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AboutDialog Abs AbstractCalculator AbstractCellEditor AbstractCommandHandler AbstractDCustomGraphics AbstractFunction AbstractGraphReader AbstractLayout AbstractMapping AbstractParserControl AbstractScaler AbstractTreeTableModel AbstractVisualProperty ACos AddRemoveTest Aliases AliasType AlignHorizontalAction AlignVerticalAction AllGraphPerspectiveMethodsTest AllRootGraphMethodsTest AlphabeticalSelectionAction AlreadySelectedException And AnimatedLayoutAction Annotation AnnotationDescription AnnotationFlatFileReader AnnotationXmlReader Appearance ApplyLayoutAction ApplyVisualStyleAction ArbitraryGraphicsCanvas ArgDescriptor ArgType ARowanBugTest ArrangeAction ArrayIntEnumerator ArrayIntIterator ArrayTestMethod1 ArrayTestMethod2 ArrayTestMethod3 ArrayTestMethod4 Arrow Arrow ArrowheadArrow ArrowIcon ArrowParser ArrowShape ArrowShapeParser ASin ATan2 AttribTopoGraphNode Attribute AttributeFilter AttributeImportPanel AttributeImportQuery AttributeSaverDialog AttributeValueVisitor Average BackgroundColorAction BackwardSlashStroke BasicCalculator BasicGraphViewHandler BasicParser BasicQuietRTreeTest BelowAndAbovePanel Bend BendSelectedEdgesAction BiModalJSplitPane BinOpNode BioDataServer BioDataServerInterface BioDataServerRmi BioDataServerUtil BiologicalProcessAnnotationReader BiologicalProcessAnnotationTester BirdsEyeView BirdsEyeViewAction BitmapExporter BitSetPerformance BList BookmarkAction BookmarkDialog BookmarkReader Bookmarks BookmarksUtil BooleanConstantNode BooleanList BooleanParser BoundaryRangeValues Bug646Test C2CMappingEditor C2DMappingEditor Calculator CalculatorCatalog CalculatorCatalogFactory CalculatorFactory CalculatorIO Category Category CellEditorFactory CellHeightManager CellRendererFactory CellularComponentAnnotationReader CellularComponentAnnotationTester CheckBoxFileChooser CheckBoxJList Child CLArgsParser clear CloneGraphInNewWindowAction CLOption CLOptionDescriptor CLUtil CodeAndSourceLocation ColorConverter ColorPaintFactory ColorParser ColorRangeValueCalculator ColorScaleTable ColorUtil ColumnResizer ColumnTypes Combin CommandLine CommandLineParser Concatenate ConsoleLogger ContentChangeListener ContiguousArrowStroke ContinuousLegend ContinuousMapping ContinuousMappingEditorPanel ContinuousMappingPoint ContinuousMappingReader ContinuousMappingWriter ContinuousRangeCalculator ContinuousTrackRenderer Cos Cosh Count CountedIterator CreateNetworkViewAction CreditScreen CustomGraphic CustomGraphicsBrowser CustomGraphicsCellRenderer CustomGraphicsCellRenderer CustomGraphicsDetailPanel CustomGraphicsManager CustomGraphicsManagerDialog CustomGraphicsPositionCalculator CustomGraphicsProperty CustomGraphicsPropertyImpl CustomGraphicsRangeValueCalculator CustomGraphicsRangeValueRenderer CustomGraphicsUtil CustomMapping CyAbstractEdit CyAttributes CyAttributesImpl CyAttributesReader CyAttributesUtils CyAttributesUtils.AttributeType CyAttributesWriter CyCollapsiblePanel CyColorCellRenderer CyColorCellRenderer.PaintIcon CyColorChooser CyColorPropertyEditor CyColorPropertyEditor.AsInt CyComboBoxPropertyEditor CyComboBoxPropertyEditor.Value CyCommandException CyCommandHandler CyCommandManager CyCommandNamespace CyCommandResult CyCustomGraphics CyCustomGraphicsEditor CyCustomGraphicsParser