Index (Cytoscape 2.4.1 API)

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aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.OboPanelDescriptor
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.SpeciesPanelDescriptor
aboutToHidePanel() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
AbstractCalculator - Class in cytoscape.visual.calculators: AbstractCalculator is the top of the tree for the Calculator classes.
AbstractCalculator(String, ObjectMapping, Class) - Constructor for class cytoscape.visual.calculators.AbstractCalculator: Create a calculator with the specified object mapping and name.
AbstractCellEditor - Class in cytoscape.util.swing
AbstractCellEditor() - Constructor for class cytoscape.util.swing.AbstractCellEditor
AbstractGraphReader - Class in cytoscape.data.readers
AbstractGraphReader(String) - Constructor for class cytoscape.data.readers.AbstractGraphReader
AbstractTreeTableModel - Class in cytoscape.util.swing
AbstractTreeTableModel(Object) - Constructor for class cytoscape.util.swing.AbstractTreeTableModel
accept(File) - Method in class cytoscape.util.CyFileFilter: Returns true if this class is capable of processing the specified file.
accept(File, String) - Method in class cytoscape.util.CyFileFilter: Returns true if this class is capable of processing the specified file.
accept(String) - Method in class cytoscape.util.CyFileFilter: Returns true if this class is capable of processing the specified file.
accept(File) - Method in class cytoscape.util.XGMMLFileFilter: Indicates which files the XGMMLFileFilter accepts.
actionHelp() - Method in class cytoscape.util.CytoscapeAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignHorizontalAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignVerticalAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlphabeticalSelectionAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AnimatedLayoutAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BackgroundColorAction: Captures User Menu Selection.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BendSelectedEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BirdsEyeViewAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BookmarkAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CloneGraphInNewWindowAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CreateNetworkViewAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CytoPanelAction: Menu item select/deselect handler.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeleteSelectedAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeselectAllAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkViewAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroySelectedAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.EdgeManipulationAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExitAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsGMLAction: User-initiated action to save the current network in GML format to a user-specified file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsGraphicsAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsInteractionsAction: User-initiated action to save the current network in SIF format to a user-specified file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsXGMMLAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportEdgeAttributesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportNodeAttributesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportVizmapAction: Get file name and execute the saving task
actionPerformed(ActionEvent) - Method in class cytoscape.actions.FitContentAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.GraphObjectSelectionAction: This Should go away
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpAboutAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpContactHelpDeskAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportBioDataServerAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportEdgeAttributesAction: User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportExpressionMatrixAction: User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportGraphFileAction: User-initiated action to load a CyNetwork into Cytoscape.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportNodeAttributesAction: User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportVizmapAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ListFromFileSelectionAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.MapOntologyAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewSessionAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesOnlyAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.OpenSessionAction: Clear current session and open the cys file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PreferenceAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PrintAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ProxyServerAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.RotateSelectedNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SaveSessionAction: If no current session file exists, open dialog box to ask user a new session file name, otherwise, overwrite the file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SaveSessionAsAction: If no current session file exists, open dialog box to save new session, and if it exists, overwrite the file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectFirstNeighborsAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SetVisualPropertiesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowAllAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.StraightenSelectedEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ToggleVisualMapperAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedEdgesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedNodesAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomSelectedAction
actionPerformed(ActionEvent) - Method in class cytoscape.data.annotation.AnnotationGui
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.OboPanelDescriptor
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.EditNetworkTitleDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ExpressionDataPopupTable.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GeneralColorDialogListener: Deprecated.
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GinyEdgeControlDialog.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GraphObjectSelection
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton.ApplyIconAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton.CancelIconAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ImportNetworkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.LabelTextPanel.BoxAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewSlider.MJTextField
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewStringPopupDialog.CancelAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewStringPopupDialog.OkAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.PopupTextArea.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog.EditBookmarkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.ProxyServerDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ShrinkExpandGraph
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog.BookmarkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.continuous.AddPointListener: User Initiated Action.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.continuous.ContinuousUI: Apply Changes.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.continuous.DeletePointListener: User Initiated Action.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.discrete.RandomColorListener: User wants to Seed the Discrete Mapper with Random Color Values.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.PopupIconChooser.ApplyIconAction
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.PopupIconChooser.CancelIconAction
activate() - Method in class cytoscape.plugin.CytoscapePlugin: If implemented, then this plugin will be activated after being initialized
add(String, int) - Method in class cytoscape.data.annotation.Annotation: create a new annotation for an entity (typically a gene) of the current species and with respect to the current ontology. an entity may have more than one classification.
add(OntologyTerm) - Method in class cytoscape.data.annotation.Ontology
add(OntologyTerm) - Method in class cytoscape.data.ontology.Ontology: Add a new ontology term to the DAG.
add(String, String) - Method in class cytoscape.data.synonyms.Aliases: Add new alias for an object.
add(String, List<String>) - Method in class cytoscape.data.synonyms.Aliases: Add list of aliases to the existing alias lists.
add(String, String) - Method in class cytoscape.data.synonyms.Thesaurus
add(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel.
add(Component, int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with specified title, icon, and tool tip.
add(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel.
add(Component, int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with specified title, icon, and tool tip.
addAction(Action) - Method in class cytoscape.util.CytoscapeMenuBar: If the given Action has a present and false inMenuBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredMenu property, or null if it does not have that property.
addAction(Action, int) - Method in class cytoscape.util.CytoscapeMenuBar
addAction(String, Action) - Method in class cytoscape.util.CytoscapeMenuBar
addAction(Action) - Method in class cytoscape.util.CytoscapeToolBar: If the given Action has an absent or false inToolBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredButtonGroup property, or null if it does not have that property.
addAction(String, Action) - Method in class cytoscape.util.CytoscapeToolBar: Note that this presently ignores the button group name.
addAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus
addAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus
addAllAnnotationToNodes(AnnotationDescription, String) - Method in class cytoscape.data.annotation.OntologyMapperDialog
addAlternateCommonName(String, String) - Method in class cytoscape.data.synonyms.Thesaurus
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServer
addAnnotation(Annotation) - Method in interface cytoscape.data.servers.BioDataServerInterface
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServerRmi: if the new annotation is to an already annotated species, curator and type, then simply add (with possible overwriting for identical
addAnnotationToNodes(AnnotationDescription, int) - Method in class cytoscape.data.annotation.AnnotationGui
addAnnotationToNodes(AnnotationDescription, int, String) - Method in class cytoscape.data.annotation.OntologyMapperDialog
addArguments(ArrayList<String>) - Method in class cytoscape.util.JnlpWriterUtil
addButtonActionListener(ActionListener) - Method in class cytoscape.data.servers.ui.AnotationPanel
addCalculator(Calculator) - Method in class cytoscape.visual.CalculatorCatalog: Add any calculator to the catalog.
addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
addChangeListener(ChangeListener, byte) - Method in class cytoscape.visual.CalculatorCatalog: Add a ChangeListener to the catalog.
addChangeListener(ChangeListener) - Method in class cytoscape.visual.calculators.AbstractCalculator: Add a ChangeListener to the calcaultor.
addChangeListener(ChangeListener) - Method in interface cytoscape.visual.calculators.Calculator: Add a ChangeListener to the calcaultor.
addChangeListener(ChangeListener) - Method in interface cytoscape.visual.mappings.ObjectMapping: Add a ChangeListener to the mapping.
addChangeListener(ChangeListener) - Method in class cytoscape.visual.mappings.PassThroughMapping: Empty implementation because PassThroughMapping has no UI.
addChangeListener(ChangeListener) - Method in class cytoscape.visual.SubjectBase: Add a ChangeListener.
addContainer(int) - Method in class cytoscape.data.annotation.OntologyTerm
addCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork: Registers the argument as a listener to this object.
addCyNetworkListener(CyNetworkListener) - Method in class cytoscape.giny.FingCyNetwork: Registers the argument as a listener to this object.
addCytoPanelListener(CytoPanelListener) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a CytoPanel listener.
addCytoPanelListener(CytoPanelListener) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a CytoPanel listener.
addCytoscapeAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus: Takes a CytoscapeAction and will add it to the MenuBar or the Toolbar as is appropriate.
addCytoscapeAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus: Add the menu item in a specific position
addDataDefinitionListener(MultiHashMapDefinitionListener) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Registers a listener for receiving events having to do with attribute definitions being created and deleted.
addDataListener(MultiHashMapListener) - Method in interface cytoscape.data.attr.MultiHashMap: Registers a listener for receiving events having to do with attribute values being assigned and removed.
addEdge(int) - Method in interface cytoscape.CyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdge(Edge) - Method in interface cytoscape.CyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdge(int) - Method in class cytoscape.giny.FingCyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdge(Edge) - Method in class cytoscape.giny.FingCyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdge(String, Object) - Method in class cytoscape.giny.FingCyNetwork: Adds a edge to this Network, by looking it up via the given attribute and value
addEdgeArrowCalculator(EdgeArrowCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeColorCalculator(EdgeColorCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
addEdgeFontFaceCalculator(EdgeFontFaceCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeFontSizeCalculator(EdgeFontSizeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeLabelCalculator(EdgeLabelCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeLineTypeCalculator(EdgeLineTypeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdgeToolTipCalculator(EdgeToolTipCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addEdit(UndoableEdit) - Method in class cytoscape.util.UndoManager
addEdit(UndoableEdit) - Method in class cytoscape.view.CytoscapeDesktop
addExtension(String) - Method in class cytoscape.util.CyFileFilter: Adds a filetype "dot" extension to filter against.
addFilter(CyFileFilter) - Method in class cytoscape.data.ImportHandler: Registers a new CyFileFilter.
addFilter(CyFileFilter[]) - Method in class cytoscape.data.ImportHandler: Registers an Array of CyFileFilter Objects.
addFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork: Adds a listener for FlagEvents to this CyNetwork
addFlagEventListener(FlagEventListener) - Method in class cytoscape.data.FlagFilter: Deprecated. If the argument is not already a listener to this object, it is added.
addFlagEventListener(FlagEventListener) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.addSelectEventListener(SelectEventListener)
addGraphView(GraphView) - Method in class cytoscape.view.GraphViewController: Adds to the set of giny.view.GraphView objects that this GraphViewController keeps synchronized with their giny.model.GraphPerspective objects.
addGraphView(GraphView, GraphViewHandler) - Method in class cytoscape.view.GraphViewController: Adds to the set of giny.view.GraphView objects that this GraphViewController keeps synchronized to their giny.model.GraphPerspective objects.
addItem(Object) - Method in class cytoscape.util.swing.FilterHistoryJList
addJars(String, ArrayList<String>, String) - Method in class cytoscape.util.JnlpWriterUtil
addMapping(String, GMLNode) - Method in class cytoscape.data.readers.GMLNode: Add a mapping from key to node
addMapping(String, Class) - Method in class cytoscape.visual.CalculatorCatalog: Add a mapping to the database of available mappings.
addMapping(ObjectMapping) - Method in class cytoscape.visual.calculators.AbstractCalculator: Add a mapping to the mappings contained by the calculator.
addNetwork(String, String) - Method in class cytoscape.view.NetworkPanel
addNode(int) - Method in interface cytoscape.CyNetwork: Add a node to this Network that already exists in Cytoscape
addNode(Node) - Method in interface cytoscape.CyNetwork: Add a node to this Network that already exists in Cytoscape
addNode(int) - Method in class cytoscape.giny.FingCyNetwork: Add a node to this Network that already exists in Cytoscape
addNode(Node) - Method in class cytoscape.giny.FingCyNetwork: Add a node to this Network that already exists in Cytoscape
addNode(String, Object) - Method in class cytoscape.giny.FingCyNetwork: Adds a node to this Network, by looking it up via the given attribute and value
addNodeAttribute(String) - Static method in class cytoscape.data.NetworkData: Attempts to add a new Attribute name, of Object type for nodes.
addNodeAttribute(String, int) - Static method in class cytoscape.data.NetworkData: Attempts to add a new Attribute name, of given type for nodes.
addNodeColorCalculator(NodeColorCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView
addNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
addNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
addNodeFontFaceCalculator(NodeFontFaceCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeFontSizeCalculator(NodeFontSizeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeLabelCalculator(NodeLabelCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeLabelColorCalculator(NodeLabelColorCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeLineTypeCalculator(NodeLineTypeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeShapeCalculator(NodeShapeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeSizeCalculator(NodeSizeCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addNodeToolTipCalculator(NodeToolTipCalculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use addCalculator(calc) instead. Will be removed 10/2007.
addOntology(Ontology) - Method in class cytoscape.data.servers.OntologyServer
addOntology(URL, OntologyServer.OntologyType, String, String) - Method in class cytoscape.data.servers.OntologyServer
addParent(int) - Method in class cytoscape.data.annotation.OntologyTerm
addPlugin(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
addPlugin(URL) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
addPluginToPropertyString(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
addPoint(double, BoundaryRangeValues) - Method in class cytoscape.visual.mappings.ContinuousMapping: Adds a New Data Point.
AddPointListener - Class in cytoscape.visual.mappings.continuous: Listens for User Request to Create New Point.
AddPointListener(ContinuousUI, ContinuousMapping, Object) - Constructor for class cytoscape.visual.mappings.continuous.AddPointListener: Constructor.
addProperty(String[]) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
addSelectButtonActionListener(ActionListener) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
addSelectEventListener(SelectEventListener) - Method in interface cytoscape.CyNetwork: Adds a listener for SelectEvents to this CyNetwork
addSelectEventListener(SelectEventListener) - Method in class cytoscape.data.SelectFilter: If the argument is not already a listener to this object, it is added.
addSelectEventListener(SelectEventListener) - Method in class cytoscape.giny.FingCyNetwork: Adds a listener for SelectEvents to this CyNetwork
addSynonym(Object) - Method in class cytoscape.data.ontology.OntologyTerm: In this implementation, key is the synonym name, and value is the synonym type.
addSynonym(Object, OntologyTerm.SynonymType) - Method in class cytoscape.data.ontology.OntologyTerm: In this implementation, key is the synonym name, and value is the synonym type.
addSynonym(Object) - Method in class cytoscape.data.ontology.Triple: Triple synonym is not supported.
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServer
addThesaurus(String, Thesaurus) - Method in interface cytoscape.data.servers.BioDataServerInterface
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServerRmi
addTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
addVisualStyle(VisualStyle) - Method in class cytoscape.visual.CalculatorCatalog
adjustColumnPreferredWidths(JTable) - Static method in class cytoscape.util.swing.ColumnResizer
ALIAS - Static variable in class cytoscape.data.synonyms.Aliases: Name of the attribute for aliases
ALIASES - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
Aliases - Class in cytoscape.data.synonyms: Simpler version of Thesaurus.
Aliases(AliasType) - Constructor for class cytoscape.data.synonyms.Aliases: Constructor for the aliases object.
AliasType - Enum in cytoscape.data.synonyms: Type of Aliases.
