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About AboutBean AboutImpl AbsConverter AbsExpression AbsoluteProgressReporter AbstractAnalysisPlugin AbstractBatcher AbstractBioAssaySetExporter AbstractDataFileHandler AbstractDbEngine AbstractEntityQuery AbstractExporterPlugin AbstractFileUnpacker AbstractFlatFileImporter AbstractItemImporter AbstractJepConversionFunction AbstractJspActionFactory AbstractJspFactory AbstractJspRendererFactory AbstractNodeLoader AbstractPlugin AbstractQuery AbstractResultList AbstractRPCClient AbstractRPCService AbstractSignalHandler AbstractSignalReceiver AbstractSignalTransporter AbstractSqlQuery AccessControlled AccountExpiredException Action ActionClassEventFilter ActionFactory ActionIterator AddAllTransformer AddConverter AddExpression Affymetrix AffymetrixFileHandler Agent AgentController AgentSignalReceiver Aggregations AllEventsFilter AllOfFilter AlreadyLoggedInException AnalysisFilterPlugin AndConverter AndRestriction Annotatable AnnotatableData AnnotatableProxy AnnotatedData AnnotatedItem AnnotatedItemInfo Annotation Annotation.QueryRuntimeFilterImpl AnnotationAssayField AnnotationBetweenRestriction AnnotationData AnnotationFlatFileImporter AnnotationFlatFileImporter.AnnotationValue AnnotationFlatFileImporter.NewAnnotations AnnotationInfo AnnotationInRestriction AnnotationLoader AnnotationNameGenerator AnnotationRestriction Annotations AnnotationSet AnnotationSet.QueryRuntimeFilterImpl AnnotationSetData AnnotationSetterPlugin AnnotationSimpleRestriction AnnotationTransfer AnnotationType AnnotationTypeCategory AnnotationTypeCategoryData AnnotationTypeClient AnnotationTypeData AnnotationTypeInfo AnnotationTypeService AnnotationTypeTransfer AnnotationUtil AnnotationUtil.AnnotatableWrapper AnnotationValidator AnyToAny AnyToAnyData Application Application.Pinger Application.SecondaryStorageControllerTask Application.SessionControlCacheCleaner ArrayBatch ArrayBatchData ArrayBatchImporter ArrayBatchLoader ArrayBatchTransfer ArrayBatchValidator ArrayBlockTransfer ArrayDesign ArrayDesignBlock ArrayDesignBlockData ArrayDesignClient ArrayDesignData ArrayDesignImporter ArrayDesignInfo ArrayDesignLoader ArrayDesignPlate ArrayDesignPlateData ArrayDesignService ArrayDesignValidator ArrayIterator ArraySlide ArraySlideData ArraySlideImporter ArraySlideLoader ArraySlideTransfer ArraySlideValidator ArrayTypePlateTransfer ArrayTypeTransfer AscOrder AssayField ASTConstantConverter ASTFunNodeConverter ASTVarNodeConverter AuthenticationException AuthenticationInformation Authenticator AutoChildNodeLoader AutoDetectFileFormat AutoDetectFileFormat.IsImportableFilter AutoDetectingImporter AutoJoiner Base Base1PluginExecuter Base1PluginExecuter.Base1JobParameterType Base1PluginExecuter.ChildBioAssay Base1PluginExecuter.RawDataProxy Base1PluginExecuter.ReporterProxy BaseException BaseFileDataSource BaseFileExporter BaseFileExporterPlugin BaseFileExporterPlugin.ExtendedDynamicField BaseFileWriter BasicBatcher BasicChildItem BasicData BasicItem BasicItemFilter BasicItemInfo BasicItemNodeLoader BasicItemNodeLoaderFactory BasicItemNodeValidatorFactory BasicItemToIdTransformer BasicNodeValidator BatchableData BatchedPropertyInfo Batcher BatchUtil BeanActionFactory BetweenRestriction BioAssay BioAssayData BioAssaySet BioAssaySetClient BioAssaySetData BioAssaySetExporter BioAssaySetFilterUtil BioAssaySetInfo BioAssaySetService BioAssaySetUtil BioMaterial BioMaterialData BioMaterialEvent BioMaterialEvent.Type BioMaterialEventData BioMaterialList BioMaterialListData BioMaterialSourceEventData BioPlate BioPlateData BioSource BioSourceData BioSourceImporter BioSourceLoader BioSourceToSampleTransformer BioSourceValidator