.biomage.HigherLevelAnalysis.NodeValue

The scale (linear, log10, ln, etc.) of the value.

scale - Variable in class org.biomage.QuantitationType.QuantitationType

Indication of how to interpret the value.

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

second line in the MAGE_ER.xml file

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

Information on the security for the instance of the class.

Security - class org.biomage.AuditAndSecurity.Security.

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

security_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

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

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

Default constructor.

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

Attribute constructor.

SecurityGroup - class org.biomage.AuditAndSecurity.SecurityGroup.

Groups contacts together based on their security privileges.

securityGroup_list - Variable in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Groups contacts together based on their security privileges.

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

Default constructor.

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

Attribute constructor.

SeqFeature - class org.biomage.BioSequence.SeqFeature.

Represents, in general, what would be a GenBank Feature Table annotation for a sequence.

SeqFeature.Basis - class org.biomage.BioSequence.SeqFeature.Basis.

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

SeqFeature() - Constructor for class org.biomage.BioSequence.SeqFeature

Default constructor.

SeqFeature(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeature

Attribute constructor.

SeqFeatureLocation - class org.biomage.BioSequence.SeqFeatureLocation.

The location of the SeqFeature annotation.

SeqFeatureLocation() - Constructor for class org.biomage.BioSequence.SeqFeatureLocation

Default constructor.

SeqFeatureLocation(Attributes) - Constructor for class org.biomage.BioSequence.SeqFeatureLocation

Attribute constructor.

seqFeatures - Variable in class org.biomage.BioSequence.BioSequence

Association to annotations for subsequences.

sequenceDatabases - Variable in class org.biomage.BioSequence.BioSequence

References an entry in a species database, like GenBank, UniGene, etc.

SequencePosition - class org.biomage.BioSequence.SequencePosition.

Designates the position of the Feature in its BioSequence.

SequencePosition() - Constructor for class org.biomage.BioSequence.SequencePosition

Default constructor.

SequencePosition(Attributes) - Constructor for class org.biomage.BioSequence.SequencePosition

Attribute constructor.

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

type of the primary key for tables

setAccession(String) - Method in class org.biomage.Description.DatabaseEntry

Set method for accession

setAccessionVersion(String) - Method in class org.biomage.Description.DatabaseEntry

Set method for accessionVersion

setAction(Audit.Action) - Method in class org.biomage.AuditAndSecurity.Audit

Set method for action

setAction(OntologyEntry) - Method in class org.biomage.BioMaterial.Treatment

Set method for action

setAction(OntologyEntry) - Method in interface org.biomage.Interface.HasAction

Set method for action

setActionMeasurement(Measurement) - Method in class org.biomage.BioMaterial.Treatment

Set method for actionMeasurement

setActionMeasurement(Measurement) - Method in interface org.biomage.Interface.HasActionMeasurement

Set method for actionMeasurement

setActivityDate(String) - Method in class org.biomage.Protocol.ProtocolApplication

Set method for activityDate

setAddress(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for address

setAdjustments(HasAdjustments.Adjustments_list) - Method in class org.biomage.Array.ArrayManufactureDeviation

Set method for adjustments

setAdjustments(HasAdjustments.Adjustments_list) - Method in interface org.biomage.Interface.HasAdjustments

Set method for adjustments

setAffiliation(Organization) - Method in class org.biomage.AuditAndSecurity.Person

Set method for affiliation

setAffiliation(Organization) - Method in interface org.biomage.Interface.HasAffiliation

Set method for affiliation

setAnalysisResults(HasAnalysisResults.AnalysisResults_list) - Method in class org.biomage.Experiment.Experiment

Set method for analysisResults

setAnalysisResults(HasAnalysisResults.AnalysisResults_list) - Method in interface org.biomage.Interface.HasAnalysisResults

Set method for analysisResults

setAnnotations(HasAnnotations.Annotations_list) - Method in class org.biomage.Description.Description

Set method for annotations

setAnnotations(HasAnnotations.Annotations_list) - Method in interface org.biomage.Interface.HasAnnotations

Set method for annotations

setArray_list(Array_package.Array_list) - Method in class org.biomage.Array.Array_package

Set method for array_list

setArray_package(Array_package) - Method in class org.biomage.Common.MAGEJava

Set method for array_package

setArray(Array) - Method in class org.biomage.BioAssay.BioAssayCreation

Set method for array

setArray(Array) - Method in interface org.biomage.Interface.HasArray

Set method for array

setArrayDesign_list(ArrayDesign_package.ArrayDesign_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Set method for arrayDesign_list

setArrayDesign_package(ArrayDesign_package) - Method in class org.biomage.Common.MAGEJava

Set method for arrayDesign_package

setArrayDesign(ArrayDesign) - Method in class org.biomage.Array.Array

Set method for arrayDesign

setArrayDesign(ArrayDesign) - Method in interface org.biomage.Interface.HasArrayDesign

Set method for arrayDesign

setArrayGroup_list(Array_package.ArrayGroup_list) - Method in class org.biomage.Array.Array_package

Set method for arrayGroup_list

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

Set method for arrayGroup

setArrayGroup(ArrayGroup) - Method in interface org.biomage.Interface.HasArrayGroup

Set method for arrayGroup

setArrayIdentifier(String) - Method in class org.biomage.Array.Array

Set method for arrayIdentifier

setArrayManufacture_list(Array_package.ArrayManufacture_list) - Method in class org.biomage.Array.Array_package

Set method for arrayManufacture_list

setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list) - Method in class org.biomage.Array.Array

Set method for arrayManufactureDeviations

setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list) - Method in interface org.biomage.Interface.HasArrayManufactureDeviations

Set method for arrayManufactureDeviations

setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list) - Method in class org.biomage.Array.ArrayManufacture

Set method for arrayManufacturers

setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list) - Method in interface org.biomage.Interface.HasArrayManufacturers

Set method for arrayManufacturers

setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayManufacture

Set method for arrays

setArrays(HasArrays.Arrays_list) - Method in class org.biomage.Array.ArrayGroup

Set method for arrays

setArrays(HasArrays.Arrays_list) - Method in interface org.biomage.Interface.HasArrays

Set method for arrays

setArraySpacingX(float) - Method in class org.biomage.Array.ArrayGroup

Set method for arraySpacingX

setArraySpacingY(float) - Method in class org.biomage.Array.ArrayGroup

Set method for arraySpacingY

setArrayXOrigin(float) - Method in class org.biomage.Array.Array

Set method for arrayXOrigin

setArrayYOrigin(float) - Method in class org.biomage.Array.Array

Set method for arrayYOrigin

setAsso(AssociationColumn) - Method in class org.biomage.tools.generate_er.Table

Description: set one association column

setAssoColumnVec(Vector) - Method in class org.biomage.tools.generate_er.Table

Description: set the vector containing all association columns

setAuditAndSecurity_package(AuditAndSecurity_package) - Method in class org.biomage.Common.MAGEJava

Set method for auditAndSecurity_package

setAuditTrail(HasAuditTrail.AuditTrail_list) - Method in class org.biomage.Common.Describable

Set method for auditTrail

setAuditTrail(HasAuditTrail.AuditTrail_list) - Method in interface org.biomage.Interface.HasAuditTrail

Set method for auditTrail

setAuthors(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for authors

setBarcode(String) - Method in class org.biomage.Array.ArrayGroup

Set method for barcode

setBaseClass(String) - Method in class org.biomage.tools.generate_er.Table

Description: set the BaseClass of this table

setBasis(SeqFeature.Basis) - Method in class org.biomage.BioSequence.SeqFeature

Set method for basis

setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list) - Method in class org.biomage.Description.Description

Set method for bibliographicReferences

setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list) - Method in interface org.biomage.Interface.HasBibliographicReferences

Set method for bibliographicReferences

setBioAssay_list(BioAssay_package.BioAssay_list) - Method in class org.biomage.BioAssay.BioAssay_package

Set method for bioAssay_list

setBioAssay_package(BioAssay_package) - Method in class org.biomage.Common.MAGEJava

Set method for bioAssay_package

setBioAssay(BioAssay) - Method in class org.biomage.BioAssayData.BioAssayDatum

Set method for bioAssay

setBioAssay(BioAssay) - Method in interface org.biomage.Interface.HasBioAssay

Set method for bioAssay

setBioAssayCreation(BioAssayCreation) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Set method for bioAssayCreation

setBioAssayCreation(BioAssayCreation) - Method in interface org.biomage.Interface.HasBioAssayCreation

Set method for bioAssayCreation

setBioAssayData_list(BioAssayData_package.BioAssayData_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for bioAssayData_list

setBioAssayData_package(BioAssayData_package) - Method in class org.biomage.Common.MAGEJava

Set method for bioAssayData_package

setBioAssayData(HasBioAssayData.BioAssayData_list) - Method in class org.biomage.Experiment.Experiment

Set method for bioAssayData

setBioAssayData(HasBioAssayData.BioAssayData_list) - Method in interface org.biomage.Interface.HasBioAssayData

Set method for bioAssayData

setBioAssayDataCluster_list(HigherLevelAnalysis_package.BioAssayDataCluster_list) - Method in class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package

Set method for bioAssayDataCluster_list

setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list) - Method in class org.biomage.BioAssayData.Transformation

