Hierarchy For All Packages

Package Hierarchies:

org.biomage.Array, org.biomage.ArrayDesign, org.biomage.AuditAndSecurity, org.biomage.BioAssay, org.biomage.BioAssayData, org.biomage.BioEvent, org.biomage.BioMaterial, org.biomage.BioSequence, org.biomage.BQS, org.biomage.Common, org.biomage.Description, org.biomage.DesignElement, org.biomage.Experiment, org.biomage.HigherLevelAnalysis, org.biomage.Interface, org.biomage.Measurement, org.biomage.Protocol, org.biomage.QuantitationType, org.biomage.tools.generate_er, org.biomage.tools.helpers, org.biomage.tools.xmlutils

Class Hierarchy

• class java.lang.Object
  • class java.util.AbstractCollection (implements java.util.Collection)
    • class java.util.AbstractList (implements java.util.List)
      • class java.util.Vector (implements java.lang.Cloneable, java.util.List, java.util.RandomAccess, java.io.Serializable)
        • class org.biomage.Array.Array_package.Array_list
        • class org.biomage.Array.Array_package.ArrayGroup_list
        • class org.biomage.Array.Array_package.ArrayManufacture_list
        • class org.biomage.ArrayDesign.ArrayDesign_package.ArrayDesign_list
        • class org.biomage.ArrayDesign.ArrayDesign_package.CompositeGroup_list
        • class org.biomage.ArrayDesign.ArrayDesign_package.ReporterGroup_list
        • class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Contact_list
        • class org.biomage.AuditAndSecurity.AuditAndSecurity_package.Security_list
        • class org.biomage.AuditAndSecurity.AuditAndSecurity_package.SecurityGroup_list
        • class org.biomage.BioAssay.BioAssay_package.BioAssay_list
        • class org.biomage.BioAssay.BioAssay_package.Channel_list
        • class org.biomage.BioAssayData.BioAssayData_package.BioAssayData_list
        • class org.biomage.BioAssayData.BioAssayData_package.BioAssayDimension_list
        • class org.biomage.BioAssayData.BioAssayData_package.BioAssayMap_list
        • class org.biomage.BioAssayData.BioAssayData_package.DesignElementDimension_list
        • class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeDimension_list
        • class org.biomage.BioAssayData.BioAssayData_package.QuantitationTypeMap_list
        • class org.biomage.BioMaterial.BioMaterial_package.BioMaterial_list
        • class org.biomage.BioMaterial.BioMaterial_package.Compound_list
        • class org.biomage.BioSequence.BioSequence_package.BioSequence_list
        • class org.biomage.Description.Description_package.Database_list
        • class org.biomage.DesignElement.DesignElement_package.CompositeCompositeMap_list
        • class org.biomage.DesignElement.DesignElement_package.CompositeSequence_list
        • class org.biomage.DesignElement.DesignElement_package.FeatureReporterMap_list
        • class org.biomage.DesignElement.DesignElement_package.Reporter_list
        • class org.biomage.DesignElement.DesignElement_package.ReporterCompositeMap_list
        • class org.biomage.Experiment.Experiment_package.Experiment_list
        • class org.biomage.Interface.HasAdjustments.Adjustments_list
        • class org.biomage.Interface.HasAnalysisResults.AnalysisResults_list
        • class org.biomage.Interface.HasAnnotations.Annotations_list
        • class org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list
        • class org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list
        • class org.biomage.Interface.HasArrays.Arrays_list
        • class org.biomage.Interface.HasAuditTrail.AuditTrail_list
        • class org.biomage.Interface.HasBibliographicReferences.BibliographicReferences_list
        • class org.biomage.Interface.HasBioAssayData.BioAssayData_list
        • class org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list
        • class org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list
        • class org.biomage.Interface.HasBioAssayMaps.BioAssayMaps_list
        • class org.biomage.Interface.HasBioAssays.BioAssays_list
        • class org.biomage.Interface.HasBioAssayTreatments.BioAssayTreatments_list
        • class org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list
        • class org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list
        • class org.biomage.Interface.HasChannels.Channels_list
        • class org.biomage.Interface.HasCharacteristics.Characteristics_list
        • class org.biomage.Interface.HasComponentCompounds.ComponentCompounds_list
        • class org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list
        • class org.biomage.Interface.HasCompositeGroups.CompositeGroups_list
        • class org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list
        • class org.biomage.Interface.HasCompositeSequences.CompositeSequences_list
        • class org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list
        • class org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list
        • class org.biomage.Interface.HasContacts.Contacts_list
        • class org.biomage.Interface.HasContainedFeatures.ContainedFeatures_list
        • class org.biomage.Interface.HasControlFeatures.ControlFeatures_list
        • class org.biomage.Interface.HasControlledFeatures.ControlledFeatures_list
        • class org.biomage.Interface.HasDatabaseReferences.DatabaseReferences_list
        • class org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list
