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AbstractDataExternalTxtReader AbstractDataFileReader AbstractIlluminaCsvReader AbstractSessionBean AbstractUseCase AbstractUseCase AbstractUseCase AbstractUseCase AccessDeniedException Action2StringFieldConversion ActionProtocolTypeMap ActionProtocolTypeMapData ActionUtils AddBioSampleTest AddBioSourceTest AddExperimentFactorAction AddExperimentPublicationAction AdditionalDataProcessing AdditionalDataProcessingData AdditionalQualifierData AdditionalUploadedFile AdditionalUploadedFileData AdminData AdminManagementTest AdminManagerDB AdminManagerDelegate AdminManagerEJB AdminUtils AffyCelFileParser AffyChpFileParser AffymetrixArrayDesignLoader AffymetrixCdfLocatorUtil Age AgeData AgilentTxtArrayDesignLoader AgilentTxtFormatException AgilentTxtReader AppendInputStream AppletValidatorCodeGenerator Array Array_package ArrayAddUpdateAction ArrayAddUpdateForm ArrayBaseForm ArrayConstants ArrayCopyAction ArrayCopyForm ArrayData ArrayDesign ArrayDesign_package ArrayDesignAction ArrayDesignAddAction ArrayDesignAddUpdateForm ArrayDesignBaseForm ArrayDesignCleaner ArrayDesignConstants ArrayDesignData ArrayDesignDataSetMapper ArrayDesignDataSource ArrayDesignDataSourceException ArrayDesignDataTableMap ArrayDesignDelimitedFileParser ArrayDesignDesc ArrayDesignDetailAction ArrayDesignDetailForm ArrayDesignFileHandler ArrayDesignFileHandlerFactory ArrayDesignFileHeaderParser ArrayDesignFileHeaderParserItf ArrayDesignFileParserMDB ArrayDesignFileParsingEntry ArrayDesignFileParsingEntryData ArrayDesignFileParsingException ArrayDesignFileParsingJob ArrayDesignFileParsingJobHandlerImpl ArrayDesignFileParsingService ArrayDesignFileProcessAction ArrayDesignFileUploadEntry ArrayDesignFileUploadEntryData ArrayDesignFileUploadGroup ArrayDesignFileUploadGroupData ArrayDesignFinder ArrayDesignFixer ArrayDesignLoaderClient ArrayDesignManagementTest ArrayDesignManager ArrayDesignManagerDB ArrayDesignManagerDelegate ArrayDesignManagerEJB ArrayDesignManagerFactory ArrayDesignRetrievalException ArrayDesignSaveException ArrayDesignSaver ArrayDesignSearchAction ArrayDesignSearchCriteria ArrayDesignSearchForm ArrayDesignSecurityHelper ArrayDesignTextFileHeaderParser ArrayDesignType ArrayDesignUpdateAction ArrayDesignUploadDelegate ArrayDesignUploadedFileData ArrayDesignUploadManagerMDB ArrayDesignUtils ArrayDesignUtils ArrayDesignValues ArrayDesignView ArrayDetailAction ArrayDetailForm ArrayGroup ArrayGroupData ArrayGroupDesc ArrayGroupManagementTest ArrayManagerDB ArrayManagerDelegate ArrayManagerEJB ArrayManufacture ArrayManufactureDeviation ArrayManufacturerFieldMapper ArrayPage ArraySearchAction ArraySearchCriteria ArraySearchForm ArrayUtils ArrayUtils AssemblerFactory AssemblerNotAvailableException AssociationColumn Audit AuditAndSecurity_package AuthenticationDAItf AuthorizationDAItf BaseAction BaseDispatchAction BaseForm BaseHttpUnitTest BaseInContainerTest BaseMicroarrayFileHeaderParser BaseMicroarrayFileParser BaseSearchCriteria BaseSecuredElement Basis2StringFieldConversion BCELCalls BeanConversionTest BeanProvider BibliographicReference BibliographicReferenceAccessionFieldMapper BibliographicReferenceAssembler BioAssay BioAssay_package BioAssayCreation BioAssayData BioAssayData_package BioAssayDataCluster BioAssayDataInfo BioAssayDataLoader BioAssayDataLoaderException BioAssayDataLoaderFactory BioAssayDimension BioAssayMap BioAssayMapping BioAssayService BioAssayTreatment BioAssayTuple BioDataCube BioDataCubeCreator BioDataTuples BioDataValues BioEvent BioEvent_package BioMaterial BioMaterial_package BiomaterialAction BiomaterialBaseForm BioMaterialCharacteristic BiomaterialCharacteristicsAction BiomaterialCharacteristicsForm BiomaterialConstants BioMaterialData BioMaterialDesc BioMaterialManagerDB BioMaterialManagerDelegate