All Classes

AbstractCalculator AbstractCellEditor AbstractGraphReader AbstractLayout AbstractTreeTableModel AbstractVisualProperty AddPointListener Aliases AliasType AlignHorizontalAction AlignVerticalAction AlphabeticalSelectionAction AnimatedLayoutAction Annotation AnnotationDescription AnnotationFlatFileReader AnnotationGui AnnotationXmlReader AnotationPanel AnotationPanelDescriptor Appearance Arrow ArrowIcon ArrowParser ArrowShape ArrowShapeParser AttributeFilter AttributeSaverDialog AttributeValueVisitor BackgroundColorAction BasicCalculator BasicGraphViewHandler BelowAndAbovePanel BendSelectedEdgesAction BiModalJSplitPane BioDataServer BioDataServerInterface BioDataServerRmi BioDataServerUtil BirdsEyeViewAction BitmapExporter BookmarkAction BookmarkDialog BookmarkReader BookmarksUtil BoundaryRangeValues C2CMappingEditor C2DMappingEditor Calculator CalculatorCatalog CalculatorCatalogFactory CalculatorFactory CalculatorIO Category CheckBoxFileChooser CheckBoxJList clear CloneGraphInNewWindowAction ColorParser ColorScaleTable ColumnResizer ContinuousLegend ContinuousMapping ContinuousMappingEditorPanel ContinuousMappingPoint ContinuousMappingReader ContinuousMappingWriter ContinuousRangeCalculator ContinuousTrackRenderer ContinuousUI CountedIterator CreateNetworkViewAction CreditScreen CyAbstractEdit CyAttributes CyAttributesImpl CyAttributesReader CyAttributesUtils CyAttributesWriter CyAttributesWriter2 CyColorCellRenderer CyColorCellRenderer.PaintIcon CyColorChooser CyColorPropertyEditor CyColorPropertyEditor.AsInt CyComboBoxPropertyEditor CyComboBoxPropertyEditor.Value CyDoublePropertyEditor CyEdge CyEdgeView CyFileFilter CyFontPropertyEditor CyGradientTrackRenderer CyGraphLOD CyGroup CyGroupChangeListener CyGroupChangeListener.ChangeType CyGroupImpl CyGroupManager CyGroupViewer CyGroupViewer.ChangeType CyHelpBroker CyInitParams CyLabelPositionPropertyEditor CyLayoutAlgorithm CyLayouts CyMain CyMenus CyNetwork CyNetworkAdapter CyNetworkData CyNetworkEvent CyNetworkListener CyNetworkNaming CyNetworkUtilities CyNetworkView CyNode CyNodeView CyStringPropertyEditor CytoPanel CytoPanelAction CytoPanelContainer CytoPanelImp CytoPanelListener CytoPanelName CytoPanelState CytoPanelUtil Cytoscape CytoscapeAction CytoscapeDesktop CytoscapeFingRootGraph CytoscapeInit CytoscapeMenuBar CytoscapeModifiedNetworkManager CytoscapePlugin CytoscapeProgressMonitor CytoscapeRootGraph CytoscapeSessionReader CytoscapeSessionWriter CytoscapeToolBar CytoscapeVersion CyUndo DBCrossReferenceReader DBCrossReferences DBReference DBXrefKeywords DefaultAppearenceBuilder DefaultPanel DefaultViewPanel DeletePointListener DeselectAllAction DeSelectAllEdgesAction DeSelectAllNodesAction DestroyNetworkAction DestroyNetworkViewAction DingNetworkView DiscreteLegend DiscreteMapping DiscreteMappingReader DiscreteMappingWriter DiscreteRangeCalculator DiscreteTrackRenderer DiscreteUI DoubleParser DropDownMenuButton DuplicateCalculatorNameException DynamicLayoutMenu EdgeAppearance EdgeAppearanceCalculator EdgeArrowCalculator EdgeAttributesPopupDetails EdgeCalculator EdgeColorCalculator EdgeColorProp 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 EditNetworkTitleDialog EditorDisplayer EditorDisplayer.EditorType Exec ExitAction ExpFileChooser ExportAction ExportAsGMLAction ExportAsGraphicsAction ExportAsGraphicsFileChooser ExportAsInteractionsAction ExportAsXGMMLAction ExportBitmapOptionsDialog ExportEdgeAttributesAction Exporter ExportNodeAttributesAction ExportVizmapAction ExpressionData ExpressionDataPopupTable ExtensibleMultiHashMapModel FileUtil FilterHistoryJList FingCyNetwork 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 GraphObjectSelection GraphObjectSelectionAction