        • class org.biomage.Interface.HasDescriptions.Descriptions_list
        • class org.biomage.Interface.HasDesignElementMaps.DesignElementMaps_list
        • class org.biomage.Interface.HasDesignProviders.DesignProviders_list
        • class org.biomage.Interface.HasExperimentalFactors.ExperimentalFactors_list
        • class org.biomage.Interface.HasFactorValues.FactorValues_list
        • class org.biomage.Interface.HasFailTypes.FailTypes_list
        • class org.biomage.Interface.HasFeatureDefects.FeatureDefects_list
        • class org.biomage.Interface.HasFeatureGroups.FeatureGroups_list
        • class org.biomage.Interface.HasFeatureInformationSources.FeatureInformationSources_list
        • class org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list
        • class org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list
        • class org.biomage.Interface.HasFeatures.Features_list
        • class org.biomage.Interface.HasFiducials.Fiducials_list
        • class org.biomage.Interface.HasHardwareApplications.HardwareApplications_list
        • class org.biomage.Interface.HasHardwareManufacturers.HardwareManufacturers_list
        • class org.biomage.Interface.HasHardwares.Hardwares_list
        • class org.biomage.Interface.HasImages.Images_list
        • class org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list
        • class org.biomage.Interface.HasLabels.Labels_list
        • class org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list
        • class org.biomage.Interface.HasMembers.Members_list
        • class org.biomage.Interface.HasMismatchInformation.MismatchInformation_list
        • class org.biomage.Interface.HasNodeContents.NodeContents_list
        • class org.biomage.Interface.HasNodes.Nodes_list
        • class org.biomage.Interface.HasNodeValue.NodeValue_list
        • class org.biomage.Interface.HasOntologyEntries.OntologyEntries_list
        • class org.biomage.Interface.HasParameters.Parameters_list
        • class org.biomage.Interface.HasParameterTypes.ParameterTypes_list
        • class org.biomage.Interface.HasParameterValues.ParameterValues_list
        • class org.biomage.Interface.HasPerformers.Performers_list
        • class org.biomage.Interface.HasPhysicalBioAssayData.PhysicalBioAssayData_list
        • class org.biomage.Interface.HasPropertySets.PropertySets_list
        • class org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
        • class org.biomage.Interface.HasProviders.Providers_list
        • class org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list
        • class org.biomage.Interface.HasQuantitationTypeMaps.QuantitationTypeMaps_list
        • class org.biomage.Interface.HasQuantitationTypes.QuantitationTypes_list
        • class org.biomage.Interface.HasReadGroups.ReadGroups_list
        • class org.biomage.Interface.HasRegions.Regions_list
        • class org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list
        • class org.biomage.Interface.HasReporterGroups.ReporterGroups_list
        • class org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list
        • class org.biomage.Interface.HasReporters.Reporters_list
        • class org.biomage.Interface.HasRoles.Roles_list
        • class org.biomage.Interface.HasSeqFeatures.SeqFeatures_list
        • class org.biomage.Interface.HasSequenceDatabases.SequenceDatabases_list
        • class org.biomage.Interface.HasSoftwareApplications.SoftwareApplications_list
        • class org.biomage.Interface.HasSoftwareManufacturers.SoftwareManufacturers_list
        • class org.biomage.Interface.HasSoftwares.Softwares_list
        • class org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list
        • class org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list
        • class org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list
        • class org.biomage.Interface.HasSubregions.Subregions_list
        • class org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list
        • class org.biomage.Interface.HasTopLevelBioAssays.TopLevelBioAssays_list
        • class org.biomage.Interface.HasTreatments.Treatments_list
        • class org.biomage.Interface.HasTypes.Types_list
        • class org.biomage.Interface.HasWriteGroups.WriteGroups_list
        • class org.biomage.Interface.HasZoneGroups.ZoneGroups_list
        • class org.biomage.Interface.HasZoneLocations.ZoneLocations_list
        • class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package.BioAssayDataCluster_list
        • class org.biomage.Protocol.Protocol_package.Hardware_list
        • class org.biomage.Protocol.Protocol_package.Protocol_list
        • class org.biomage.Protocol.Protocol_package.Software_list
        • class org.biomage.QuantitationType.QuantitationType_package.QuantitationType_list
  • class java.util.AbstractMap (implements java.util.Map)
    • class java.util.HashMap (implements java.lang.Cloneable, java.util.Map, java.io.Serializable)
      • class org.biomage.tools.xmlutils.MultiHashMap (implements org.biomage.tools.xmlutils.MultiMap)
  • class org.biomage.Array.Array_package (implements java.io.Serializable)
  • class org.biomage.ArrayDesign.ArrayDesign_package (implements java.io.Serializable)
  • class org.biomage.Array.ArrayGroup.OrientationMarkPosition
  • class org.biomage.AuditAndSecurity.Audit.Action