Set method for bioAssayDataSources

setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list) - Method in interface org.biomage.Interface.HasBioAssayDataSources

Set method for bioAssayDataSources

setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for bioAssayDimension_list

setBioAssayDimension(BioAssayDimension) - Method in class org.biomage.BioAssayData.BioAssayData

Set method for bioAssayDimension

setBioAssayDimension(BioAssayDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents

Set method for bioAssayDimension

setBioAssayDimension(BioAssayDimension) - Method in interface org.biomage.Interface.HasBioAssayDimension

Set method for bioAssayDimension

setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list) - Method in class org.biomage.BioAssay.BioAssay

Set method for bioAssayFactorValues

setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list) - Method in interface org.biomage.Interface.HasBioAssayFactorValues

Set method for bioAssayFactorValues

setBioAssayMap_list(BioAssayData_package.BioAssayMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for bioAssayMap_list

setBioAssayMapping(BioAssayMapping) - Method in class org.biomage.BioAssayData.Transformation

Set method for bioAssayMapping

setBioAssayMapping(BioAssayMapping) - Method in interface org.biomage.Interface.HasBioAssayMapping

Set method for bioAssayMapping

setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list) - Method in class org.biomage.BioAssayData.BioAssayMapping

Set method for bioAssayMaps

setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list) - Method in interface org.biomage.Interface.HasBioAssayMaps

Set method for bioAssayMaps

setBioAssayMapTarget(DerivedBioAssay) - Method in class org.biomage.BioAssayData.BioAssayMap

Set method for bioAssayMapTarget

setBioAssayMapTarget(DerivedBioAssay) - Method in interface org.biomage.Interface.HasBioAssayMapTarget

Set method for bioAssayMapTarget

setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayDimension

Set method for bioAssays

setBioAssays(HasBioAssays.BioAssays_list) - Method in class org.biomage.Experiment.Experiment

Set method for bioAssays

setBioAssays(HasBioAssays.BioAssays_list) - Method in interface org.biomage.Interface.HasBioAssays

Set method for bioAssays

setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Set method for bioAssayTreatments

setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list) - Method in interface org.biomage.Interface.HasBioAssayTreatments

Set method for bioAssayTreatments

setBioAssayTupleData(HasBioAssayTupleData.BioAssayTupleData_list) - Method in class org.biomage.BioAssayData.BioDataTuples

Set method for bioAssayTupleData

setBioAssayTupleData(HasBioAssayTupleData.BioAssayTupleData_list) - Method in interface org.biomage.Interface.HasBioAssayTupleData

Set method for bioAssayTupleData

setBioDataValues(BioDataValues) - Method in class org.biomage.BioAssayData.BioAssayData

Set method for bioDataValues

setBioDataValues(BioDataValues) - Method in interface org.biomage.Interface.HasBioDataValues

Set method for bioDataValues

setBioEvent_package(BioEvent_package) - Method in class org.biomage.Common.MAGEJava

Set method for bioEvent_package

setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list) - Method in class org.biomage.DesignElement.CompositeSequence

Set method for biologicalCharacteristics

setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list) - Method in interface org.biomage.Interface.HasBiologicalCharacteristics

Set method for biologicalCharacteristics

setBioMaterial_list(BioMaterial_package.BioMaterial_list) - Method in class org.biomage.BioMaterial.BioMaterial_package

Set method for bioMaterial_list

setBioMaterial_package(BioMaterial_package) - Method in class org.biomage.Common.MAGEJava

Set method for bioMaterial_package

setBioMaterial(BioMaterial) - Method in class org.biomage.Array.ManufactureLIMS

Set method for bioMaterial

setBioMaterial(BioMaterial) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement

Set method for bioMaterial

setBioMaterial(BioMaterial) - Method in interface org.biomage.Interface.HasBioMaterial

Set method for bioMaterial

setBioMaterialPlateCol(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial

Set method for bioMaterialPlateCol

setBioMaterialPlateIdentifier(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial

Set method for bioMaterialPlateIdentifier

setBioMaterialPlateRow(String) - Method in class org.biomage.Array.ManufactureLIMSBiomaterial

Set method for bioMaterialPlateRow

setBioSequence_list(BioSequence_package.BioSequence_list) - Method in class org.biomage.BioSequence.BioSequence_package

Set method for bioSequence_list

setBioSequence_package(BioSequence_package) - Method in class org.biomage.Common.MAGEJava

Set method for bioSequence_package

setBQS_package(BQS_package) - Method in class org.biomage.Common.MAGEJava

Set method for bQS_package

setCanBeNull(String) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the canBeNull field of this column

setCascade(String) - Method in class org.biomage.tools.generate_er.ForeignKey

Description: set if the foreign table owns this table

setCategory(OntologyEntry) - Method in class org.biomage.Experiment.ExperimentalFactor

Set method for category

setCategory(OntologyEntry) - Method in interface org.biomage.Interface.HasCategory

Set method for category

setCategory(String) - Method in class org.biomage.Description.OntologyEntry

Set method for category

setChannel_list(BioAssay_package.Channel_list) - Method in class org.biomage.BioAssay.BioAssay_package

Set method for channel_list

setChannel(Channel) - Method in interface org.biomage.Interface.HasChannel

Set method for channel

setChannel(Channel) - Method in class org.biomage.QuantitationType.QuantitationType

Set method for channel

setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.Image

Set method for channels

setChannels(HasChannels.Channels_list) - Method in class org.biomage.BioAssay.BioAssay

Set method for channels

setChannels(HasChannels.Channels_list) - Method in interface org.biomage.Interface.HasChannels

Set method for channels

setCharacteristics(HasCharacteristics.Characteristics_list) - Method in class org.biomage.BioMaterial.BioMaterial

Set method for characteristics

setCharacteristics(HasCharacteristics.Characteristics_list) - Method in interface org.biomage.Interface.HasCharacteristics

Set method for characteristics

setClusterBioAssayData(BioAssayData) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Set method for clusterBioAssayData

setClusterBioAssayData(BioAssayData) - Method in interface org.biomage.Interface.HasClusterBioAssayData

Set method for clusterBioAssayData

setColumn(int) - Method in class org.biomage.ArrayDesign.Zone

Set method for column

setColumn(int) - Method in class org.biomage.DesignElement.FeatureLocation

Set method for column

setColumnId(String) - Method in class org.biomage.tools.generate_er.ForeignKey

Description: set the column id of the foreign key

setComment(String) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the Comment of this column

setComment(String) - Method in class org.biomage.tools.generate_er.Table

Description: set the Comment of this table

setComponentCompounds(HasComponentCompounds.ComponentCompounds_list) - Method in class org.biomage.BioMaterial.Compound

Set method for componentCompounds

setComponentCompounds(HasComponentCompounds.ComponentCompounds_list) - Method in interface org.biomage.Interface.HasComponentCompounds

Set method for componentCompounds

setComposite(CompositeSequence) - Method in class org.biomage.DesignElement.CompositePosition

Set method for composite

setComposite(CompositeSequence) - Method in interface org.biomage.Interface.HasComposite

Set method for composite

setCompositeCompositeMap_list(DesignElement_package.CompositeCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package

Set method for compositeCompositeMap_list

setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence

Set method for compositeCompositeMaps

setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list) - Method in interface org.biomage.Interface.HasCompositeCompositeMaps

Set method for compositeCompositeMaps

setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Set method for compositeGroup_list

setCompositeGroups(HasCompositeGroups.CompositeGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for compositeGroups

setCompositeGroups(HasCompositeGroups.CompositeGroups_list) - Method in interface org.biomage.Interface.HasCompositeGroups

Set method for compositeGroups

setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list) - Method in class org.biomage.DesignElement.CompositeCompositeMap

Set method for compositePositionSources

setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list) - Method in interface org.biomage.Interface.HasCompositePositionSources

Set method for compositePositionSources

setCompositeSequence_list(DesignElement_package.CompositeSequence_list) - Method in class org.biomage.DesignElement.DesignElement_package

Set method for compositeSequence_list

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

Set method for compositeSequence

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

Set method for compositeSequence

setCompositeSequence(CompositeSequence) - Method in interface org.biomage.Interface.HasCompositeSequence

Set method for compositeSequence

setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.ArrayDesign.CompositeGroup

Set method for compositeSequences

setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in class org.biomage.BioAssayData.CompositeSequenceDimension

Set method for compositeSequences

setCompositeSequences(HasCompositeSequences.CompositeSequences_list) - Method in interface org.biomage.Interface.HasCompositeSequences

Set method for compositeSequences

setCompound_list(BioMaterial_package.Compound_list) - Method in class org.biomage.BioMaterial.BioMaterial_package

Set method for compound_list

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

Set method for compound

setCompound(Compound) - Method in interface org.biomage.Interface.HasCompound

Set method for compound

setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list) - Method in class org.biomage.BioMaterial.Treatment

Set method for compoundMeasurements

setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list) - Method in interface org.biomage.Interface.HasCompoundMeasurements

Set method for compoundMeasurements

setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list) - Method in interface org.biomage.Interface.HasConfidenceIndicators

Set method for confidenceIndicators

setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list) - Method in class org.biomage.QuantitationType.QuantitationType