BioWell BioWellData BlockInfo Body BooleanFormatter BooleanFormatter.Type BooleanParameterType BooleanParameterValueData Button Button ButtonAction ButtonBean ButtonGroup Bzip2FilePacker CaseExpression CdfFileHandler CdfFileReporterImporter CelFileHandler Cell CellValue ChainedProgressReporter ChannelFunction CharacterEncodingFilter ChildItem ChildNodeDirection ClassLocal ClassMapErrorHandler ClassUtil Client ClientContext ClientData ClientDefaultSetting ClientDefaultSettingData CmdLine ColFunction CollectionTransformer ColorFormatter ColorGenerator Coloring ColoringData ColumnDef ColumnMapper Columns CombiningEventFilter CommonData CommonItem CommonItemInfo CommonItemTransfer CompactButtonRenderer CompactButtonRendererFactory CompileAll ComponentData CompoundMapper Config ConfigurableServiceFactory ConfigurationException ConfigureByExample ConnectionClosedException ConsoleProgressReporter ConstantMapper ContextData ContextIndex ContextKey ContextUtil ContextUtil.ContextResult ContextUtil.IsInContextFilter Controlled ConverterFactory Coordinate CountExpression CropStringMapper Data DatabaseException DataCube DataCube.RawMappingQuery DataCubeColumn DataCubeColumnData DataCubeData DataCubeExtraValue DataCubeExtraValueData DataCubeFilter DataCubeFilterData DataCubeLayer DataCubeLayerData DataFileHandler DataFileLoader DataFileMetadataReader DataFileType DataFileTypeData DataFileTypeInfo DataFileValidator DataFileValidator DataLoader DataNoFunction DataQuery DataQueryWrapper DataResultIterator DateFormatter DateParameterType DateParameterValueData DateUtil DbControl DbControl.SaveIf DbEngine DefaultDbEngine DefaultFilter DefaultRequestHandler DelegatingSignalHandler DescOrder DetachedItemException Diff3 DirectionalCacheKey Directory DirectoryData DisallowedValueException DiskConsumable DiskConsumableData DiskUsage DiskUsageData DiskUsageStatistics DivideConverter DivideExpression DoubleParameterType DoubleParameterValueData Download DummyJobExecutor DummyService DuplicateWizardException Dynamic DynamicExtraValueQuery DynamicField DynamicFilter DynamicJoin DynamicPositionQuery DynamicPositionQueryJoiners DynamicPositionQueryJoiners.ExtraValueJoiner DynamicPositionQueryJoiners.ReporterJoiner DynamicQuery DynamicQueryWrapper DynamicRawDataQuery DynamicReporterQuery DynamicRestriction DynamicResultIterator DynamicSpotQuery DynamicSpotQueryJoiners DynamicSpotQueryJoiners.ExtraValueJoiner DynamicSpotQueryJoiners.RawDataJoiner DynamicSpotQueryJoiners.ReporterJoiner DynamicSpotQueryJoiners.ReporterListJoiner DynamicUtil DynamicUtil.SelectedInfo EngineFactory EntityQuery EntityQueryWrapper Enumeration Enumeration.Entry EqRestriction EqualsConverter EqualsFilter ErrorHandler EventFilter EventHandler EventType EventTypeFilter ExceptionCatcher ExecuteUpdateWork ExpConverter Experiment ExperimentalFactorLoader ExperimentalFactorValidator ExperimentClient ExperimentData ExperimentExplorer ExperimentExplorer.AnnotationGroup ExperimentExplorer.AnnotationSummary ExperimentExplorer.ReporterPositions ExperimentInfo ExperimentLoader ExperimentOverview ExperimentService ExperimentTransfer ExperimentValidator ExpExpression ExportableField ExportableFieldFactory ExportableFieldFormatter ExportedProperty ExportOutputStream ExportTemplate Expression Expressions ExpressionSelect ExtendableData ExtendedProperties ExtendedProperty ExtendedPropertyAccessor ExtendedPropertyAccessor.GetterSetter ExtendedPropertyFormatter ExtendedPropertyInfo ExtendedPropertyLinker Extension ExtensionBean ExtensionContext ExtensionPoint ExtensionPointBean ExtensionPointContext ExtensionPointEventFilter ExtensionsControl ExtensionsControl.AutoInstallTask ExtensionsDirectory