  • class org.biomage.AuditAndSecurity.AuditAndSecurity_package (implements java.io.Serializable)
  • class org.biomage.BioAssay.BioAssay_package (implements java.io.Serializable)
  • class org.biomage.BioAssayData.BioAssayData_package (implements java.io.Serializable)
  • class org.biomage.BioAssayData.BioDataCube.Order
  • class org.biomage.BioEvent.BioEvent_package (implements java.io.Serializable)
  • class org.biomage.BioMaterial.BioMaterial_package (implements java.io.Serializable)
  • class org.biomage.BioSequence.BioSequence_package (implements java.io.Serializable)
  • class org.biomage.BQS.BQS_package (implements java.io.Serializable)
  • class org.biomage.Measurement.ConcentrationUnit.UnitNameCV
  • class org.biomage.tools.generate_er.CreateMageER
  • class org.biomage.tools.generate_er.DataColumn
    • class org.biomage.tools.generate_er.AssociationColumn
  • class org.biomage.Description.Description_package (implements java.io.Serializable)
  • class org.biomage.DesignElement.DesignElement_package (implements java.io.Serializable)
  • class java.util.Dictionary
    • class java.util.Hashtable (implements java.lang.Cloneable, java.util.Map, java.io.Serializable)
      • class org.biomage.tools.xmlutils.MultiHashtable (implements org.biomage.tools.xmlutils.MultiMap)
  • class org.biomage.Measurement.DistanceUnit.UnitNameCV
  • class org.biomage.Experiment.Experiment_package (implements java.io.Serializable)
  • class org.biomage.Common.Extendable (implements org.biomage.Interface.HasPropertySets, java.io.Serializable)
    • class org.biomage.Array.ArrayManufactureDeviation (implements org.biomage.Interface.HasAdjustments, org.biomage.Interface.HasFeatureDefects, java.io.Serializable)
    • class org.biomage.BioAssayData.BioAssayDatum (implements org.biomage.Interface.HasBioAssay, org.biomage.Interface.HasDesignElement, org.biomage.Interface.HasQuantitationType, java.io.Serializable)
    • class org.biomage.BioAssayData.BioAssayMapping (implements org.biomage.Interface.HasBioAssayMaps, java.io.Serializable)
    • class org.biomage.BioAssayData.BioDataValues (implements java.io.Serializable)
      • class org.biomage.BioAssayData.BioDataCube (implements java.io.Serializable)
      • class org.biomage.BioAssayData.BioDataTuples (implements org.biomage.Interface.HasBioAssayTupleData, java.io.Serializable)
    • class org.biomage.BioMaterial.BioMaterialMeasurement (implements org.biomage.Interface.HasBioMaterial, org.biomage.Interface.HasMeasurement, java.io.Serializable)
    • class org.biomage.BioMaterial.CompoundMeasurement (implements org.biomage.Interface.HasCompound, org.biomage.Interface.HasMeasurement, java.io.Serializable)
    • class org.biomage.Description.DatabaseEntry (implements org.biomage.Interface.HasDatabase, org.biomage.Interface.HasType, java.io.Serializable)
    • class org.biomage.Common.Describable (implements org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasSecurity, java.io.Serializable)
      • class org.biomage.AuditAndSecurity.Audit (implements org.biomage.Interface.HasPerformer, java.io.Serializable)
      • class org.biomage.BQS.BibliographicReference (implements org.biomage.Interface.HasParameters, java.io.Serializable)
      • class org.biomage.Description.Description (implements org.biomage.Interface.HasAnnotations, org.biomage.Interface.HasBibliographicReferences, org.biomage.Interface.HasDatabaseReferences, org.biomage.Interface.HasExternalReference, java.io.Serializable)
      • class org.biomage.Experiment.ExperimentDesign (implements org.biomage.Interface.HasExperimentalFactors, org.biomage.Interface.HasNormalizationDescription, org.biomage.Interface.HasQualityControlDescription, org.biomage.Interface.HasReplicateDescription, org.biomage.Interface.HasTopLevelBioAssays, org.biomage.Interface.HasTypes, java.io.Serializable)
      • class org.biomage.Array.Fiducial (implements org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFiducialType, org.biomage.Interface.HasPosition, java.io.Serializable)
      • class org.biomage.Common.Identifiable (implements java.io.Serializable)
        • class org.biomage.Array.Array (implements org.biomage.Interface.HasArrayDesign, org.biomage.Interface.HasArrayGroup, org.biomage.Interface.HasArrayManufactureDeviations, org.biomage.Interface.HasInformation, java.io.Serializable)
        • class org.biomage.ArrayDesign.ArrayDesign (implements org.biomage.Interface.HasCompositeGroups, org.biomage.Interface.HasDesignProviders, org.biomage.Interface.HasFeatureGroups, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasReporterGroups, java.io.Serializable)
          • class org.biomage.ArrayDesign.PhysicalArrayDesign (implements org.biomage.Interface.HasSurfaceType, org.biomage.Interface.HasZoneGroups, java.io.Serializable)
        • class org.biomage.Array.ArrayGroup (implements org.biomage.Interface.HasArrays, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFiducials, org.biomage.Interface.HasSubstrateType, java.io.Serializable)
        • class org.biomage.Array.ArrayManufacture (implements org.biomage.Interface.HasArrayManufacturers, org.biomage.Interface.HasArrays, org.biomage.Interface.HasFeatureLIMSs, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasQualityControlStatistics, java.io.Serializable)
        • class org.biomage.BioAssay.BioAssay (implements org.biomage.Interface.HasBioAssayFactorValues, org.biomage.Interface.HasChannels, java.io.Serializable)