CyCustomGraphicsParserFactory CyCustomGraphicsParserFactoryImpl CyCustomGraphicsTableCellRenderer CyCustomGraphicsTreeCellRenderer CyCustomGraphicsTreeNode CyDesktopManager CyDesktopManager.Arrange CyDoublePropertyEditor CyEdge CyEdgeView CyFileFilter CyFontPropertyEditor CyGradientTrackRenderer CyGraphAllLOD CyGraphLOD CyGroup CyGroupChangeListener CyGroupChangeListener.ChangeType CyGroupImpl CyGroupManager CyGroupViewer CyGroupViewer.ChangeType CyHelpBroker CyInitParams CyLayoutAlgorithm CyLayouts CyLogger CyLogHandler CyMain CyMenus CyNetwork CyNetworkAdapter CyNetworkData CyNetworkEvent CyNetworkListener CyNetworkNaming CyNetworkTitleChange CyNetworkUtilities CyNetworkView CyNode CyNodeView CyObjectPositionPropertyEditor Cysession CyStartupListener CyStringPropertyEditor Cytopanel CytoPanel CytoPanelAction CytoPanelContainer CytoPanelImp CytoPanelListener CytoPanelName Cytopanels CytoPanelState CytoPanelUtil Cytoscape CytoscapeAction CytoscapeDesktop CytoscapeFingRootGraph CytoscapeInit CytoscapeMenuBar CytoscapeModifiedNetworkManager CytoscapePlugin CytoscapeProgressMonitor CytoscapeRootGraph CytoscapeSessionReader CytoscapeSessionWriter CytoscapeToolBar CytoscapeVersion CyUndo CyWebServiceEvent CyWebServiceEvent.WSEventType CyWebServiceEvent.WSResponseType CyWebServiceEventListener CyWebServiceEventSupport CyWebServiceException CyWebServiceException.WSErrorCode DashDotStroke DatabaseSearchResult DataSource DBCrossReferenceReader DBCrossReferences DBReference DBXrefKeywords DefaultAppearenceBuilder DefaultCyCustomGraphicsParser DefaultViewPanel Degrees DeleteAction DeltaArrow DeselectAllAction DeSelectAllEdgesAction DeSelectAllNodesAction Desktop DesktopSize DestroyNetworkAction DestroyNetworkViewAction DGraphView DGraphView.Canvas DGraphView.ShapeType DiamondArrow DiamondNodeShape DingCanvas DingNetworkView DiscArrow DiscreteLegend DiscreteMapping DiscreteMappingReader DiscreteMappingWriter DiscretePropertySetter DiscreteRangeCalculator DiscreteTrackRenderer DLayer DNodeView DotStroke DoubleList DoubleParser DoubleRangeValueCalculator DownloadableInfo DownloadableType DropDownMenuButton DuplicateCalculatorNameException DuplicatePluginClassException DynamicGraph DynamicGraphFactory DynamicLayoutMenu Edge Edge EdgeAnchors EdgeAppearance EdgeAppearanceCalculator EdgeAttributesPopupDetails EdgeColorProp EdgeContextMenuListener EdgeDetails EdgeFontFaceProp EdgeFontSizeProp EdgeLabelColorProp EdgeLabelOpacityProp EdgeLabelPositionProp EdgeLabelProp EdgeLabelWidthProp EdgeLineStyleProp EdgeLineWidthProp EdgeManipulationAction EdgeOpacityProp EdgeSourceArrowColorProp EdgeSourceArrowOpacityProp EdgeSourceArrowShapeProp EdgeTargetArrowColorProp EdgeTargetArrowOpacityProp EdgeTargetArrowShapeProp EdgeToolTipProp EdgeView EditBookmarkDialog EditNetworkTitleDialog EditorDisplayer EditorDisplayer.EditorType EditorManager EditorValueRangeTracer EllipseNodeShape EqnAttrTracker EqnCompiler EqnParser EqualDashStroke Equation EquationUtil Error Exec ExitAction Exp ExpFileChooser ExportAction ExportAsGMLAction ExportAsGraphicsAction ExportAsGraphicsFileChooser ExportAsInteractionsAction ExportAsXGMMLAction ExportBitmapOptionsDialog ExportEdgeAttributesAction Exporter ExportNetworksAsNNFAction ExportNodeAttributesAction ExportVizmapAction ExpressionData ExpressionDataPopupTable