AlignHorizontalAction - Class in cytoscape.actions
AlignHorizontalAction(CyNetworkView) - Constructor for class cytoscape.actions.AlignHorizontalAction
AlignVerticalAction - Class in cytoscape.actions
AlignVerticalAction(CyNetworkView) - Constructor for class cytoscape.actions.AlignVerticalAction
ALL_ATTRIBUTES_FILTER - Static variable in class cytoscape.data.CyAttributesUtils: An AttributeFilter that produces all attributes--none are filtered out.
allAttributeValuesRemoved(String, String) - Method in interface cytoscape.data.attr.MultiHashMapListener: This listener method gets called as a result of MultiHashMap.removeAllAttributeValues(objectKey, attributeName), but only if objectKey has at least one attribute value bound in attributeName.
AlphabeticalSelectionAction - Class in cytoscape.actions
AlphabeticalSelectionAction() - Constructor for class cytoscape.actions.AlphabeticalSelectionAction
AnimatedLayoutAction - Class in cytoscape.actions
AnimatedLayoutAction(CyNetworkView) - Constructor for class cytoscape.actions.AnimatedLayoutAction
Annotation - Class in cytoscape.data.annotation: Store any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from an ontology (a controlled vocabulary for some subject domain, expressed as a directed acyclic graph).
Annotation(String, String, Ontology) - Constructor for class cytoscape.data.annotation.Annotation
Annotation(String, String, String) - Constructor for class cytoscape.data.annotation.Annotation
AnnotationDescription - Class in cytoscape.data.annotation: Distinguish among different ontologies, by curator and type.
AnnotationDescription(String, String, String) - Constructor for class cytoscape.data.annotation.AnnotationDescription
AnnotationFlatFileReader - Class in cytoscape.data.annotation.readers
AnnotationFlatFileReader(File) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
AnnotationFlatFileReader(BufferedReader, Thesaurus, boolean) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
AnnotationFlatFileReader(String, Thesaurus) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
AnnotationGui - Class in cytoscape.data.annotation
AnnotationGui() - Constructor for class cytoscape.data.annotation.AnnotationGui
AnnotationGui(boolean, ImageIcon) - Constructor for class cytoscape.data.annotation.AnnotationGui
AnnotationXmlReader - Class in cytoscape.data.annotation.readers
AnnotationXmlReader(File) - Constructor for class cytoscape.data.annotation.readers.AnnotationXmlReader
AnotationPanel - Class in cytoscape.data.servers.ui
AnotationPanel() - Constructor for class cytoscape.data.servers.ui.AnotationPanel: Creates new form GeneOntologyPanel2
AnotationPanelDescriptor - Class in cytoscape.data.servers.ui
AnotationPanelDescriptor() - Constructor for class cytoscape.data.servers.ui.AnotationPanelDescriptor
appendNetwork(CyNetwork) - Method in interface cytoscape.CyNetwork: Appends all of the nodes and edges in the given Network to this Network
appendNetwork(CyNetwork) - Method in class cytoscape.giny.FingCyNetwork: Appends all of the nodes and edges in teh given Network to this Network
appendSpecies(String) - Method in class cytoscape.data.servers.ui.GeneOntologyWizard
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator
apply(NodeAppearance, Node, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.EdgeCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. DOCUMENT ME!
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeColorCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeLabelCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: DOCUMENT ME!
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: DOCUMENT ME!
apply(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFillColorCalculator: DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeHeightCalculator: DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeToolTipCalculator
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeWidthCalculator: DOCUMENT ME!
apply(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.NodeCalculator
applyAppearance(EdgeView, boolean) - Method in class cytoscape.visual.EdgeAppearance: Deprecated. Use applyAppearance(edgeView) instead - now we always optimize. Will be removed 10/2007
applyAppearance(EdgeView) - Method in class cytoscape.visual.EdgeAppearance
applyAppearance(NodeView, boolean) - Method in class cytoscape.visual.NodeAppearance: Deprecated. use applyAppearance(nodeView) instead - now we always optimize. will be removed 10/2007
applyAppearance(NodeView) - Method in class cytoscape.visual.NodeAppearance
applyAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the node, edge, and global visual attributes.
applyBypass(Edge) - Method in class cytoscape.visual.EdgeAppearance
applyBypass(Node) - Method in class cytoscape.visual.NodeAppearance
applyDefaultProperties(Properties, String) - Method in class cytoscape.visual.EdgeAppearance
applyDefaultProperties(Properties, String) - Method in class cytoscape.visual.NodeAppearance
applyEdgeAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the edge appearances.
applyEdgeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the edge appearances.
applyGlobalAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies the global visual attributes.
applyGlobalAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies the global visual attributes.
applyLayout(LayoutAlgorithm) - Method in class cytoscape.ding.DingNetworkView
applyLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView
applyLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView
applyLayout(LayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView
applyLayout(LayoutAlgorithm) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to the entire CyNetworkView
applyLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given Nodes and Edges
applyLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(LayoutAlgorithm, int[], int[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given Nodes and Edges
applyLayout(LayoutAlgorithm) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView
applyLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(LayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(GraphView) - Method in interface cytoscape.view.NetworkView: Deprecated. added for giny, applies the layout on the view
applyLockedLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView
applyLockedLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView
applyLockedLayout(LayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView
applyLockedLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
applyLockedLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to the entire CyNetworkView, but locks the given NodeViews and EdgeViews in place
applyLockedLayout(LayoutAlgorithm, int[], int[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
applyLockedLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
applyLockedLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given NodeViews and EdgeViews in place
applyLockedLayout(LayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
applyMaps(String, String) - Method in class cytoscape.data.readers.GMLReader
applyNamingServices(CyNetwork) - Static method in class cytoscape.data.Semantics: This method should be called in the process of creating a new network, or upon loading a new bioDataServer.
applyNodeAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the node appearances.
applyNodeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the node appearances.
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.EdgeAppearanceCalculator
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.GlobalAppearanceCalculator: This method customizes this object by searching the supplied properties object for keys identifying default values and calculators.
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.ContinuousMapping: Customizes this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.DiscreteMapping: Customizes this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(Properties, String, ValueParser) - Method in interface cytoscape.visual.mappings.ObjectMapping
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.PassThroughMapping: Customize this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.NodeAppearanceCalculator
applyVizMap(CyEdge) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(EdgeView) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(CyNode) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(NodeView) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(CyEdge, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(EdgeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(CyNode, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(NodeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
applyVizMap(CyEdge) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given edge to the given vizmapper
applyVizMap(EdgeView) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given edge to the given vizmapper
applyVizMap(CyEdge, VisualStyle) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given edge to the given vizmapper
applyVizMap(EdgeView, VisualStyle) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given edge to the given vizmapper
applyVizMap(CyNode) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given node to the given vizmapper
applyVizMap(NodeView) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given node to the given vizmapper
applyVizMap(CyNode, VisualStyle) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given node to the given vizmapper
applyVizMap(NodeView, VisualStyle) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given node to the given vizmapper
applyVizMap(CyEdge) - Method in interface cytoscape.view.CyNetworkView: Applies the given edge to the given vizmapper
applyVizMap(EdgeView) - Method in interface cytoscape.view.CyNetworkView: Applies the given edge to the given vizmapper
applyVizMap(CyNode) - Method in interface cytoscape.view.CyNetworkView: Applies the given node to the given vizmapper
applyVizMap(NodeView) - Method in interface cytoscape.view.CyNetworkView: Applies the given node to the given vizmapper
applyVizMap(CyEdge, VisualStyle) - Method in interface cytoscape.view.CyNetworkView: Applies the given edge to the given vizmapper
applyVizMap(EdgeView, VisualStyle) - Method in interface cytoscape.view.CyNetworkView: Applies the given edge to the given vizmapper
applyVizMap(CyNode, VisualStyle) - Method in interface cytoscape.view.CyNetworkView: Applies the given node to the given vizmapper
applyVizMap(NodeView, VisualStyle) - Method in interface cytoscape.view.CyNetworkView: Applies the given node to the given vizmapper
applyVizmapper(VisualStyle) - Method in class cytoscape.ding.DingNetworkView
applyVizmapper(VisualStyle) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
applyVizmapper(VisualStyle) - Method in interface cytoscape.view.CyNetworkView
areSynonyms(String, String, CyNetwork) - Static method in class cytoscape.data.Semantics: This method is used to determine if two, potentially different names really refer to the same thing; that is, the two names are synonyms.
Arrow - Class in cytoscape.visual: This class is a replacement for the yFiles Arrow class.
Arrow(String) - Constructor for class cytoscape.visual.Arrow
ARROW - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for an arrowhead
ArrowParser - Class in cytoscape.visual.parsers: Parses a String into a yFiles Arrow object.
ArrowParser() - Constructor for class cytoscape.visual.parsers.ArrowParser
assignCommonNames(CyNetwork, BioDataServer) - Static method in class cytoscape.data.Semantics: This method takes every canonical name defines in the node attributes of the given network, and attempts to assign a common name by getting a list of synonyms for the canonical name from the bioDataServer and using the first synonym as the common name.
assignNodeAliases(CyNode, String, BioDataServer) - Static method in class cytoscape.data.Semantics: Use the given BioDataServer to set all of the aliases for a node, given its species.
assignSpecies(CyNetwork) - Static method in class cytoscape.data.Semantics: This method attempts to set a species attribute for every canonical name defined in the node attributes member of the supplied network.
ATTRIBUTE_ALREADY_ASSIGNED - Static variable in class cytoscape.data.NetworkData
attributeDefined(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinitionListener: This method is called by a MultiHashMapDefinition implementation as a result of a new attribute being defined (MultiHashMapDefinition.defineAttribute()).
AttributeFilter - Interface in cytoscape.data: Interface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such as CyAttributesUtils.copyAttributes().
ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape: Deprecated. this event should not be used, it is not fired. Will be removed June 2007.
AttributeSaverDialog - Class in cytoscape.data: Dialog box to save various attributes.
AttributeSaverDialog(int) - Constructor for class cytoscape.data.AttributeSaverDialog: Create a dialog box of the specified type.
attributeUndefined(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinitionListener: This method is called by a MultiHashMapDefinition implementation as a result of an attribute being undefined (MultiHashMapDefinition.undefineAttribute()).
attributeValueAssigned(String, String, Object[], Object, Object) - Method in interface cytoscape.data.attr.MultiHashMapListener
attributeValueRemoved(String, String, Object[], Object) - Method in interface cytoscape.data.attr.MultiHashMapListener: This listener method gets called as a result of MultiHashMap.removeAttributeValue(objectKey, attributeName, keyIntoValue), but only if an attribute value was found [and removed] for specified key.
AttributeValueVisitor - Interface in cytoscape.data: Interface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils.traverseAttributeValues().

B

BACKGROUND - Static variable in class cytoscape.data.writers.XGMMLWriter
BackgroundColorAction - Class in cytoscape.actions: Prompts User for New Background Color.
BackgroundColorAction() - Constructor for class cytoscape.actions.BackgroundColorAction: Constructor.
BasicGraphViewHandler - Class in cytoscape.view: A basic GraphViewHandler that simply reflects GraphPerspective changes on a given GraphView
BasicGraphViewHandler() - Constructor for class cytoscape.view.BasicGraphViewHandler: Constructor
BEGIN - Static variable in class cytoscape.CyNetworkEvent: Indicates that someone is beginning to work with the network.
BendSelectedEdgesAction - Class in cytoscape.actions
BendSelectedEdgesAction() - Constructor for class cytoscape.actions.BendSelectedEdgesAction
BiModalJSplitPane - Class in cytoscape.view.cytopanels: The BiModalJSplitPane class extends JSplitPane to provide two modes: MODE_SHOW_SPLIT: The split in the split pane appears as it normally would, and the user can resize the split pane as needed.
BiModalJSplitPane(JFrame, int, int, Component, Component) - Constructor for class cytoscape.view.cytopanels.BiModalJSplitPane: Constructor.
BioDataServer - Class in cytoscape.data.servers
BioDataServer(String) - Constructor for class cytoscape.data.servers.BioDataServer: serverName is either an RMI URI, or a manifest file which says what files to load into an in-process server; the manifest, the annotations, and the ontologies, may be files on a filesystem, files in a jar, or files retrieved by HTTP Mod. by Kei (9/10/2005): 1.
BioDataServer() - Constructor for class cytoscape.data.servers.BioDataServer
BioDataServerInterface - Interface in cytoscape.data.servers
BioDataServerRmi - Class in cytoscape.data.servers: This is the actual class which implements BioDataServer Methods.
BioDataServerRmi() - Constructor for class cytoscape.data.servers.BioDataServerRmi
BioDataServerUtil - Class in cytoscape.util
BioDataServerUtil() - Constructor for class cytoscape.util.BioDataServerUtil
BIOLOGICAL_PROCESS - Static variable in class cytoscape.data.Semantics
BirdsEyeViewAction - Class in cytoscape.actions
BirdsEyeViewAction() - Constructor for class cytoscape.actions.BirdsEyeViewAction
BLACK_ARROW - Static variable in class cytoscape.visual.Arrow
BLACK_CIRCLE - Static variable in class cytoscape.visual.Arrow
BLACK_DELTA - Static variable in class cytoscape.visual.Arrow
BLACK_DIAMOND - Static variable in class cytoscape.visual.Arrow
BLACK_T - Static variable in class cytoscape.visual.Arrow
BOOKMARK_PACKAGE_NAME - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
BookmarkAction - Class in cytoscape.actions
BookmarkAction() - Constructor for class cytoscape.actions.BookmarkAction
BookmarkDialog - Class in cytoscape.dialogs.preferences
BookmarkDialog(JFrame) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog: Creates new BookmarkDialog
BookmarkDialog() - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog
BookmarkDialog.EditBookmarkDialog - Class in cytoscape.dialogs.preferences
BookmarkDialog.EditBookmarkDialog(JDialog, boolean, Bookmarks, String, String, DataSource) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog.EditBookmarkDialog: Creates new form NewBookmarkDialog
BookmarkReader - Class in cytoscape.data.readers
BookmarkReader() - Constructor for class cytoscape.data.readers.BookmarkReader
BookmarksUtil - Class in cytoscape.util: Utility methods for getting entries in the bookmark object.
BookmarksUtil() - Constructor for class cytoscape.util.BookmarksUtil
BoundaryRangeValues - Class in cytoscape.visual.mappings: This class defines a data object representing the range values associated with a particular domain value, called a boundary value.
BoundaryRangeValues() - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues
BoundaryRangeValues(Object, Object, Object) - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues
buildOntologyServer() - Static method in class cytoscape.Cytoscape: This will replace the bioDataServer.
buildStyle() - Method in class cytoscape.data.readers.VisualStyleBuilder
buttonAndColor(JDialog, MutableColor, JLabel, String) - Static method in class cytoscape.dialogs.MiscGB: Deprecated. No one uses this so don't start. Will be removed 12/2006.