          • class org.biomage.BioAssay.DerivedBioAssay (implements org.biomage.Interface.HasDerivedBioAssayData, org.biomage.Interface.HasType, java.io.Serializable)
          • class org.biomage.BioAssay.MeasuredBioAssay (implements org.biomage.Interface.HasFeatureExtraction, org.biomage.Interface.HasMeasuredBioAssayData, java.io.Serializable)
          • class org.biomage.BioAssay.PhysicalBioAssay (implements org.biomage.Interface.HasBioAssayCreation, org.biomage.Interface.HasBioAssayTreatments, org.biomage.Interface.HasPhysicalBioAssayData, java.io.Serializable)
        • class org.biomage.BioAssayData.BioAssayData (implements org.biomage.Interface.HasBioAssayDimension, org.biomage.Interface.HasBioDataValues, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasQuantitationTypeDimension, org.biomage.Interface.HasSummaryStatistics, java.io.Serializable)
          • class org.biomage.BioAssayData.DerivedBioAssayData (implements org.biomage.Interface.HasProducerTransformation, java.io.Serializable)
          • class org.biomage.BioAssayData.MeasuredBioAssayData (implements java.io.Serializable)
        • class org.biomage.HigherLevelAnalysis.BioAssayDataCluster (implements org.biomage.Interface.HasClusterBioAssayData, org.biomage.Interface.HasNodes, java.io.Serializable)
        • class org.biomage.BioAssayData.BioAssayDimension (implements org.biomage.Interface.HasBioAssays, java.io.Serializable)
        • class org.biomage.BioEvent.BioEvent (implements org.biomage.Interface.HasProtocolApplications, java.io.Serializable)
          • class org.biomage.BioAssay.BioAssayCreation (implements org.biomage.Interface.HasArray, org.biomage.Interface.HasPhysicalBioAssayTarget, org.biomage.Interface.HasSourceBioMaterialMeasurements, java.io.Serializable)
            • class org.biomage.BioAssay.Hybridization (implements java.io.Serializable)
          • class org.biomage.BioAssay.BioAssayTreatment (implements org.biomage.Interface.HasPhysicalBioAssay, org.biomage.Interface.HasTarget, java.io.Serializable)
            • class org.biomage.BioAssay.ImageAcquisition (implements org.biomage.Interface.HasImages, java.io.Serializable)
          • class org.biomage.BioAssay.FeatureExtraction (implements org.biomage.Interface.HasMeasuredBioAssayTarget, org.biomage.Interface.HasPhysicalBioAssaySource, java.io.Serializable)
          • class org.biomage.BioEvent.Map (implements java.io.Serializable)
            • class org.biomage.BioAssayData.BioAssayMap (implements org.biomage.Interface.HasBioAssayMapTarget, org.biomage.Interface.HasSourceBioAssays, java.io.Serializable)
            • class org.biomage.BioAssayData.DesignElementMap (implements java.io.Serializable)
              • class org.biomage.DesignElement.CompositeCompositeMap (implements org.biomage.Interface.HasCompositePositionSources, org.biomage.Interface.HasCompositeSequence, java.io.Serializable)
              • class org.biomage.DesignElement.FeatureReporterMap (implements org.biomage.Interface.HasFeatureInformationSources, org.biomage.Interface.HasReporter, java.io.Serializable)
              • class org.biomage.DesignElement.ReporterCompositeMap (implements org.biomage.Interface.HasCompositeSequence, org.biomage.Interface.HasReporterPositionSources, java.io.Serializable)
            • class org.biomage.BioAssayData.QuantitationTypeMap (implements org.biomage.Interface.HasSourcesQuantitationType, org.biomage.Interface.HasTargetQuantitationType, java.io.Serializable)
          • class org.biomage.BioAssayData.Transformation (implements org.biomage.Interface.HasBioAssayDataSources, org.biomage.Interface.HasBioAssayMapping, org.biomage.Interface.HasDerivedBioAssayDataTarget, org.biomage.Interface.HasDesignElementMapping, org.biomage.Interface.HasQuantitationTypeMapping, java.io.Serializable)
          • class org.biomage.BioMaterial.Treatment (implements org.biomage.Interface.HasAction, org.biomage.Interface.HasActionMeasurement, org.biomage.Interface.HasCompoundMeasurements, org.biomage.Interface.HasSourceBioMaterialMeasurements, java.io.Serializable)
        • class org.biomage.BioMaterial.BioMaterial (implements org.biomage.Interface.HasCharacteristics, org.biomage.Interface.HasMaterialType, org.biomage.Interface.HasQualityControlStatistics, org.biomage.Interface.HasTreatments, java.io.Serializable)
          • class org.biomage.BioMaterial.BioSample (implements org.biomage.Interface.HasType, java.io.Serializable)
          • class org.biomage.BioMaterial.BioSource (implements org.biomage.Interface.HasSourceContact, java.io.Serializable)
          • class org.biomage.BioMaterial.LabeledExtract (implements org.biomage.Interface.HasLabels, java.io.Serializable)
        • class org.biomage.BioSequence.BioSequence (implements org.biomage.Interface.HasOntologyEntries, org.biomage.Interface.HasPolymerType, org.biomage.Interface.HasSeqFeatures, org.biomage.Interface.HasSequenceDatabases, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasType, java.io.Serializable)
        • class org.biomage.BioAssay.Channel (implements org.biomage.Interface.HasLabels, java.io.Serializable)
        • class org.biomage.BioMaterial.Compound (implements org.biomage.Interface.HasComponentCompounds, org.biomage.Interface.HasMerckIndex, java.io.Serializable)
        • class org.biomage.AuditAndSecurity.Contact (implements org.biomage.Interface.HasRoles, java.io.Serializable)
