All Classes

AbstractCalculator AbstractCellEditor AbstractGraphReader AbstractTreeTableModel AddPointListener Aliases AliasType AlignHorizontalAction AlignVerticalAction AlphabeticalSelectionAction AnimatedLayoutAction Annotation AnnotationDescription AnnotationFlatFileReader AnnotationGui AnnotationXmlReader AnotationPanel AnotationPanelDescriptor Arrow ArrowParser AttributeFilter AttributeSaverDialog AttributeValueVisitor BackgroundColorAction BasicGraphViewHandler BendSelectedEdgesAction BiModalJSplitPane BioDataServer BioDataServerInterface BioDataServerRmi BioDataServerUtil BirdsEyeViewAction BookmarkAction BookmarkDialog BookmarkReader BookmarksUtil BoundaryRangeValues Calculator CalculatorCatalog CalculatorCatalogFactory CalculatorFactory CalculatorIO CheckBoxFileChooser clear CloneGraphInNewWindowAction ColorParser ColorScaleTable ColumnResizer ContinuousLegend ContinuousMapping ContinuousMappingPoint ContinuousMappingReader ContinuousMappingWriter ContinuousRangeCalculator ContinuousUI CountedIterator CreateNetworkViewAction CreditScreen CyAttributes CyAttributesImpl CyAttributesReader CyAttributesUtils CyAttributesWriter CyAttributesWriter2 CyColorChooser CyEdge CyEdgeView CyFileFilter CyGraphLOD CyHelpBroker CyInitParams CyMain CyMenus CyNetwork CyNetworkAdapter CyNetworkData CyNetworkEvent CyNetworkListener CyNetworkNaming CyNetworkUtilities CyNetworkView CyNode CyNodeView CytoPanel CytoPanelAction CytoPanelContainer CytoPanelImp CytoPanelListener CytoPanelState CytoPanelUtil Cytoscape CytoscapeAction CytoscapeConfig CytoscapeDesktop CytoscapeFingRootGraph CytoscapeInit CytoscapeMenuBar CytoscapeModifiedNetworkManager CytoscapePlugin CytoscapeProgressMonitor CytoscapeRootGraph CytoscapeSessionReader CytoscapeSessionWriter CytoscapeToolBar CytoscapeVersion DBCrossReferenceReader DBCrossReferences DBReference DBXrefKeywords DefaultPanel DeletePointListener DeleteSelectedAction DeselectAllAction DeSelectAllEdgesAction DeSelectAllNodesAction DestroyNetworkAction DestroyNetworkViewAction DestroySelectedAction DingNetworkView DiscreteLegend DiscreteMapping DiscreteMappingReader DiscreteMappingWriter DiscreteRangeCalculator DiscreteUI DoubleParser DuplicateCalculatorNameException EdgeAppearance EdgeAppearanceCalculator EdgeArrowCalculator EdgeAttributesPopupDetails EdgeCalculator EdgeColorCalculator EdgeFontFaceCalculator EdgeFontSizeCalculator EdgeLabelCalculator EdgeLineTypeCalculator EdgeManipulationAction EdgeToolTipCalculator EditNetworkTitleDialog Exec ExitAction ExpFileChooser ExportAction ExportAsGMLAction ExportAsGraphicsAction ExportAsInteractionsAction ExportAsXGMMLAction ExportEdgeAttributesAction ExportNodeAttributesAction ExportVizmapAction ExpressionData ExpressionDataPopupTable ExtensibleMultiHashMapModel FileUtil FilterHistoryJList FingCyNetwork FitContentAction FlagAndSelectionHandler FlagEvent FlagEventListener FlagFilter FlatInterpolator FlattenIntVectors FontChooser FontParser FontRenderer GeneOntology GeneOntology.GOAspect GeneOntologyWizard GeneralColorDialogListener GenericEdgeArrowCalculator GenericEdgeColorCalculator GenericEdgeFontFaceCalculator GenericEdgeFontSizeCalculator GenericEdgeLabelCalculator GenericEdgeLabelColorCalculator GenericEdgeLineTypeCalculator GenericEdgeSourceArrowCalculator GenericEdgeTargetArrowCalculator GenericEdgeToolTipCalculator GenericNodeBorderColorCalculator GenericNodeColorCalculator GenericNodeFillColorCalculator GenericNodeFontFaceCalculator