C

calcName - Static variable in class cytoscape.visual.OldStyleCalculatorIO: Deprecated.
calculateBackgroundColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: Currently no calculators are supported for global visual attributes, so this method simply returns the default background color.
calculateEdgeAppearance(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
calculateEdgeAppearance(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
calculateEdgeArrow(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeArrowCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeArrow(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. DOCUMENT ME!
calculateEdgeArrow(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: DOCUMENT ME!
calculateEdgeArrow(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: DOCUMENT ME!
calculateEdgeColor(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeColorCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeColor(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeColorCalculator
calculateEdgeColor(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeFont(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeFontFace(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeFontFaceCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeFontFace(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
calculateEdgeFontSize(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeFontSizeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeFontSize(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
calculateEdgeLabel(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeLabelCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeLabel(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeLabelCalculator
calculateEdgeLabel(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeLineType(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeLineTypeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeLineType(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
calculateEdgeLineType(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
calculateEdgeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
calculateEdgeSourceArrow(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeTargetArrow(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateEdgeToolTip(Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.EdgeToolTipCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateEdgeToolTip(Edge, CyNetwork) - Method in class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
calculateEdgeToolTip(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use calculateEdgeAppearance() instead. This method will be removed Sept. 2007.
calculateGlobalAppearance(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: Constructs a new GlobalAppearance object containing the values for the known global visual attributes.
calculateGlobalAppearance(GlobalAppearance, CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: The supplied GlobalAppearance object will be changed to hold new values for the known global visual attributes.
calculateNodeAppearance(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
calculateNodeAppearance(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
calculateNodeBorderColor(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeColor(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: DOCUMENT ME!
calculateNodeColor(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. DOCUMENT ME!
calculateNodeColor(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFillColorCalculator: DOCUMENT ME!
calculateNodeColor(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeColorCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeFillColor(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeFont(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeFontFace(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
calculateNodeFontFace(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeFontFaceCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeFontSize(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
calculateNodeFontSize(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeFontSizeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeHeight(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeLabel(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator
calculateNodeLabel(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLabelCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLabel(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeLabelColor(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
calculateNodeLabelColor(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLabelColorCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLabelColor(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeLineType(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
calculateNodeLineType(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLineTypeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLineType(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
calculateNodeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
calculateNodeShape(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator
calculateNodeShape(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeShapeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeShape(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeSize(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeHeightCalculator: DOCUMENT ME!
calculateNodeSize(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. DOCUMENT ME!
calculateNodeSize(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: DOCUMENT ME!
calculateNodeSize(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeWidthCalculator: DOCUMENT ME!
calculateNodeSize(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeSizeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeToolTip(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeToolTipCalculator
calculateNodeToolTip(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeToolTipCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeToolTip(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateNodeWidth(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculateNodeAppearance() and get the value from the NodeAppearance. This method will be removed Sept 2007.
calculateRangeValue(String) - Method in class cytoscape.visual.mappings.continuous.ContinuousRangeCalculator: Calculates Range Value.
calculateRangeValue(Map) - Method in class cytoscape.visual.mappings.ContinuousMapping: Calculates the Range Value.
calculateRangeValue(Map) - Method in class cytoscape.visual.mappings.discrete.DiscreteRangeCalculator: Calculates Range Value.
calculateRangeValue(Map) - Method in class cytoscape.visual.mappings.DiscreteMapping: Calculates the Range Value.
calculateRangeValue(Map) - Method in interface cytoscape.visual.mappings.ObjectMapping
calculateRangeValue(Map) - Method in class cytoscape.visual.mappings.PassThroughMapping
calculateSloppySelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: Currently no calculators are supported for global visual attributes, so this method simply returns the default sloppy selection color.
Calculator - Interface in cytoscape.visual.calculators: Calculator specifies a super-interface for all calculator interfaces.
CalculatorCatalog - Class in cytoscape.visual: Stores various types of Calculators from data attributes to an attribute of a specified type.
CalculatorCatalog() - Constructor for class cytoscape.visual.CalculatorCatalog
CalculatorCatalog(Properties) - Constructor for class cytoscape.visual.CalculatorCatalog
CalculatorCatalogFactory - Class in cytoscape.visual: This class provides a static method for reading a CalculatorCatalog object from file, using parameters specified in a supplied CytoscapeConfig.
CalculatorCatalogFactory() - Constructor for class cytoscape.visual.CalculatorCatalogFactory
CalculatorFactory - Class in cytoscape.visual.calculators: This class provides static factory methods for constructing instances of Calculators as specified by arguments and static methods for getting names and labels based on calculator type.
CalculatorFactory() - Constructor for class cytoscape.visual.calculators.CalculatorFactory
CalculatorIO - Class in cytoscape.visual: This class defines static methods for reading calculator definitions from a properties object and installing them into a CalculatorCatalog, and for constructing a properties object that describes all the calculators in a CalculatorCatalog.
CalculatorIO() - Constructor for class cytoscape.visual.CalculatorIO
cancel() - Method in interface cytoscape.util.MonitoredTask: Gets called by the CytoscapeProgressMonitor when the user click on the Cancel button.
cancelCellEditing() - Method in class cytoscape.util.swing.AbstractCellEditor
CANONICAL_NAME - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
CELLULAR_COMPONENT - Static variable in class cytoscape.data.Semantics
centerName - Static variable in class cytoscape.visual.LabelPosition
centerWindowLocation(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
centerWindowOnScreen(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
centerWindowSize(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
CheckBoxFileChooser - Class in cytoscape.actions: extends JFileChooser by adding a JCheckBox at the bottom of the chooser
CheckBoxFileChooser(File, String) - Constructor for class cytoscape.actions.CheckBoxFileChooser
checkCalculatorName(String, byte) - Method in class cytoscape.visual.CalculatorCatalog: Checks whether a name for a calculator is valid
checkCalculatorName(byte, String) - Method in class cytoscape.visual.CalculatorCatalog
checkCalculatorUsage(Calculator) - Method in class cytoscape.visual.ui.VizMapUI: Ensure that the calculator to be removed isn't used in other visual styles.
checkConflictingCalculator(Calculator) - Method in class cytoscape.visual.VisualStyle: Check if contained appearance calculators are using given calculator
checkEdgeArrowCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeColorCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeFontFaceCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeFontSizeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeLabelCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeLineTypeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkEdgeToolTipCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkForCalculators(Properties, CalculatorCatalog) - Static method in class cytoscape.visual.OldStyleCalculatorIO: Deprecated. Use CalculatorIO instead. Will be removed 10/2007
checkMappingName(String) - Method in class cytoscape.visual.CalculatorCatalog
checkNodeColorCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeFontFaceCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeFontSizeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeLabelCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeLabelColorCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeLineTypeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeShapeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeSizeCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkNodeToolTipCalculatorName(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use checkCalculatorName(type,name) instead. Will be removed 10/2007.
checkSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
checkVisualStyleName(String) - Method in class cytoscape.visual.CalculatorCatalog
CLEAN - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
clear() - Method in class cytoscape.data.servers.BioDataServer
clear() - Method in interface cytoscape.data.servers.BioDataServerInterface
clear() - Method in class cytoscape.data.servers.BioDataServerRmi
clear - Class in cytoscape.data.servers
clear() - Constructor for class cytoscape.data.servers.clear
clear() - Method in class cytoscape.visual.CalculatorCatalog
clearStatusBar() - Method in class cytoscape.view.CytoscapeDesktop: Clears the Status Bar Message.
clearVector() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
clone() - Method in class cytoscape.util.CytoscapeAction: The default clone() implementation delegates to the create() method of DataTypeUtilities.getDataTypeFactory( this.getClass() ).
clone() - Method in class cytoscape.visual.calculators.AbstractCalculator: Clone the calculator.
clone() - Method in interface cytoscape.visual.calculators.Calculator: Clone the calculator.
clone() - Method in class cytoscape.visual.EdgeAppearance
clone() - Method in class cytoscape.visual.GlobalAppearanceCalculator: Make shallow copy of this object
clone() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Clones the object.
clone() - Method in class cytoscape.visual.mappings.ContinuousMapping: Clones the Mapping Object.
clone() - Method in class cytoscape.visual.mappings.DiscreteMapping: Clones the Object.
clone() - Method in interface cytoscape.visual.mappings.ObjectMapping
clone() - Method in class cytoscape.visual.mappings.PassThroughMapping
clone() - Method in class cytoscape.visual.NodeAppearance
clone() - Method in class cytoscape.visual.VisualStyle: Perform deep copy of this VisualStyle.
CloneGraphInNewWindowAction - Class in cytoscape.actions
CloneGraphInNewWindowAction() - Constructor for class cytoscape.actions.CloneGraphInNewWindowAction
COLOR - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for a color
COLOR_ARROW - Static variable in class cytoscape.visual.Arrow
COLOR_CIRCLE - Static variable in class cytoscape.visual.Arrow
COLOR_DELTA - Static variable in class cytoscape.visual.Arrow
COLOR_DIAMOND - Static variable in class cytoscape.visual.Arrow
COLOR_T - Static variable in class cytoscape.visual.Arrow
ColorParser - Class in cytoscape.visual.parsers: Parses a String into a Color object.
ColorParser() - Constructor for class cytoscape.visual.parsers.ColorParser
ColorScaleTable - Class in cytoscape.dialogs
ColorScaleTable(int, int, double[][]) - Constructor for class cytoscape.dialogs.ColorScaleTable
ColumnResizer - Class in cytoscape.util.swing: Automatically resize column based on the objects in the cell.
ColumnResizer() - Constructor for class cytoscape.util.swing.ColumnResizer
COMMON_NAME - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
compare(Object, Object) - Method in class cytoscape.data.readers.GMLNode
completions() - Method in class cytoscape.util.CytoscapeAction
compressFast(int, boolean) - Method in class cytoscape.util.ZipUtil: Faster version of compression method.
configure() - Method in class cytoscape.util.MacAppConfig: Configures the Info.plist list with all cytoscape/*.jar files.
constraints - Variable in class cytoscape.dialogs.GridBagGroup
construct() - Method in class cytoscape.util.SwingWorker: Compute the value to be returned by the get method.
containsGraphView(GraphView) - Method in class cytoscape.view.GraphViewController: Whether or not the given giny.view.GraphView is kept synchronized with its giny.model.GraphPerspective member by this GraphViewController.
containsTerm(int) - Method in class cytoscape.data.annotation.Ontology
containsTerm(String) - Method in class cytoscape.data.ontology.Ontology
containsTriple(Term, Term, Term) - Method in class cytoscape.data.ontology.Ontology: See if a triple exists in this ontology.
ContinuousLegend - Class in cytoscape.visual.mappings.continuous
ContinuousLegend(String, String, List, Object, byte) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousLegend
ContinuousMapping - Class in cytoscape.visual.mappings: Implements an interpolation table mapping data to values of a particular class.
ContinuousMapping(Object, byte) - Constructor for class cytoscape.visual.mappings.ContinuousMapping: Constructor.
ContinuousMappingPoint - Class in cytoscape.visual.mappings.continuous: Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(double, BoundaryRangeValues) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Constructor.
ContinuousMappingReader - Class in cytoscape.visual.mappings.continuous: Reads in ContinuousMapping Properties.
ContinuousMappingReader(Properties, String, ValueParser) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingReader: Constructor.
ContinuousMappingWriter - Class in cytoscape.visual.mappings.continuous: Writes out ContinuousMapping Properties.
ContinuousMappingWriter(ArrayList, String, String, Interpolator) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingWriter: Constructor.
ContinuousRangeCalculator - Class in cytoscape.visual.mappings.continuous: Calculates the Range for Continuous Mappers.
ContinuousRangeCalculator(ArrayList, Interpolator, Map) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousRangeCalculator: Constructor.
ContinuousUI - Class in cytoscape.visual.mappings.continuous: Provides User Interface Controls for Continuous Mappers.
ContinuousUI(JDialog, Object, CyNetwork, ContinuousMapping) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousUI: Constructor.
convert() - Method in class cytoscape.util.Transform
convert(int) - Static method in class cytoscape.visual.LabelPosition
convert(String) - Static method in class cytoscape.visual.LabelPosition
convertLambdasToPvals() - Method in class cytoscape.data.ExpressionData: Converts all lambdas to p-values.
copy(EdgeAppearance) - Method in class cytoscape.visual.EdgeAppearance
copy(NodeAppearance) - Method in class cytoscape.visual.NodeAppearance
copyAttribute(String, String, String, CyAttributes, boolean) - Static method in class cytoscape.data.CyAttributesUtils: Copy a specific attribute of a given object to another object.
copyAttributes(String, String, CyAttributes, boolean) - Static method in class cytoscape.data.CyAttributesUtils: Copy all the attributes of a given object to another object.
copyAttributes(String, String, CyAttributes, AttributeFilter, boolean) - Static method in class cytoscape.data.CyAttributesUtils: Copy all the attributes of a given object that pass a given filter to another object.
copyToAttribs(CyAttributes, TaskMonitor) - Method in class cytoscape.data.ExpressionData: Copies ExpressionData data structure into CyAttributes data structure.
count() - Method in class cytoscape.data.annotation.Annotation: total number of entities, usually ORFs.