          • class org.biomage.AuditAndSecurity.Organization (implements org.biomage.Interface.HasParent, java.io.Serializable)
          • class org.biomage.AuditAndSecurity.Person (implements org.biomage.Interface.HasAffiliation, java.io.Serializable)
        • class org.biomage.Description.Database (implements org.biomage.Interface.HasContacts, java.io.Serializable)
        • class org.biomage.DesignElement.DesignElement (implements org.biomage.Interface.HasControlType, java.io.Serializable)
          • class org.biomage.DesignElement.CompositeSequence (implements org.biomage.Interface.HasBiologicalCharacteristics, org.biomage.Interface.HasCompositeCompositeMaps, org.biomage.Interface.HasReporterCompositeMaps, java.io.Serializable)
          • class org.biomage.DesignElement.Feature (implements org.biomage.Interface.HasControlFeatures, org.biomage.Interface.HasControlledFeatures, org.biomage.Interface.HasFeatureGroup, org.biomage.Interface.HasFeatureLocation, org.biomage.Interface.HasPosition, org.biomage.Interface.HasZone, java.io.Serializable)
          • class org.biomage.DesignElement.Reporter (implements org.biomage.Interface.HasFailTypes, org.biomage.Interface.HasFeatureReporterMaps, org.biomage.Interface.HasImmobilizedCharacteristics, org.biomage.Interface.HasWarningType, java.io.Serializable)
        • class org.biomage.BioAssayData.DesignElementDimension (implements java.io.Serializable)
          • class org.biomage.BioAssayData.CompositeSequenceDimension (implements org.biomage.Interface.HasCompositeSequences, java.io.Serializable)
          • class org.biomage.BioAssayData.FeatureDimension (implements org.biomage.Interface.HasContainedFeatures, java.io.Serializable)
          • class org.biomage.BioAssayData.ReporterDimension (implements org.biomage.Interface.HasReporters, java.io.Serializable)
        • class org.biomage.ArrayDesign.DesignElementGroup (implements org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes, java.io.Serializable)
          • class org.biomage.ArrayDesign.CompositeGroup (implements org.biomage.Interface.HasCompositeSequences, java.io.Serializable)
          • class org.biomage.ArrayDesign.FeatureGroup (implements org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFeatures, org.biomage.Interface.HasFeatureShape, org.biomage.Interface.HasTechnologyType, java.io.Serializable)
          • class org.biomage.ArrayDesign.ReporterGroup (implements org.biomage.Interface.HasReporters, java.io.Serializable)
        • class org.biomage.Experiment.Experiment (implements org.biomage.Interface.HasAnalysisResults, org.biomage.Interface.HasBioAssayData, org.biomage.Interface.HasBioAssays, org.biomage.Interface.HasExperimentDesign, org.biomage.Interface.HasProviders, java.io.Serializable)
        • class org.biomage.Experiment.ExperimentalFactor (implements org.biomage.Interface.HasCategory, org.biomage.Interface.HasFactorValues, java.io.Serializable)
        • class org.biomage.Experiment.FactorValue (implements org.biomage.Interface.HasExperimentalFactor, org.biomage.Interface.HasMeasurement, java.io.Serializable)
        • class org.biomage.BioAssay.Image (implements org.biomage.Interface.HasChannels, org.biomage.Interface.HasFormat, java.io.Serializable)
        • class org.biomage.Protocol.Parameter (implements org.biomage.Interface.HasDataType, org.biomage.Interface.HasUnit, java.io.Serializable)
        • class org.biomage.Protocol.Parameterizable (implements org.biomage.Interface.HasParameterTypes, java.io.Serializable)
          • class org.biomage.Protocol.Hardware (implements org.biomage.Interface.HasHardwareManufacturers, org.biomage.Interface.HasSoftwares, org.biomage.Interface.HasType, java.io.Serializable)
          • class org.biomage.Protocol.Protocol (implements org.biomage.Interface.HasHardwares, org.biomage.Interface.HasSoftwares, org.biomage.Interface.HasType, java.io.Serializable)
          • class org.biomage.Protocol.Software (implements org.biomage.Interface.HasHardware, org.biomage.Interface.HasSoftwareManufacturers, org.biomage.Interface.HasSoftwares, org.biomage.Interface.HasType, java.io.Serializable)
        • class org.biomage.QuantitationType.QuantitationType (implements org.biomage.Interface.HasChannel, org.biomage.Interface.HasConfidenceIndicators, org.biomage.Interface.HasDataType, org.biomage.Interface.HasScale, java.io.Serializable)
          • class org.biomage.QuantitationType.SpecializedQuantitationType (implements java.io.Serializable)
          • class org.biomage.QuantitationType.StandardQuantitationType (implements java.io.Serializable)
            • class org.biomage.QuantitationType.ConfidenceIndicator (implements org.biomage.Interface.HasTargetQuantitationType, java.io.Serializable)
              • class org.biomage.QuantitationType.Error (implements java.io.Serializable)
              • class org.biomage.QuantitationType.ExpectedValue (implements java.io.Serializable)
              • class org.biomage.QuantitationType.PValue (implements java.io.Serializable)
            • class org.biomage.QuantitationType.DerivedSignal (implements java.io.Serializable)
            • class org.biomage.QuantitationType.MeasuredSignal (implements java.io.Serializable)
            • class org.biomage.QuantitationType.PresentAbsent (implements java.io.Serializable)
            • class org.biomage.QuantitationType.Ratio (implements java.io.Serializable)
