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AboutDialog AbstractCalculator AbstractCellEditor AbstractGraphReader AbstractLayout AbstractTreeTableModel AbstractVisualProperty AddPointListener Aliases AliasType AlignHorizontalAction AlignVerticalAction AlphabeticalSelectionAction AnimatedLayoutAction Annotation AnnotationDescription AnnotationFlatFileReader AnnotationGui AnnotationXmlReader AnotationPanel AnotationPanelDescriptor Appearance ArbitraryGraphicsCanvas ArrangeAction ArrayIntEnumerator ArrayIntIterator Arrow ArrowIcon ArrowParser ArrowShape ArrowShapeParser AttributeFilter AttributeImportPanel AttributeImportQuery AttributeSaverDialog AttributeValueVisitor BackgroundColorAction BasicCalculator BasicGraphViewHandler BelowAndAbovePanel Bend BendSelectedEdgesAction BiModalJSplitPane BioDataServer BioDataServerInterface BioDataServerRmi BioDataServerUtil BirdsEyeView BirdsEyeViewAction BitmapExporter BookmarkAction BookmarkDialog BookmarkReader BookmarksUtil BoundaryRangeValues C2CMappingEditor C2DMappingEditor Calculator CalculatorCatalog CalculatorCatalogFactory CalculatorFactory CalculatorIO Category CheckBoxFileChooser CheckBoxJList clear CloneGraphInNewWindowAction ColorParser ColorScaleTable ColumnResizer ConsoleLogger ContentChangeListener ContinuousLegend ContinuousMapping ContinuousMappingEditorPanel ContinuousMappingPoint ContinuousMappingReader ContinuousMappingWriter ContinuousRangeCalculator ContinuousTrackRenderer ContinuousUI CountedIterator CreateNetworkViewAction CreditScreen CyAbstractEdit CyAttributes CyAttributesImpl CyAttributesReader CyAttributesUtils CyAttributesUtils.AttributeType CyAttributesWriter CyColorCellRenderer CyColorCellRenderer.PaintIcon CyColorChooser CyColorPropertyEditor CyColorPropertyEditor.AsInt CyComboBoxPropertyEditor CyComboBoxPropertyEditor.Value CyDesktopManager CyDesktopManager.Arrange CyDoublePropertyEditor CyEdge CyEdgeView CyFileFilter CyFontPropertyEditor CyGradientTrackRenderer CyGraphAllLOD CyGraphLOD CyGroup CyGroupChangeListener CyGroupChangeListener.ChangeType CyGroupImpl CyGroupManager CyGroupViewer CyGroupViewer.ChangeType CyHelpBroker CyInitParams CyLabelPositionPropertyEditor CyLayoutAlgorithm CyLayouts CyLogger CyLogHandler CyMain CyMenus CyNetwork CyNetworkAdapter CyNetworkData CyNetworkEvent CyNetworkListener CyNetworkNaming CyNetworkTitleChange CyNetworkUtilities CyNetworkView CyNode CyNodeView CyStartupListener CyStringPropertyEditor CytoPanel CytoPanelAction CytoPanelContainer CytoPanelImp CytoPanelListener CytoPanelName 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 DatabaseSearchResult DBCrossReferenceReader DBCrossReferences DBReference DBXrefKeywords DefaultAppearenceBuilder DefaultPanel DefaultViewPanel DeleteAction DeletePointListener DeselectAllAction DeSelectAllEdgesAction DeSelectAllNodesAction DestroyNetworkAction DestroyNetworkViewAction DGraphView DGraphView.Canvas DGraphView.ShapeType DingCanvas DingNetworkView DiscreteLegend DiscreteMapping DiscreteMappingReader DiscreteMappingWriter DiscreteRangeCalculator DiscreteTrackRenderer DiscreteUI DNodeView DoubleParser DownloadableInfo DownloadableType DropDownMenuButton DuplicateCalculatorNameException DuplicatePluginClassException DynamicLayoutMenu Edge EdgeAppearance EdgeAppearanceCalculator EdgeArrowCalculator EdgeAttributesPopupDetails EdgeCalculator EdgeColorCalculator EdgeColorProp EdgeContextMenuListener EdgeFontFaceCalculator EdgeFontFaceProp EdgeFontSizeCalculator EdgeFontSizeProp EdgeLabelCalculator EdgeLabelColorProp EdgeLabelOpacityProp EdgeLabelPositionProp EdgeLabelProp EdgeLineStyleProp EdgeLineTypeCalculator EdgeLineTypeProp EdgeLineWidthProp EdgeManipulationAction EdgeOpacityProp EdgeSourceArrowColorProp EdgeSourceArrowOpacityProp EdgeSourceArrowProp EdgeSourceArrowShapeProp EdgeTargetArrowColorProp EdgeTargetArrowOpacityProp EdgeTargetArrowProp EdgeTargetArrowShapeProp EdgeToolTipCalculator EdgeToolTipProp EdgeView EditNetworkTitleDialog EditorDisplayer EditorDisplayer.EditorType EditorValueRangeTracer Exec ExitAction ExpFileChooser ExportAction ExportAsGMLAction ExportAsGraphicsAction