CountedIterator - Interface in cytoscape.data.attr: A java.util.Iterator with knowledge of how many elements are remaining.
createAlignTab() - Method in class cytoscape.dialogs.PhoebeNodeControl
createBasicOntology(URL, String, String) - Method in class cytoscape.data.ontology.OntologyFactory
createColorLabel(Color) - Static method in class cytoscape.dialogs.MiscGB
createDefaultVisualStyle() - Method in class cytoscape.visual.CalculatorCatalog
createDifferenceGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils: Create a new graph which is the difference of multiple graphs.
createEdge(int, int, boolean) - Method in class cytoscape.giny.FingCyNetwork: This method will create a new edge.
createGeneOntology(URL, String, String) - Method in class cytoscape.data.ontology.OntologyFactory
createHorizontalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
createHorizontalAlignLeft() - Method in class cytoscape.dialogs.PhoebeNodeControl
createHorizontalAlignRight() - Method in class cytoscape.dialogs.PhoebeNodeControl
createHorizontalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
createIdentifier(String, String, String) - Static method in class cytoscape.CyEdge: A static method used to create edge identifiers.
createInfoTag() - Method in class cytoscape.util.JnlpWriterUtil
createIntersectionGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils: Create a new graph which is the intersection of multiple graphs.
createJMenu(String) - Method in class cytoscape.util.CytoscapeMenuBar: Factory method for instantiating objects of type JMenu
createManifestFileChooser() - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
createNetwork(String) - Static method in class cytoscape.Cytoscape: Creates a new, empty Network.
createNetwork(String, boolean) - Static method in class cytoscape.Cytoscape: Creates a new, empty Network.
createNetwork(String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: Creates a new, empty Network.
createNetwork(int[], int[], String) - Static method in class cytoscape.Cytoscape: Creates a new Network.
createNetwork(Collection, Collection, String) - Static method in class cytoscape.Cytoscape: Creates a new Network.
createNetwork(int[], int[], String, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(int[], int[], String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork
createNetwork(Collection, Collection, String, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(Collection, Collection, String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(String, int, boolean, BioDataServer, String) - Static method in class cytoscape.Cytoscape: Deprecated. It will be removed in April 2007 Use CyNetwork createNetworkFromFile(String location, boolean create_view) instead. File type is no longer needed as ImportHandler now manages all file types.
createNetwork(GraphReader, boolean, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a cytoscape.data.CyNetwork from a reader.
createNetwork(Collection, Collection) - Method in class cytoscape.giny.CytoscapeFingRootGraph
createNetwork(Node[], Edge[]) - Method in class cytoscape.giny.CytoscapeFingRootGraph: Creates a new Network
createNetwork(int[], int[]) - Method in class cytoscape.giny.CytoscapeFingRootGraph: Uses Code copied from ColtRootGraph to create a new Network.
createNetwork(Node[], Edge[]) - Method in interface cytoscape.giny.CytoscapeRootGraph: Uses Code copied from ColtRootGraph to create a new CyNetwork.
createNetwork(Collection, Collection) - Method in interface cytoscape.giny.CytoscapeRootGraph
createNetwork(int[], int[]) - Method in interface cytoscape.giny.CytoscapeRootGraph: Uses Code copied from ColtRootGraph to create a new Network.
createNetworkFromFile(String) - Static method in class cytoscape.Cytoscape: Creates a CyNetwork from a file.
createNetworkFromFile(String, boolean) - Static method in class cytoscape.Cytoscape: Creates a CyNetwork from a file.
createNetworkFromURL(URL, boolean) - Static method in class cytoscape.Cytoscape: Creates a CyNetwork from a URL.
createNetworkView(CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a CyNetworkView, but doesn't do anything with it.
createNetworkView(CyNetwork, String) - Static method in class cytoscape.Cytoscape: Creates a CyNetworkView, but doesn't do anything with it.
CreateNetworkViewAction - Class in cytoscape.actions
CreateNetworkViewAction() - Constructor for class cytoscape.actions.CreateNetworkViewAction
CreateNetworkViewAction(boolean) - Constructor for class cytoscape.actions.CreateNetworkViewAction
createNewSession() - Static method in class cytoscape.Cytoscape: Clear all networks and attributes and start a new session.
createNode() - Method in class cytoscape.giny.FingCyNetwork: This method will create a new node.
createPointPanel() - Method in class cytoscape.visual.mappings.continuous.ContinuousUI: Generates the main UI Panel.
createResourcesTag() - Method in class cytoscape.util.JnlpWriterUtil
createTerm(String, String) - Method in class cytoscape.data.ontology.Ontology: Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class cytoscape.data.ontology.Ontology
createTriple(Term, Term, Term, String, String) - Method in class cytoscape.data.ontology.Ontology
createUnionGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils: Create a new graph which is the union of multiple graphs.
createVariable(String, String) - Method in class cytoscape.data.ontology.Ontology
createVerticalAlignBottom() - Method in class cytoscape.dialogs.PhoebeNodeControl
createVerticalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
createVerticalAlignTop() - Method in class cytoscape.dialogs.PhoebeNodeControl
createVerticalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
createViewFromCurrentNetwork(CyNetwork) - Static method in class cytoscape.actions.CreateNetworkViewAction
CreditScreen - Class in cytoscape.util
CreditScreen() - Constructor for class cytoscape.util.CreditScreen
CUSTOM - Static variable in class cytoscape.util.FileUtil
customGraphics(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render custom graphics on nodes.
CY_PROPS - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
CyAttributes - Interface in cytoscape.data: CyAttributes provides access to node and edge attributes within Cytoscape.
CyAttributesImpl - Class in cytoscape.data
CyAttributesImpl() - Constructor for class cytoscape.data.CyAttributesImpl
CyAttributesReader - Class in cytoscape.data.readers
CyAttributesReader() - Constructor for class cytoscape.data.readers.CyAttributesReader
CyAttributesUtils - Class in cytoscape.data
CyAttributesUtils() - Constructor for class cytoscape.data.CyAttributesUtils
CyAttributesWriter - Class in cytoscape.data.writers
CyAttributesWriter() - Constructor for class cytoscape.data.writers.CyAttributesWriter
CyAttributesWriter2 - Class in cytoscape.data.writers: CyAttributeWriter extracted from AttributeSaverDialog.
CyAttributesWriter2(CyAttributes, String, Writer) - Constructor for class cytoscape.data.writers.CyAttributesWriter2
CyColorChooser - Class in cytoscape.util: This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColorChooser() - Constructor for class cytoscape.util.CyColorChooser
CyEdge - Class in cytoscape
CyEdge(RootGraph, int) - Constructor for class cytoscape.CyEdge
CyEdgeView - Interface in cytoscape.view
CyFileFilter - Class in cytoscape.util: A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
CyFileFilter() - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter.
CyFileFilter(String) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter that accepts files with the given extension.
CyFileFilter(String, String) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter that accepts the given file type.
CyFileFilter(String[]) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter from the given string array.
CyFileFilter(String[], String) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter from the given string array and description.
CyFileFilter(String, String, String) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter that accepts the given file type.
CyFileFilter(String[], String, String) - Constructor for class cytoscape.util.CyFileFilter: Creates a file filter from the given string array and description.
CyGraphLOD - Class in cytoscape.ding: An instance of this class defines the level of detail that goes into a single rendering of a graph.
CyGraphLOD() - Constructor for class cytoscape.ding.CyGraphLOD
CyHelpBroker - Class in cytoscape.view: This class creates the Cytoscape Help Broker for managing the JavaHelp system and help set access
CyHelpBroker() - Constructor for class cytoscape.view.CyHelpBroker
CyInitParams - Interface in cytoscape.init: An interface that describes the initialization parameters needed by cytoscape.
CyMain - Class in cytoscape: This is the main startup class for Cytoscape.
CyMain(String[]) - Constructor for class cytoscape.CyMain: Creates a new CyMain object.
CyMenus - Class in cytoscape.view: Creates the menu and tool bars for a Cytoscape window object.
CyMenus() - Constructor for class cytoscape.view.CyMenus
CyNetwork - Interface in cytoscape: CyNetwork is the primary class for algorithm writing.
CyNetworkAdapter - Class in cytoscape: Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes.
CyNetworkAdapter() - Constructor for class cytoscape.CyNetworkAdapter
CyNetworkData - Interface in cytoscape: This will be the interface where things like multi-dimensional data are accessed.
CyNetworkEvent - Class in cytoscape: Events of this class are fired from a CyNetwork object when something happens to the network.
CyNetworkEvent(CyNetwork, int) - Constructor for class cytoscape.CyNetworkEvent
CyNetworkListener - Interface in cytoscape: Interface for listeners that respond to CyNetwork events.
CyNetworkNaming - Class in cytoscape.util
CyNetworkNaming() - Constructor for class cytoscape.util.CyNetworkNaming
CyNetworkUtilities - Class in cytoscape.data: This class provides static methods that operate on a CyNetwork to perform various useful tasks.
CyNetworkUtilities() - Constructor for class cytoscape.data.CyNetworkUtilities
CyNetworkView - Interface in cytoscape.view: CyNetworkView is responsible for actually getting a graph to show up on the screen.
CyNode - Class in cytoscape
CyNode(RootGraph, int) - Constructor for class cytoscape.CyNode
CyNodeView - Interface in cytoscape.view
CYSESSION - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
CytoPanel - Interface in cytoscape.view.cytopanels: Interface to a CytoPanel.
CytoPanelAction - Class in cytoscape.actions: Menu item handler for CytoPanels
CytoPanelAction(JCheckBoxMenuItem, CytoPanel) - Constructor for class cytoscape.actions.CytoPanelAction: Constructor.
CytoPanelContainer - Interface in cytoscape.view.cytopanels: Interface for Container of CytoPanel Objects.
CytoPanelImp - Class in cytoscape.view.cytopanels: The CytoPanel class extends JPanel to provide the following functionality: Floating/Docking of Panel.
CytoPanelImp(int, int, CytoPanelState) - Constructor for class cytoscape.view.cytopanels.CytoPanelImp: Constructor.
CytoPanelListener - Interface in cytoscape.view.cytopanels: This listener interface provides the mechanism to respond to CytoPanel Events.
CytoPanelState - Class in cytoscape.view.cytopanels: CytoPanelState Class.
CytoPanelUtil - Class in cytoscape.view.cytopanels: Contains methods to assist with various tasks performed by the CytoPanel API.
CytoPanelUtil() - Constructor for class cytoscape.view.cytopanels.CytoPanelUtil
cytoscape - package cytoscape: Core Cytoscape Classes.
Cytoscape - Class in cytoscape: This class, Cytoscape is the primary class in the API.
Cytoscape() - Constructor for class cytoscape.Cytoscape
cytoscape.actions - package cytoscape.actions: UI classes that are attached to menu items in the menu or tool bar of the window.
cytoscape.data - package cytoscape.data: Basic data classes used by Cytoscape.
cytoscape.data.annotation - package cytoscape.data.annotation: Classes used to represent generic annotation data in Cytoscape.
cytoscape.data.annotation.readers - package cytoscape.data.annotation.readers: Reader classes for generic annotation data.
cytoscape.data.attr - package cytoscape.data.attr
cytoscape.data.attr.util - package cytoscape.data.attr.util
cytoscape.data.ontology - package cytoscape.data.ontology
cytoscape.data.ontology.readers - package cytoscape.data.ontology.readers
cytoscape.data.readers - package cytoscape.data.readers: Reader classes for the basic data types in cytoscape.data.
cytoscape.data.servers - package cytoscape.data.servers: An interface for annotation data providers and various implementations of that interface, including both remote and in-process implementations.
cytoscape.data.servers.ui - package cytoscape.data.servers.ui
cytoscape.data.synonyms - package cytoscape.data.synonyms: Classes providing synonym funcationality, that is identifying multiple names that refer to the same entity.
cytoscape.data.synonyms.readers - package cytoscape.data.synonyms.readers: Readers for classes in the cytoscape.data.synonyms package.
cytoscape.data.writers - package cytoscape.data.writers
cytoscape.dialogs - package cytoscape.dialogs: UI classes for performing some action, generally more complicated than those contained in the cytoscape.actions package.
cytoscape.dialogs.preferences - package cytoscape.dialogs.preferences
cytoscape.ding - package cytoscape.ding
cytoscape.giny - package cytoscape.giny
cytoscape.init - package cytoscape.init
cytoscape.layout - package cytoscape.layout: Classes providing some kind of graph layout functionality.
cytoscape.plugin - package cytoscape.plugin: Classes related to Cytoscape plugins.
cytoscape.util - package cytoscape.util: This package contains utility classes which are deemed generally useful, but which do not clearly belong to any other package.
cytoscape.util.shadegrown - package cytoscape.util.shadegrown
cytoscape.util.swing - package cytoscape.util.swing
cytoscape.view - package cytoscape.view: Classes that provide a window to display a graph and UI components connected to that window, such as the menus.
cytoscape.view.cytopanels - package cytoscape.view.cytopanels: CytoPanels Framework.
cytoscape.visual - package cytoscape.visual: Framework for generalized mappings from graph attributes to visual attributes.
cytoscape.visual.calculators - package cytoscape.visual.calculators: Objects that calculate from the data attributes the value for one visual attribute, such as color, shape, or size.
cytoscape.visual.mappings - package cytoscape.visual.mappings: The Mappings are used by Calculators to map graph attributes to visual attribute values.
cytoscape.visual.mappings.continuous - package cytoscape.visual.mappings.continuous: Mappings from a continuous numerical input to a particular visual attribute.
cytoscape.visual.mappings.discrete - package cytoscape.visual.mappings.discrete: Mappings from a discrete-valued input to a particular visual attribute.
cytoscape.visual.parsers - package cytoscape.visual.parsers: Translates visual attribute values to and from their String representation.
cytoscape.visual.ui - package cytoscape.visual.ui: Top-level UI components for the cytoscape.visual package.
CYTOSCAPE_EXIT - Static variable in class cytoscape.Cytoscape
CYTOSCAPE_INITIALIZED - Static variable in class cytoscape.Cytoscape
CytoscapeAction - Class in cytoscape.util
CytoscapeAction() - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeAction(String) - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeAction(String, Icon) - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeConfig - Class in cytoscape: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
CytoscapeConfig() - Constructor for class cytoscape.CytoscapeConfig: Deprecated.
CytoscapeDesktop - Class in cytoscape.view: The CytoscapeDesktop is the central Window for working with Cytoscape
CytoscapeDesktop() - Constructor for class cytoscape.view.CytoscapeDesktop: The Default constructor uses a TabbedView
CytoscapeDesktop(int) - Constructor for class cytoscape.view.CytoscapeDesktop: Create a CytoscapeDesktop that conforms the given view type.
CytoscapeFingRootGraph - Class in cytoscape.giny
CytoscapeFingRootGraph() - Constructor for class cytoscape.giny.CytoscapeFingRootGraph
CytoscapeInit - Class in cytoscape: Cytoscape Init is responsible for starting Cytoscape in a way that makes sense.
CytoscapeInit() - Constructor for class cytoscape.CytoscapeInit: Creates a new CytoscapeInit object.
CytoscapeMenuBar - Class in cytoscape.util
CytoscapeMenuBar() - Constructor for class cytoscape.util.CytoscapeMenuBar: Default constructor.
CytoscapeModifiedNetworkManager - Class in cytoscape: CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents.
CytoscapeModifiedNetworkManager() - Constructor for class cytoscape.CytoscapeModifiedNetworkManager
CytoscapePlugin - Class in cytoscape.plugin: A CytoscapePlugin is the new "Global" plugin.
CytoscapePlugin() - Constructor for class cytoscape.plugin.CytoscapePlugin: There are no arguments required or allowed in a CytoscapePlugin constructor.
CytoscapeProgressMonitor - Class in cytoscape.util: CytoscapeProgressMonitor.
CytoscapeProgressMonitor(MonitoredTask) - Constructor for class cytoscape.util.CytoscapeProgressMonitor: Construtor.
CytoscapeProgressMonitor(MonitoredTask, Component) - Constructor for class cytoscape.util.CytoscapeProgressMonitor: Constructor.
CytoscapeRootGraph - Interface in cytoscape.giny
CytoscapeSessionReader - Class in cytoscape.data.readers: Reaser to load CYtoscape Session file (.cys).
CytoscapeSessionReader(URL) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Constructor for remote file (specified by an URL)
CytoscapeSessionReader(String) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Constructor.
CytoscapeSessionWriter - Class in cytoscape.data.writers: Write session states into files.