        • class org.biomage.BioAssayData.QuantitationTypeDimension (implements org.biomage.Interface.HasQuantitationTypes, java.io.Serializable)
        • class org.biomage.AuditAndSecurity.Security (implements org.biomage.Interface.HasOwner, org.biomage.Interface.HasReadGroups, org.biomage.Interface.HasWriteGroups, java.io.Serializable)
        • class org.biomage.AuditAndSecurity.SecurityGroup (implements org.biomage.Interface.HasMembers, java.io.Serializable)
        • class org.biomage.ArrayDesign.Zone (implements org.biomage.Interface.HasDistanceUnit, java.io.Serializable)
      • class org.biomage.Array.ManufactureLIMS (implements org.biomage.Interface.HasBioMaterial, org.biomage.Interface.HasFeature, org.biomage.Interface.HasIdentifierLIMS, java.io.Serializable)
        • class org.biomage.Array.ManufactureLIMSBiomaterial (implements java.io.Serializable)
      • class org.biomage.HigherLevelAnalysis.Node (implements org.biomage.Interface.HasNodeContents, org.biomage.Interface.HasNodes, org.biomage.Interface.HasNodeValue, java.io.Serializable)
      • class org.biomage.HigherLevelAnalysis.NodeContents (implements org.biomage.Interface.HasBioAssayDimension, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasQuantitationDimension, java.io.Serializable)
      • class org.biomage.Protocol.ParameterizableApplication (implements org.biomage.Interface.HasParameterValues, java.io.Serializable)
        • class org.biomage.Protocol.HardwareApplication (implements org.biomage.Interface.HasHardware, java.io.Serializable)
        • class org.biomage.Protocol.ProtocolApplication (implements org.biomage.Interface.HasHardwareApplications, org.biomage.Interface.HasPerformers, org.biomage.Interface.HasProtocol, org.biomage.Interface.HasSoftwareApplications, java.io.Serializable)
        • class org.biomage.Protocol.SoftwareApplication (implements org.biomage.Interface.HasSoftware, java.io.Serializable)
      • class org.biomage.BioSequence.SeqFeature (implements org.biomage.Interface.HasRegions, java.io.Serializable)
    • class org.biomage.BioAssayData.DesignElementMapping (implements org.biomage.Interface.HasDesignElementMaps, java.io.Serializable)
    • class org.biomage.Description.ExternalReference (implements java.io.Serializable)
    • class org.biomage.Array.FeatureDefect (implements org.biomage.Interface.HasDefectType, org.biomage.Interface.HasFeature, org.biomage.Interface.HasPositionDelta, java.io.Serializable)
    • class org.biomage.DesignElement.FeatureInformation (implements org.biomage.Interface.HasFeature, org.biomage.Interface.HasMismatchInformation, java.io.Serializable)
    • class org.biomage.Measurement.Measurement (implements org.biomage.Interface.HasUnit, java.io.Serializable)
    • class org.biomage.DesignElement.MismatchInformation (implements java.io.Serializable)
    • class org.biomage.HigherLevelAnalysis.NodeValue (implements org.biomage.Interface.HasDataType, org.biomage.Interface.HasScale, org.biomage.Interface.HasType, java.io.Serializable)
    • class org.biomage.Description.OntologyEntry (implements org.biomage.Interface.HasOntologyReference, java.io.Serializable)
    • class org.biomage.Protocol.ParameterValue (implements org.biomage.Interface.HasParameterType, java.io.Serializable)
    • class org.biomage.DesignElement.Position (implements org.biomage.Interface.HasDistanceUnit, java.io.Serializable)
    • class org.biomage.Array.PositionDelta (implements org.biomage.Interface.HasDistanceUnit, java.io.Serializable)
    • class org.biomage.BioAssayData.QuantitationTypeMapping (implements org.biomage.Interface.HasQuantitationTypeMaps, java.io.Serializable)
    • class org.biomage.BioSequence.SeqFeatureLocation (implements org.biomage.Interface.HasCoordinate, org.biomage.Interface.HasSubregions, java.io.Serializable)
    • class org.biomage.BioSequence.SequencePosition (implements java.io.Serializable)
      • class org.biomage.DesignElement.CompositePosition (implements org.biomage.Interface.HasComposite, org.biomage.Interface.HasMismatchInformation, java.io.Serializable)
      • class org.biomage.DesignElement.ReporterPosition (implements org.biomage.Interface.HasMismatchInformation, org.biomage.Interface.HasReporter, java.io.Serializable)
    • class org.biomage.Measurement.Unit (implements java.io.Serializable)
      • class org.biomage.Measurement.ConcentrationUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.DistanceUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.MassUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.QuantityUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.TemperatureUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.TimeUnit (implements java.io.Serializable)
      • class org.biomage.Measurement.VolumeUnit (implements java.io.Serializable)
    • class org.biomage.Array.ZoneDefect (implements org.biomage.Interface.HasDefectType, org.biomage.Interface.HasPositionDelta, org.biomage.Interface.HasZone, java.io.Serializable)
    • class org.biomage.ArrayDesign.ZoneGroup (implements org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasZoneLayout, org.biomage.Interface.HasZoneLocations, java.io.Serializable)
    • class org.biomage.ArrayDesign.ZoneLayout (implements org.biomage.Interface.HasDistanceUnit, java.io.Serializable)
  • class org.biomage.DesignElement.FeatureLocation (implements java.io.Serializable)
