All Classes

AbstractCalculator AbstractCellEditor AbstractTreeTableModel AbstractUnmarshallingEventHandlerImpl AbstractUnmarshallingEventHandlerImpl AddPointListener AlignHorizontalAction AlignVerticalAction AlphabeticalSelectionAction AnimatedLayoutAction Annotation AnnotationDescription AnnotationFlatFileReader AnnotationGui AnnotationXmlReader AnotationPanel AnotationPanelDescriptor AnyType AnyTypeImpl Arrow ArrowParser Att AttImpl AttributeLayout AttributeSaverDialog AttType AttTypeImpl BackgroundColorAction BasicGraphViewHandler BiModalJSplitPane BioDataServer BioDataServerInterface BioDataServerRmi BioDataServerUtil BirdsEyeViewAction BoundaryRangeValues Calculator CalculatorCatalog CalculatorCatalogFactory CalculatorFactory CalculatorIO Center CenterImpl CenterType CenterTypeImpl CheckBoxFileChooser Child ChildImpl ChildType ChildTypeImpl clear CloneGraphInNewWindowAction ColorParser ColorScaleTable ContentHandlerAdaptor ContentHandlerAdaptor ContinuousMapping ContinuousMappingPoint ContinuousMappingReader ContinuousMappingWriter ContinuousRangeCalculator ContinuousUI Contributor ContributorImpl ContributorType ContributorTypeImpl CountedIterator Coverage CoverageImpl CoverageType CoverageTypeImpl CreateNetworkViewAction Creator CreatorImpl CreatorType CreatorTypeImpl CreditScreen CyAttributes CyAttributesImpl CyAttributesReader CyAttributesUtils CyAttributesWriter CyEdge CyEdgeView CyFileFilter CyGraphLOD CyHelpBroker CyInitParams CyMain CyMenus CyNetwork CyNetworkAdapter CyNetworkData CyNetworkEvent CyNetworkListener CyNetworkNaming CyNetworkUtilities CyNetworkView CyNode CyNodeView CyProject Cysession CysessionImpl CysessionType CysessionTypeImpl Cytopanel CytoPanel CytoPanelAction CytoPanelContainer CytoPanelImp CytopanelImpl CytoPanelListener Cytopanels CytopanelsImpl CytoPanelState CytopanelsType CytopanelsTypeImpl CytopanelType CytopanelTypeImpl CytoPanelUtil Cytoscape CytoscapeAction CytoscapeConfig CytoscapeDesktop CytoscapeFingRootGraph CytoscapeInit CytoscapeMenuBar CytoscapeModifiedNetworkManager CytoscapeObj CytoscapePlugin CytoscapeProgressMonitor CytoscapeRootGraph CytoscapeSessionReader CytoscapeSessionWriter CytoscapeToolBar CytoscapeVersion Date DateImpl DateType DateTypeImpl Dcmes DcmesImpl DefaultJAXBContextImpl DefaultJAXBContextImpl DefaultPanel DeletePointListener DeleteSelectedAction Description DescriptionImpl DescriptionType DescriptionTypeImpl DeselectAllAction DeSelectAllEdgesAction DeSelectAllNodesAction DestroyNetworkAction DestroyNetworkViewAction DestroySelectedAction DingNetworkView DiscreteMapping DiscreteMappingReader DiscreteMappingWriter DiscreteRangeCalculator DiscreteUI DoubleParser DuplicateCalculatorNameException Edge Edge EdgeAppearance EdgeAppearanceCalculator EdgeArrowCalculator EdgeAttributesPopupDetails EdgeCalculator EdgeColorCalculator EdgeFontFaceCalculator EdgeFontSizeCalculator EdgeImpl EdgeImpl EdgeLabelCalculator EdgeLineTypeCalculator EdgeManipulationAction EdgeToolTipCalculator EdgeType EdgeTypeImpl ErrorHandlerAdaptor ErrorHandlerAdaptor Exec ExitAction ExpFileChooser ExportAction ExportAsGMLAction ExportAsGraphicsAction ExportAsInteractionsAction ExportAsXGMMLAction ExportEdgeAttributesAction ExportNodeAttributesAction ExportVizmapAction ExpressionData ExpressionDataPopupTable ExtensibleMultiHashMapModel FileUtil FingCyNetwork FitContentAction