Set method for confidenceIndicators

setContact_list(AuditAndSecurity_package.Contact_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Set method for contact_list

setContacts(HasContacts.Contacts_list) - Method in class org.biomage.Description.Database

Set method for contacts

setContacts(HasContacts.Contacts_list) - Method in interface org.biomage.Interface.HasContacts

Set method for contacts

setContainedFeatures(HasContainedFeatures.ContainedFeatures_list) - Method in class org.biomage.BioAssayData.FeatureDimension

Set method for containedFeatures

setContainedFeatures(HasContainedFeatures.ContainedFeatures_list) - Method in interface org.biomage.Interface.HasContainedFeatures

Set method for containedFeatures

setControlFeatures(HasControlFeatures.ControlFeatures_list) - Method in class org.biomage.DesignElement.Feature

Set method for controlFeatures

setControlFeatures(HasControlFeatures.ControlFeatures_list) - Method in interface org.biomage.Interface.HasControlFeatures

Set method for controlFeatures

setControlledFeatures(HasControlledFeatures.ControlledFeatures_list) - Method in class org.biomage.DesignElement.Feature

Set method for controlledFeatures

setControlledFeatures(HasControlledFeatures.ControlledFeatures_list) - Method in interface org.biomage.Interface.HasControlledFeatures

Set method for controlledFeatures

setControlType(OntologyEntry) - Method in class org.biomage.DesignElement.DesignElement

Set method for controlType

setControlType(OntologyEntry) - Method in interface org.biomage.Interface.HasControlType

Set method for controlType

setCoordinate(SequencePosition) - Method in class org.biomage.BioSequence.SeqFeatureLocation

Set method for coordinate

setCoordinate(SequencePosition) - Method in interface org.biomage.Interface.HasCoordinate

Set method for coordinate

setCube(Object[][][]) - Method in class org.biomage.BioAssayData.BioDataCube

Set method for cube

setData(DataColumn) - Method in class org.biomage.tools.generate_er.Table

Description: set one simple data column

setDatabase_list(Description_package.Database_list) - Method in class org.biomage.Description.Description_package

Set method for database_list

setDatabase(Database) - Method in class org.biomage.Description.DatabaseEntry

Set method for database

setDatabase(Database) - Method in interface org.biomage.Interface.HasDatabase

Set method for database

setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list) - Method in class org.biomage.Description.Description

Set method for databaseReferences

setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list) - Method in interface org.biomage.Interface.HasDatabaseReferences

Set method for databaseReferences

setDataColumn(DataColumn) - Method in class org.biomage.tools.generate_er.PrimaryKey

Description: set the primary key column

setDataColumnVec(Vector) - Method in class org.biomage.tools.generate_er.Table

Description: set the vector containing all simple data columns

setDataType(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue

Set method for dataType

setDataType(OntologyEntry) - Method in interface org.biomage.Interface.HasDataType

Set method for dataType

setDataType(OntologyEntry) - Method in class org.biomage.Protocol.Parameter

Set method for dataType

setDataType(OntologyEntry) - Method in class org.biomage.QuantitationType.QuantitationType

Set method for dataType

setDate(Date) - Method in class org.biomage.AuditAndSecurity.Audit

Set method for date

setDefectType(OntologyEntry) - Method in class org.biomage.Array.ZoneDefect

Set method for defectType

setDefectType(OntologyEntry) - Method in class org.biomage.Array.FeatureDefect

Set method for defectType

setDefectType(OntologyEntry) - Method in interface org.biomage.Interface.HasDefectType

Set method for defectType

setDeltaX(float) - Method in class org.biomage.Array.PositionDelta

Set method for deltaX

setDeltaY(float) - Method in class org.biomage.Array.PositionDelta

Set method for deltaY

setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list) - Method in class org.biomage.BioAssay.DerivedBioAssay

Set method for derivedBioAssayData

setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list) - Method in interface org.biomage.Interface.HasDerivedBioAssayData

Set method for derivedBioAssayData

setDerivedBioAssayDataTarget(DerivedBioAssayData) - Method in class org.biomage.BioAssayData.Transformation

Set method for derivedBioAssayDataTarget

setDerivedBioAssayDataTarget(DerivedBioAssayData) - Method in interface org.biomage.Interface.HasDerivedBioAssayDataTarget

Set method for derivedBioAssayDataTarget

setDescription_package(Description_package) - Method in class org.biomage.Common.MAGEJava

Set method for description_package

setDescription(String) - Method in class org.biomage.Description.OntologyEntry

Set method for description

setDescriptions(HasDescriptions.Descriptions_list) - Method in class org.biomage.Common.Describable

Set method for descriptions

setDescriptions(HasDescriptions.Descriptions_list) - Method in interface org.biomage.Interface.HasDescriptions

Set method for descriptions

setDesignElement_package(DesignElement_package) - Method in class org.biomage.Common.MAGEJava

Set method for designElement_package

setDesignElement(DesignElement) - Method in class org.biomage.BioAssayData.BioAssayDatum

Set method for designElement

setDesignElement(DesignElement) - Method in interface org.biomage.Interface.HasDesignElement

Set method for designElement

setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for designElementDimension_list

setDesignElementDimension(DesignElementDimension) - Method in class org.biomage.BioAssayData.BioAssayData

Set method for designElementDimension

setDesignElementDimension(DesignElementDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents

Set method for designElementDimension

setDesignElementDimension(DesignElementDimension) - Method in interface org.biomage.Interface.HasDesignElementDimension

Set method for designElementDimension

setDesignElementMapping(DesignElementMapping) - Method in class org.biomage.BioAssayData.Transformation

Set method for designElementMapping

setDesignElementMapping(DesignElementMapping) - Method in interface org.biomage.Interface.HasDesignElementMapping

Set method for designElementMapping

setDesignElementMaps(HasDesignElementMaps.DesignElementMaps_list) - Method in class org.biomage.BioAssayData.DesignElementMapping

Set method for designElementMaps

setDesignElementMaps(HasDesignElementMaps.DesignElementMaps_list) - Method in interface org.biomage.Interface.HasDesignElementMaps

Set method for designElementMaps

setDesignProviders(HasDesignProviders.DesignProviders_list) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for designProviders

setDesignProviders(HasDesignProviders.DesignProviders_list) - Method in interface org.biomage.Interface.HasDesignProviders

Set method for designProviders

setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.PositionDelta

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.Fiducial

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.Array.ArrayGroup

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneLayout

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.Zone

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in class org.biomage.DesignElement.Position

Set method for distanceUnit

setDistanceUnit(DistanceUnit) - Method in interface org.biomage.Interface.HasDistanceUnit

Set method for distanceUnit

setDocumentLocator(Locator) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

setEditor(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for editor

setEmail(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for email

setEnd(int) - Method in class org.biomage.BioSequence.SequencePosition

Set method for end

setEnumVector(Vector) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the all enum values

setExperiment_list(Experiment_package.Experiment_list) - Method in class org.biomage.Experiment.Experiment_package

Set method for experiment_list

setExperiment_package(Experiment_package) - Method in class org.biomage.Common.MAGEJava

Set method for experiment_package

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

Set method for experimentalFactor

setExperimentalFactor(ExperimentalFactor) - Method in interface org.biomage.Interface.HasExperimentalFactor

Set method for experimentalFactor

setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for experimentalFactors

setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list) - Method in interface org.biomage.Interface.HasExperimentalFactors

Set method for experimentalFactors

setExperimentDesign(ExperimentDesign) - Method in class org.biomage.Experiment.Experiment

Set method for experimentDesign

setExperimentDesign(ExperimentDesign) - Method in interface org.biomage.Interface.HasExperimentDesign

Set method for experimentDesign

setExportedFromDB(String) - Method in class org.biomage.Description.ExternalReference

Set method for exportedFromDB

setExportedFromServer(String) - Method in class org.biomage.Description.ExternalReference

Set method for exportedFromServer

setExportID(String) - Method in class org.biomage.Description.ExternalReference

Set method for exportID

setExportName(String) - Method in class org.biomage.Description.ExternalReference

Set method for exportName

setExternalReference(ExternalReference) - Method in class org.biomage.Description.Description

Set method for externalReference

setExternalReference(ExternalReference) - Method in interface org.biomage.Interface.HasExternalReference

Set method for externalReference

setFactorValues(HasFactorValues.FactorValues_list) - Method in class org.biomage.Experiment.ExperimentalFactor

Set method for factorValues

setFactorValues(HasFactorValues.FactorValues_list) - Method in interface org.biomage.Interface.HasFactorValues

Set method for factorValues

setFailTypes(HasFailTypes.FailTypes_list) - Method in class org.biomage.DesignElement.Reporter

Set method for failTypes

setFailTypes(HasFailTypes.FailTypes_list) - Method in interface org.biomage.Interface.HasFailTypes

Set method for failTypes

setFax(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for fax

setFeature(Feature) - Method in class org.biomage.Array.ManufactureLIMS

Set method for feature

setFeature(Feature) - Method in class org.biomage.Array.FeatureDefect

Set method for feature

setFeature(Feature) - Method in class org.biomage.DesignElement.FeatureInformation