BioMaterialManagerEJB BioMaterialMeasurement BioMaterialParentsFieldMapper BioMaterialSearchCriteria BioMaterialUIUtils BioMaterialUtils BioMaterialView Biometrics BiometricsData BioSample BioSampleComparator BioSampleData BioSampleDesc BioSampleManagementTest BioSampleView BioSequence BioSequence_package BioSource BiosourceAddUpdateAction BiosourceAddUpdateForm BiosourceBaseForm BioSourceData BioSourceDesc BiosourceDetailAction BiosourceDetailForm BioSourceManagementTest BioSourceProviderFieldMapper BiosourceSearchAction BiosourceSearchForm BioSourceView Boolean2IntFieldConversion BQS_package CaArrayArrayDesignSecurityHelper CaArrayCache CaArrayCache2 CaarrayCallBackHandler CaArrayConstants CaarrayDecorator CAArrayDesignFileUploadEntry CAArrayDesignFileUploadEntryData CaArrayLoginModule CaArrayPrincipal CaArrayProperties CaArraySequenceManagerHighLowImpl CaArrayToMageConversion CaArrayTransactionHandler CAFileUploadEntry CAFileUploadEntryData CAFileUploadHistory CAFileUploadHistoryData CAMagemlFileUploadEntry CAMagemlFileUploadEntryData CanGetBioAssayDatum CanGetByQuantitationType CanParseFiles CanUserAccessElement CanUserAccessElementItf CanUserAccessElementItfPG CaSecurityManagerDelegate CaSecurityManagerEJB CaSecurityManagerHelper CdfFileNotFoundException Channel ChromosomalAberration ChromosomalAberrationData ClassGenerator ClassGenerator.DirectLoader ClassMapper ClassMapperRepository ClassMapperRepository.ConvertField ClassMapperRepository.DTOClass ClassMapperRepository.TargetClass CollectionField CompositeCompositeMap CompositeGroup CompositeGroupData CompositeGroupDesc CompositeGroupManagerDB CompositeGroupSearchCriteria CompositePosition CompositeSequence CompositeSequenceData CompositeSequenceDesc CompositeSequenceDimension Compound CompoundAttrsProperties CompoundMeasurement CompoundMeasurementData ConcentrationUnit ConfidenceIndicator ConfigurationException Contact Contact ContactData ContactManagementTest ContactManagerDB ContactManagerDelegate ContactManagerEJB ContactsAction ContactUtils CreateClassFile CreateCPPFile CreateDocFile CreateFile CreateInterfaceFile CreateJavaClasses CreateJavaClassFile CreateJavaFile CreateJavaMAGEFile CreateJavaPackageFile CreateMageClasses CreateMageClasses.CreateClassTransformer CreateMageClassFileList CreateMageDTDClasses CreateMageER CreateMAGEFile CreateObjectException CreatePackageFile CreateSecuredElement CreateSecuredElementException CreateTransformedClassFile CreateTransformedInterfaceFile CubeCreator CustomCommonsFormFile CustomDataCubeIOHelpers CustomFormFile CustomMAGEContentHandler CustomMultipartRequestHandler Database DatabaseComparator DatabaseData DatabaseEntry DatabaseImportMAGEContentHandler DatabaseImportMAGEReader DataColumn DataColumnDescriptor DataConverter DataDescInterface DataExternal DataFileAssessment DataFileLoaderClient DataFileParseException DataFileProcessor DataFileProcessorFactory DataFileReloadConfiguration DataFileReloadResults DataFileRepairResults DataHandlerDataSourceException DataHeaderMap DataInternal DataJobHandlerImpl DataLoader DataMatrix DataRow DataSet DataSetMapper DataSetMapperMap DataTable DataTableDescriptor DataTableMap DataTypeEnum Date2NameValueTypeFieldMapper Date2StringFieldMapper Datum DbArrayDesignDataSource DbConnectionBroker DBException DbFileUploadEntrySaver DBUtils DefaultAssembler DefaultJMSMessageCollection DefaultJMSMessageHandler DefaultSecuredElementIdUpdater DefaultZoneMatcher DeleteTreatmentFromBioMaterial DelimitedExporter DelimitedFileReader DelimitedFileWriter DelimitedImportDefaultListener DelimitedImportListener DelimitedImportParser DerivedBioAssay DerivedBioAssayData DerivedSignal Describable Description Description_package DescriptionFieldMapper DesignElement DesignElement_package DesignElementColumnsMap DesignElementDimension DesignElementDimensionCreator