ExtensibleMultiHashMapModel FConvNode FileUtil Filter FilterHistoryJList FingCyNetwork FingEdgeDepot FingExtensibleGraphPerspective FingExtensibleRootGraph FingNodeDepot FingRootGraphFactory First FitContentAction FixedGraph FlagAndSelectionHandler FlatInterpolator FlattenIntVectors FList FloatConstantNode FloatParser FloatRangeValueCalculator FontCellRenderer FontChooser FontConverter FontParser FontRenderer ForwardSlashStroke FuncCallNode Function FunctionError FunctionUtil GCTest GeneOntology GeneOntology.GOAspect GenericNodeCustomGraphicCalculator GeoMean getCanonicalName getCommonName GinyEdgeControlDialog GinyUtils GlobalAppearance GlobalAppearanceCalculator GMLException GMLFileFilter GMLNode GMLParser GMLReader GMLTag GMLTree GMLWriter GnuParser GOTerm GradientEditorPanel GradientLayerCustomGraphics GradientOvalLayer GradientPaintFactory GradientRoundRectangleLayer GraphGraphics GraphicsParser GraphLOD GraphObject GraphObjectSelection GraphObjectSelectionAction GraphPerspective GraphPerspectiveChangeEvent GraphPerspectiveChangeListener GraphReader GraphRenderer GraphSetUtils GraphView GraphViewChangeEvent GraphViewChangeListener GraphViewController GraphViewHandler GridBagGroup GridNodeLayout HalfBottomArrow HalfTopArrow Haltable HarMean HelpAboutAction HelpContactHelpDeskAction HelpContentsAction HelpFormatter HexagonNodeShape HiddenEdges HiddenNodes HideEdgeListener HideNodeListener HideSelectedAction HideSelectedEdgesAction HideSelectedNodesAction IconPopupButton IconTableCellRenderer IdentDescriptor IdentNode IDGenerator If IList ImageImposter ImageUtil ImplementsGraphTest ImportAttributeMatrixDialog ImportEdgeAttributesAction ImportExpressionMatrixAction ImportGraphFileAction ImportHandler ImportNetworkDialog ImportNodeAttributesAction ImportVizmapAction IndeterminateProgressBar InnerCanvas InnerCanvasEvent InnerCanvasListener Installable InstallablePlugin InstallableTheme Instruction IntArray IntBTree IntBTreeConstructionTuner IntBTreePerformance IntBTreeQueryTuner IntegerEntryField IntEnumerator Interaction InteractionsReader InteractionWriter InternalFrameComponent Interpolator InterpolatorFactory Interpreter IntHash IntHashPerformance IntIntHash IntIterator IntObjHash IntQueue IntStack IntTHash InvalidDownloadable InvertSelectedEdgesAction InvertSelectedNodesAction JErrorPanel JnlpWriterUtil JointIntegerEntry JStatusBar JTask JTaskConfig JTreeTable Justification KeyValue Label LabelPlacerGraphic LabelPosition LabelPositionParser LabelTextPanel Largest Last Layer LayoutAdapter LayoutAlgorithm LayoutMenu LayoutMenuManager LayoutProperties LayoutSettingsDialog LayoutTask Left LegacyCustomNodeShape LegendDialog LegendTable Len LicenseDialog LinearNumberInterpolator LinearNumberToColorInterpolator LinearNumberToNumberInterpolator LineStyle LineStyleParser LineTypeIcon ListFromFileSelectionAction ListToString Ln loadAnnotation loadAnnotationFromFlatFiles LoadImageTask LoadNetworkTask loadThesaurus Log LoggerAction LoggerDialog LogLevel LongDashStroke LongEnumerator LongList LongLongHash Lower MacAppConfig ManagerException ManagerModel ManagerUtil MapperAndAttribute MappingFactory MappingKeyFactory MappingManager MappingManagerImpl MappingType MappingUtil MathUtil Max Median MemoryReporter MemoryUsageAction MetadataEntries MetadataParser Mid