Set method for feature

setFeature(Feature) - Method in interface org.biomage.Interface.HasFeature

Set method for feature

setFeatureDefects(HasFeatureDefects.FeatureDefects_list) - Method in class org.biomage.Array.ArrayManufactureDeviation

Set method for featureDefects

setFeatureDefects(HasFeatureDefects.FeatureDefects_list) - Method in interface org.biomage.Interface.HasFeatureDefects

Set method for featureDefects

setFeatureExtraction(FeatureExtraction) - Method in class org.biomage.BioAssay.MeasuredBioAssay

Set method for featureExtraction

setFeatureExtraction(FeatureExtraction) - Method in interface org.biomage.Interface.HasFeatureExtraction

Set method for featureExtraction

setFeatureGroup(FeatureGroup) - Method in class org.biomage.DesignElement.Feature

Set method for featureGroup

setFeatureGroup(FeatureGroup) - Method in interface org.biomage.Interface.HasFeatureGroup

Set method for featureGroup

setFeatureGroups(HasFeatureGroups.FeatureGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for featureGroups

setFeatureGroups(HasFeatureGroups.FeatureGroups_list) - Method in interface org.biomage.Interface.HasFeatureGroups

Set method for featureGroups

setFeatureHeight(float) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for featureHeight

setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list) - Method in class org.biomage.DesignElement.FeatureReporterMap

Set method for featureInformationSources

setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list) - Method in interface org.biomage.Interface.HasFeatureInformationSources

Set method for featureInformationSources

setFeatureLength(float) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for featureLength

setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list) - Method in class org.biomage.Array.ArrayManufacture

Set method for featureLIMSs

setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list) - Method in interface org.biomage.Interface.HasFeatureLIMSs

Set method for featureLIMSs

setFeatureLocation(FeatureLocation) - Method in class org.biomage.DesignElement.Feature

Set method for featureLocation

setFeatureLocation(FeatureLocation) - Method in interface org.biomage.Interface.HasFeatureLocation

Set method for featureLocation

setFeatureReporterMap_list(DesignElement_package.FeatureReporterMap_list) - Method in class org.biomage.DesignElement.DesignElement_package

Set method for featureReporterMap_list

setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list) - Method in class org.biomage.DesignElement.Reporter

Set method for featureReporterMaps

setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list) - Method in interface org.biomage.Interface.HasFeatureReporterMaps

Set method for featureReporterMaps

setFeatures(HasFeatures.Features_list) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for features

setFeatures(HasFeatures.Features_list) - Method in interface org.biomage.Interface.HasFeatures

Set method for features

setFeatureShape(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for featureShape

setFeatureShape(OntologyEntry) - Method in interface org.biomage.Interface.HasFeatureShape

Set method for featureShape

setFeatureWidth(float) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for featureWidth

setFiducials(HasFiducials.Fiducials_list) - Method in class org.biomage.Array.ArrayGroup

Set method for fiducials

setFiducials(HasFiducials.Fiducials_list) - Method in interface org.biomage.Interface.HasFiducials

Set method for fiducials

setFiducialType(OntologyEntry) - Method in class org.biomage.Array.Fiducial

Set method for fiducialType

setFiducialType(OntologyEntry) - Method in interface org.biomage.Interface.HasFiducialType

Set method for fiducialType

setFirstName(String) - Method in class org.biomage.AuditAndSecurity.Person

Set method for firstName

setForeignKey(ForeignKey) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the foreign key object of this table

setForeignKeyType(String) - Method in class org.biomage.tools.generate_er.ForeignKey

Description: set the type of the foreign key

setForeignTable(String) - Method in class org.biomage.tools.generate_er.ForeignKey

Description: set the foreign table object for this table

setForeignTablePrimaryKey(String) - Method in class org.biomage.tools.generate_er.ForeignKey

Description: set the primary key of the foreign table object

setFormat(OntologyEntry) - Method in class org.biomage.BioAssay.Image

Set method for format

setFormat(OntologyEntry) - Method in interface org.biomage.Interface.HasFormat

Set method for format

setFullName(String) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the full name of this column

setHardware_list(Protocol_package.Hardware_list) - Method in class org.biomage.Protocol.Protocol_package

Set method for hardware_list

setHardware(Hardware) - Method in interface org.biomage.Interface.HasHardware

Set method for hardware

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

Set method for hardware

setHardware(Hardware) - Method in class org.biomage.Protocol.HardwareApplication

Set method for hardware

setHardwareApplications(HasHardwareApplications.HardwareApplications_list) - Method in interface org.biomage.Interface.HasHardwareApplications

Set method for hardwareApplications

setHardwareApplications(HasHardwareApplications.HardwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication

Set method for hardwareApplications

setHardwareManufacturers(HasHardwareManufacturers.HardwareManufacturers_list) - Method in interface org.biomage.Interface.HasHardwareManufacturers

Set method for hardwareManufacturers

setHardwareManufacturers(HasHardwareManufacturers.HardwareManufacturers_list) - Method in class org.biomage.Protocol.Hardware

Set method for hardwareManufacturers

setHardwares(HasHardwares.Hardwares_list) - Method in interface org.biomage.Interface.HasHardwares

Set method for hardwares

setHardwares(HasHardwares.Hardwares_list) - Method in class org.biomage.Protocol.Protocol

Set method for hardwares

setHigherLevelAnalysis_package(HigherLevelAnalysis_package) - Method in class org.biomage.Common.MAGEJava

Set method for higherLevelAnalysis_package

setIdentifier(String) - Method in class org.biomage.Common.Identifiable

Set method for identifier

setIdentifierLIMS(DatabaseEntry) - Method in class org.biomage.Array.ManufactureLIMS

Set method for identifierLIMS

setIdentifierLIMS(DatabaseEntry) - Method in interface org.biomage.Interface.HasIdentifierLIMS

Set method for identifierLIMS

setImages(HasImages.Images_list) - Method in class org.biomage.BioAssay.ImageAcquisition

Set method for images

setImages(HasImages.Images_list) - Method in interface org.biomage.Interface.HasImages

Set method for images

setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list) - Method in class org.biomage.DesignElement.Reporter

Set method for immobilizedCharacteristics

setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list) - Method in interface org.biomage.Interface.HasImmobilizedCharacteristics

Set method for immobilizedCharacteristics

setIndex(Index) - Method in class org.biomage.tools.generate_er.Table

Description: set one index

setIndexColumn(AssociationColumn) - Method in class org.biomage.tools.generate_er.Index

Description: set column id for the index

setIndexVector(Vector) - Method in class org.biomage.tools.generate_er.Table

Description: set the vector for all index

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

Set method for information

setInformation(ArrayManufacture) - Method in interface org.biomage.Interface.HasInformation

Set method for information

setIsAbstract(String) - Method in class org.biomage.tools.generate_er.Table

Description: set if the table is for an abstract class

setIsApproximateLength(boolean) - Method in class org.biomage.BioSequence.BioSequence

Set method for isApproximateLength

setIsBackground(boolean) - Method in class org.biomage.QuantitationType.QuantitationType

Set method for isBackground

setIsCircular(boolean) - Method in class org.biomage.BioSequence.BioSequence

Set method for isCircular

setIsSolvent(boolean) - Method in class org.biomage.BioMaterial.Compound

Set method for isSolvent

setIssue(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for issue

setKindCV(Measurement.KindCV) - Method in class org.biomage.Measurement.Measurement

Set method for kindCV

setLabels(HasLabels.Labels_list) - Method in class org.biomage.BioAssay.Channel

Set method for labels

setLabels(HasLabels.Labels_list) - Method in class org.biomage.BioMaterial.LabeledExtract

Set method for labels

setLabels(HasLabels.Labels_list) - Method in interface org.biomage.Interface.HasLabels

Set method for labels

setLastName(String) - Method in class org.biomage.AuditAndSecurity.Person

Set method for lastName

setLength(float) - Method in class org.biomage.Array.ArrayGroup

Set method for length

setLength(int) - Method in class org.biomage.BioSequence.BioSequence

Set method for length

setLinkingKey(LinkingKey) - Method in class org.biomage.tools.generate_er.Table

Description: set linking key column

setLinkOne(AssociationColumn) - Method in class org.biomage.tools.generate_er.LinkingKey

Description: set one linking key for the table

setLinkTwo(AssociationColumn) - Method in class org.biomage.tools.generate_er.LinkingKey

Description: set the other linking key for the table

setLowerRightX(float) - Method in class org.biomage.ArrayDesign.Zone

Set method for lowerRightX

setLowerRightY(float) - Method in class org.biomage.ArrayDesign.Zone

Set method for lowerRightY

setMake(String) - Method in class org.biomage.Protocol.Hardware

Set method for make

setManufacturingDate(String) - Method in class org.biomage.Array.ArrayManufacture

Set method for manufacturingDate

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

Set method for materialType

setMaterialType(OntologyEntry) - Method in interface org.biomage.Interface.HasMaterialType

Set method for materialType

setMaxCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the maximum cardinality of the assocaition class

setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list) - Method in class org.biomage.BioAssay.MeasuredBioAssay

Set method for measuredBioAssayData

setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list) - Method in interface org.biomage.Interface.HasMeasuredBioAssayData

Set method for measuredBioAssayData

setMeasuredBioAssayTarget(MeasuredBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction

Set method for measuredBioAssayTarget

setMeasuredBioAssayTarget(MeasuredBioAssay) - Method in interface org.biomage.Interface.HasMeasuredBioAssayTarget

Set method for measuredBioAssayTarget

setMeasurement_package(Measurement_package) - Method in class org.biomage.Common.MAGEJava

Set method for measurement_package

setMeasurement(Measurement) - Method in class org.biomage.BioMaterial.CompoundMeasurement

Set method for measurement

setMeasurement(Measurement) - Method in class org.biomage.BioMaterial.BioMaterialMeasurement

Set method for measurement

setMeasurement(Measurement) - Method in class org.biomage.Experiment.FactorValue

Set method for measurement

setMeasurement(Measurement) - Method in interface org.biomage.Interface.HasMeasurement

Set method for measurement

setMembers(HasMembers.Members_list) - Method in class org.biomage.AuditAndSecurity.SecurityGroup

Set method for members

setMembers(HasMembers.Members_list) - Method in interface org.biomage.Interface.HasMembers

Set method for members

setMerckIndex(OntologyEntry) - Method in class org.biomage.BioMaterial.Compound

Set method for merckIndex

setMerckIndex(OntologyEntry) - Method in interface org.biomage.Interface.HasMerckIndex

Set method for merckIndex

setMidInitials(String) - Method in class org.biomage.AuditAndSecurity.Person

Set method for midInitials

setMinCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the minimum cardinality of the assocaition class

setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.ReporterPosition

Set method for mismatchInformation

setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.FeatureInformation

Set method for mismatchInformation

setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in class org.biomage.DesignElement.CompositePosition

Set method for mismatchInformation

setMismatchInformation(HasMismatchInformation.MismatchInformation_list) - Method in interface org.biomage.Interface.HasMismatchInformation

Set method for mismatchInformation

setModel(String) - Method in class org.biomage.Protocol.Hardware

Set method for model

setName(String) - Method in class org.biomage.Common.NameValueType

Set method for name

setName(String) - Method in class org.biomage.Common.Identifiable

Set method for name

setName(String) - Method in class org.biomage.HigherLevelAnalysis.NodeValue

Set method for name

setName(String) - Method in class org.biomage.tools.generate_er.Index

Description: set name of the index

setName(String) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the name of this column

setName(String) - Method in class org.biomage.tools.generate_er.Table

Description: set the name of this table

setNameByValue(int) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition

setNameByValue(int) - Method in class org.biomage.AuditAndSecurity.Audit.Action

setNameByValue(int) - Method in class org.biomage.BioAssayData.BioDataCube.Order

setNameByValue(int) - Method in class org.biomage.BioSequence.SeqFeature.Basis

setNameByValue(int) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.Measurement.Type

setNameByValue(int) - Method in class org.biomage.Measurement.Measurement.KindCV

setNameByValue(int) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV

setNameByValue(int) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV

setNameByValueAction(int) - Method in class org.biomage.AuditAndSecurity.Audit

For Action set the Name of the Enumeration type by passing a value (int)

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

For Basis set the Name of the Enumeration type by passing a value (int)

setNameByValueKindCV(int) - Method in class org.biomage.Measurement.Measurement

For KindCV set the Name of the Enumeration type by passing a value (int)

setNameByValueOrder(int) - Method in class org.biomage.BioAssayData.BioDataCube

For Order set the Name of the Enumeration type by passing a value (int)

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

For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)

setNameByValueType(int) - Method in class org.biomage.Measurement.Measurement

For Type set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.VolumeUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TimeUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.TemperatureUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.QuantityUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.MassUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.DistanceUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNameByValueUnitNameCV(int) - Method in class org.biomage.Measurement.ConcentrationUnit

For UnitNameCV set the Name of the Enumeration type by passing a value (int)

setNewSequence(String) - Method in class org.biomage.DesignElement.MismatchInformation

Set method for newSequence

setNodeContents(HasNodeContents.NodeContents_list) - Method in class org.biomage.HigherLevelAnalysis.Node

Set method for nodeContents

setNodeContents(HasNodeContents.NodeContents_list) - Method in interface org.biomage.Interface.HasNodeContents

Set method for nodeContents

setNodes(HasNodes.Nodes_list) - Method in class org.biomage.HigherLevelAnalysis.Node

Set method for nodes

setNodes(HasNodes.Nodes_list) - Method in class org.biomage.HigherLevelAnalysis.BioAssayDataCluster

Set method for nodes

setNodes(HasNodes.Nodes_list) - Method in interface org.biomage.Interface.HasNodes

Set method for nodes

setNodeValue(HasNodeValue.NodeValue_list) - Method in class org.biomage.HigherLevelAnalysis.Node

Set method for nodeValue

setNodeValue(HasNodeValue.NodeValue_list) - Method in interface org.biomage.Interface.HasNodeValue

Set method for nodeValue

setNormalizationDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for normalizationDescription

setNormalizationDescription(Description) - Method in interface org.biomage.Interface.HasNormalizationDescription

Set method for normalizationDescription

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

Set method for numArrays

setNumberOfFeatures(int) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for numberOfFeatures

setNumFeaturesPerCol(int) - Method in class org.biomage.ArrayDesign.ZoneLayout

Set method for numFeaturesPerCol

setNumFeaturesPerRow(int) - Method in class org.biomage.ArrayDesign.ZoneLayout

Set method for numFeaturesPerRow

setOneColumn(DataColumn) - Method in class org.biomage.tools.generate_er.Unique

Description: set the one of the columns consisting the Unique

setOntologyEntries(HasOntologyEntries.OntologyEntries_list) - Method in class org.biomage.BioSequence.BioSequence

Set method for ontologyEntries

setOntologyEntries(HasOntologyEntries.OntologyEntries_list) - Method in interface org.biomage.Interface.HasOntologyEntries

Set method for ontologyEntries

setOntologyReference(DatabaseEntry) - Method in class org.biomage.Description.OntologyEntry

Set method for ontologyReference

setOntologyReference(DatabaseEntry) - Method in interface org.biomage.Interface.HasOntologyReference

Set method for ontologyReference

setOrder(BioDataCube.Order) - Method in class org.biomage.BioAssayData.BioDataCube

Set method for order

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

Set method for order

setOrientationMark(String) - Method in class org.biomage.Array.ArrayGroup

Set method for orientationMark

setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition) - Method in class org.biomage.Array.ArrayGroup

Set method for orientationMarkPosition

setOriginRelativeTo(String) - Method in class org.biomage.Array.Array

Set method for originRelativeTo

setOtherKind(String) - Method in class org.biomage.Measurement.Measurement

Set method for otherKind

setOwner(Contact) - Method in class org.biomage.AuditAndSecurity.Security

Set method for owner

setOwner(Contact) - Method in interface org.biomage.Interface.HasOwner

Set method for owner

setOwner(String) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the owner of the association relationship

setPages(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for pages

setParameters(HasParameters.Parameters_list) - Method in class org.biomage.BQS.BibliographicReference

Set method for parameters

setParameters(HasParameters.Parameters_list) - Method in interface org.biomage.Interface.HasParameters

Set method for parameters

setParameterType(Parameter) - Method in interface org.biomage.Interface.HasParameterType

Set method for parameterType

setParameterType(Parameter) - Method in class org.biomage.Protocol.ParameterValue

Set method for parameterType

setParameterTypes(HasParameterTypes.ParameterTypes_list) - Method in interface org.biomage.Interface.HasParameterTypes

Set method for parameterTypes

setParameterTypes(HasParameterTypes.ParameterTypes_list) - Method in class org.biomage.Protocol.Parameterizable

Set method for parameterTypes

setParameterValues(HasParameterValues.ParameterValues_list) - Method in interface org.biomage.Interface.HasParameterValues

Set method for parameterValues

setParameterValues(HasParameterValues.ParameterValues_list) - Method in class org.biomage.Protocol.ParameterizableApplication

Set method for parameterValues

setParent(Organization) - Method in class org.biomage.AuditAndSecurity.Organization

Set method for parent

setParent(Organization) - Method in interface org.biomage.Interface.HasParent

Set method for parent

setPerformer(Contact) - Method in class org.biomage.AuditAndSecurity.Audit

Set method for performer

setPerformer(Contact) - Method in interface org.biomage.Interface.HasPerformer

Set method for performer

setPerformers(HasPerformers.Performers_list) - Method in interface org.biomage.Interface.HasPerformers

Set method for performers

setPerformers(HasPerformers.Performers_list) - Method in class org.biomage.Protocol.ProtocolApplication

Set method for performers

setPhone(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for phone

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

Set method for physicalBioAssay

setPhysicalBioAssay(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssay

Set method for physicalBioAssay

setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list) - Method in class org.biomage.BioAssay.PhysicalBioAssay

Set method for physicalBioAssayData

setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list) - Method in interface org.biomage.Interface.HasPhysicalBioAssayData

Set method for physicalBioAssayData

setPhysicalBioAssaySource(PhysicalBioAssay) - Method in class org.biomage.BioAssay.FeatureExtraction

Set method for physicalBioAssaySource

setPhysicalBioAssaySource(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssaySource

Set method for physicalBioAssaySource

setPhysicalBioAssayTarget(PhysicalBioAssay) - Method in class org.biomage.BioAssay.BioAssayCreation