ExportAsGraphicsFileChooser ExportAsInteractionsAction ExportAsXGMMLAction ExportBitmapOptionsDialog ExportEdgeAttributesAction Exporter ExportNodeAttributesAction ExportVizmapAction ExpressionData ExpressionDataPopupTable ExtensibleMultiHashMapModel FileUtil Filter FilterHistoryJList FingCyNetwork FingEdgeDepot FingExtensibleGraphPerspective FingExtensibleRootGraph FingNodeDepot FingRootGraphFactory FitContentAction FlagAndSelectionHandler FlatInterpolator FlattenIntVectors FloatParser FontCellRenderer FontChooser FontParser FontRenderer GeneOntology GeneOntology.GOAspect GeneOntologyWizard GenericEdgeArrowCalculator GenericEdgeColorCalculator GenericEdgeFontFaceCalculator GenericEdgeFontSizeCalculator GenericEdgeLabelCalculator GenericEdgeLabelColorCalculator GenericEdgeLineStyleCalculator GenericEdgeLineTypeCalculator GenericEdgeLineWidthCalculator GenericEdgeSourceArrowCalculator GenericEdgeSourceArrowColorCalculator GenericEdgeSourceArrowShapeCalculator GenericEdgeTargetArrowCalculator GenericEdgeTargetArrowColorCalculator GenericEdgeTargetArrowShapeCalculator GenericEdgeToolTipCalculator GenericNodeBorderColorCalculator GenericNodeColorCalculator GenericNodeFillColorCalculator GenericNodeFontFaceCalculator GenericNodeFontSizeCalculator GenericNodeHeightCalculator GenericNodeLabelCalculator GenericNodeLabelColorCalculator GenericNodeLabelPositionCalculator GenericNodeLineStyleCalculator GenericNodeLineTypeCalculator GenericNodeLineWidthCalculator GenericNodeShapeCalculator GenericNodeSizeCalculator GenericNodeToolTipCalculator GenericNodeUniformSizeCalculator GenericNodeWidthCalculator getCanonicalName getCommonName GinyEdgeControlDialog GinyUtils GlobalAppearance GlobalAppearanceCalculator GMLException GMLFileFilter GMLNode GMLParser GMLReader GMLTag GMLTree GMLWriter GOTerm GradientEditorPanel GraphObject GraphObjectSelection GraphObjectSelectionAction GraphPerspective GraphPerspectiveChangeEvent GraphPerspectiveChangeListener GraphReader GraphSetUtils GraphView GraphViewChangeEvent GraphViewChangeListener GraphViewController GraphViewHandler GridBagGroup GridNodeLayout Haltable HelpAboutAction HelpContactHelpDeskAction HelpContentsAction HideSelectedAction HideSelectedEdgesAction HideSelectedNodesAction IconPopupButton IconSupport ImportAttributeMatrixDialog ImportBioDataServerAction ImportEdgeAttributesAction ImportExpressionMatrixAction ImportGraphFileAction ImportHandler ImportNetworkDialog ImportNodeAttributesAction ImportVizmapAction IndeterminateProgressBar InnerCanvas InnerCanvasEvent InnerCanvasListener Installable InstallablePlugin InstallableTheme IntArray IntBTree IntegerEntryField IntEnumerator Interaction InteractionsReader InteractionWriter InternalFrameComponent Interpolator InterpolatorFactory IntHash IntIntHash IntIterator IntObjHash IntQueue IntStack IntTHash InvalidDownloadable InvertSelectedEdgesAction InvertSelectedNodesAction JErrorPanel JnlpWriterUtil JointIntegerEntry JStatusBar JTask JTaskConfig JTreeTable KeyValue Label LabelPlacerGraphic LabelPosition LabelPositionCellRenderer LabelPositionParser LabelTextPanel LayoutAdapter LayoutAlgorithm LayoutMenu LayoutMenuManager LayoutProperties LayoutSettingsDialog LayoutTask LegendDialog LegendTable LicenseDialog LinearNumberInterpolator LinearNumberToColorInterpolator LinearNumberToNumberInterpolator LineStyle LineStyleParser LineType LineTypeIcon LineTypeParser ListFromFileSelectionAction loadAnnotation loadAnnotationFromFlatFiles LoadNetworkTask loadThesaurus LoggerAction LoggerDialog LogLevel LongEnumerator LongLongHash MacAppConfig ManagerException ManagerModel ManagerUtil ManifestfileSelectionPanel ManifestFileSelectionPanelDescriptor MapOntologyAction MapperAndAttribute MappingFactory MappingType MappingUtil MetadataEntries MetadataParser MinIntHeap MinMaxDialog MinMaxDouble MinMaxInt Misc MiscDialog MiscGB ModuleProperties ModulePropertiesImpl MonitoredTask mRNAMeasurement MultiHashMap MultiHashMapDefinition MultiHashMapDefinitionListener MultiHashMapFactory MultiHashMapHelpers MultiHashMapListener MutableBool MutableInt MutableString NetworkData NetworkExpansionMenu