ExtensionsFile ExtensionsFilter ExtensionsInvoker ExtensionsServlet Extract ExtractData ExtractImporter ExtractLoader ExtractToLabeledExtractTransformer ExtractToSampleTransformer ExtractTransfer ExtractValidator ExtraValue ExtraValue.CoordinateType ExtraValueData ExtraValueExpression ExtraValueFunction ExtraValueJoin ExtraValueType ExtraValueTypeData Factories Failure FallbackIdMethod Feature FeatureBatcher FeatureCoordinate FeatureData FeatureIdentificationMethod FieldConverter File File.Action FileAttachable FileAttachableData FileData FileExportOutputStream FileImportInputStream FilePacker FileParameterType FileSet FileSet.DataFileHandlerWrapper FileSet.QueryRuntimeFilterImpl FileSetData FileSetMember FileSetMember.QueryRuntimeFilterImpl FileSetMemberData FileSetMemberNameGenerator FileStoreEnabled FileStoreEnabledData FileStoreUtil FileTransfer FileType FileTypeData FileTypeIndex FileUnpacker FileUpload FileUpload.SectionHeaders FileUpload.UploadStatus FileUploadProgress FileUtil Filter FilterBatcher FilterUtil Fix FixedButtonFactory FixedMenuItemFactory FlatFileParser FlatFileParser.Data FlatFileParser.Line FlatFileParser.LineType FloatConverter FloatExpression FloatParameterType FloatParameterValueData Formatter FormatterFactory FormatterSettings Formula Formula.AverageMethod Formula.Parser Formula.Type FormulaData FormulaFilter ForwardingSignalHandler GalExporter GenericOverview GeometricMeanExpression GlobalDefaultSetting GlobalDefaultSettingData GreaterConverter GreaterEqualsConverter Group Group.QueryRuntimeFilterImpl GroupData GroupGroups GroupKeys GroupPermissions GroupProjects GroupTransfer GteqRestriction GtRestriction GuiContext GuiContext.Type GuiContextData GzipFilePacker Hardware HardwareData HardwareLoader HardwareTransfer HardwareType HardwareTypeData HardwareValidator HasAnnotationRestriction Head Header Help Help HelpData HelpExporter HelpImporter HibernateUtil Hidden HideableSection HistogramPlot HistogramPlot.HistogramBin HistogramPlot.HistogramDataset HistogramPlot.HistogramSeries HistogramPlot.TempSeries HistogramPlot.YAggregate Hql HqlElementsExpression HqlEntityExpression HqlExpression HqlIndexExpression HqlInnerJoin HqlLeftJoin HqlPropertyExpression HqlQuery HqlQueryJoiners HqlQueryJoiners.ReporterListJoiner HqlRightJoin HqlSizeExpression HTML Hybridization HybridizationData HybridizationImporter HybridizationLoader HybridizationTransfer HybridizationValidator Icon Identifiable IdentifiableData IdentifiableFormatter IdentityFilter IdentityUnitConverter IdMethod IfConverter IlluminaRawDataImporter IlluminaRawDataImporter.BatchAndMapHolder Image Image.Format ImageData ImageFileTransfer ImageLoader ImmediateDownloadExporter ImportInputStream Include IncludeExcludeFilter IndexedCacheKey InfoRequestHandler InputStreamSplitter InputStreamTracker InReporterListFunction InRestriction Install Install.PlatformFT InstanceOfFilter IntegerConverter IntegerExpression IntegerFormatter IntegerParameterType IntegerParameterValueData IntegerUtil IntensityCalculator IntensityCalculatorPlugin IntensityCalculatorUtil IntensityCalculatorUtil.JepIntensityCalculatorImpl IntensityFormula IntensityTransform InteractivePlugin InternalIdMethod InternalJobQueue InternalJobQueue.JobQueueKeyring InternalStorageController InternalStorageController.StorageKeyring InvalidAnnotationException InvalidDataException InvalidPasswordException InvalidPasswordException InvalidPathException InvalidRelationException InvalidUseOfNullException InverseFilter InvokationContext Item Item.DefinedPermissions ItemAlreadyExistsException ItemContext ItemContext.SortDirection ItemInUseException ItemKey ItemKeyData ItemModifiedException