  • class org.biomage.tools.generate_er.ForeignKey
  • class org.biomage.HigherLevelAnalysis.HigherLevelAnalysis_package (implements java.io.Serializable)
  • class org.biomage.tools.xmlutils.Importer
  • class org.biomage.tools.xmlutils.ImportExportTest
  • class org.biomage.tools.generate_er.Index
  • class org.biomage.tools.generate_er.LinkingKey
  • class org.biomage.tools.xmlutils.MAGEContentHandler (implements org.xml.sax.ContentHandler)
  • class org.biomage.tools.xmlutils.MAGEContentHandler.UnresolvedRef
  • class org.biomage.Common.MAGEJava (implements java.io.Serializable)
  • class org.biomage.Measurement.MassUnit.UnitNameCV
  • class org.biomage.Measurement.Measurement_package (implements java.io.Serializable)
  • class org.biomage.Measurement.Measurement.KindCV
  • class org.biomage.Measurement.Measurement.Type
  • class org.biomage.Common.NameValueType (implements org.biomage.Interface.HasPropertySets, java.io.Serializable)
  • class org.biomage.tools.generate_er.PrimaryKey
  • class org.biomage.Protocol.Protocol_package (implements java.io.Serializable)
  • class org.biomage.QuantitationType.QuantitationType_package (implements java.io.Serializable)
  • class org.biomage.Measurement.QuantityUnit.UnitNameCV
  • class org.biomage.BioSequence.SeqFeature.Basis
  • class org.biomage.tools.helpers.StringOutputHelpers
  • class org.biomage.tools.generate_er.Table
  • class org.biomage.Measurement.TemperatureUnit.UnitNameCV
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class org.biomage.Common.MAGEException
  • class org.biomage.Measurement.TimeUnit.UnitNameCV
  • class org.biomage.tools.generate_er.Unique
  • class org.biomage.Measurement.VolumeUnit.UnitNameCV

Interface Hierarchy

• interface org.biomage.Interface.HasAction
• interface org.biomage.Interface.HasActionMeasurement
• interface org.biomage.Interface.HasAdjustments
• interface org.biomage.Interface.HasAffiliation
• interface org.biomage.Interface.HasAnalysisResults
• interface org.biomage.Interface.HasAnnotations
• interface org.biomage.Interface.HasArray
• interface org.biomage.Interface.HasArrayDesign
• interface org.biomage.Interface.HasArrayGroup
• interface org.biomage.Interface.HasArrayManufactureDeviations
• interface org.biomage.Interface.HasArrayManufacturers
• interface org.biomage.Interface.HasArrays
• interface org.biomage.Interface.HasAuditTrail
• interface org.biomage.Interface.HasBibliographicReferences
• interface org.biomage.Interface.HasBioAssay
• interface org.biomage.Interface.HasBioAssayCreation
• interface org.biomage.Interface.HasBioAssayData
• interface org.biomage.Interface.HasBioAssayDataSources
• interface org.biomage.Interface.HasBioAssayDimension
• interface org.biomage.Interface.HasBioAssayFactorValues
• interface org.biomage.Interface.HasBioAssayMapping
• interface org.biomage.Interface.HasBioAssayMaps
• interface org.biomage.Interface.HasBioAssayMapTarget
• interface org.biomage.Interface.HasBioAssays
• interface org.biomage.Interface.HasBioAssayTreatments
• interface org.biomage.Interface.HasBioAssayTupleData
• interface org.biomage.Interface.HasBioDataValues
• interface org.biomage.Interface.HasBiologicalCharacteristics
• interface org.biomage.Interface.HasBioMaterial
• interface org.biomage.Interface.HasCategory
• interface org.biomage.Interface.HasChannel
• interface org.biomage.Interface.HasChannels
• interface org.biomage.Interface.HasCharacteristics
• interface org.biomage.Interface.HasClusterBioAssayData
• interface org.biomage.Interface.HasComponentCompounds
• interface org.biomage.Interface.HasComposite
• interface org.biomage.Interface.HasCompositeCompositeMaps
• interface org.biomage.Interface.HasCompositeGroups
• interface org.biomage.Interface.HasCompositePositionSources
• interface org.biomage.Interface.HasCompositeSequence
• interface org.biomage.Interface.HasCompositeSequences
• interface org.biomage.Interface.HasCompound
• interface org.biomage.Interface.HasCompoundMeasurements
• interface org.biomage.Interface.HasConfidenceIndicators
• interface org.biomage.Interface.HasContacts
• interface org.biomage.Interface.HasContainedFeatures
• interface org.biomage.Interface.HasControlFeatures
• interface org.biomage.Interface.HasControlledFeatures
• interface org.biomage.Interface.HasControlType
• interface org.biomage.Interface.HasCoordinate
• interface org.biomage.Interface.HasDatabase
• interface org.biomage.Interface.HasDatabaseReferences
• interface org.biomage.Interface.HasDataType
• interface org.biomage.Interface.HasDefectType
• interface org.biomage.Interface.HasDerivedBioAssayData
• interface org.biomage.Interface.HasDerivedBioAssayDataTarget
• interface org.biomage.Interface.HasDescriptions
• interface org.biomage.Interface.HasDesignElement
• interface org.biomage.Interface.HasDesignElementDimension
• interface org.biomage.Interface.HasDesignElementMapping
• interface org.biomage.Interface.HasDesignElementMaps
• interface org.biomage.Interface.HasDesignProviders
• interface org.biomage.Interface.HasDistanceUnit
• interface org.biomage.Interface.HasExperimentalFactor
• interface org.biomage.Interface.HasExperimentalFactors
• interface org.biomage.Interface.HasExperimentDesign
• interface org.biomage.Interface.HasExternalReference
• interface org.biomage.Interface.HasFactorValues
• interface org.biomage.Interface.HasFailTypes
• interface org.biomage.Interface.HasFeature