DesignElementFinder DesignElementGroup DesignElementManagerDB DesignElementMap DesignElementMapping DesignElementRetrievalSettings DesignElementRetrievalSettings.AttributeInfo DesignElementService DesignElementServiceFactory DesignElementTuple DesignProviderRole DesignProviderRoleData DistanceUnit DownloadFile DuplicateBioSourceTest EHCacheHelper EJBUtils EntrySaveException Error ExpectedValue Experiment Experiment_package ExperimentAction ExperimentAddAdditionalHybPageAction ExperimentAddHybPageAction ExperimentAdditionalQualifierAction ExperimentAdditionalUploadFilePageAction ExperimentalFactor ExperimentalFactorData ExperimentAssembler ExperimentBaseForm ExperimentBatchDownloadAction ExperimentCleanerClient ExperimentCleaningConfiguration ExperimentContactPageAction ExperimentData ExperimentDataProcessingPageAction ExperimentDeletionResult ExperimentDesc ExperimentDesign ExperimentDetailForm ExperimentDetailPageAction ExperimentFileDownloadServlet ExperimentFileTypeConstants ExperimentFtpData ExperimentHybridizationAction ExperimentHybridizationAnnotationAction ExperimentHybridizationDetailDoneAction ExperimentImportMageMLAction ExperimentManagementTest ExperimentManagerDB ExperimentManagerDelegate ExperimentManagerEJB ExperimentNewAdditionalQualifierAction ExperimentNewDataObject ExperimentNewPageAction ExperimentNewPageContinueAction ExperimentProviderRole ExperimentProviderRoleData ExperimentSearchAction ExperimentSearchCriteria ExperimentSearchForm ExperimentSearchTest ExperimentShortDesc ExperimentTypeFieldMapper ExperimentUIConstants ExperimentUploadAction ExperimentUtils ExperimentUtils ExperimentValidationUtil ExperimentView ExportMAGEML Extendable ExternalDataCubeIOHelpers ExternalReference ExtractData ExtractDropDownData FactorDropDownData FactorValue FactorValueData Failed Feature FeatureDefect FeatureDimension FeatureExtraction FeatureGroup FeatureGroupData FeatureGroupDesc FeatureGroupManagerDB FeatureGroupSearchCriteria FeatureInformation FeatureLocation FeatureReporterMap FetchFileListTest Fiducial FieldMapper FileData FileDataObject FileLocatorUtils FileMessageInterface FileMessageTypes FilePacker FileParseManagerDB FileParserDelegate FileParsingDelegate FileParsingEntry FileParsingEntryData FileParsingService FileType FileTypeFactory FileTypeGroupMap FileTypeManager FileTypeMap FileUploadDelegate FileUploadEntry FileUploadEntryData FileUploadEntryLookupException FileUploadEntrySaver FileUploadGroup FileUploadGroupData FileUploadHandlerMDB FileUploadHistory FileUploadHistoryData FileUploadHistorySearchCriteria FileUploadManagerDB FileUploadManagerDelegate FileUploadManagerEJB FileUploadManagerMDB FileUploadUtils FileUtility FileValidator FileZipper FloatValidator ForeignKey FormUtils GalBlockData GalFeatureData GalFileParseHandler GalHeaderListener GalHeaderParser GalIdGenerator GalImportService GalToMageMapping GenePixDataMatrix GenePixDesignElement GenePixDesignElementService GenepixGalArrayDesignLoader GenePixGALFileHeaderParser GenepixGalFormatException GenePixGALZoneMatcher GenepixGprArrayDesignLoader GenepixGprFormatException GenepixGprReader GenePixQuantificationService GenePixQuantitationType GeneralException GeneralSecuredElementUpdateTester GetElementProtectionGroups GetProtectionGroups GetTreatmentTest GetUserRole GprDataRow GprFileParseHandler GprHeaderListener GprHeaderParser GprParsingService GroupAddUpdateAction GroupAddUpdateForm GroupData GroupDetailAction GroupDetailForm GroupSearchAction GroupSearchCriteria GroupSearchForm GuiSet Hardware HardwareAddUpdateAction HardwareAddUpdateForm HardwareApplication HardwareApplicationData HardwareBaseForm HardwareData HardwareDesc HardwareDetailAction HardwareDetailForm HardwareManagerDB HardwareManagerDelegate HardwareManagerEJB HardwareSearchAction HardwareSearchCriteria HardwareSearchForm