GenericNodeFontSizeCalculator GenericNodeHeightCalculator GenericNodeLabelCalculator GenericNodeLabelColorCalculator GenericNodeLabelPositionCalculator GenericNodeLineTypeCalculator GenericNodeShapeCalculator GenericNodeSizeCalculator GenericNodeToolTipCalculator GenericNodeUniformSizeCalculator GenericNodeWidthCalculator getCanonicalName getCommonName GinyEdgeControlDialog GinyUtils GlobalAppearance GlobalAppearanceCalculator GMLException GMLFileFilter GMLNode GMLParser GMLReader GMLTree GMLWriter GOTerm GraphObjectSelection GraphObjectSelectionAction GraphReader GraphSetUtils GraphViewController GraphViewHandler GridBagGroup HelpAboutAction HelpContactHelpDeskAction 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 LabelPosition LabelPositionParser LabelTextPanel LayoutAlgorithm LegendDialog LegendTable LinearNumberInterpolator LinearNumberToColorInterpolator LinearNumberToNumberInterpolator LineType LineTypeParser ListFromFileSelectionAction loadAnnotation loadAnnotationFromFlatFiles LoadNetworkTask loadThesaurus MacAppConfig ManifestfileSelectionPanel ManifestFileSelectionPanelDescriptor MapOntologyAction MapperAndAttribute MappingFactory MappingUtil MetadataEntries MetadataParser MinMaxDouble MinMaxInt Misc MiscDialog MiscGB MonitoredTask mRNAMeasurement MultiHashMap MultiHashMapDefinition MultiHashMapDefinitionListener MultiHashMapFactory MultiHashMapHelpers MultiHashMapListener MutableBool MutableColor MutableInt MutableString NetworkData NetworkMetaDataDialog NetworkMetaDataTableModel NetworkPanel NetworkView NetworkViewManager NewSessionAction NewSlider NewStringPopupDialog NewWindowSelectedNodesEdgesAction NewWindowSelectedNodesOnlyAction NodeAppearance NodeAppearanceCalculator NodeCalculator NodeColorCalculator NodeFontFaceCalculator NodeFontSizeCalculator NodeLabelCalculator NodeLabelColorCalculator NodeLineTypeCalculator NodeShapeCalculator NodeShapeParser NodeSizeCalculator NodeToolTipCalculator 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 PercentUtil PhoebeNetworkView PhoebeNodeControl PluginsTableModel PointTextListener PopupFontChooser PopupIconChooser PopupLabelPositionChooser PopupStringChooser PopupTextArea PreferenceAction PreferencesDialog PreferenceTableModel PreferenceValueDialog PrintAction ProxyHandler ProxyServerAction ProxyServerDialog RandomColorListener RotateSelectedNodesAction SaveSessionAction SaveSessionAsAction SelectAllAction SelectAllEdgesAction SelectAllNodesAction SelectEvent SelectEventListener SelectFilter SelectFirstNeighborsAction SelectFormatPanel SelectFormatPanelDescriptor SelectionModeAction Semantics SetVisualPropertiesAction ShapeNodeRealizer ShowAllAction ShrinkExpandGraph ShrinkExpandGraphUI SIFFileFilter SpeciesPanel SpeciesPanelDescriptor status StraightenSelectedEdgesAction StringParser SubjectBase SwingWorker TextFileReader TextHttpReader TextJarReader Thesaurus ThesaurusFlatFileReader ToggleVisualMapperAction Transform TreeTableModel TreeTableModelAdapter Triple UndoManager UnHideSelectedAction UnHideSelectedEdgesAction UnHideSelectedNodesAction URLimportAdvancedDialog URLUtil ValueChangeListener ValueDisplayer ValueListener ValueParser VisualMappingManager VisualStyle VisualStyleBuilder VisualStyleBuilderDialog VizMapAttrTab VizMapBypassNetworkListener VizMapFontTab VizMapSizeTab VizMapTab VizMapUI VizUIUtilities WindowUtilities XGMMLException XGMMLFileFilter XGMMLReader XGMMLWriter ZipUtil ZoomAction ZoomSelectedAction