Set method for physicalBioAssayTarget

setPhysicalBioAssayTarget(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasPhysicalBioAssayTarget

Set method for physicalBioAssayTarget

setPK(PrimaryKey) - Method in class org.biomage.tools.generate_er.Table

Description: set the primary key for the table

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

Set method for polymerType

setPolymerType(OntologyEntry) - Method in interface org.biomage.Interface.HasPolymerType

Set method for polymerType

setPosition(Position) - Method in class org.biomage.Array.Fiducial

Set method for position

setPosition(Position) - Method in class org.biomage.DesignElement.Feature

Set method for position

setPosition(Position) - Method in interface org.biomage.Interface.HasPosition

Set method for position

setPositionDelta(PositionDelta) - Method in class org.biomage.Array.ZoneDefect

Set method for positionDelta

setPositionDelta(PositionDelta) - Method in class org.biomage.Array.FeatureDefect

Set method for positionDelta

setPositionDelta(PositionDelta) - Method in interface org.biomage.Interface.HasPositionDelta

Set method for positionDelta

setProducerTransformation(Transformation) - Method in class org.biomage.BioAssayData.DerivedBioAssayData

Set method for producerTransformation

setProducerTransformation(Transformation) - Method in interface org.biomage.Interface.HasProducerTransformation

Set method for producerTransformation

setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.NameValueType

Set method for propertySets

setPropertySets(HasPropertySets.PropertySets_list) - Method in class org.biomage.Common.Extendable

Set method for propertySets

setPropertySets(HasPropertySets.PropertySets_list) - Method in interface org.biomage.Interface.HasPropertySets

Set method for propertySets

setProtocol_list(Protocol_package.Protocol_list) - Method in class org.biomage.Protocol.Protocol_package

Set method for protocol_list

setProtocol_package(Protocol_package) - Method in class org.biomage.Common.MAGEJava

Set method for protocol_package

setProtocol(Protocol) - Method in interface org.biomage.Interface.HasProtocol

Set method for protocol

setProtocol(Protocol) - Method in class org.biomage.Protocol.ProtocolApplication

Set method for protocol

setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.Array.ArrayManufacture

Set method for protocolApplications

setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for protocolApplications

setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in class org.biomage.BioEvent.BioEvent

Set method for protocolApplications

setProtocolApplications(HasProtocolApplications.ProtocolApplications_list) - Method in interface org.biomage.Interface.HasProtocolApplications

Set method for protocolApplications

setProviders(HasProviders.Providers_list) - Method in class org.biomage.Experiment.Experiment

Set method for providers

setProviders(HasProviders.Providers_list) - Method in interface org.biomage.Interface.HasProviders

Set method for providers

setPublication(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for publication

setPublisher(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for publisher

setQuality(String) - Method in class org.biomage.Array.ManufactureLIMS

Set method for quality

setQualityControlDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for qualityControlDescription

setQualityControlDescription(Description) - Method in interface org.biomage.Interface.HasQualityControlDescription

Set method for qualityControlDescription

setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in class org.biomage.Array.ArrayManufacture

Set method for qualityControlStatistics

setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in class org.biomage.BioMaterial.BioMaterial

Set method for qualityControlStatistics

setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list) - Method in interface org.biomage.Interface.HasQualityControlStatistics

Set method for qualityControlStatistics

setQuantitationDimension(QuantitationTypeDimension) - Method in class org.biomage.HigherLevelAnalysis.NodeContents

Set method for quantitationDimension

setQuantitationDimension(QuantitationTypeDimension) - Method in interface org.biomage.Interface.HasQuantitationDimension

Set method for quantitationDimension

setQuantitationType_list(QuantitationType_package.QuantitationType_list) - Method in class org.biomage.QuantitationType.QuantitationType_package

Set method for quantitationType_list

setQuantitationType_package(QuantitationType_package) - Method in class org.biomage.Common.MAGEJava

Set method for quantitationType_package

setQuantitationType(QuantitationType) - Method in class org.biomage.BioAssayData.BioAssayDatum

Set method for quantitationType

setQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasQuantitationType

Set method for quantitationType

setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for quantitationTypeDimension_list

setQuantitationTypeDimension(QuantitationTypeDimension) - Method in class org.biomage.BioAssayData.BioAssayData

Set method for quantitationTypeDimension

setQuantitationTypeDimension(QuantitationTypeDimension) - Method in interface org.biomage.Interface.HasQuantitationTypeDimension

Set method for quantitationTypeDimension

setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list) - Method in class org.biomage.BioAssayData.BioAssayData_package

Set method for quantitationTypeMap_list

setQuantitationTypeMapping(QuantitationTypeMapping) - Method in class org.biomage.BioAssayData.Transformation

Set method for quantitationTypeMapping

setQuantitationTypeMapping(QuantitationTypeMapping) - Method in interface org.biomage.Interface.HasQuantitationTypeMapping

Set method for quantitationTypeMapping

setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMapping

Set method for quantitationTypeMaps

setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list) - Method in interface org.biomage.Interface.HasQuantitationTypeMaps

Set method for quantitationTypeMaps

setQuantitationTypes(HasQuantitationTypes.QuantitationTypes_list) - Method in class org.biomage.BioAssayData.QuantitationTypeDimension

Set method for quantitationTypes

setQuantitationTypes(HasQuantitationTypes.QuantitationTypes_list) - Method in interface org.biomage.Interface.HasQuantitationTypes

Set method for quantitationTypes

setReadGroups(HasReadGroups.ReadGroups_list) - Method in class org.biomage.AuditAndSecurity.Security

Set method for readGroups

setReadGroups(HasReadGroups.ReadGroups_list) - Method in interface org.biomage.Interface.HasReadGroups

Set method for readGroups

setRegions(HasRegions.Regions_list) - Method in class org.biomage.BioSequence.SeqFeature

Set method for regions

setRegions(HasRegions.Regions_list) - Method in interface org.biomage.Interface.HasRegions

Set method for regions

setReleaseDate(Date) - Method in class org.biomage.Protocol.SoftwareApplication

Set method for releaseDate

setReplacedLength(int) - Method in class org.biomage.DesignElement.MismatchInformation

Set method for replacedLength

setReplicateDescription(Description) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for replicateDescription

setReplicateDescription(Description) - Method in interface org.biomage.Interface.HasReplicateDescription

Set method for replicateDescription

setReporter_list(DesignElement_package.Reporter_list) - Method in class org.biomage.DesignElement.DesignElement_package

Set method for reporter_list

setReporter(Reporter) - Method in class org.biomage.DesignElement.ReporterPosition

Set method for reporter

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

Set method for reporter

setReporter(Reporter) - Method in interface org.biomage.Interface.HasReporter

Set method for reporter

setReporterCompositeMap_list(DesignElement_package.ReporterCompositeMap_list) - Method in class org.biomage.DesignElement.DesignElement_package

Set method for reporterCompositeMap_list

setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list) - Method in class org.biomage.DesignElement.CompositeSequence

Set method for reporterCompositeMaps

setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list) - Method in interface org.biomage.Interface.HasReporterCompositeMaps

Set method for reporterCompositeMaps

setReporterGroup_list(ArrayDesign_package.ReporterGroup_list) - Method in class org.biomage.ArrayDesign.ArrayDesign_package

Set method for reporterGroup_list

setReporterGroups(HasReporterGroups.ReporterGroups_list) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for reporterGroups

setReporterGroups(HasReporterGroups.ReporterGroups_list) - Method in interface org.biomage.Interface.HasReporterGroups

Set method for reporterGroups

setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list) - Method in class org.biomage.DesignElement.ReporterCompositeMap

Set method for reporterPositionSources

setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list) - Method in interface org.biomage.Interface.HasReporterPositionSources

Set method for reporterPositionSources

setReporters(HasReporters.Reporters_list) - Method in class org.biomage.ArrayDesign.ReporterGroup

Set method for reporters

setReporters(HasReporters.Reporters_list) - Method in class org.biomage.BioAssayData.ReporterDimension

Set method for reporters

setReporters(HasReporters.Reporters_list) - Method in interface org.biomage.Interface.HasReporters

Set method for reporters

setRoles(HasRoles.Roles_list) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for roles

setRoles(HasRoles.Roles_list) - Method in interface org.biomage.Interface.HasRoles

Set method for roles

setRow(int) - Method in class org.biomage.ArrayDesign.Zone

Set method for row

setRow(int) - Method in class org.biomage.DesignElement.FeatureLocation

Set method for row

setScale(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue

Set method for scale

setScale(OntologyEntry) - Method in interface org.biomage.Interface.HasScale

Set method for scale

setScale(OntologyEntry) - Method in class org.biomage.QuantitationType.QuantitationType

Set method for scale

setSecurity_list(AuditAndSecurity_package.Security_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Set method for security_list

setSecurity(Security) - Method in class org.biomage.Common.Describable

Set method for security

setSecurity(Security) - Method in interface org.biomage.Interface.HasSecurity

Set method for security

setSecurityGroup_list(AuditAndSecurity_package.SecurityGroup_list) - Method in class org.biomage.AuditAndSecurity.AuditAndSecurity_package