ItemNotFoundException ItemParameterType ItemParameterValueData ItemProxy ItemQuery ItemQueryLoader ItemQueryWrapper ItemResultIterator ItemResultList ItemTypeFilter JarClassLoader JarClassLoader.JarInfo JdbcWork Jep JepConversionFunction JepDynamicField JepExpressionFunction JepExtraValueCalculator JepFunction JepIntensityTransformer JepMapper JepRestrictionFunction Job Job.ExecutionTime Job.ProgressReporterImpl Job.Status Job.Type JobAgent JobAgentConnection JobAgentData JobAgentInfo JobAgentServerConnection JobAgentServerConnection.ListenerThread JobAgentServerConnection.RequestHandlerThread JobAgentSettings JobAgentSettingsData JobData JobExecutor JobInfo JobQueueChecker JobRunner Join JoinType JspContext Key KeyData KeyPermission Keyring Label Label LabelData LabeledExtract LabeledExtractData LabeledExtractImporter LabeledExtractLoader LabeledExtractNameGenerator LabeledExtractToExtractTransformer LabeledExtractTransfer LabeledExtractValidator LabelTransfer LessConverter LessEqualsConverter LikeRestriction LinearUnitConverter LineNoFunction ListUtil LocalSignalReceiver LocalSignalTransporter Location Log2Function LogarithmConverter LogExpression LogUtil LongParameterType LongParameterValueData LookupFormatter LowessNormalization LowessNormalization.SpotData LteqRestriction LtRestriction Manager ManualTransformCreator MAPlotFactory MappedPlateTransfer Mapper MappingBatcher MappingCoordinate MatrixBaseFileExporter MaxExpression MD5 MeanExpression MeanFunction MeanRawDataPropertyExpression MeasuredBioMaterial MeasuredBioMaterialData MeasuredBioMaterialTransfer MedianRatioNormalization MedianRatioNormalization.SpotData Menu Menuitem MenuItemAction MenuItemAction.MenuType MenuItemBean Menuseparator Message MessageData Metadata Migrater MimeType MimeTypeData MinExpression ModeInfo MultiFormatter MultiPermissions MultiplyConverter MultiplyExpression MultiPropertyIdMethod MultiStepCollectionTransformer MultiUpdateWork MySQLEngine Nameable NameableComparator NameableData NameableFormatter NameableInfo NameableNameGenerator NameableNodeValidator NameablePluginAdaptor NameableUtil NaturalLogarithmConverter Navigator NegateExpression NeqRestriction NestedIterator News News.QueryRuntimeFilterImpl NewsData NewsTransfer Node Node.Type NodeCache NodeFactory NodeLoader NodeLoaderFactory NodeNameGenerator NodeValidator NodeValidatorFactory NoneOfFilter NotConverter Note NotEqualsConverter NotInReporterListFunction NotLoggedInException NotNullFilter NotRestriction NullIfExceptionMapper NullNodeLoader NullNodeValidator NumberFormatter NumberFormatUtil NumberOutOfRangeException OlderThanFileFilter OneOfFilter Operator OrConverter Order Orders OrRestriction OverviewContext OverviewPlotAction OverviewPlotBean OverviewUtil Ownable OwnableData OwnableUtil OwnableUtil OwnedData OwnedItem OwnedItemInfo PackedFileExporter Page Panel ParameterException ParameterExpression ParameterInfo Parameters ParameterType ParameterValueData ParameterValues ParameterValuesImpl ParameterValuesWrapper ParentBioMaterialLoader PasswordData Path Path Path.Type PathConverter PathElement PathParameterType PathSetter PauseRequestHandler PerformanceTimer Permission PermissionButtonFactory PermissionDeniedException PermissionMenuItemFactory Permissions PermissionUtil PingRequestHandler PlainTextTemplate Plate PlateCoordinate PlateData PlateEvent PlateEventData PlateEventTransfer PlateEventType PlateEventTypeData PlateEventTypeTransfer PlateFlatFileImporter PlateGeometry PlateGeometryData PlateMapping PlateMappingData PlateMappingExporter PlateMappingImporter PlateType PlateTypeData PlateTypeTransfer Platform PlatformData PlatformFileType PlatformFileTypeData PlatformLoader