CytoscapeSessionWriter(String) - Constructor for class cytoscape.data.writers.CytoscapeSessionWriter: Constructor.
CytoscapeToolBar - Class in cytoscape.util
CytoscapeToolBar() - Constructor for class cytoscape.util.CytoscapeToolBar: Default constructor delegates to the superclass void constructor and then calls CytoscapeToolBar.initializeCytoscapeToolBar().
CytoscapeVersion - Class in cytoscape: CytoscapeVersion: identify (and describe) successive versions of cytoscape.
CytoscapeVersion() - Constructor for class cytoscape.CytoscapeVersion

D

DASHED_1 - Static variable in class cytoscape.visual.LineType
DASHED_2 - Static variable in class cytoscape.visual.LineType
DASHED_3 - Static variable in class cytoscape.visual.LineType
DASHED_4 - Static variable in class cytoscape.visual.LineType
DASHED_5 - Static variable in class cytoscape.visual.LineType
dashedEdges(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to honor dashed edges.
DATASERVER_CHANGED - Static variable in class cytoscape.Cytoscape
DBCrossReferenceReader - Class in cytoscape.data.ontology.readers: Reader for database cross reference file.
DBCrossReferenceReader() - Constructor for class cytoscape.data.ontology.readers.DBCrossReferenceReader: Constructor.
DBCrossReferences - Class in cytoscape.data.ontology: Database cress reference.
DBCrossReferences() - Constructor for class cytoscape.data.ontology.DBCrossReferences
DBReference - Class in cytoscape.data.ontology: Represents an entry in the database cross reference.
DBReference(String, String, String) - Constructor for class cytoscape.data.ontology.DBReference
DBReference(String, String, String, String, String) - Constructor for class cytoscape.data.ontology.DBReference
DBXrefKeywords - Enum in cytoscape.data.ontology.readers
deactivate() - Method in class cytoscape.plugin.CytoscapePlugin: If implemented then this plugin can remove itself from the Menu system, and anything else, when the user decides to deactivate it.
DEF_COMPRESSION_LEVEL - Static variable in class cytoscape.util.ZipUtil
DEFAULT - Static variable in class cytoscape.visual.LabelPosition
DEFAULT_GRAPH_VIEW_HANDLER - Static variable in class cytoscape.view.GraphViewController
DEFAULT_MENU_SPECIFIER - Static variable in class cytoscape.util.CytoscapeMenuBar
DEFAULT_NETWORK_METADATA_LABEL - Static variable in class cytoscape.data.readers.MetadataParser
DefaultPanel - Class in cytoscape.visual.ui: Defines a class to provide the interface for specifying global defaults such as background color.
DefaultPanel(VizMapUI, VisualMappingManager) - Constructor for class cytoscape.visual.ui.DefaultPanel: Constructor.
defineAttribute(String, byte, byte[]) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Creates an attribute definition.
deleteAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Deletes the id/attributeName pair.
deleteAttribute(String) - Method in interface cytoscape.data.CyAttributes: Deletes the specified attribute.
deleteAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
deleteAttribute(String) - Method in class cytoscape.data.CyAttributesImpl
deleteBookmark(String, Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
deleteBookmark(Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
deleteEdgeAttribute(String) - Method in class cytoscape.giny.FingCyNetwork: Deletes the attribute with the given name from edge attributes
deleteNodeAttribute(String) - Method in class cytoscape.giny.FingCyNetwork: Deletes the attribute with the given name from node attributes
deletePlugins(String[]) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
DeletePointListener - Class in cytoscape.visual.mappings.continuous: Listens for User Request to Delete Existing Point.
DeletePointListener(ContinuousUI, ContinuousMapping, int) - Constructor for class cytoscape.visual.mappings.continuous.DeletePointListener: Constructor.
deleteProperty(String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DeleteSelectedAction - Class in cytoscape.actions: Giny version of the original class.
DeleteSelectedAction(CyNetworkView) - Constructor for class cytoscape.actions.DeleteSelectedAction
deleteTerm(Term) - Method in class cytoscape.data.ontology.Ontology: Delete a term from DAG (CyNetwork)
describe() - Method in class cytoscape.data.servers.BioDataServer
describe() - Method in interface cytoscape.data.servers.BioDataServerInterface
describe() - Method in class cytoscape.data.servers.BioDataServerRmi
describe() - Method in class cytoscape.plugin.CytoscapePlugin: method returning a String description of the plugin.
DeselectAllAction - Class in cytoscape.actions
DeselectAllAction() - Constructor for class cytoscape.actions.DeselectAllAction
deselectAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
DeSelectAllEdgesAction - Class in cytoscape.actions
DeSelectAllEdgesAction() - Constructor for class cytoscape.actions.DeSelectAllEdgesAction
deselectAllNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
DeSelectAllNodesAction - Class in cytoscape.actions
DeSelectAllNodesAction() - Constructor for class cytoscape.actions.DeSelectAllNodesAction
destroyCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkAction
destroyNetwork(String) - Static method in class cytoscape.Cytoscape: destroys the given network
destroyNetwork(CyNetwork) - Static method in class cytoscape.Cytoscape: destroys the given network
destroyNetwork(CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: destroys the given network
DestroyNetworkAction - Class in cytoscape.actions
DestroyNetworkAction() - Constructor for class cytoscape.actions.DestroyNetworkAction
DestroyNetworkAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkAction
destroyNetworkView(CyNetworkView) - Static method in class cytoscape.Cytoscape: destroys the networkview, including any layout information
destroyNetworkView(String) - Static method in class cytoscape.Cytoscape: destroys the networkview, including any layout information
destroyNetworkView(CyNetwork) - Static method in class cytoscape.Cytoscape: destroys the networkview, including any layout information
DestroyNetworkViewAction - Class in cytoscape.actions
DestroyNetworkViewAction() - Constructor for class cytoscape.actions.DestroyNetworkViewAction
DestroyNetworkViewAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkViewAction
DestroySelectedAction - Class in cytoscape.actions
DestroySelectedAction() - Constructor for class cytoscape.actions.DestroySelectedAction
DestroySelectedAction(boolean) - Constructor for class cytoscape.actions.DestroySelectedAction
destroyViewFromCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkViewAction
detail(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render a graph at full detail.
DIAMOND - Static variable in class cytoscape.visual.ShapeNodeRealizer
DingNetworkView - Class in cytoscape.ding
DingNetworkView(CyNetwork, String) - Constructor for class cytoscape.ding.DingNetworkView
dirHeader - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
discardAllEdits() - Method in class cytoscape.util.UndoManager: called when a network view switches
DiscreteLegend - Class in cytoscape.visual.mappings.discrete
DiscreteLegend(Map, String, String, byte) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteLegend
DiscreteMapping - Class in cytoscape.visual.mappings: Implements a lookup table mapping data to values of a particular class.
DiscreteMapping(Object, byte) - Constructor for class cytoscape.visual.mappings.DiscreteMapping: Constructor.
DiscreteMapping(Object, String, byte) - Constructor for class cytoscape.visual.mappings.DiscreteMapping: Constructor.
DiscreteMappingReader - Class in cytoscape.visual.mappings.discrete: Reads in DiscreteMapping Properties.
DiscreteMappingReader(Properties, String, ValueParser) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteMappingReader: Constructor.
DiscreteMappingWriter - Class in cytoscape.visual.mappings.discrete: Writes DiscreteMapping Properties.
DiscreteMappingWriter(String, String, TreeMap) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteMappingWriter: Constructor.
DiscreteRangeCalculator - Class in cytoscape.visual.mappings.discrete: Range Calculator for the Discrete Mapper.
DiscreteRangeCalculator(TreeMap, String) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteRangeCalculator: Constructor.
DiscreteUI - Class in cytoscape.visual.mappings.discrete: Provides User Interface Controls for Discrete Mappers.
DiscreteUI(JDialog, CyNetwork, String, Object, byte, DiscreteMapping) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteUI: Constructor.
DNA - Static variable in class cytoscape.data.Semantics
Doc - Variable in class cytoscape.util.JnlpWriterUtil
DOCK - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Dock state of a CytoPanel.
doLayout() - Method in interface cytoscape.layout.LayoutAlgorithm
done() - Method in interface cytoscape.util.MonitoredTask: Returns true if the task is done.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.AbstractGraphReader: Executes post-processing: no-op.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.GMLReader
doPostProcessing(CyNetwork) - Method in interface cytoscape.data.readers.GraphReader: Execute whatever post-processing is required.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.XGMMLReader
DOUBLE - Static variable in class cytoscape.data.readers.GMLTree: When getting a vector, used to specify the type for the contained objects
DOUBLE - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for a double
DOUBLE_TYPE - Static variable in class cytoscape.data.NetworkData
DoubleParser - Class in cytoscape.visual.parsers: Parses a String into a Double object.
DoubleParser() - Constructor for class cytoscape.visual.parsers.DoubleParser
doubleValue() - Method in class cytoscape.data.readers.GMLNode: Get the value of this node as a Double
downloadFromURL(URL, TaskMonitor) - Method in class cytoscape.data.ImportHandler: Download a temporary file from the given URL.
dump() - Method in class cytoscape.data.synonyms.Thesaurus
DuplicateCalculatorNameException - Exception in cytoscape.visual: This Exception is thrown when one attempts to add a Calculator to a CalculatorCatalog that already has a Calculator of the same name and interface type.
DuplicateCalculatorNameException(String) - Constructor for exception cytoscape.visual.DuplicateCalculatorNameException

E

eastName - Static variable in class cytoscape.visual.LabelPosition
EDGE - Static variable in class cytoscape.data.writers.CytoscapeSessionWriter
EDGE_ATTRIBUTE_ADDED - Static variable in class cytoscape.data.NetworkData
EDGE_ATTRIBUTE_REMOVED - Static variable in class cytoscape.data.NetworkData
EDGE_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_FONT_FACE - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_FONT_SIZE - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_LABEL - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_LABEL_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_LABEL_FONT - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_LABEL_POSITION - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_LINETYPE - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_MAPPING - Static variable in interface cytoscape.visual.mappings.ObjectMapping
EDGE_NATURE - Static variable in class cytoscape.data.ImportHandler: Filter Type: EDGE.
EDGE_SET - Static variable in class cytoscape.data.FlagEvent: Deprecated. Static constant indicating a change to a group of Edges.
EDGE_SET - Static variable in class cytoscape.data.SelectEvent: Static constant indicating a change to a group of Edges.
EDGE_SRCARROW - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_TGTARROW - Static variable in class cytoscape.visual.ui.VizMapUI
EDGE_TOOLTIP - Static variable in class cytoscape.visual.ui.VizMapUI
edgeAnchors(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to honor edge anchors.
EdgeAppearance - Class in cytoscape.visual: Objects of this class hold data describing the appearance of an Edge.
EdgeAppearance() - Constructor for class cytoscape.visual.EdgeAppearance
EdgeAppearanceCalculator - Class in cytoscape.visual: This class calculates the appearance of an Edge.
EdgeAppearanceCalculator() - Constructor for class cytoscape.visual.EdgeAppearanceCalculator
EdgeAppearanceCalculator(EdgeAppearanceCalculator) - Constructor for class cytoscape.visual.EdgeAppearanceCalculator: Copy constructor.
EdgeAppearanceCalculator(String, Properties, String, CalculatorCatalog) - Constructor for class cytoscape.visual.EdgeAppearanceCalculator: Creates a new EdgeAppearanceCalculator and immediately customizes it by calling applyProperties with the supplied arguments.
edgeArrowBaseKey - Static variable in class cytoscape.visual.CalculatorIO
EdgeArrowCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeArrowClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
edgeArrows(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render edge arrows.
EdgeAttributesPopupDetails - Class in cytoscape.dialogs: This class provides a detailed list of attribute information for a given edge.
EdgeAttributesPopupDetails(Frame, String, CyAttributes) - Constructor for class cytoscape.dialogs.EdgeAttributesPopupDetails
EdgeCalculator - Class in cytoscape.visual.calculators: EdgeCalculator implements some UI features for calculators lower in the object tree.
EdgeCalculator(String, ObjectMapping, Class) - Constructor for class cytoscape.visual.calculators.EdgeCalculator
EdgeCalculator(String, Properties, String, ValueParser, Object) - Constructor for class cytoscape.visual.calculators.EdgeCalculator: Constructor that calls MappingFactory to construct a new ObjectMapping based on the supplied arguments.
edgeColorBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeColorCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeColorClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
edgeFontFaceBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeFontFaceCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeFontFaceClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
edgeFontSizeBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeFontSizeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeFontSizeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
edgeLabelBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeLabelCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeLabelClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
edgeLabels(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render edge labels.
edgeLineTypeBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeLineTypeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeLineTypeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
EdgeManipulationAction - Class in cytoscape.actions
EdgeManipulationAction(CyNetworkView) - Constructor for class cytoscape.actions.EdgeManipulationAction
EDGES - Static variable in class cytoscape.data.AttributeSaverDialog: Constant to specify edges
edgeToolTipBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
EdgeToolTipCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeToolTipClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
editNetworkTitle(CyNetwork) - Static method in class cytoscape.util.CyNetworkNaming: This will prompt the user to edit the title of a given CyNetork, and after ensuring that the network title is not already in use, this will assign that title to the given CyNetwork
EditNetworkTitleDialog - Class in cytoscape.dialogs
EditNetworkTitleDialog(Component, boolean, String) - Constructor for class cytoscape.dialogs.EditNetworkTitleDialog
ELLIPSE - Static variable in class cytoscape.visual.ShapeNodeRealizer
EMBEDDED_WINDOW - Static variable in interface cytoscape.init.CyInitParams
END - Static variable in class cytoscape.CyNetworkEvent: Indicates that someone is done working with the network.
ensureCapacity(int, int) - Static method in class cytoscape.Cytoscape: Ensure the capacity of Cytoscapce.
EQUAL - Static variable in class cytoscape.visual.mappings.continuous.ContinuousUI
equals(Object) - Method in class cytoscape.data.annotation.AnnotationDescription: redefine equals so that instances with the same contents are equal. this emulates the way that String equality is judged.
equals(Object) - Method in class cytoscape.util.CytoscapeMenuBar: CytoscapeMenuBars are unique -- this equals() method returns true iff the other object == this.
equals(Object) - Method in class cytoscape.util.CytoscapeToolBar: CytoscapeToolBars are unique -- this equals() method returns true iff the other object == this.
equals(Object) - Method in class cytoscape.visual.LabelPosition
equals(Object) - Method in class cytoscape.visual.LineType
equalValue - Variable in class cytoscape.visual.mappings.BoundaryRangeValues
ERROR - Static variable in interface cytoscape.init.CyInitParams
Exec - Class in cytoscape.util
Exec() - Constructor for class cytoscape.util.Exec
Exec(String[]) - Constructor for class cytoscape.util.Exec
exit(int) - Static method in class cytoscape.Cytoscape: Shuts down Cytoscape, after giving plugins time to react.