HardwaresSoftwaresParameterTypesFieldMapper HasAccessions HasAccessions.Accessions_list HasAction HasActionMeasurement HasAdjustments HasAdjustments.Adjustments_list HasAffiliation HasAnalysisResults HasAnalysisResults.AnalysisResults_list HasAnnotations HasAnnotations.Annotations_list HasArray HasArrayDesign HasArrayGroup HasArrayManufactureDeviations HasArrayManufactureDeviations.ArrayManufactureDeviations_list HasArrayManufacturers HasArrayManufacturers.ArrayManufacturers_list HasArrays HasArrays.Arrays_list HasAssociations HasAssociations.Associations_list HasAuditTrail HasAuditTrail.AuditTrail_list HasBibliographicReferences HasBibliographicReferences.BibliographicReferences_list HasBioAssay HasBioAssayCreation HasBioAssayData HasBioAssayData.BioAssayData_list HasBioAssayDataSources HasBioAssayDataSources.BioAssayDataSources_list HasBioAssayDimension HasBioAssayFactorValues HasBioAssayFactorValues.BioAssayFactorValues_list HasBioAssayMapping HasBioAssayMaps HasBioAssayMaps.BioAssayMaps_list HasBioAssayMapTarget HasBioAssays HasBioAssays.BioAssays_list HasBioAssayTreatments HasBioAssayTreatments.BioAssayTreatments_list HasBioAssayTupleData HasBioAssayTupleData.BioAssayTuples_list HasBioDataValues HasBiologicalCharacteristics HasBiologicalCharacteristics.BiologicalCharacteristics_list HasBioMaterial HasCategory HasChannel HasChannels HasChannels.Channels_list HasCharacteristics HasCharacteristics.Characteristics_list HasClusterBioAssayData HasComponentCompounds HasComponentCompounds.ComponentCompounds_list HasComposite HasCompositeCompositeMaps HasCompositeCompositeMaps.CompositeCompositeMaps_list HasCompositeGroups HasCompositeGroups.CompositeGroups_list HasCompositePositionSources HasCompositePositionSources.CompositePositionSources_list HasCompositeSequence HasCompositeSequences HasCompositeSequences.CompositeSequences_list HasCompound HasCompoundIndices HasCompoundIndices.CompoundIndices_list HasCompoundMeasurements HasCompoundMeasurements.CompoundMeasurements_list HasConfidenceIndicators HasConfidenceIndicators.ConfidenceIndicators_list HasContacts HasContacts.Contacts_list HasContainedFeatures HasContainedFeatures.ContainedFeatures_list HasControlFeatures HasControlFeatures.ControlFeatures_list HasControlledFeatures HasControlledFeatures.ControlledFeatures_list HasControlType HasCoordinate HasDatabase HasDatabaseReferences HasDatabaseReferences.DatabaseReferences_list HasDataType HasDefaultValue HasDefectType HasDerivedBioAssayData HasDerivedBioAssayData.DerivedBioAssayData_list HasDerivedBioAssayDataTarget HasDerivedBioAssayMap HasDerivedBioAssayMap.DerivedBioAssayMap_list HasDescriptions HasDescriptions.Descriptions_list HasDesignElement HasDesignElementDimension HasDesignElementMapping HasDesignElementMaps HasDesignElementMaps.DesignElementMaps_list HasDesignElementTuples HasDesignElementTuples.DesignElementTuples_list HasDesignProviders HasDesignProviders.DesignProviders_list HasDistanceUnit HasExperimentalFactor HasExperimentalFactors HasExperimentalFactors.ExperimentalFactors_list HasExperimentDesigns HasExperimentDesigns.ExperimentDesigns_list HasExternalLIMS HasExternalReference HasFactorValues HasFactorValues.FactorValues_list HasFailTypes HasFailTypes.FailTypes_list HasFeature HasFeatureDefects HasFeatureDefects.FeatureDefects_list HasFeatureExtraction HasFeatureGroup HasFeatureGroups HasFeatureGroups.FeatureGroups_list HasFeatureInformationSources HasFeatureInformationSources.FeatureInformationSources_list HasFeatureLIMSs HasFeatureLIMSs.FeatureLIMSs_list HasFeatureLocation HasFeatureReporterMaps HasFeatureReporterMaps.FeatureReporterMaps_list HasFeatures HasFeatures.Features_list HasFeatureShape HasFiducials HasFiducials.Fiducials_list HasFiducialType HasFormat HasHardware HasHardwareApplications HasHardwareApplications.HardwareApplications_list