PlatformValidator PlatformVariant PlatformVariantData PlotAnnotation PlotGenerator PlotGeneratorBean PlotServlet PlotServlet.CFResultIterator PlotServlet.CFSqlResult Plugin Plugin.MainType PluginConfigInfo PluginConfiguration PluginConfigurationData PluginConfigurationExporter PluginConfigurationImporter PluginConfigurationRequest PluginDefinition PluginDefinitionData PluginExecutionRequest PluginInfo PluginKeys PluginParameter PluginPermission PluginPermission PluginRequest PluginResponse PluginSessionControl PluginTransfer PluginType PluginTypeData PooledChildrenTransformer PooledParentsTransformer POP3Authenticator PositionBatcher PositionExtraValueBatcher PositionFunction PostgresDbEngine PowerExpression PredefinedQuery PrefixSuffixFormatter PrefixSuffixRenderer Presets PresetSelector PrintMapFlatFileImporter PrintMapFlatFileImporter.FormatType PrintMapFlatFileImporter.Section ProcessJobExecutor ProcessJobExecutor.StreamRedirector ProgressReporter ProgressReporterSignalHandler ProgressThread Project Project.Default Project.QueryRuntimeFilterImpl ProjectClient ProjectData ProjectInfo ProjectKey ProjectKeyData ProjectKeys ProjectPermission ProjectPermissions ProjectService PropertyFilter PropertyFilter PropertyFilterData PropertyIdMethod PropertyValue Protocol ProtocolData ProtocolLoader ProtocolParameterLoader ProtocolParameterValidator ProtocolTransfer ProtocolType ProtocolTypeData ProtocolTypeTransfer ProtocolValidator ProxyActionFactory QuadraticMeanExpression Quantity QuantityData Query QueryElement QueryExecutor QueryExecutor.Cancelable QueryExecutor.CancelableSession QueryExecutor.CancelableStatelessSession QueryExecutor.CancelableStatement QueryExecutor.FutureItem QueryExecutor.FutureResultSet QueryExecutor.FutureScrollIterator QueryExecutor.FutureUpdate QueryOptions QueryParameter QueryParameter QueryParameters QueryResult QueryRuntimeFilter QueryRuntimeFilterFactory QueryRuntimeFilterFactory.AnnotatableFilter QueryRuntimeFilterFactory.BasicFilter QueryRuntimeFilterFactory.ChainedFilter QueryRuntimeFilterFactory.ChildFilter QueryRuntimeFilterFactory.DenyAllFilter QueryRuntimeFilterFactory.OwnableFilter QueryRuntimeFilterFactory.RemovableFilter QueryRuntimeFilterFactory.ShareableFilter QueryRuntimeFilterManager QuerySection QueryType QueryWrapper QueryWrapper Quota Quota.QueryRuntimeFilterImpl QuotaData QuotaException QuotaIndex QuotaTransfer QuotaType QuotaTypeData RawBioAssay RawBioAssayClient RawBioAssayData RawBioAssayDataTransfer RawBioAssayImporter RawBioAssayInfo RawBioAssayLoader RawBioAssayService RawBioAssayTransfer RawBioAssayValidator RawChannelFunction RawData RawDataBatcher RawDataFlatFileImporter RawDataProperty RawDataPropertyExpression RawDataType RawDataTypes RawDataUtil RawFunction RealJoin RealTable RegexpFileFilter Registered RegisteredData Registry Registry.AttributeKey Registry.RegisteredAbout Registry.RegisteredExtension Registry.RegisteredExtensionPoint Removable RemovableData RemovableUtil RemoveAllTransformer Render Renderer RendererFactory Reporter ReporterBatcher ReporterClient ReporterData ReporterFlatFileImporter ReporterFunction ReporterList ReporterListData ReporterListExpression ReporterListInfo ReporterListJoin ReporterListScoreData ReporterMapFlatFileImporter ReporterPropertyExpression ReporterProxy ReporterScore ReporterScoreQuery ReporterScoreQueryWrapper ReporterScoreResultIterator ReporterService ReporterTransfer ReporterType ReporterTypeData Request RequestHandler RequestInformation RequestWrapper Response Response.Status Restriction Restrictions ResultIterator ResultList ResultSetWork RlikeRestriction Role Role.QueryRuntimeFilterImpl RoleData RoleKey RoleKeyData