ExitAction - Class in cytoscape.actions
ExitAction() - Constructor for class cytoscape.actions.ExitAction
ExpFileChooser - Class in cytoscape.actions: extends JFileChooser in the following way: adds a JCheckBox at the bottom of the chooser, asking whether to copy expression data to attributes.
ExpFileChooser(File) - Constructor for class cytoscape.actions.ExpFileChooser
ExportAction - Class in cytoscape.actions
ExportAction() - Constructor for class cytoscape.actions.ExportAction
ExportAsGMLAction - Class in cytoscape.actions
ExportAsGMLAction() - Constructor for class cytoscape.actions.ExportAsGMLAction
ExportAsGMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsGMLAction
ExportAsGraphicsAction - Class in cytoscape.actions
ExportAsGraphicsAction() - Constructor for class cytoscape.actions.ExportAsGraphicsAction
ExportAsInteractionsAction - Class in cytoscape.actions: write out the current graph to the specified file, using the standard interactions format: nodeA edgeType nodeB.
ExportAsInteractionsAction() - Constructor for class cytoscape.actions.ExportAsInteractionsAction: Constructor.
ExportAsXGMMLAction - Class in cytoscape.actions: This action is for exporting network and attributes in XGMML file.
ExportAsXGMMLAction() - Constructor for class cytoscape.actions.ExportAsXGMMLAction
ExportAsXGMMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsXGMMLAction
ExportEdgeAttributesAction - Class in cytoscape.actions
ExportEdgeAttributesAction() - Constructor for class cytoscape.actions.ExportEdgeAttributesAction
ExportNodeAttributesAction - Class in cytoscape.actions
ExportNodeAttributesAction() - Constructor for class cytoscape.actions.ExportNodeAttributesAction
ExportVizmapAction - Class in cytoscape.actions: Export visual styles as a vizmap.props file
ExportVizmapAction() - Constructor for class cytoscape.actions.ExportVizmapAction
EXPRESSION_DATA_LOADED - Static variable in class cytoscape.Cytoscape
ExpressionData - Class in cytoscape.data: This class provides a reader for the common file format for expression data and an interface to access the data.
ExpressionData() - Constructor for class cytoscape.data.ExpressionData: Constructor.
ExpressionData(String) - Constructor for class cytoscape.data.ExpressionData: Constructor.
ExpressionData(String, String) - Constructor for class cytoscape.data.ExpressionData: Constructor.
ExpressionData(String, TaskMonitor) - Constructor for class cytoscape.data.ExpressionData: Constructor.
ExpressionData(String, String, TaskMonitor) - Constructor for class cytoscape.data.ExpressionData: Constructor.
ExpressionDataPopupTable - Class in cytoscape.dialogs
ExpressionDataPopupTable(Frame, String[], String, ExpressionData) - Constructor for class cytoscape.dialogs.ExpressionDataPopupTable
ExpressionDataPopupTable(Frame, String, String[], ExpressionData) - Constructor for class cytoscape.dialogs.ExpressionDataPopupTable
ExpressionDataPopupTable.OKAction - Class in cytoscape.dialogs
ExtensibleMultiHashMapModel - Class in cytoscape.data.attr.util: Deprecated. Use MultiHashMapFactory instead.
ExtensibleMultiHashMapModel() - Constructor for class cytoscape.data.attr.util.ExtensibleMultiHashMapModel: Deprecated.
EXTERNAL_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in JFrames, so each Network has its own window. ( like the GIMP )
extract() - Method in class cytoscape.data.readers.GMLReader

F

FILE_BIOPAX - Static variable in class cytoscape.Cytoscape
FILE_BY_SUFFIX - Static variable in class cytoscape.Cytoscape: When creating a network, use one of the standard suffixes to have it parsed correctly
sif -- Simple Interaction File gml -- Graph Markup Languange sbml -- SBML xgmml -- XGMML
FILE_GML - Static variable in class cytoscape.Cytoscape
FILE_PSI_MI - Static variable in class cytoscape.Cytoscape
FILE_SBML - Static variable in class cytoscape.Cytoscape
FILE_SIF - Static variable in class cytoscape.Cytoscape
FILE_XGMML - Static variable in class cytoscape.Cytoscape
FileUtil - Class in cytoscape.util: Provides a platform-dependent way to open files.
FileUtil() - Constructor for class cytoscape.util.FileUtil
FilterHistoryJList - Class in cytoscape.util.swing: JList with incremntal search & search history.
FilterHistoryJList() - Constructor for class cytoscape.util.swing.FilterHistoryJList
FingCyNetwork - Class in cytoscape.giny: FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the functionality formally provided by GraphObjAttributes.
FingCyNetwork(FingExtensibleRootGraph, IntIterator, IntIterator) - Constructor for class cytoscape.giny.FingCyNetwork: rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor.
finished() - Method in class cytoscape.util.SwingWorker: Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
fireFocus(String) - Method in class cytoscape.view.NetworkPanel
firePropertyChange(String, Object, Object) - Static method in class cytoscape.Cytoscape
firePropertyChange(String, Object, Object) - Method in class cytoscape.view.NetworkViewManager: Fires a PropertyChangeEvent
fireStateChanged() - Method in class cytoscape.visual.SubjectBase: Notifies all listeners that have registered interest for notification on this event type.
FitContentAction - Class in cytoscape.actions
FitContentAction() - Constructor for class cytoscape.actions.FitContentAction
flagAllEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.selectAllEdges()
flagAllEdges() - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state to true for all Edges in the GraphPerspective.
flagAllEdges() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.selectAllEdges()
flagAllNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.selectAllNodes()
flagAllNodes() - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state to true for all Nodes in the GraphPerspective.
flagAllNodes() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.selectAllNodes()
FlagAndSelectionHandler - Class in cytoscape.view: This class synchronizes the flagged status of nodes and edges as held by a FlagFilter object of a network with the selection status of the corresponding node and edge views in a GraphView.
FlagAndSelectionHandler(FlagFilter, GraphView) - Constructor for class cytoscape.view.FlagAndSelectionHandler: Standard constructor takes the flag filter and the view that should be synchronized.
FlagEvent - Class in cytoscape.data: Deprecated. As of 2.3, replaced with SelectEvent
FlagEvent(FlagFilter, Object, boolean) - Constructor for class cytoscape.data.FlagEvent: Deprecated. Standard constructor.
FlagEventListener - Interface in cytoscape.data: Listener for FlagEvents fired by a FlagFilter object
FlagFilter - Class in cytoscape.data: Deprecated. As of 2.3, replaced with SelectFilter
FlagFilter(GraphPerspective) - Constructor for class cytoscape.data.FlagFilter: Deprecated. Standard Constructor.
FlagFilter(SelectFilter) - Constructor for class cytoscape.data.FlagFilter: Deprecated. Constructor added so that FlagFilter can be properly deprecated
FlatInterpolator - Class in cytoscape.visual.mappings: This simple Interpolator returns the value at either the lower or upper boundary of the domain.
FlatInterpolator() - Constructor for class cytoscape.visual.mappings.FlatInterpolator: The default FlatInterpolator returns the range value at the lower boundary.
FlatInterpolator(Integer) - Constructor for class cytoscape.visual.mappings.FlatInterpolator: Constructs a FlatInterpolator which returns the range value at the lower boundary unless the argument 'mode' is equal to FlatInterpolator.UPPER.
FlattenIntVectors - Class in cytoscape.data.annotation: given a vector which nests other vectors, each resolving eventually to a list of Integers, flatten it out into a simple 1-level-deep vector of Integer vectors.
FlattenIntVectors(Vector) - Constructor for class cytoscape.data.annotation.FlattenIntVectors
FLOAT - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Float state of a CytoPanel.
focusGained(FocusEvent) - Method in class cytoscape.dialogs.IntegerEntryField.PositiveIntegerListener
focusGained(FocusEvent) - Method in class cytoscape.dialogs.JointIntegerEntry.CopyField1To2Listener
focusLost(FocusEvent) - Method in class cytoscape.dialogs.IntegerEntryField.PositiveIntegerListener
focusLost(FocusEvent) - Method in class cytoscape.dialogs.JointIntegerEntry.CopyField1To2Listener
focusLost(FocusEvent) - Method in class cytoscape.visual.mappings.continuous.PointTextListener: User now clicks outside of Text Box.
focusNetworkNode(String) - Method in class cytoscape.view.NetworkPanel
FONT - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for a font
FontChooser - Class in cytoscape.visual.ui: Defines a generalized font chooser class.
FontChooser() - Constructor for class cytoscape.visual.ui.FontChooser: Create a FontChooser to choose between all fonts available on the system.
FontChooser(Font) - Constructor for class cytoscape.visual.ui.FontChooser
FontChooser(Font[], Font) - Constructor for class cytoscape.visual.ui.FontChooser: Create a FontChooser to choose between the given array of fonts.
FontParser - Class in cytoscape.visual.parsers: Parses a String into a Font object.
FontParser() - Constructor for class cytoscape.visual.parsers.FontParser
FontRenderer - Class in cytoscape.visual.ui: FontRenderer describes a class that renders each font name in a FontChooser JList or JComboBox in the face specified.
FontRenderer() - Constructor for class cytoscape.visual.ui.FontRenderer
formatter - Static variable in class cytoscape.visual.ui.ValueDisplayer: Formatting for numeric types.

G

GeneOntology - Class in cytoscape.data.ontology: Gene Ontology object based on general Ontology.
GeneOntology(String, String, String, CyNetwork) - Constructor for class cytoscape.data.ontology.GeneOntology
GeneOntology.GOAspect - Enum in cytoscape.data.ontology
GeneOntologyWizard - Class in cytoscape.data.servers.ui
GeneOntologyWizard() - Constructor for class cytoscape.data.servers.ui.GeneOntologyWizard
GeneralColorDialogListener - Class in cytoscape.dialogs: Deprecated. No one uses this, so don't start. Will be removed 12/2006. If you need a JColorChooser, use CyColorChooser instead.
GeneralColorDialogListener(Component, MutableColor, String) - Constructor for class cytoscape.dialogs.GeneralColorDialogListener: Deprecated.
GeneralColorDialogListener(Component, MutableColor, JLabel, String) - Constructor for class cytoscape.dialogs.GeneralColorDialogListener: Deprecated.
GenericEdgeArrowCalculator - Class in cytoscape.visual.calculators: Deprecated. Use EdgeSourceArrow or EdgeTargetArrow instead. will be removed 10/2007
GenericEdgeArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. Creates a new GenericEdgeArrowCalculator object.
GenericEdgeArrowCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. Creates a new GenericEdgeArrowCalculator object.
GenericEdgeColorCalculator - Class in cytoscape.visual.calculators
GenericEdgeColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeColorCalculator
GenericEdgeColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeColorCalculator
GenericEdgeFontFaceCalculator - Class in cytoscape.visual.calculators
GenericEdgeFontFaceCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
GenericEdgeFontFaceCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
GenericEdgeFontSizeCalculator - Class in cytoscape.visual.calculators
GenericEdgeFontSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
GenericEdgeFontSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
GenericEdgeLabelCalculator - Class in cytoscape.visual.calculators
GenericEdgeLabelCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelCalculator
GenericEdgeLabelCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelCalculator
GenericEdgeLabelColorCalculator - Class in cytoscape.visual.calculators
GenericEdgeLabelColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
GenericEdgeLabelColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
GenericEdgeLineTypeCalculator - Class in cytoscape.visual.calculators
GenericEdgeLineTypeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
GenericEdgeLineTypeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
GenericEdgeSourceArrowCalculator - Class in cytoscape.visual.calculators
GenericEdgeSourceArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: Creates a new GenericEdgeSourceArrowCalculator object.
GenericEdgeSourceArrowCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: Creates a new GenericEdgeSourceArrowCalculator object.
GenericEdgeTargetArrowCalculator - Class in cytoscape.visual.calculators
GenericEdgeTargetArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: Creates a new GenericEdgeTargetArrowCalculator object.
GenericEdgeTargetArrowCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: Creates a new GenericEdgeTargetArrowCalculator object.
GenericEdgeToolTipCalculator - Class in cytoscape.visual.calculators
GenericEdgeToolTipCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
GenericEdgeToolTipCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
GenericNodeBorderColorCalculator - Class in cytoscape.visual.calculators
GenericNodeBorderColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: Creates a new GenericNodeBorderColorCalculator object.
GenericNodeBorderColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: Creates a new GenericNodeBorderColorCalculator object.
GenericNodeColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use NodeFillColor or NodeBorderColor instead. will be removed 10/2007
GenericNodeColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. Creates a new GenericNodeColorCalculator object.
GenericNodeColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. Creates a new GenericNodeColorCalculator object.
GenericNodeFillColorCalculator - Class in cytoscape.visual.calculators
GenericNodeFillColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFillColorCalculator: Creates a new GenericNodeFillColorCalculator object.
GenericNodeFillColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFillColorCalculator: Creates a new GenericNodeFillColorCalculator object.
GenericNodeFontFaceCalculator - Class in cytoscape.visual.calculators
GenericNodeFontFaceCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
GenericNodeFontFaceCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
GenericNodeFontSizeCalculator - Class in cytoscape.visual.calculators
GenericNodeFontSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
GenericNodeFontSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
GenericNodeHeightCalculator - Class in cytoscape.visual.calculators
GenericNodeHeightCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeHeightCalculator: Creates a new GenericNodeHeightCalculator object.
GenericNodeHeightCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeHeightCalculator: Creates a new GenericNodeHeightCalculator object.
GenericNodeLabelCalculator - Class in cytoscape.visual.calculators
GenericNodeLabelCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelCalculator
GenericNodeLabelCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelCalculator
GenericNodeLabelColorCalculator - Class in cytoscape.visual.calculators
GenericNodeLabelColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
GenericNodeLabelColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
GenericNodeLabelPositionCalculator - Class in cytoscape.visual.calculators
GenericNodeLabelPositionCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
GenericNodeLabelPositionCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
GenericNodeLineTypeCalculator - Class in cytoscape.visual.calculators
GenericNodeLineTypeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
GenericNodeLineTypeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
GenericNodeShapeCalculator - Class in cytoscape.visual.calculators
GenericNodeShapeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeShapeCalculator
GenericNodeShapeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeShapeCalculator
GenericNodeSizeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use NodeWidth,NodeHeight, or NodeUniformSize instead. will be removed 10/2007
GenericNodeSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. Creates a new GenericNodeSizeCalculator object.
GenericNodeSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. Creates a new GenericNodeSizeCalculator object.
GenericNodeToolTipCalculator - Class in cytoscape.visual.calculators
GenericNodeToolTipCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeToolTipCalculator
GenericNodeToolTipCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeToolTipCalculator
GenericNodeUniformSizeCalculator - Class in cytoscape.visual.calculators
GenericNodeUniformSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: Creates a new GenericNodeUniformSizeCalculator object.
GenericNodeUniformSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: Creates a new GenericNodeUniformSizeCalculator object.
GenericNodeWidthCalculator - Class in cytoscape.visual.calculators
GenericNodeWidthCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeWidthCalculator: Creates a new GenericNodeWidthCalculator object.
GenericNodeWidthCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeWidthCalculator: Creates a new GenericNodeWidthCalculator object.
get() - Method in class cytoscape.util.SwingWorker: Return the value created by the construct method.
get(byte) - Method in class cytoscape.visual.EdgeAppearance
get(byte) - Method in class cytoscape.visual.NodeAppearance
getAbbreviation() - Method in class cytoscape.data.ontology.DBReference
getAcceptedDataClasses() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets Accepted Data Classes.
getAcceptedDataClasses() - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets Accepted Data Classes.
getAcceptedDataClasses() - Method in interface cytoscape.visual.mappings.ObjectMapping: Return the classes that the ObjectMapping can map from, eg. the contents of the data of the controlling attribute.
getAcceptedDataClasses() - Method in class cytoscape.visual.mappings.PassThroughMapping
getActionList() - Static method in class cytoscape.util.CytoscapeAction
getAliases(String) - Method in class cytoscape.data.synonyms.Aliases
getAll() - Method in class cytoscape.visual.mappings.DiscreteMapping: gets all map values
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
getAllAnnotations(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAllAttributeKeys(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all key sequnces that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeKeysAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all key sequences having a given prefix that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeValues(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all attribute values on an object in a given attribute definition; this method is only useful with attribute definitions that have nonzero key spaces.
getAllAttributeValuesAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering attribute values along a specified key prefix; this method is only useful with attribute definitions that have nonzero key spaces.
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServer
getAllCommonNames(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAllCommonNames(String) - Method in class cytoscape.data.synonyms.Thesaurus
getAllDescriptions() - Method in class cytoscape.data.ImportHandler: Gets a collection of all registered filter descriptions.
getAllExtensions() - Method in class cytoscape.data.ImportHandler: Gets a collection of all registered file extensions.
getAllFilters() - Method in class cytoscape.data.ImportHandler: Gets a list of all registered filters plus a catch-all super set filter.
getAllFilters(String) - Method in class cytoscape.data.ImportHandler: Gets a list of all registered filters, which are of type: fileNature, plus a catch-all super set filter.
getAllHierarchyPaths(int) - Method in class cytoscape.data.annotation.Ontology: get all unique paths from the termID to the root of the ontology, in reverse order, with the most general classification first, and most specific last.
getAllHierarchyPathsAsNames(String) - Method in class cytoscape.data.annotation.Annotation
getAllHierarchyPathsAsNames(int) - Method in class cytoscape.data.annotation.Ontology: get all unique paths as a set of names, from termID to the root of the ontology, in reverse order, from most general to most specific.
getAllInteractions() - Method in class cytoscape.data.readers.InteractionsReader
getAllMeasurements() - Method in class cytoscape.data.ExpressionData: Gets all Measurements.
getAllNamesInGroup(String) - Method in class cytoscape.data.synonyms.Thesaurus
getAllPoints() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets all Data Points.
getAllSynonyms(String, CyNetwork) - Static method in class cytoscape.data.Semantics: This method returns a list of all names that are synonyms of the given name.
getAllTypes(String) - Method in class cytoscape.data.ImportHandler: Gets descriptions for all registered filters, which are of the type: fileNature.
getAlternateCommonNames(String) - Method in class cytoscape.data.synonyms.Thesaurus
getAnchorNames() - Static method in class cytoscape.visual.LabelPosition
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationFlatFileReader
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationXmlReader
getAnnotation() - Method in class cytoscape.data.ontology.OntologyTerm: Always return empty annotation object.
getAnnotation() - Method in class cytoscape.data.ontology.Triple: Always return empty annotation object.
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServer
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServer
getAnnotation(String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotation(AnnotationDescription) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServer
getAnnotationCount() - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServer
getAnnotationDescriptions() - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServerRmi
getAnotationFiles() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
getArgs() - Method in class cytoscape.CyMain: DOCUMENT ME!
getArgs() - Method in class cytoscape.CytoscapeConfig: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
getArgs() - Static method in class cytoscape.CytoscapeInit: Deprecated. Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007.
getArgs() - Method in interface cytoscape.init.CyInitParams
getArrowIcons() - Static method in class cytoscape.visual.ui.IconSupport
getArrowIcons() - Method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getArrowToStringHashMap(int) - Static method in class cytoscape.visual.ui.IconSupport
getArrowToStringHashMap(int) - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getAspect(String) - Method in class cytoscape.data.ontology.GeneOntology: Returns Aspect/name space of the GO term.
getAttribute(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
getAttribute(DataSource, String) - Static method in class cytoscape.util.BookmarksUtil
getAttributeDescription(String) - Method in interface cytoscape.data.CyAttributes: Gets the human readable description of a specific attribute.
getAttributeDescription(String) - Method in class cytoscape.data.CyAttributesImpl
getAttributeKeyspaceDimensionTypes(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Returns information about the dimensionality and types in the key space of specified attribute.
getAttributeKeyspan(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: For all key sequences, having specified prefix, that map into bound values on objectKey in attributeName, returns the [unique] representatives from dimension keyPrefix.length + 1.
getAttributeList(String, String) - Method in interface cytoscape.data.CyAttributes: Deprecated. Use getListAttribute() instead. Will be removed 11/2007.
getAttributeList(String, String) - Method in class cytoscape.data.CyAttributesImpl
getAttributeMap(String, String) - Method in interface cytoscape.data.CyAttributes: Deprecated. Use getMapAttribute() instead. Will be removed 11/2007.
getAttributeMap(String, String) - Method in class cytoscape.data.CyAttributesImpl
getAttributeNames() - Method in interface cytoscape.data.CyAttributes: Gets an array of all attribute names.
getAttributeNames() - Method in class cytoscape.data.CyAttributesImpl
getAttributeNamesForObj(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils: Return a non-null List of all the attribute names associated with a given identifier for a given CyAttributes.
getAttributes(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
getAttributeType(String, String) - Static method in class cytoscape.visual.mappings.MappingUtil: This method determines the type of the attribute used for the mapping.
getAttributeTypeString(String, String) - Static method in class cytoscape.visual.mappings.MappingUtil: This method determines the type of the attr used and returns a string representation of it.
getAttributeValue(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: Retrieves a bound attribute value from an object.
getAttributeValueType(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Returns the type of attribute values that exist in specified attribute space.
getBackgroundColor() - Method in class cytoscape.data.readers.XGMMLReader
getBackgroundColor() - Method in class cytoscape.visual.GlobalAppearance
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.OboPanelDescriptor
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.SelectFormatPanelDescriptor
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.SpeciesPanelDescriptor
getBioDataServer() - Static method in class cytoscape.Cytoscape
getBioDataServer() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getProperty("bioDataServer") instead.
getBlankDisplayFor(JDialog, String, byte) - Static method in class cytoscape.visual.ui.ValueDisplayer: Get a blank or default display/input pair for a given type of input.
getBlankDisplayFor(JDialog, String, Object) - Static method in class cytoscape.visual.ui.ValueDisplayer: Get a blank or default display/input pair for the given sample object, which itself is ignored.
getBookmarks() - Static method in class cytoscape.Cytoscape
getBookmarks() - Method in class cytoscape.data.readers.BookmarkReader: Get loaded bookmark.
getBookmarks(URL) - Static method in class cytoscape.util.BookmarksUtil
getBookmarks(File) - Static method in class cytoscape.util.BookmarksUtil
getBool() - Method in class cytoscape.util.MutableBool
getBooleanAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a Boolean value at the specified id/attributeName.
getBooleanAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getBorderColor() - Method in class cytoscape.visual.NodeAppearance
getBorderLineType() - Method in class cytoscape.visual.NodeAppearance
getBounds() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the bounds of the applications mainframe.
getBounds() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Gets Bounds of Container, relative to parent component.
getBriefHistory() - Method in class cytoscape.CytoscapeVersion: Deprecated. See cytoscape.org for history. Will be removed 10/2007
getButton() - Method in class cytoscape.dialogs.IconPopupButton
getCalculator(byte, String) - Method in class cytoscape.visual.CalculatorCatalog
getCalculatorCatalog() - Method in class cytoscape.visual.VisualMappingManager
getCalculators() - Method in class cytoscape.visual.CalculatorCatalog
getCalculators(byte) - Method in class cytoscape.visual.CalculatorCatalog
getCalculatorTypes() - Method in class cytoscape.visual.CalculatorCatalog
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServer
getCanonicalName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getCanonicalName - Class in cytoscape.data.servers
getCanonicalName() - Constructor for class cytoscape.data.servers.getCanonicalName
getCategory(String, List<Category>) - Static method in class cytoscape.util.BookmarksUtil: Select specific category from a list of categories.
getCellEditorValue() - Method in class cytoscape.util.swing.AbstractCellEditor
getCheckBoxState() - Method in class cytoscape.actions.CheckBoxFileChooser: method for accessing last state of JCheckBox jcb
getClass(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
getClassifications() - Method in class cytoscape.data.annotation.Annotation: returns an array of all the classifications in the current annotation
getClassifications(String) - Method in class cytoscape.data.annotation.Annotation: all of the ontology identifiers registered for the specified entity
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServer
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
getClassifications(String, String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getClassifications(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getClassificationsVector(String) - Method in class cytoscape.data.annotation.Annotation: all of the ontology identifiers registered for the specified entity, as a Vector of Integers
getClassLoader() - Static method in class cytoscape.CytoscapeInit: DOCUMENT ME!
getClientData(String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientData(String) - Method in class cytoscape.ding.DingNetworkView
getClientData(String) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. Get Some client data
getClientData(String) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Get Some client data
getClientData(String) - Method in interface cytoscape.view.CyNetworkView: Get Some client data
getClientDataNames() - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientDataNames() - Method in class cytoscape.ding.DingNetworkView
getClientDataNames() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. Get a list of all currently available ClientData objects
getClientDataNames() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Get a list of all currently available ClientData objects
getClientDataNames() - Method in interface cytoscape.view.CyNetworkView: Get a list of all currently available ClientData objects
getCmd() - Method in class cytoscape.util.Exec
getColor(String) - Method in class cytoscape.data.readers.GMLReader: Create a color object from the string like it is stored in a gml file
getColor(String) - Method in class cytoscape.data.readers.XGMMLReader: Convert a valid string into Color object.
getColor() - Method in class cytoscape.util.MutableColor: Deprecated.
getColor() - Method in class cytoscape.visual.EdgeAppearance
getColorHexString(Color) - Method in class cytoscape.data.readers.GMLTree: Get the String representation of the 6 character hexidecimal RGB values i.e.
getColorIcon(Color) - Static method in class cytoscape.visual.ui.IconSupport
getColumnClass(int) - Method in class cytoscape.util.swing.AbstractTreeTableModel
getColumnClass(int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the type for column number column.
getColumnClass(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getColumnCount() - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
getColumnCount() - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getColumnCount() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getColumnCount() - Method in interface cytoscape.util.swing.TreeTableModel: Returns the number of availible columns.
getColumnCount() - Method in class cytoscape.util.swing.TreeTableModelAdapter
getColumnName(int) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getColumnName(int) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getColumnName(int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the name for column number column.
getColumnName(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServer
getCommonName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getCommonName - Class in cytoscape.data.servers
getCommonName() - Constructor for class cytoscape.data.servers.getCommonName
getCommonName(String) - Method in class cytoscape.data.synonyms.Thesaurus
getComponentAt(int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the component at index.
getComponentAt(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the component at index.
getConditionIndex(String) - Method in class cytoscape.data.ExpressionData: Gets the index value of the specified experimenal conditon.
getConditionNames() - Method in class cytoscape.data.ExpressionData: Gets an Array of All Experimental Conditions.
getConfigDirectory() - Static method in class cytoscape.CytoscapeInit: If .cytoscape directory does not exist, it creates it and returns it
getConfigDirectoy() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method is only deprecated because it is misspelled. Just use the correctly spelled method: getConfigDirectory(). This method will be removed 12/2006.
getConfigFile(String) - Static method in class cytoscape.CytoscapeInit: DOCUMENT ME!
getConstraintBox() - Method in class cytoscape.dialogs.JointIntegerEntry
getConstraintLabel() - Method in class cytoscape.dialogs.JointIntegerEntry
getContainers() - Method in class cytoscape.data.annotation.OntologyTerm
getControllingAttributeName() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingReader: Gets Controlling Attribute Name.
getControllingAttributeName() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets the Name of the Controlling Attribute.
getControllingAttributeName() - Method in class cytoscape.visual.mappings.discrete.DiscreteMappingReader: Gets Controlling Attribute Name.
getControllingAttributeName() - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets the Name of the Controlling Attribute.
getControllingAttributeName() - Method in interface cytoscape.visual.mappings.ObjectMapping: Get the controlling attribute name
getControllingAttributeName() - Method in class cytoscape.visual.mappings.PassThroughMapping
getCount() - Method in class cytoscape.data.readers.InteractionsReader
getCrossReferences() - Method in class cytoscape.data.ontology.GOTerm
getCrossReferences() - Method in class cytoscape.data.servers.OntologyServer
getCurator() - Method in class cytoscape.data.annotation.Annotation
getCurator() - Method in class cytoscape.data.annotation.AnnotationDescription
getCurator() - Method in class cytoscape.data.annotation.Ontology
getCurator() - Method in class cytoscape.data.annotation.OntologyDescription
getCurator() - Method in class cytoscape.data.ontology.GeneOntology
getCurator() - Method in class cytoscape.data.ontology.Ontology
getCurrent() - Method in interface cytoscape.util.MonitoredTask: Returns the currentProgress parameter.
getCurrentIcon() - Method in class cytoscape.visual.ui.IconSupport
getCurrentNetwork() - Static method in class cytoscape.Cytoscape: Return the Network that currently has the Focus.
getCurrentNetworkView() - Static method in class cytoscape.Cytoscape: Return the CyNetworkView that currently has the focus.
getCurrentSessionFileName() - Static method in class cytoscape.Cytoscape: Get name of the current session file.
getCyEdge(Node, Node, String, Object, boolean) - Static method in class cytoscape.Cytoscape: Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.
getCyEdge(Node, Node, String, Object, boolean, boolean) - Static method in class cytoscape.Cytoscape: Gets the first CyEdge found between the two nodes that has the given value for the given attribute.
getCyEdge(String, String, String, String) - Static method in class cytoscape.Cytoscape: Returns and edge if it exists, otherwise creates a directed edge.
getCyEdgesList() - Static method in class cytoscape.Cytoscape
getCyInitParams() - Static method in class cytoscape.CytoscapeInit: Returns the CyInitParams object used to initialize Cytoscape.