• interface org.biomage.Interface.HasFeatureDefects
• interface org.biomage.Interface.HasFeatureExtraction
• interface org.biomage.Interface.HasFeatureGroup
• interface org.biomage.Interface.HasFeatureGroups
• interface org.biomage.Interface.HasFeatureInformationSources
• interface org.biomage.Interface.HasFeatureLIMSs
• interface org.biomage.Interface.HasFeatureLocation
• interface org.biomage.Interface.HasFeatureReporterMaps
• interface org.biomage.Interface.HasFeatures
• interface org.biomage.Interface.HasFeatureShape
• interface org.biomage.Interface.HasFiducials
• interface org.biomage.Interface.HasFiducialType
• interface org.biomage.Interface.HasFormat
• interface org.biomage.Interface.HasHardware
• interface org.biomage.Interface.HasHardwareApplications
• interface org.biomage.Interface.HasHardwareManufacturers
• interface org.biomage.Interface.HasHardwares
• interface org.biomage.Interface.HasIdentifierLIMS
• interface org.biomage.Interface.HasImages
• interface org.biomage.Interface.HasImmobilizedCharacteristics
• interface org.biomage.Interface.HasInformation
• interface org.biomage.Interface.HasLabels
• interface org.biomage.Interface.HasMaterialType
• interface org.biomage.Interface.HasMeasuredBioAssayData
• interface org.biomage.Interface.HasMeasuredBioAssayTarget
• interface org.biomage.Interface.HasMeasurement
• interface org.biomage.Interface.HasMembers
• interface org.biomage.Interface.HasMerckIndex
• interface org.biomage.Interface.HasMismatchInformation
• interface org.biomage.Interface.HasNodeContents
• interface org.biomage.Interface.HasNodes
• interface org.biomage.Interface.HasNodeValue
• interface org.biomage.Interface.HasNormalizationDescription
• interface org.biomage.Interface.HasOntologyEntries
• interface org.biomage.Interface.HasOntologyReference
• interface org.biomage.Interface.HasOwner
• interface org.biomage.Interface.HasParameters
• interface org.biomage.Interface.HasParameterType
• interface org.biomage.Interface.HasParameterTypes
• interface org.biomage.Interface.HasParameterValues
• interface org.biomage.Interface.HasParent
• interface org.biomage.Interface.HasPerformer
• interface org.biomage.Interface.HasPerformers
• interface org.biomage.Interface.HasPhysicalBioAssay
• interface org.biomage.Interface.HasPhysicalBioAssayData
• interface org.biomage.Interface.HasPhysicalBioAssaySource
• interface org.biomage.Interface.HasPhysicalBioAssayTarget
• interface org.biomage.Interface.HasPolymerType
• interface org.biomage.Interface.HasPosition
• interface org.biomage.Interface.HasPositionDelta
• interface org.biomage.Interface.HasProducerTransformation
• interface org.biomage.Interface.HasPropertySets
• interface org.biomage.Interface.HasProtocol
• interface org.biomage.Interface.HasProtocolApplications
• interface org.biomage.Interface.HasProviders
• interface org.biomage.Interface.HasQualityControlDescription
• interface org.biomage.Interface.HasQualityControlStatistics
• interface org.biomage.Interface.HasQuantitationDimension
• interface org.biomage.Interface.HasQuantitationType
• interface org.biomage.Interface.HasQuantitationTypeDimension
• interface org.biomage.Interface.HasQuantitationTypeMapping
• interface org.biomage.Interface.HasQuantitationTypeMaps
• interface org.biomage.Interface.HasQuantitationTypes
• interface org.biomage.Interface.HasReadGroups
• interface org.biomage.Interface.HasRegions
• interface org.biomage.Interface.HasReplicateDescription
• interface org.biomage.Interface.HasReporter
• interface org.biomage.Interface.HasReporterCompositeMaps
• interface org.biomage.Interface.HasReporterGroups
• interface org.biomage.Interface.HasReporterPositionSources
• interface org.biomage.Interface.HasReporters
• interface org.biomage.Interface.HasRoles
• interface org.biomage.Interface.HasScale
• interface org.biomage.Interface.HasSecurity
• interface org.biomage.Interface.HasSeqFeatures
• interface org.biomage.Interface.HasSequenceDatabases
• interface org.biomage.Interface.HasSoftware
• interface org.biomage.Interface.HasSoftwareApplications
• interface org.biomage.Interface.HasSoftwareManufacturers
• interface org.biomage.Interface.HasSoftwares
• interface org.biomage.Interface.HasSourceBioAssays
• interface org.biomage.Interface.HasSourceBioMaterialMeasurements
• interface org.biomage.Interface.HasSourceContact
• interface org.biomage.Interface.HasSourcesQuantitationType
• interface org.biomage.Interface.HasSpecies
• interface org.biomage.Interface.HasSubregions
• interface org.biomage.Interface.HasSubstrateType
• interface org.biomage.Interface.HasSummaryStatistics
• interface org.biomage.Interface.HasSurfaceType
• interface org.biomage.Interface.HasTarget
• interface org.biomage.Interface.HasTargetQuantitationType
• interface org.biomage.Interface.HasTechnologyType
• interface org.biomage.Interface.HasTopLevelBioAssays
• interface org.biomage.Interface.HasTreatments
• interface org.biomage.Interface.HasType
• interface org.biomage.Interface.HasTypes
• interface org.biomage.Interface.HasUnit
• interface org.biomage.Interface.HasWarningType
• interface org.biomage.Interface.HasWriteGroups
• interface org.biomage.Interface.HasZone
• interface org.biomage.Interface.HasZoneGroups
• interface org.biomage.Interface.HasZoneLayout
• interface org.biomage.Interface.HasZoneLocations
• interface java.util.Map
  • interface org.biomage.tools.xmlutils.MultiMap