HasHardwareManufacturers HasHardwareManufacturers.HardwareManufacturers_list HasHardwares HasHardwares.Hardwares_list HasIdentifierLIMS HasImages HasImages.Images_list HasImmobilizedCharacteristics HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list HasInformation HasLabels HasLabels.Labels_list HasMaterialType HasMeasuredBioAssayData HasMeasuredBioAssayData.MeasuredBioAssayData_list HasMeasuredBioAssayTarget HasMeasurement HasMembers HasMembers.Members_list HasMismatchInformation HasMismatchInformation.MismatchInformation_list HasNodeContents HasNodeContents.NodeContents_list HasNodes HasNodes.Nodes_list HasNodeValue HasNodeValue.NodeValue_list HasNormalizationDescription HasOntologyEntries HasOntologyEntries.OntologyEntries_list HasOntologyReference HasOwner HasOwner.Owner_list HasParameters HasParameters.Parameters_list HasParameterType HasParameterTypes HasParameterTypes.ParameterTypes_list HasParameterValues HasParameterValues.ParameterValues_list HasParent HasPerformer HasPerformers HasPerformers.Performers_list HasPhysicalBioAssay HasPhysicalBioAssayData HasPhysicalBioAssayData.PhysicalBioAssayData_list HasPhysicalBioAssaySource HasPhysicalBioAssayTarget HasPolymerType HasPosition HasPositionDelta HasProducerTransformation HasPropertySets HasPropertySets.PropertySets_list HasProtocol HasProtocolApplications HasProtocolApplications.ProtocolApplications_list HasProviders HasProviders.Providers_list HasQualityControlDescription HasQualityControlStatistics HasQualityControlStatistics.QualityControlStatistics_list HasQuantitationDimension HasQuantitationType HasQuantitationTypeDimension HasQuantitationTypeMapping HasQuantitationTypeMaps HasQuantitationTypeMaps.QuantitationTypeMaps_list HasQuantitationTypes HasQuantitationTypes.QuantitationTypes_list HasQuantitationTypeTuples HasQuantitationTypeTuples.QuantitationTypeTuples_list HasRegions HasRegions.Regions_list HasReplicateDescription HasReporter HasReporterCompositeMaps HasReporterCompositeMaps.ReporterCompositeMaps_list HasReporterGroups HasReporterGroups.ReporterGroups_list HasReporterPositionSources HasReporterPositionSources.ReporterPositionSources_list HasReporters HasReporters.Reporters_list HasRoles HasRoles.Roles_list HasScale HasSecurity HasSecurityGroups HasSecurityGroups.SecurityGroups_list HasSeqFeatures HasSeqFeatures.SeqFeatures_list HasSequenceDatabases HasSequenceDatabases.SequenceDatabases_list HasSoftware HasSoftwareApplications HasSoftwareApplications.SoftwareApplications_list HasSoftwareManufacturers HasSoftwareManufacturers.SoftwareManufacturers_list HasSoftwares HasSoftwares.Softwares_list HasSourceBioAssays HasSourceBioAssays.SourceBioAssays_list HasSourceBioMaterialMeasurements HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list HasSourceContact HasSourceContact.SourceContact_list HasSourcesQuantitationType HasSourcesQuantitationType.SourcesQuantitationType_list HasSpecies HasSubregions HasSubregions.Subregions_list HasSubstrateType HasSummaryStatistics HasSummaryStatistics.SummaryStatistics_list HasSurfaceType HasTarget HasTargetQuantitationType HasTechnologyType HasTopBioMaterial HasTopBioMaterial.TopLevelBioMaterials_list HasTopLevelBioAssays HasTopLevelBioAssays.TopLevelBioAssays_list HasTreatments HasTreatments.Treatments_list HasType HasTypes HasTypes.Types_list HasUnit HasValue HasWarningType HasZone HasZoneGroups HasZoneGroups.ZoneGroups_list HasZoneLayout HasZoneLocations HasZoneLocations.ZoneLocations_list HigherLevelAnalysis_package HolderBean HomeAction HttpFileProperties HttpFileUploadApplet HttpFileUploadAppletParams HttpFileUploadAppletParams HttpFileUploadCache HttpFileUploader HttpFileUploadSessionData HttpFileUploadThread HttpTunnelingFetchFileList HttpUploadedFileData HttpUploadedFileData HttpUploadFile HttpUploadParameters Hybridization Hybridization