FlagAndSelectionHandler FlagEvent FlagEventListener FlagFilter FlatInterpolator FlattenIntVectors FontChooser FontParser FontRenderer Format FormatImpl FormatType FormatTypeImpl GeneOntologyWizard GeneralColorDialogListener GenericEdgeArrowCalculator GenericEdgeColorCalculator GenericEdgeFontFaceCalculator GenericEdgeFontSizeCalculator GenericEdgeLabelCalculator GenericEdgeLineTypeCalculator GenericEdgeToolTipCalculator GenericNodeColorCalculator GenericNodeFontFaceCalculator GenericNodeFontSizeCalculator GenericNodeLabelCalculator GenericNodeLabelColorCalculator GenericNodeLineTypeCalculator GenericNodeShapeCalculator GenericNodeSizeCalculator GenericNodeToolTipCalculator getCanonicalName getCommonName GinyEdgeControlDialog GinyUtils GlobalAppearance GlobalAppearanceCalculator GMLException GMLNode GMLParser GMLReader2 GMLTree GMLWriter GrammarInfo GrammarInfo GrammarInfoImpl GrammarInfoImpl Graph GraphConverter GraphConverter2 GraphicEdge GraphicEdgeImpl GraphicGraph GraphicGraphImpl GraphicNode GraphicNodeImpl Graphics GraphicsImpl GraphicsType GraphicsTypeImpl GraphImpl GraphObjAttributes GraphObjectSelection GraphObjectSelectionAction GraphReader GraphSetUtils GraphViewController GraphViewHandler GridBagGroup HelpAboutAction HiddenEdges HiddenEdgesImpl HiddenEdgesType HiddenEdgesTypeImpl HiddenNodes HiddenNodesImpl HiddenNodesType HiddenNodesTypeImpl HideSelectedAction HideSelectedEdgesAction HideSelectedNodesAction IconPopupButton Identifier IdentifierImpl IdentifierType IdentifierTypeImpl ImportBioDataServerAction ImportEdgeAttributesAction ImportExpressionMatrixAction ImportGraphFileAction ImportNetworkDialog ImportNodeAttributesAction ImportVizmapAction IndeterminateProgressBar IntegerEntryField Interaction InteractionsReader InterleaveDispatcher Interpolator InterpolatorFactory InvertSelectedEdgesAction InvertSelectedNodesAction JAXBVersion JAXBVersion JointIntegerEntry JTreeTable KeyValue LabelTextPanel Language LanguageImpl LanguageType LanguageTypeImpl LayoutAction LayoutAlgorithm LayoutUtils Line LinearNumberInterpolator LinearNumberToColorInterpolator LinearNumberToNumberInterpolator LineImpl LineType LineType LineTypeImpl LineTypeParser ListFromFileSelectionAction loadAnnotation loadAnnotationFromFlatFiles loadThesaurus MacAppConfig ManifestfileSelectionPanel ManifestFileSelectionPanelDescriptor MapOntologyAction MapperAndAttribute MappingFactory MarshallerImpl MarshallerImpl MetadataParser MinMaxDouble MinMaxInt Misc MiscDialog MiscGB MonitoredTask mRNAMeasurement MSVValidator MSVValidator MultiHashMap MultiHashMapDefinition MultiHashMapDefinitionListener MultiHashMapFactory MultiHashMapHelpers MultiHashMapListener MutableBool MutableColor MutableInt MutableString NamespaceContext2 NamespaceContext2 NamespaceContextImpl NamespaceContextImpl Network NetworkData NetworkImpl NetworkMetaDataDialog NetworkMetaDataTableModel NetworkPanel NetworkTree NetworkTreeImpl NetworkTreeType NetworkTreeTypeImpl NetworkType NetworkTypeImpl NetworkView NetworkViewManager NewSessionAction NewSlider NewStringPopupDialog NewWindowSelectedNodesEdgesAction NewWindowSelectedNodesOnlyAction Node Node NodeAppearance NodeAppearanceCalculator NodeCalculator NodeColorCalculator NodeFontFaceCalculator NodeFontSizeCalculator NodeImpl NodeImpl NodeLabelCalculator NodeLabelColorCalculator NodeLineTypeCalculator NodeShapeCalculator NodeShapeParser