Set method for securityGroup_list

setSeqFeatures(HasSeqFeatures.SeqFeatures_list) - Method in class org.biomage.BioSequence.BioSequence

Set method for seqFeatures

setSeqFeatures(HasSeqFeatures.SeqFeatures_list) - Method in interface org.biomage.Interface.HasSeqFeatures

Set method for seqFeatures

setSequence(String) - Method in class org.biomage.BioSequence.BioSequence

Set method for sequence

setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list) - Method in class org.biomage.BioSequence.BioSequence

Set method for sequenceDatabases

setSequenceDatabases(HasSequenceDatabases.SequenceDatabases_list) - Method in interface org.biomage.Interface.HasSequenceDatabases

Set method for sequenceDatabases

setSerialNumber(String) - Method in class org.biomage.Protocol.HardwareApplication

Set method for serialNumber

setSoftware_list(Protocol_package.Software_list) - Method in class org.biomage.Protocol.Protocol_package

Set method for software_list

setSoftware(Software) - Method in interface org.biomage.Interface.HasSoftware

Set method for software

setSoftware(Software) - Method in class org.biomage.Protocol.SoftwareApplication

Set method for software

setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list) - Method in interface org.biomage.Interface.HasSoftwareApplications

Set method for softwareApplications

setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list) - Method in class org.biomage.Protocol.ProtocolApplication

Set method for softwareApplications

setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list) - Method in interface org.biomage.Interface.HasSoftwareManufacturers

Set method for softwareManufacturers

setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list) - Method in class org.biomage.Protocol.Software

Set method for softwareManufacturers

setSoftwares(HasSoftwares.Softwares_list) - Method in interface org.biomage.Interface.HasSoftwares

Set method for softwares

setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Software

Set method for softwares

setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Protocol

Set method for softwares

setSoftwares(HasSoftwares.Softwares_list) - Method in class org.biomage.Protocol.Hardware

Set method for softwares

setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list) - Method in class org.biomage.BioAssayData.BioAssayMap

Set method for sourceBioAssays

setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list) - Method in interface org.biomage.Interface.HasSourceBioAssays

Set method for sourceBioAssays

setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in class org.biomage.BioAssay.BioAssayCreation

Set method for sourceBioMaterialMeasurements

setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in class org.biomage.BioMaterial.Treatment

Set method for sourceBioMaterialMeasurements

setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list) - Method in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

Set method for sourceBioMaterialMeasurements

setSourceContact(Contact) - Method in class org.biomage.BioMaterial.BioSource

Set method for sourceContact

setSourceContact(Contact) - Method in interface org.biomage.Interface.HasSourceContact

Set method for sourceContact

setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list) - Method in class org.biomage.BioAssayData.QuantitationTypeMap

Set method for sourcesQuantitationType

setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list) - Method in interface org.biomage.Interface.HasSourcesQuantitationType

Set method for sourcesQuantitationType

setSpacingBetweenCols(float) - Method in class org.biomage.ArrayDesign.ZoneLayout

Set method for spacingBetweenCols

setSpacingBetweenRows(float) - Method in class org.biomage.ArrayDesign.ZoneLayout

Set method for spacingBetweenRows

setSpacingsBetweenZonesX(float) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for spacingsBetweenZonesX

setSpacingsBetweenZonesY(float) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for spacingsBetweenZonesY

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

Set method for species

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

Set method for species

setSpecies(OntologyEntry) - Method in interface org.biomage.Interface.HasSpecies

Set method for species

setStart(int) - Method in class org.biomage.BioSequence.SequencePosition

Set method for start

setStartCoord(int) - Method in class org.biomage.DesignElement.MismatchInformation

Set method for startCoord

setStrandType(String) - Method in class org.biomage.BioSequence.SeqFeatureLocation

Set method for strandType

setSubregions(HasSubregions.Subregions_list) - Method in class org.biomage.BioSequence.SeqFeatureLocation

Set method for subregions

setSubregions(HasSubregions.Subregions_list) - Method in interface org.biomage.Interface.HasSubregions

Set method for subregions

setSubstrateType(OntologyEntry) - Method in class org.biomage.Array.ArrayGroup

Set method for substrateType

setSubstrateType(OntologyEntry) - Method in interface org.biomage.Interface.HasSubstrateType

Set method for substrateType

setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list) - Method in class org.biomage.BioAssayData.BioAssayData

Set method for summaryStatistics

setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list) - Method in interface org.biomage.Interface.HasSummaryStatistics

Set method for summaryStatistics

setSurfaceType(OntologyEntry) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign

Set method for surfaceType

setSurfaceType(OntologyEntry) - Method in interface org.biomage.Interface.HasSurfaceType

Set method for surfaceType

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

Set method for target

setTarget(PhysicalBioAssay) - Method in interface org.biomage.Interface.HasTarget

Set method for target

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

Set method for targetQuantitationType

setTargetQuantitationType(QuantitationType) - Method in interface org.biomage.Interface.HasTargetQuantitationType

Set method for targetQuantitationType

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

Set method for targetQuantitationType

setTechnologyType(OntologyEntry) - Method in class org.biomage.ArrayDesign.FeatureGroup

Set method for technologyType

setTechnologyType(OntologyEntry) - Method in interface org.biomage.Interface.HasTechnologyType

Set method for technologyType

setText(String) - Method in class org.biomage.Description.Description

Set method for text

setText(String) - Method in class org.biomage.Protocol.Protocol

Set method for text

setThisMaxCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the maximum cardinality of this table for the association relationship

setThisMinCard(String) - Method in class org.biomage.tools.generate_er.AssociationColumn

Description: set the maximum cardinality of this table for the association relationship

setTitle(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for title

setTitle(String) - Method in class org.biomage.Protocol.Protocol

Set method for title

setTolerance(float) - Method in class org.biomage.Array.ArrayManufacture

Set method for tolerance

setTollFreePhone(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for tollFreePhone

setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for topLevelBioAssays

setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list) - Method in interface org.biomage.Interface.HasTopLevelBioAssays

Set method for topLevelBioAssays

setTreatments(HasTreatments.Treatments_list) - Method in class org.biomage.BioMaterial.BioMaterial

Set method for treatments

setTreatments(HasTreatments.Treatments_list) - Method in interface org.biomage.Interface.HasTreatments

Set method for treatments

setType(Measurement.Type) - Method in class org.biomage.Measurement.Measurement

Set method for type

setType(OntologyEntry) - Method in class org.biomage.BioAssay.DerivedBioAssay

Set method for type

setType(OntologyEntry) - Method in class org.biomage.BioMaterial.BioSample

Set method for type

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

Set method for type

setType(OntologyEntry) - Method in class org.biomage.Description.DatabaseEntry

Set method for type

setType(OntologyEntry) - Method in class org.biomage.HigherLevelAnalysis.NodeValue

Set method for type

setType(OntologyEntry) - Method in interface org.biomage.Interface.HasType

Set method for type

setType(OntologyEntry) - Method in class org.biomage.Protocol.Software

Set method for type

setType(OntologyEntry) - Method in class org.biomage.Protocol.Protocol

Set method for type

setType(OntologyEntry) - Method in class org.biomage.Protocol.Hardware

Set method for type

setType(String) - Method in class org.biomage.Common.NameValueType

Set method for type

setType(String) - Method in class org.biomage.tools.generate_er.DataColumn

Description: set the Type of this column

setType(String) - Method in class org.biomage.tools.generate_er.Table

Description: set the Type of this table

setTypes(HasTypes.Types_list) - Method in class org.biomage.ArrayDesign.DesignElementGroup

Set method for types

setTypes(HasTypes.Types_list) - Method in class org.biomage.Experiment.ExperimentDesign

Set method for types

setTypes(HasTypes.Types_list) - Method in interface org.biomage.Interface.HasTypes

Set method for types

setUnique(Unique) - Method in class org.biomage.tools.generate_er.Table

Description: set the unique column

setUniqueVector(Vector) - Method in class org.biomage.tools.generate_er.Unique

Description: set the vector holding all columns that consists the Unique

setUnit(Unit) - Method in interface org.biomage.Interface.HasUnit

Set method for unit

setUnit(Unit) - Method in class org.biomage.Measurement.Measurement

Set method for unit

setUnit(Unit) - Method in class org.biomage.Protocol.Parameter

Set method for unit

setUnitName(String) - Method in class org.biomage.Measurement.Unit

Set method for unitName

setUnitNameCV(ConcentrationUnit.UnitNameCV) - Method in class org.biomage.Measurement.ConcentrationUnit

Set method for unitNameCV

setUnitNameCV(DistanceUnit.UnitNameCV) - Method in class org.biomage.Measurement.DistanceUnit

Set method for unitNameCV

setUnitNameCV(MassUnit.UnitNameCV) - Method in class org.biomage.Measurement.MassUnit

Set method for unitNameCV

setUnitNameCV(QuantityUnit.UnitNameCV) - Method in class org.biomage.Measurement.QuantityUnit

Set method for unitNameCV

setUnitNameCV(TemperatureUnit.UnitNameCV) - Method in class org.biomage.Measurement.TemperatureUnit

Set method for unitNameCV

setUnitNameCV(TimeUnit.UnitNameCV) - Method in class org.biomage.Measurement.TimeUnit