HybridizationAnnotationForm HybridizationAnnotationMiniForm HybridizationCommonData HybridizationDataJob HybridizationDataJobHandlerImpl HybridizationDataObj HybridizationDataObject HybridizationDataTableMap HybridizationDeletionConfiguration HybridizationDeletionResult HybridizationDelimitedFileParser HybridizationDetailForm HybridizationFactorDataObject HybridizationFileHandler HybridizationFileHandlerDelegate HybridizationFileHandlerEJB HybridizationFileHandlerFactory HybridizationFileParserMDB HybridizationFileParsingEntry HybridizationFileParsingEntryData HybridizationFileParsingService HybridizationFileProcessAction HybridizationFileType HybridizationFileUpload HybridizationFileUploadAction HybridizationFileUploadAssembler HybridizationFileUploadData HybridizationFileUploadEntry HybridizationFileUploadEntryAssembler HybridizationFileUploadEntryData HybridizationFileUploadEntrySummaryData HybridizationFileUploadForm HybridizationFileUploadGroup HybridizationFileUploadGroupData HybridizationManagerDB HybridizationRowWrapper IAccess Id2ObjectFieldMapper Identifiable IdFieldMapper IlluminaArrayDesignLoader IlluminaCsvFormatException IlluminaDataHandlerDataSourceManagerDB IlluminaDbDataHanderDataSource Image ImageAcquisition ImageneTxtArrayDesignLoader ImageneTxtFormatException ImageneTxtReader ImportException ImportExportTest InContainerTest Index IndexAction InheritedAccessDeniedException InsertObjectException InternalFeatureIdGenerator InternalTable IntValidator IsUsrElementOwner JavassistCalls JCSHelper JdbcAccessImpl JDBCConnection2 JDBCConnectionImpl2 JDBCParms JDBCParms JMSMessageCollection JMSMessageHandler JMSMessageManagerDB KindCV2StringFieldConversion LabelAddUpdateAction LabeledExtract LabeledExtractBaseForm LabeledExtractData LabeledExtractDesc LabeledExtractDetailAction LabeledExtractDetailForm LabeledExtractManagementTest LabeledExtractSearchAction LabeledExtractSearchForm LabeledExtractView LabelFieldMapper LdapAuthenticationDAObj LDAPConnection LineSplitter LineSplitterImpl LinkingKey LoadDuplicateFileNameProcessor LocalDynaBean LocalDynaBean LocalDynaBeanImpl LocalDynaBeanImpl LocalDynaBeanWrapper LocalDynaBeanWrapper LoggingSecuredElementOrphanHandler LoggingUserTransaction LoginAction LoginForm LogoutAction Long2LongObjectFieldConversion MAGEContentHandler MAGECubeBuilder MAGEException MAGEJava MAGEManagerDB MAGEMLExportManagerDB MAGEMLFileUploadEntry MAGEMLFileUploadEntryData MAGEMLFileUploadSearchCriteria MAGEMLFileValues MAGEMLGeneratorDelegate MAGEMLGeneratorMDB MAGEMLImportManagerDB MAGEMLImportSecuredElementBuilder MAGEMLManagerDelegate MAGEMLManagerEJB MAGEReader MAGEReader MAGEResolver MAGEWriter MageXMLConverter ManagerDB MandatoryFloat MandatoryInt MandatoryText ManufactureLIMS ManufactureLIMSBiomaterial Map MassUnit MeasuredBioAssay MeasuredBioAssayAssembler MeasuredBioAssayData MeasuredSignal Measurement Measurement_package MeasurementData MeasurementManagerDB MessageData MGEDOntologyClassEntry MGEDOntologyEntry MGEDOntologyEntry.OntologyDatabaseEntry MGEDOntologyPropertyEntry MicroarrayDelimitedFileParser MicroarrayTextFileHeaderParser MismatchInformation MissingSecuredElementIdException ModifyExperimentAdditionalQualifierAction ModifyExperimentContactAction ModifyExperimentDetailAction ModifyExperimentFactorAction ModifyExperimentGeneralInfoAction ModifyExperimentPublicationAction ModifyExperimentQualityAction ModifyProtocolApplicationAction ModifyTreatmentAction MultiHashMap MultiHashtable MultiMap NameValueType NETCDFCreator NETCDFException NETCDFFileReader Node NodeContents NodeValue NonNumericQuantitationTypes NonNumericQuantitationTypesService Notifiable NumberOfChannelsFieldMapper ObjectCacheEHCacheImpl ObjectCacheEHCachePerClassImpl ObjectInUseException ObjectNotExistException ODMGImplementationManager OjbInitializer