RoleKeys RoleTransfer RoleTransfer.ItemPermission Row Rows Sample SampleData SampleImporter SampleLoader SampleTissueTransfer SampleToBioSourceTransformer SampleToExtractTransformer SampleTransfer SampleValidator Scan ScanData ScanImporter ScanLoader ScanResults ScanResults.FileResults ScanTransfer ScanValidator ScatterPlot Scheduler SchemaVersionData ScoreFunction Scripts ScrollIterator SecondaryStorageController Select Select SelectedExpression Selects SerialBaseFileExporter ServiceControllerAction ServiceFactory Services ServicesEventHandler ServicesUtil ServletExportOutputStream ServletLoader ServletWrapper Session SessionClient SessionControl SessionControl.LoginInfo SessionControl.SettingInfo SessionData SessionService Setting SettingData Settings Severity Shareable ShareableData ShareableUtil ShareableUtil SharedData SharedItem SharedItemInfo SharedItemTransfer Signal SignalException SignalHandler SignalReceivedException SignalReceiver SignalRequestHandler SignalTarget SignalTransporter SimpleAbsoluteProgressReporter SimpleAuthenticator SimpleDynamicField SimpleErrorHandler SimpleExport SimpleProgressReporter SimpleSignalProgressReporter SingleExtensionFilter SocketSignalReceiver SocketSignalTransporter SocketUtil Software SoftwareData SoftwareLoader SoftwareTransfer SoftwareType SoftwareTypeData SoftwareValidator SpotBatcher SpotExtraValueBatcher SpotImage SpotImageCreator SpotImageFormatter SpotImages SpotImagesData SqlColumnExpression SqlQuery SqlResult SqlResultIterator SqlResultList SqrtExpression SquareRootConverter StartRequestHandler StartServiceRenderer StartStopServlet StaticCache StaticCache.LockEntry StaticCache.LockSafeInputStream StaticCache.LockSafeOutputStream StaticFilter StopRequestHandler StopServiceRenderer StringConverter StringConverter StringFormatter StringMatcher StringMatcher.FuzzyMatch StringParameterType StringParameterValueData StringTooLongException StringUtil Stylesheets Submenu SubqueryExpression SubtractConverter SubtractExpression SumExpression SystemData SystemItem SystemItems Tab TabControl Table TableColumn TableExistsWork TableInfo TableInfo.ColumnInfo TableInfo.ForeignKeyInfo TableInfo.PrimaryKeyInfo TableInfoWork TableWriter TarFilePacker TarFileUnpacker TarUtil TempFileDataSource TextParameterValueData ThreadJobExecutor ThreadJobExecutor.ShutdownHook ThreadSignalHandler ThreadTimerTask ThrowableUtil Toolbar ToolbarButtonRenderer ToolbarButtonRendererFactory ToolbarUtil ToStringComparator ToStringFormatter ToTransferable Transactional Transactional.Action Transfer Transferable Transformation TransformationData Trashcan Tree Tree.Entry Type UMinusConverter Unit UnitCache UnitCache.CacheKey UnitConverter UnitData UnitSymbolData UnitUtil UnknownLoginException UnmappedPlateTransfer UnmodifiableResultList UnsavedItemException UnsupportedFileFormatException UnsupportedSignalException Update UploadAbortedException UploadedFile UploadFileTransfer UsedQuantity User User.QueryRuntimeFilterImpl UserClientSetting UserClientSettingData UserData UserDefaultSetting UserDefaultSettingData UserGroups UserKeys UserPermissions UserProjects UserRoles UserTransfer Validatable ValidationOptions Validator ValueConverter Values Values VariableConverter VariableSetter Version VersionedParameter VersionInfo ViewSpotImage VirtualColumn VirtualColumnExpression VirtualColumnExpression.WrappedExpression VirtualDb VirtualDbData VirtualTable WebException Well WellCoordinateFormatter WellData WellTransfer WhenStatement WizzzardTransfer WrappedConfigureByExample WrappedDataItem WrappedItem WrappingRenderer XJspCompiler XmlLoader XMLTemplate XMLUtil XMLUtil.Validator ZipFilePacker ZipFileUnpacker ZipUnpacker