GraphReader GraphSetUtils GraphViewController GraphViewHandler GridBagGroup GridNodeLayout HelpAboutAction HelpContactHelpDeskAction HelpContentsAction HideSelectedAction HideSelectedEdgesAction HideSelectedNodesAction IconPopupButton IconSupport ImportAttributeMatrixDialog ImportBioDataServerAction ImportEdgeAttributesAction ImportExpressionMatrixAction ImportGraphFileAction ImportHandler ImportNetworkDialog ImportNodeAttributesAction ImportVizmapAction IndeterminateProgressBar IntegerEntryField Interaction InteractionsReader InteractionWriter InternalFrameComponent Interpolator InterpolatorFactory InvertSelectedEdgesAction InvertSelectedNodesAction JnlpWriterUtil JointIntegerEntry JStatusBar JTreeTable KeyValue 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 MacAppConfig ManagerException ManagerModel ManagerUtil ManifestfileSelectionPanel ManifestFileSelectionPanelDescriptor MapOntologyAction MapperAndAttribute MappingFactory MappingType MappingUtil MetadataEntries MetadataParser MinMaxDouble MinMaxInt Misc MiscDialog MiscGB MonitoredTask mRNAMeasurement MultiHashMap MultiHashMapDefinition MultiHashMapDefinitionListener MultiHashMapFactory MultiHashMapHelpers MultiHashMapListener MutableBool MutableInt MutableString NetworkData NetworkMetaDataDialog NetworkMetaDataTableModel NetworkPanel NetworkView NetworkViewManager NewSessionAction NewSlider NewStringPopupDialog NewWindowSelectedNodesEdgesAction NewWindowSelectedNodesOnlyAction NodeAppearance NodeAppearanceCalculator NodeBorderColorProp NodeBorderOpacityProp NodeCalculator NodeColorCalculator 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 NodeWidthProp NotAPluginException NumberInterpolator ObjectMapping ObjectToString OBOFlatFileReader OBOHeaderTags OboPanel OboPanelDescriptor OBOTags OldStyleCalculatorIO 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 PluginProperties PluginProperties.PluginProperty PluginsTableModel PluginStatus PluginTracker PluginUpdateAction PluginUpdateDialog PluginUrlDialog PluginXml PointTextListener PopupFontChooser PopupIconChooser PopupLabelPositionChooser PopupStringChooser PopupTextArea PreferenceAction PreferencesDialog PreferenceTableModel PreferenceValueDialog PrintAction ProxyHandler ProxyServerAction ProxyServerDialog RandomColorListener RedoAction RotateSelectedNodesAction SaveSessionAction SaveSessionAsAction SelectAllAction SelectAllEdgesAction SelectAllNodesAction SelectEvent SelectEventListener SelectFilter SelectFirstNeighborsAction SelectFormatPanel SelectFormatPanelDescriptor SelectionModeAction Semantics SettingsAction SetVisualPropertiesAction ShapeCellRenderer ShapeNodeRealizer ShowAllAction ShrinkExpandGraph ShrinkExpandGraphUI SIFFileFilter SpeciesPanel SpeciesPanelDescriptor StaticLayoutMenu status StraightenSelectedEdgesAction StringParser SubjectBase SVGExporter SwingWorker TextFileReader TextHttpReader TextJarReader Thesaurus ThesaurusFlatFileReader ToggleVisualMapperAction Transform TreeNode TreeTableModel TreeTableModelAdapter TriangleThumbRenderer Triple Tunable UndoAction UnHideSelectedAction UnHideSelectedEdgesAction UnHideSelectedNodesAction URLimportAdvancedDialog URLUtil ValueChangeListener ValueDisplayer ValueListener ValueParser ValueSelectDialog VisualMappingManager VisualProperty VisualPropertyIcon VisualPropertyType VisualStyle VisualStyleBuilder VisualStyleBuilderDialog VizMapAttrTab VizMapBypassNetworkListener VizMapFontTab VizMapperMainPanel VizMapperMainPanel.DefaultEditor VizMapperProperty VizMapperTrackRenderer VizMapSizeTab VizMapTab VizMapUI VizUIUtilities WebstartException WindowUtilities XGMMLException XGMMLFileFilter XGMMLReader XGMMLWriter YValueLegendPanel ZipUtil ZoomAction ZoomSelectedAction