OntologyAction OntologyActionForm OntologyAddUpdateAction OntologyCategoriesProperties OntologyConstants OntologyDetailAction OntologyEntry OntologyEntryAttrsProperties OntologyHelper OntologyImport OntologySearchAction OntologyStrainLineActionForm OptionData Order2StringFieldConversion Organization OrganizationAddUpdateAction OrganizationAddUpdateForm OrganizationComparator OrganizationData OrganizationDesc OrganizationDescriptor OrganizationDetailAction OrganizationDetailForm OrganizationSearchAction OrganizationSearchCriteria OrganizationSearchForm OrientationMarkPosition2StringFieldConversion OtherUnit PagePanel PageRecord Parameter ParameterAddAction ParameterAddForm ParameterData Parameterizable ParameterizableApplication ParameterizableApplicationData ParameterValue ParameterValueData ParsedFeature ParseException ParserBeanPropertiesInterface ParserUtils ParsingBioAssay ParsingDataMatrix ParsingDesignElement ParsingProperties ParsingQuantitationType ParsingSucceededFieldMapper ParsingTest PathElement PathInfo PBLifeCycleAdapter PBLifeCycleListenerAbstractClassPKPersistence PBLifeCycleListenerCompoundResolver PBLifeCycleListenerDescriptorModifier PBLifeCycleListenerMAGEIdentifierAssigner PBLifeCycleListenerOntologyEntryResolver PCData PCDataImpl PeopleSearchAction PeopleSearchForm PerformExperimentAdditionalUploadFileAction PerformExperimentAddPublicationAction PerformExperimentDataProcessingAction PerformExperimentImportMageMLAction PerformExperimentNewAdditionalQualifierAction PerformExperimentNewPageContinueAction PerformExperimentSearchAction PerformExperimentUploadHybridizationAction PerfTest PersistArrayDesign PersistenceBrokerManager PersistenceBrokerManagerInitializationException PersistExperiment PersistProtocol Person PersonAddUpdateAction PersonAddUpdateForm PersonComparator PersonData PersonDesc PersonDetailAction PersonDetailForm PersonSearchCriteria PhysicalArrayDesign PhysicalBioAssay PoolAction PoolException PoolForm Position PositionDelta PresentAbsent PrimaryInfo PrimaryKey ProcessBatchFileDownload ProcessDuplicatedFileName ProcessFetchFileList ProcessFileUpload PropertiesReader ProtectionAppGroupElement ProtectionElement ProtectionGroupData Protocol Protocol_package ProtocolAction ProtocolActionMappingsAction ProtocolActionMappingsForm ProtocolAddUpdateAction ProtocolAddUpdateForm ProtocolApplication ProtocolApplicationAction ProtocolApplicationData ProtocolApplicationFieldMapper ProtocolApplicationForm ProtocolApplicationPerformerFieldMapper ProtocolBaseForm ProtocolData ProtocolDesc ProtocolDetailAction ProtocolDetailForm ProtocolManagerAddTest ProtocolManagerDB ProtocolManagerDelegate ProtocolManagerEJB ProtocolManagerGetTest ProtocolManagerParameterAddTest ProtocolManagerUpdateTest ProtocolSearchAction ProtocolSearchCriteria ProtocolSearchForm ProtocolUIUtils ProtocolUtils ProviderFieldMapper PublicationData PublicExperimentDetailAction PublicSearchAction PValue QualityControlData QuantitationNamesProperties QuantitationType QuantitationType_package QuantitationTypeColumnsMap QuantitationTypeDescriptor QuantitationTypeDimension QuantitationTypeFinder QuantitationTypeManagerDB QuantitationTypeMap QuantitationTypeMapping QuantitationTypeName2JavaPropertyNameMap QuantitationTypeService QuantitationTypeServiceFactory QuantitationTypeTuple QuantityUnit QueryCustomizerExcludingObjectsMarkedAsDeleted Ratio RdbmsAuthenticationDAObj RdbmsAuthorizationDAObj ReadZipFileContent ReflectAccess RegisterAction RegisterForm RemoveSecuredElement Reporter ReporterCompositeMap ReporterDimension ReporterGroup ReporterGroupData ReporterGroupDesc ReporterGroupManagerDB ReporterGroupSearchCriteria ReporterPosition ReporterTypeData Role RoleAssignmentData RoleData RowReaderBioSequence RowReaderUnit RuntimeCacheException SampleBaseForm SampleDetailAction