Min MinIntHeap MinIntHeapPerformance MinMaxDialog MinMaxDouble MinMaxInt Misc MiscGB MissingArgumentException MissingOptionException Mod Mode ModuleProperties ModulePropertiesImpl MolecularFunctionAnnotationReader MolecularFunctionAnnotationTester MonitoredTask mRNAMeasurement MultiHashMap MultiHashMapDefinition MultiHashMapDefinitionListener MultiHashMapFactory MultiHashMapHelpers MultiHashMapListener MutableBool MutableInt MutableSpacialIndex2D MutableString NestedNetworkChangeEvent NestedNetworkChangeEventListener NestedNetworkListener NestedNetworkReader NestedNetworkViewUpdater Network NetworkData NetworkExpansionMenu NetworkFrame NetworkFrames NetworkImportWebServiceClient NetworkMetaDataDialog NetworkMetaDataTableModel NetworkPanel NetworkSelectorPanel NetworkTree NetworkTreeNode NetworkTreeTableModel NetworkViewManager NewMappingBuilder NewNetworkAction NewSessionAction NewSlider NewStringPopupDialog NewWindowSelectedNodesEdgesAction NewWindowSelectedNodesOnlyAction NNFFileFilter NNFParser NNFReader NoArrow Node Node Node NodeAppearance NodeAppearanceCalculator NodeBorderColorProp NodeBorderOpacityProp NodeContextMenuListener NodeCustomGraphicsPositionProp NodeCustomGraphicsProp NodeDetails NodeFillColorProp NodeFontFaceProp NodeFontSizeProp NodeHeightProp NodeIcon NodeLabelColorProp NodeLabelOpacityProp NodeLabelPositionProp NodeLabelProp NodeLabelWidthProp NodeLineStyleProp NodeLineWidthProp NodeOpacityProp NodeShape NodeShape NodeShapeConverter NodeShapeParser NodeShapeProp NodeShapeRangeValueCalculator NodeShowNestedNetworkProp NodeSizeProp NodeToolTipProp NodeView NodeWidthProp NormDist NoRTreeQueryPerformance Not NotAPluginException Now Nth NullCustomGraphics NumberInterpolator ObjectFactory ObjectFactory ObjectMapping ObjectPlacerControl ObjectPlacerGraphic ObjectPosition ObjectPositionCellRenderer ObjectPositionConverter ObjectPositionImpl ObjectPositionParser ObjectToString OBOFlatFileReader OBOHeaderTags OboOntologyReader OboOntologyReader2 OboOntologyTester OBOTags OctagonNodeShape Ontology Ontology Ontology OntologyDescription OntologyFactory OntologyFlatFileReader OntologyReader OntologyServer OntologyServer OntologyServer.OntologyType OntologyTerm OntologyTerm OntologyTerm.SynonymType OntologyXmlReader OpenBrowser OpenSessionAction Option OptionBuilder OptionGroup Options OptionValidator Or PaintFactory Panel Panels ParallelogramNodeShape ParallelStroke Parent ParseException Parser Parser ParserControl PassThroughMapping PatternOptionBuilder PDFExporter PercentUtil Permut PersistImageTask PhoebeCanvasDropEvent PhoebeCanvasDropListener PhoebeCanvasDroppable PhoebeNodeControl Pi PipeStroke PipeStroke.Type Plugin PluginException PluginFileReader PluginIndex PluginInfo PluginInfo.FileType PluginInquireAction PluginManageDialog PluginManageDialog.CommonError PluginManageDialog.PluginInstallStatus PluginManager PluginManagerAction PluginManagerInquireTask PluginProperties PluginProperties.PluginProperty Plugins PluginsTableModel PluginStatus PluginTracker PluginUpdateAction PluginUpdateDialog PluginUrlDialog PluginVersionUtils PluginXml PointTextListener PopupFontChooser PopupIconChooser PopupObjectPositionChooser PopupStringChooser PopupTextArea Position PosixParser PreferenceAction PreferencesDialog PreferenceTableModel PreferenceValueDialog