Set method for unitNameCV

setUnitNameCV(VolumeUnit.UnitNameCV) - Method in class org.biomage.Measurement.VolumeUnit

Set method for unitNameCV

setUpperLeftX(float) - Method in class org.biomage.ArrayDesign.Zone

Set method for upperLeftX

setUpperLeftY(float) - Method in class org.biomage.ArrayDesign.Zone

Set method for upperLeftY

setURI(String) - Method in class org.biomage.AuditAndSecurity.Contact

Set method for URI

setURI(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for URI

setURI(String) - Method in class org.biomage.BioAssay.Image

Set method for URI

setURI(String) - Method in class org.biomage.Description.DatabaseEntry

Set method for URI

setURI(String) - Method in class org.biomage.Description.Database

Set method for URI

setURI(String) - Method in class org.biomage.Protocol.Parameterizable

Set method for URI

setValue(Object) - Method in class org.biomage.BioAssayData.BioAssayDatum

Set method for value

setValue(Object) - Method in class org.biomage.HigherLevelAnalysis.NodeValue

Set method for value

setValue(Object) - Method in class org.biomage.Measurement.Measurement

Set method for value

setValue(Object) - Method in class org.biomage.Protocol.ParameterValue

Set method for value

setValue(String) - Method in class org.biomage.Common.NameValueType

Set method for value

setValue(String) - Method in class org.biomage.Description.OntologyEntry

Set method for value

setValueByName(String) - Method in class org.biomage.Array.ArrayGroup.OrientationMarkPosition

setValueByName(String) - Method in class org.biomage.AuditAndSecurity.Audit.Action

setValueByName(String) - Method in class org.biomage.BioAssayData.BioDataCube.Order

setValueByName(String) - Method in class org.biomage.BioSequence.SeqFeature.Basis

setValueByName(String) - Method in class org.biomage.Measurement.VolumeUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.TimeUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.TemperatureUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.QuantityUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.Measurement.Type

setValueByName(String) - Method in class org.biomage.Measurement.Measurement.KindCV

setValueByName(String) - Method in class org.biomage.Measurement.MassUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.DistanceUnit.UnitNameCV

setValueByName(String) - Method in class org.biomage.Measurement.ConcentrationUnit.UnitNameCV

setValueByNameAction(String) - Method in class org.biomage.AuditAndSecurity.Audit

For Action set the Value of the Enumeration type by passing a Name to it.

setValueByNameBasis(String) - Method in class org.biomage.BioSequence.SeqFeature

For Basis set the Value of the Enumeration type by passing a Name to it.

setValueByNameKindCV(String) - Method in class org.biomage.Measurement.Measurement

For KindCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameOrder(String) - Method in class org.biomage.BioAssayData.BioDataCube

For Order set the Value of the Enumeration type by passing a Name to it.

setValueByNameOrientationMarkPosition(String) - Method in class org.biomage.Array.ArrayGroup

For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.

setValueByNameType(String) - Method in class org.biomage.Measurement.Measurement

For Type set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.VolumeUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TimeUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.TemperatureUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.QuantityUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.MassUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.DistanceUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setValueByNameUnitNameCV(String) - Method in class org.biomage.Measurement.ConcentrationUnit

For UnitNameCV set the Value of the Enumeration type by passing a Name to it.

setVerbose(int) - Static method in class org.biomage.tools.helpers.StringOutputHelpers

Description: Looks for verboseness argument to set the level of output.

setVersion(String) - Method in class org.biomage.ArrayDesign.ArrayDesign

Set method for version

setVersion(String) - Method in class org.biomage.Description.Database

Set method for version

setVersion(String) - Method in class org.biomage.Protocol.SoftwareApplication

Set method for version

setVolume(String) - Method in class org.biomage.BQS.BibliographicReference

Set method for volume

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

Set method for warningType

setWarningType(OntologyEntry) - Method in interface org.biomage.Interface.HasWarningType

Set method for warningType

setWidth(float) - Method in class org.biomage.Array.ArrayGroup

Set method for width

setWriteGroups(HasWriteGroups.WriteGroups_list) - Method in class org.biomage.AuditAndSecurity.Security

Set method for writeGroups

setWriteGroups(HasWriteGroups.WriteGroups_list) - Method in interface org.biomage.Interface.HasWriteGroups

Set method for writeGroups

setX(float) - Method in class org.biomage.DesignElement.Position

Set method for x

setY(float) - Method in class org.biomage.DesignElement.Position

Set method for y

setYear(Date) - Method in class org.biomage.BQS.BibliographicReference

Set method for year

setZone(Zone) - Method in class org.biomage.Array.ZoneDefect

Set method for zone

setZone(Zone) - Method in class org.biomage.DesignElement.Feature

Set method for zone

setZone(Zone) - Method in interface org.biomage.Interface.HasZone

Set method for zone

setZoneGroups(HasZoneGroups.ZoneGroups_list) - Method in class org.biomage.ArrayDesign.PhysicalArrayDesign

Set method for zoneGroups

setZoneGroups(HasZoneGroups.ZoneGroups_list) - Method in interface org.biomage.Interface.HasZoneGroups

Set method for zoneGroups

setZoneLayout(ZoneLayout) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for zoneLayout

setZoneLayout(ZoneLayout) - Method in interface org.biomage.Interface.HasZoneLayout

Set method for zoneLayout

setZoneLocations(HasZoneLocations.ZoneLocations_list) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for zoneLocations

setZoneLocations(HasZoneLocations.ZoneLocations_list) - Method in interface org.biomage.Interface.HasZoneLocations

Set method for zoneLocations

setZonesPerX(int) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for zonesPerX

setZonesPerY(int) - Method in class org.biomage.ArrayDesign.ZoneGroup

Set method for zonesPerY

skippedEntity(String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

software - Variable in class org.biomage.Protocol.SoftwareApplication

The underlying software.

Software - class org.biomage.Protocol.Software.

Software represents the software used.

software_list - Variable in class org.biomage.Protocol.Protocol_package

Software represents the software used.

Software() - Constructor for class org.biomage.Protocol.Software

Default constructor.

Software(Attributes) - Constructor for class org.biomage.Protocol.Software

Attribute constructor.

SoftwareApplication - class org.biomage.Protocol.SoftwareApplication.

The use of a piece of software with the requisite Parameters and ParameterValues.

SoftwareApplication() - Constructor for class org.biomage.Protocol.SoftwareApplication

Default constructor.

SoftwareApplication(Attributes) - Constructor for class org.biomage.Protocol.SoftwareApplication

Attribute constructor.

softwareApplications - Variable in class org.biomage.Protocol.ProtocolApplication

The use of software for the application of the protocol.

softwareManufacturers - Variable in class org.biomage.Protocol.Software

Contact for information on the software.

softwares - Variable in class org.biomage.Protocol.Software

Software packages this software uses, i.e.

softwares - Variable in class org.biomage.Protocol.Protocol

Software used by this Protocol.

softwares - Variable in class org.biomage.Protocol.Hardware

Associates Hardware and Software together.

sourceBioAssays - Variable in class org.biomage.BioAssayData.BioAssayMap

The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

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

The BioSample and its amount used in the BioAssayCreation event.

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

The BioMaterials and the amounts used in the treatment

sourceContact - Variable in class org.biomage.BioMaterial.BioSource

The BioSource's source is the provider of the biological material (a cell line, strain, etc...).

sourcesQuantitationType - Variable in class org.biomage.BioAssayData.QuantitationTypeMap

The QuantitationType sources for values for the transformation.

SpecializedQuantitationType - class org.biomage.QuantitationType.SpecializedQuantitationType.

User defined quantitation type.

SpecializedQuantitationType() - Constructor for class org.biomage.QuantitationType.SpecializedQuantitationType

Default constructor.

SpecializedQuantitationType(Attributes) - Constructor for class org.biomage.QuantitationType.SpecializedQuantitationType

Attribute constructor.

species - Variable in class org.biomage.ArrayDesign.DesignElementGroup

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

species - Variable in class org.biomage.BioSequence.BioSequence

The organism from which this sequence was obtained.

StandardQuantitationType - class org.biomage.QuantitationType.StandardQuantitationType.

Superclass for the named quantitation type.

StandardQuantitationType() - Constructor for class org.biomage.QuantitationType.StandardQuantitationType

Default constructor.

StandardQuantitationType(Attributes) - Constructor for class org.biomage.QuantitationType.StandardQuantitationType

Attribute constructor.

startDocument() - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

startElement(String, String, String, Attributes) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

startPrefixMapping(String, String) - Method in class org.biomage.tools.xmlutils.MAGEContentHandler

StringOutputHelpers - class org.biomage.tools.helpers.StringOutputHelpers.

Description: Class that provides static helper metheds for outputting strings.

StringOutputHelpers() - Constructor for class org.biomage.tools.helpers.StringOutputHelpers

subregions - Variable in class org.biomage.BioSequence.SeqFeatureLocation

Regions within the SeqFeature.

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

table type is subset

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

Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.

summaryStatistics - Variable in class org.biomage.BioAssayData.BioAssayData

Statistics on the Quality of the BioAssayData.

surfaceType - Variable in class org.biomage.ArrayDesign.PhysicalArrayDesign

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