SampleDetailForm SampleSearchAction SampleSearchForm SampleUpdateAction SampleUpdateForm ScaleEnum SearchCriteriaConverter SecondaryInfo SecuredElementBuilder SecuredElementData SecuredElementIdUpdater SecuredElementIdUpdaterFactory SecuredElementIdUpdaterMDB SecuredElementInfo SecuredElementItf SecuredElementOrphanHandler SecuredElementOrphanHandlerFactory SecuredElementUpdateListener SecuredElementUpdateMessage Security SecurityAdminService SecurityConstants SecurityContextFilter SecurityDSConnectionUtil SecurityDSConnectionUtil.CustomRowMap SecurityException SecurityGroup SecurityManagerDelegate SecurityManagerEJB SecurityObjFactory SecurityServiceItf SecurityServiceObj SecurityTester SecurityUtils SelectedFiles SendMail SeqFeature SeqFeatureLocation SequenceInputFile SequencePosition SerializableFileUploadBean SerializableFileUploadDataBean ServerMessageConstants ServiceLocator ServiceLookupException SetSecuredElementOwner SetSecuredElementProtectionGroups SimpleDesignElement SimpleField SimpleQuantitationType Software SoftwareAddUpdateAction SoftwareAddUpdateForm SoftwareApplication SoftwareApplicationData SoftwareBaseForm SoftwareData SoftwareDesc SoftwareDetailAction SoftwareDetailForm SoftwareManagerAddTest SoftwareManagerDB SoftwareManagerDelegate SoftwareManagerEJB SoftwareManagerGetTest SoftwareManagerUpdateTest SoftwareOrHardwareManufacturerFieldMapper SoftwareSearchAction SoftwareSearchCriteria SoftwareSearchForm SourceType SourceType2StringFieldConversion SpecializedQuantitationType SplitAction SplitBioSampleData SplitForm SqlDate2JavaDateFieldMapper SqlUtil StandardQuantitationType StringFormatter StringManipHelpers StringOutputHelpers TabDelimitedTxtReader Table TechnologyTypeFieldMapper TemperatureUnit TestArrayDesignConversion TestBioMaterialConversion TestCallbackHandler TestDataConverter Tester Tester Tester Tester TestException TestExperimentConversion TestManagerEJB TestParameterConversion TestProtocolConversion TestTreatmentConversion TestUtils TestVocabConversion ThreeDArrayTransformer TilesController TimeCalls TimeCalls.DirectLoader TimeUnit TransactionException TransactionHandler TransactionHandler Transformation TransformBioAssayData TransformBioAssayData Treatment TreatmentActionOne TreatmentActionThree TreatmentActionTwo TreatmentAssembler TreatmentData TreatmentEvent TreatmentFormOne TreatmentFormThree TreatmentFormTwo TreatmentModifyForm Type2StringFieldConversion UcsfGalArrayDesignLoader UcsfGalFormatException UcsfGprArrayDesignLoader UcsfGprFormatException UCSFSpotFileHeaderParser UCSFSpotGprReader UCSFSpotZoneMatcher UIConstants UIMessageConstants Unique Unit UnitData UnitDataFieldMapper UnitNameCV2StringFieldConversion UpdateBioSourceCharacteristicsTest UpdateTreatmentTest UploadApplet UploadedFileData UploadFile UploadFileTypes UploadFileValues UploadTypeData UseCase UseCase UseCase UseCase User UserAddUpdateAction UserAddUpdateForm UserAdminAction UserData UserData UserDesc UserDetailAction UserDetailForm UserGroupAddUpdateAction UserGroupAddUpdateForm UserGroupData UserInfo UserInfo UserManagementAction UserRoleData UserRoleData UserSearchAction UserSearchCriteria UserSearchForm Value2StringFieldConversion VisibilityComparator VisibilityData VocabCategory VocabData VocabDataFieldMapper VocabDesc VocabManagerAddTest VocabManagerDB VocabManagerDelegate VocabManagerDeleteTest VocabManagerEJB VocabManagerGetTest VocabManagerUpdateTest VocabSearchCriteria VocabUtils VolumeUnit WhiteSpaceDelimitedTxtReader WriteDTDClassElement WriteDTDElement WriteDTDFile WriteDTDFile.CreateClassTransformer WriteDTDFile.PackageDependencies WriteDTDMageElement WriteDTDPackageElement XMIParseHelpers XMIParseHelpers.IDREFException XMLConvertInputVerifier Zipper ZipUtil Zone ZoneDefect ZoneGroup ZoneGroupManagerDB ZoneLayout ZoneLocationZoneMatcher ZoneMatcher