PrimesGenerator PrintAction PrintLOD Product PropUtil ProxyHandler ProxyServerAction ProxyServerDialog PSExporter Radians RandomColorListener RangeValueCalculator RangeValueCalculatorFactory RangeValueCalculatorFactoryImpl RecentlyOpenedTracker RectangleNodeShape RedoAction RedrawTask RenderingContext RepeatedAllRootGraphMethodsTest RestoreImageTask Right RootGraph RootGraphAddRemoveTest RootGraphChangeEvent RootGraphChangeListener RootGraphPerformanceTest RotateSelectedNodesAction Round RoundedRectangleNodeShape RTree RTreeQueryPerformance RTreeSerializationPerformance RTreeUpdatePerformance RunBareBones RunSampleTask SampleTask SanityTest SaveImageTask SaveSessionAction SaveSessionAsAction Scaler ScalerFactory ScalingMethod SConvNode SelectAdjacentEdgesAction SelectAllAction SelectAllEdgesAction SelectAllNodesAction SelectConnectedNodesAction SelectedEdges SelectedNodes SelectEvent SelectEventListener SelectFilter SelectFirstNeighborsAction SelectionModeAction Semantics SeparateArrowStroke Server SessionState SetNestedNetworkDialog SettingsAction SetVisualPropertiesAction ShapeCellRenderer ShapeStroke ShowAllAction ShowCustomGraphicsManagerAction ShowGraphicsDetailsAction ShrinkExpandGraph ShrinkExpandGraphUI SIFFileFilter Sign Sin SineWaveStroke Sinh SList SolidStroke SpacialEntry2DEnumerator SpacialIndex2D Sqrt StaticLayoutMenu status StDev StraightenSelectedEdgesAction StringConstantNode StringList StringParser StringRangeValueCalculator StringUtils StringWrap SubjectBase Substitute Sum SVGExporter SwingWorker SynonymReader SynonymTester Taggable Tan Tanh Task TaskManager TaskMonitor TeeArrow Text TextFileReader TextHttpReader TextJarReader TexturePaintFactory ThemeInfo Thesaurus ThesaurusFlatFileReader Today ToggleVisualMapperAction Token Tokeniser TopoGraphNode TopologicalSort TrackerException Transform TreeCellRenderer TreeCellRenderer TreeNode TreeTableModel TreeTableModelAdapter TriangleNodeShape TriangleThumbRenderer Triple Trunc Tunable TunableListener TypeHandler UnaryOpNode Undo UndoAction UnHideSelectedAction UnHideSelectedEdgesAction UnHideSelectedNodesAction UnifiedNetworkImportDialog UnrecognizedOptionException Upper URLImageCustomGraphics URLImageCustomGraphicsParser URLUtil Value ValueParser ValueSelectDialog ValueToStringConverter ValueToStringConverterManager Var VectorCustomGraphics VeeNodeShape VerticalSlashStroke ViewableNodes ViewChangeEdit ViewChangeEdit.SavedObjs ViewportChangeListener VisualMappingManager VisualProperty VisualPropertyDependency VisualPropertyDependency.Definition VisualPropertyIcon VisualPropertyType VisualStyle VisualStyleBuilder VizMapBypassNetworkListener VizMapperMainPanel VizMapperMainPanel.DefaultEditor VizMapperProperty VizMapperTrackRenderer WebServiceClient WebServiceClientGUI WebServiceClientGUI.IconSize WebServiceClientImpl WebServiceClientImplWithGUI WebServiceClientManager WebServiceClientManager.ClientType WebServiceContextMenu WebServiceContextMenuListener WebServiceNetworkImportAction WebServiceThemeInstall WebstartException WidestStringComboBoxModel WidestStringComboBoxPopupMenuListener WidestStringProvider WidthStroke WindowUtilities WSImportResultDialog XGMMLException XGMMLFileFilter XGMMLReader XGMMLWriter YValueLegendPanel ZeroStroke ZigzagStroke ZipUtil ZoomAction ZoomSelectedAction