NodeSizeCalculator NodeToolTipCalculator NodeType NodeTypeImpl NotAPluginException NumberInterpolator ObjectFactory ObjectFactory ObjectMapping ObjectToString OboPanel OboPanelDescriptor OldStyleCalculatorIO Ontology OntologyDescription OntologyFlatFileReader OntologyMapperDialog OntologyTerm OntologyXmlReader OpenBrowser OpenSessionAction Panel PanelImpl Panels PanelsImpl PanelState PanelStateImpl PanelsType PanelsTypeImpl PanelType PanelTypeImpl Parent ParentImpl ParentType ParentTypeImpl PassThroughMapping PercentUtil PhoebeNetworkView PhoebeNodeControl Plugin PluginImpl Plugins PluginsImpl PluginsTableModel PluginsType PluginsTypeImpl PluginType PluginTypeImpl Point PointImpl PointTextListener PointType PointTypeImpl PopupIconChooser PopupTextArea PreferenceAction PreferencesDialog PreferenceTableModel PreferenceValueDialog PrefixCallback PrefixCallback PrintAction PropertiesTester Publisher PublisherImpl PublisherType PublisherTypeImpl RandomColorListener RandomRenderableSubgraphLogic RdfDescription RdfDescriptionImpl RdfDescriptionType RdfDescriptionTypeImpl RdfRDF RdfRDFImpl RdfRDFType RdfRDFTypeImpl Relation RelationImpl RelationType RelationTypeImpl Rights RightsImpl RightsType RightsTypeImpl RotateSelectedNodesAction SaveSessionAction SaveSessionAsAction SAXMarshaller SAXMarshaller SAXUnmarshallerHandler SAXUnmarshallerHandler SAXUnmarshallerHandlerImpl SAXUnmarshallerHandlerImpl SelectAllAction SelectAllEdgesAction SelectAllNodesAction SelectedEdges SelectedEdgesImpl SelectedEdgesType SelectedEdgesTypeImpl SelectedNodes SelectedNodesImpl SelectedNodesType SelectedNodesTypeImpl SelectedPanel SelectedPanelImpl SelectEvent SelectEventListener SelectFilter SelectFirstNeighborsAction SelectFormatPanel SelectFormatPanelDescriptor SelectionModeAction Semantics SessionNote SessionNoteImpl SessionState SessionStateImpl SessionStateType SessionStateTypeImpl SetVisualPropertiesAction ShapeNodeRealizer ShowAllAction ShrinkExpandGraph ShrinkExpandGraphUI SimpleEdge SimpleEdgeImpl SimpleGraph SimpleGraphImpl SimpleNode SimpleNodeImpl Source SourceImpl SourceType SourceTypeImpl SpeciesPanel SpeciesPanelDescriptor SquiggleAction status StringParser Subject SubjectBase SubjectImpl SubjectType SubjectTypeImpl SwingWorker TestMultiHashMap TextFileReader TextHttpReader TextJarReader Thesaurus ThesaurusFlatFileReader Title TitleImpl TitleType TitleTypeImpl ToggleVisualMapperAction Transform TreeTableModel TreeTableModelAdapter Type TypeImpl TypeType TypeTypeImpl UndoManager UnHideSelectedAction UnHideSelectedEdgesAction UnHideSelectedNodesAction UnmarshallableObject UnmarshallableObject UnmarshallerImpl UnmarshallerImpl UnmarshallingContext UnmarshallingContext UnmarshallingEventHandler UnmarshallingEventHandler UnmarshallingEventHandlerAdaptor UnmarshallingEventHandlerAdaptor Util Util ValidatableObject ValidatableObject ValidatingUnmarshaller ValidatingUnmarshaller ValidatorImpl ValidatorImpl ValueChangeListener ValueDisplayer ValueListener ValueParser ViewableNodes ViewableNodesImpl ViewableNodesType ViewableNodesTypeImpl VisualMappingManager VisualStyle VisualStyleBuilder VisualStyleBuilderDialog VizMapAttrTab VizMapFontTab VizMapSizeTab VizMapTab VizMapUI VizUIUtilities WindowUtilities XGMMLReader XGMMLWriter XMLSerializable XMLSerializable XMLSerializer XMLSerializer ZipMultipleFiles ZoomAction ZoomSelectedAction