NetworkImportWebServiceClient NetworkMetaDataDialog NetworkMetaDataTableModel NetworkPanel NetworkViewManager NewNetworkAction NewSessionAction NewSlider NewStringPopupDialog NewWindowSelectedNodesEdgesAction NewWindowSelectedNodesOnlyAction Node NodeAppearance NodeAppearanceCalculator NodeBorderColorProp NodeBorderOpacityProp NodeCalculator NodeColorCalculator NodeContextMenuListener NodeFillColorProp NodeFontFaceCalculator NodeFontFaceProp NodeFontSizeCalculator NodeFontSizeProp NodeHeightProp NodeIcon NodeLabelCalculator NodeLabelColorCalculator NodeLabelColorProp NodeLabelOpacityProp NodeLabelPositionProp NodeLabelProp NodeLineStyleProp NodeLineTypeCalculator NodeLineTypeProp NodeLineWidthProp NodeOpacityProp NodeShape NodeShapeCalculator NodeShapeParser NodeShapeProp NodeSizeCalculator NodeSizeProp NodeToolTipCalculator NodeToolTipProp NodeView NodeWidthProp NotAPluginException NumberInterpolator ObjectMapping ObjectToString OBOFlatFileReader OBOHeaderTags OboPanel OboPanelDescriptor OBOTags Ontology Ontology OntologyDescription OntologyFactory OntologyFlatFileReader OntologyMapperDialog OntologyReader OntologyServer OntologyServer.OntologyType OntologyTerm OntologyTerm OntologyTerm.SynonymType OntologyXmlReader OpenBrowser OpenSessionAction ParserFactory PassThroughMapping PDFExporter PercentUtil PhoebeNetworkView PhoebeNodeControl PluginException PluginFileReader PluginInfo PluginInfo.FileType PluginInquireAction PluginManageDialog PluginManageDialog.CommonError PluginManageDialog.PluginInstallStatus PluginManager PluginManagerAction PluginManagerInquireTask PluginProperties PluginProperties.PluginProperty PluginsTableModel PluginStatus PluginTracker PluginUpdateAction PluginUpdateDialog PluginUrlDialog PluginVersionUtils PluginXml PointTextListener PopupFontChooser PopupIconChooser PopupLabelPositionChooser PopupStringChooser PopupTextArea PreferenceAction PreferencesDialog PreferenceTableModel PreferenceValueDialog PrintAction PrintLOD ProxyHandler ProxyServerAction ProxyServerDialog PSExporter RandomColorListener RedoAction RootGraph RootGraphChangeEvent RootGraphChangeListener RotateSelectedNodesAction RunBareBones RunSampleTask SampleTask SaveSessionAction SaveSessionAsAction SelectAdjacentEdgesAction SelectAllAction SelectAllEdgesAction SelectAllNodesAction SelectConnectedNodesAction SelectEvent SelectEventListener SelectFilter SelectFirstNeighborsAction SelectFormatPanel SelectFormatPanelDescriptor SelectionModeAction Semantics SettingsAction SetVisualPropertiesAction ShapeCellRenderer ShapeNodeRealizer ShowAllAction ShowGraphicsDetailsAction ShrinkExpandGraph ShrinkExpandGraphUI SIFFileFilter SpeciesPanel SpeciesPanelDescriptor StaticLayoutMenu status StraightenSelectedEdgesAction StringParser StringUtils StringWrap SubjectBase SVGExporter SwingWorker Task TaskManager TaskMonitor TextFileReader TextHttpReader TextJarReader ThemeInfo Thesaurus ThesaurusFlatFileReader ToggleVisualMapperAction TrackerException Transform TreeCellRenderer TreeNode TreeTableModel TreeTableModelAdapter TriangleThumbRenderer Triple Tunable TunableListener Undo UndoAction UnHideSelectedAction UnHideSelectedEdgesAction UnHideSelectedNodesAction UnifiedNetworkImportDialog URLimportAdvancedDialog URLUtil ValueChangeListener ValueDisplayer ValueListener ValueParser ValueSelectDialog ViewChangeEdit ViewChangeEdit.SavedObjs ViewportChangeListener VisualMappingManager VisualProperty VisualPropertyIcon VisualPropertyType VisualStyle VisualStyleBuilder VizMapAttrTab VizMapBypassNetworkListener VizMapFontTab VizMapperMainPanel VizMapperMainPanel.DefaultEditor VizMapperProperty VizMapperTrackRenderer VizMapSizeTab VizMapTab VizMapUI VizUIUtilities WebServiceClient WebServiceClientGUI WebServiceClientGUI.IconSize WebServiceClientImpl WebServiceClientImplWithGUI WebServiceClientManager WebServiceClientManager.ClientType WebServiceContextMenu WebServiceContextMenuListener WebServiceNetworkImportAction WebServiceThemeInstall WebstartException WindowUtilities WSImportResultDialog XGMMLException XGMMLFileFilter XGMMLReader XGMMLWriter YValueLegendPanel ZipUtil ZoomAction ZoomSelectedAction