getCyMenus() - Method in class cytoscape.view.CytoscapeDesktop
getCyNetworkListeners() - Method in interface cytoscape.CyNetwork: Returns the set of listeners registered with this object.
getCyNetworkListeners() - Method in class cytoscape.giny.FingCyNetwork: Returns the set of listeners registered with this object.
getCyNode(String) - Static method in class cytoscape.Cytoscape
getCyNode(String, boolean) - Static method in class cytoscape.Cytoscape
getCyNodesList() - Static method in class cytoscape.Cytoscape
getCysessionNote() - Method in class cytoscape.data.readers.CytoscapeSessionReader: Extract Session Note test field in cysession.xml
getCytoPanel(int) - Method in class cytoscape.view.CytoscapeDesktop: Gets a cytoPanel given a Compass direction.
getCytoPanelComponentCount() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the number of components in the CytoPanel.
getCytoPanelComponentCount() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the number of components in the CytoPanel.
getCytoPanelMenu() - Method in class cytoscape.view.CyMenus: Returns the cytopanels menu.
getDag() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
getDag() - Method in interface cytoscape.data.ontology.readers.OntologyReader
getDataSourceList(String, List<Category>) - Static method in class cytoscape.util.BookmarksUtil: Traverse bookmark tree and get a list of data sources from the specified category.
getDBNames() - Method in class cytoscape.data.ontology.DBCrossReferences
getDBReference(String) - Method in class cytoscape.data.ontology.DBCrossReferences
getDefaultAppearance() - Method in class cytoscape.visual.EdgeAppearanceCalculator
getDefaultAppearance() - Method in class cytoscape.visual.NodeAppearanceCalculator
getDefaultBackgroundColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultEdgeColor() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeFont() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeFontFace() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeFontSize() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeLabel() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeLineType() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultEdgeSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultEdgeSourceArrow() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeTargetArrow() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultEdgeToolTip() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getDefaultAppearance() instead. This method will be removed Sept. 2007.
getDefaultMenuSpecifier() - Method in class cytoscape.util.CytoscapeMenuBar
getDefaultNodeBorderColor() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeFillColor() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeFont() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeFontFace() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeFontSize() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeHeight() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeLabel() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeLabelColor() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeLineType() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultNodeSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultNodeShape() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeToolTip() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultNodeWidth() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept 2007.
getDefaultProperties(String) - Method in class cytoscape.visual.EdgeAppearance
getDefaultProperties(String) - Method in class cytoscape.visual.NodeAppearance
getDefaultSloppySelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
getDefaultSpeciesName() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead.
getDefaultVisualStyle() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead.
getDefinedAttributes() - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Returns all defined attributeNames.
getDescription() - Method in class cytoscape.data.annotation.Ontology
getDescription() - Method in class cytoscape.data.ExpressionData: Returns a text description of this data object.
getDescription() - Method in class cytoscape.data.ontology.GOTerm
getDescription() - Method in class cytoscape.data.ontology.Ontology
getDescription() - Method in class cytoscape.data.ontology.OntologyTerm: Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in enum cytoscape.data.ontology.readers.OBOTags
getDescription() - Method in class cytoscape.data.ontology.Triple: Description for triple is not supported.
getDescription() - Method in class cytoscape.dialogs.NetworkMetaDataTableModel: Get Desctiption entry, which will not be included in the table.
getDescription() - Method in class cytoscape.util.CyFileFilter: Returns the human readable description of this filter.
getDescription(String) - Method in class cytoscape.visual.EdgeAppearance
getDescription() - Method in class cytoscape.visual.EdgeAppearance
getDescription() - Method in class cytoscape.visual.EdgeAppearanceCalculator
getDescription() - Method in class cytoscape.visual.GlobalAppearanceCalculator: Returns a text description of this object's current state.
getDescription(String) - Method in class cytoscape.visual.NodeAppearance
getDescription() - Method in class cytoscape.visual.NodeAppearance
getDescription() - Method in class cytoscape.visual.NodeAppearanceCalculator: Returns a text description of the current default values and calculator names.
getDesktop() - Static method in class cytoscape.Cytoscape
getDesktopPane() - Method in class cytoscape.view.NetworkViewManager
getDisplayFor(JDialog, String, Object) - Static method in class cytoscape.visual.ui.ValueDisplayer: Get a display/input pair initialized to a given type of input.
getDisplayForColor(JDialog, String, Color) - Static method in class cytoscape.visual.ui.ValueDisplayer
getDisplayForLabelPosition(JDialog, String, LabelPosition) - Static method in class cytoscape.visual.ui.ValueDisplayer
getDoubleAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a Double value at the specified id/attributeName.
getDoubleAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getDoubleValue() - Method in class cytoscape.dialogs.NewSlider
getDupeCount() - Method in class cytoscape.visual.calculators.AbstractCalculator: Get how many times this calculator has been duplicated.
getDupeCount() - Method in class cytoscape.visual.VisualStyle: Get how many times this style has been cloned.
getEdge(String) - Method in class cytoscape.giny.CytoscapeFingRootGraph
getEdge(String) - Method in interface cytoscape.giny.CytoscapeRootGraph
getEdgeAliases() - Method in class cytoscape.data.servers.OntologyServer
getEdgeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the EdgeAppearanceCalculator for this visual style.
getEdgeArrowCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeArrowCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeAttributeFiles() - Method in class cytoscape.CyMain: DOCUMENT ME!
getEdgeAttributeFiles() - Method in interface cytoscape.init.CyInitParams
getEdgeAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Edge Attributes
getEdgeAttributes() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getEdgeAttributes() - Method in class cytoscape.data.readers.AbstractGraphReader: Deprecated. Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006.
getEdgeAttributes() - Method in interface cytoscape.data.readers.GraphReader: Deprecated. Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006.
getEdgeAttributesList() - Method in class cytoscape.giny.FingCyNetwork: Return all availble Attributes for the Edges in this CyNetwork
getEdgeAttributeValue(Edge, String) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Edge
getEdgeAttributeValue(int, String) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Edge
getEdgeColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeColorCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeColorCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeFontFaceCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeFontFaceCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeFontFaceCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeFontSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeFontSizeCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeFontSizeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeIndicesArray() - Method in class cytoscape.data.readers.AbstractGraphReader
getEdgeIndicesArray() - Method in class cytoscape.data.readers.GMLReader: Part of interace contract
getEdgeIndicesArray() - Method in interface cytoscape.data.readers.GraphReader: Gets an array of edges indices that participate in the newly created graph.
getEdgeIndicesArray() - Method in class cytoscape.data.readers.InteractionsReader
getEdgeIndicesArray() - Method in class cytoscape.data.readers.XGMMLReader: Part of interace contract
getEdgeLabelCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeLabelCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeLabelCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeLineTypeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeLineTypeCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeLineTypeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEdgeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
getEdgeSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
getEdgeSourceArrowCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeTargetArrowCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeToolTipCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getEdgeToolTipCalculator() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept. 2007.
getEdgeToolTipCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getEditingRow() - Method in class cytoscape.util.swing.JTreeTable
getEditMenu() - Method in class cytoscape.view.CyMenus: returns the menu with items related to editing the graph.
getEventType() - Method in class cytoscape.data.FlagEvent: Deprecated. Returns a boolean identifying the type of event, true if the change is setting the flag for these objects, or false if the change is removing the flag.
getEventType() - Method in class cytoscape.data.SelectEvent: Returns a boolean identifying the type of event, true the selectes state was set to true, false if it was set to false
getExpressionData() - Static method in class cytoscape.Cytoscape
getExpressionData() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. @see{getNetworkData} Returns the expression data object associated with this network. Will be removed Feb 2007.
getExpressionFiles() - Method in class cytoscape.CyMain: DOCUMENT ME!
getExpressionFiles() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getExpressionFiles() - Method in interface cytoscape.init.CyInitParams
getExtension(File) - Method in class cytoscape.util.CyFileFilter: Return the extension portion of the file's name.
getExtension(String) - Method in class cytoscape.util.CyFileFilter
getExtensionSet() - Method in class cytoscape.util.CyFileFilter: Returns the Set of file extension names.
getExtremeValues() - Method in class cytoscape.data.ExpressionData: Returns a 2D Matrix of Extreme Values.
getFaceComboBox() - Method in class cytoscape.visual.ui.FontChooser
getField() - Method in class cytoscape.dialogs.IntegerEntryField
getField(String) - Method in class cytoscape.dialogs.JointIntegerEntry
getFile() - Method in class cytoscape.dialogs.ImportNetworkDialog: Get first file only.
getFile(String, int) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileFormatRadioButtonSelected() - Method in class cytoscape.data.servers.ui.SelectFormatPanel
getFileMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to file operations.
getFileName() - Method in class cytoscape.data.ExpressionData: Gets the Name of the Expression Data File.
getFilename() - Method in class cytoscape.dialogs.ImportAttributeMatrixDialog
getFileNature() - Method in class cytoscape.util.CyFileFilter: Returns the nature of the file.
getFiles() - Method in class cytoscape.dialogs.ImportNetworkDialog: Get all files selected.
getFiles(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil: Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String, boolean) - Static method in class cytoscape.util.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFileType(String) - Method in class cytoscape.data.ImportHandler: Gets the name of the filter which is capable of reading the specified file.
getFillColor() - Method in class cytoscape.visual.NodeAppearance
getFilterField() - Method in class cytoscape.util.swing.FilterHistoryJList
getFinalState() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
getFlagEventListeners() - Method in class cytoscape.data.FlagFilter: Deprecated. Gets a List of All Registered Listeners.
getFlaggedEdgeIndicesArray() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedEdges()
getFlaggedEdgeIndicesArray() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.getSelectedEdges()
getFlaggedEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedEdges()
getFlaggedEdges() - Method in class cytoscape.data.FlagFilter: Deprecated. Returns the set of all flagged edges in the referenced GraphPespective.
getFlaggedEdges() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.getSelectedEdges()
getFlaggedNodeIndicesArray() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedNodes()
getFlaggedNodeIndicesArray() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.getSelectedNodes()
getFlaggedNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedNodes()
getFlaggedNodes() - Method in class cytoscape.data.FlagFilter: Deprecated. Returns the set of all flagged nodes in the referenced GraphPespective.
getFlaggedNodes() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.getSelectedNodes()
getFlagger() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectFilter()
getFlagger() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.getSelectFilter()
getFlip() - Method in class cytoscape.data.servers.ui.GeneOntologyWizard
getFlipCheckBoxStatus() - Method in class cytoscape.data.servers.ui.AnotationPanel
getFont() - Method in class cytoscape.visual.EdgeAppearance
getFont() - Method in class cytoscape.visual.NodeAppearance
getFontSize() - Method in class cytoscape.visual.EdgeAppearance
getFontSize() - Method in class cytoscape.visual.NodeAppearance
getFullName() - Method in class cytoscape.data.ontology.DBReference
getFullName() - Method in class cytoscape.data.ontology.GOTerm
getFullPath() - Method in class cytoscape.data.ExpressionData: Gets the File representation of the Expression Data Object.
getGAFiles() - Method in class cytoscape.data.servers.ui.AnotationPanel
getGeneDescriptor(String) - Method in class cytoscape.data.ExpressionData: Gets the Gene Descriptor for the specified gene.
getGeneDescriptors() - Method in class cytoscape.data.ExpressionData: Gets an Array of GeneDescriptors.
getGeneDescriptorsVector() - Method in class cytoscape.data.ExpressionData: Gets a Vector Gene Descriptors.
getGeneNames() - Method in class cytoscape.data.ExpressionData: Gets a List of All Gene Names.
getGeneNamesVector() - Method in class cytoscape.data.ExpressionData: Gets a List of All Gene Names.
getGenericURL() - Method in class cytoscape.data.ontology.DBReference
getGinyArrow() - Method in class cytoscape.visual.Arrow
getGinyShape(byte) - Static method in class cytoscape.visual.ShapeNodeRealizer
getGlobalAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the GlobalAppearanceCalculator for this visual style.
getGlobalPercent(int, int, int) - Method in class cytoscape.util.PercentUtil: Calculates Global Percent Based on Current Step, Current Value, and MaxValue.
getGOTerm(String) - Method in class cytoscape.data.ontology.GeneOntology
getGraphFiles() - Method in class cytoscape.CyMain: DOCUMENT ME!
getGraphFiles() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getGraphFiles() - Method in interface cytoscape.init.CyInitParams
getGraphPerspective() - Method in class cytoscape.CyNode
getGraphViewCenter() - Method in class cytoscape.data.readers.XGMMLReader: Returns the graph view center.
getGraphViewController() - Method in class cytoscape.view.CytoscapeDesktop: TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
getGraphViewController() - Method in interface cytoscape.view.NetworkView: Deprecated.
getGraphViewHandler(GraphView) - Method in class cytoscape.view.GraphViewController: Gets the cytoscape.view.GraphViewHandler for the given giny.view.GraphView
getGraphViewHandlersMap() - Method in class cytoscape.view.GraphViewController: Gets a Map with giny.view.GraphView objects as keys, and cytoscape.view.GraphViewHandler objects as values, two or more different keys can share the same value.
getGraphViews() - Method in class cytoscape.view.GraphViewController: Gets an array of giny.view.GraphView objects that this GraphViewController will keep synchronized with their corresponding giny.model.GraphPerspective objects available through their getGraphPerspective() method
getGraphViewZoomLevel() - Method in class cytoscape.data.readers.XGMMLReader: Returns the zoom level read from the the xgmml file.
getHeader() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
getHeader() - Method in interface cytoscape.data.ontology.readers.OntologyReader
getHeader() - Static method in class cytoscape.visual.mappings.LegendTable
getHeight() - Method in class cytoscape.visual.NodeAppearance
getHelp() - Method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.
getHelpBroker() - Method in class cytoscape.view.CyHelpBroker
getHelpBroker() - Method in class cytoscape.view.CytoscapeDesktop
getHelpMenu() - Method in class cytoscape.view.CyMenus: Returns the help menu.
getHelpSet() - Method in class cytoscape.view.CyHelpBroker
getHelpSet() - Method in class cytoscape.view.CytoscapeDesktop
getIconName() - Method in class cytoscape.dialogs.IconPopupButton
getIconObject() - Method in class cytoscape.dialogs.IconPopupButton
getIcons() - Method in class cytoscape.visual.ui.IconSupport
getIconType(ImageIcon) - Method in class cytoscape.visual.ui.IconSupport
getId() - Method in class cytoscape.data.annotation.OntologyTerm
getIdentifier() - Method in class cytoscape.CyEdge
getIdentifier() - Method in interface cytoscape.CyNetwork: Can't Change
getIdentifier() - Method in class cytoscape.CyNode
getIdentifier() - Method in class cytoscape.giny.FingCyNetwork
getIdentifier() - Method in class cytoscape.util.CytoscapeMenuBar
getIdSet(String) - Method in class cytoscape.data.synonyms.Aliases: Return set of all names for the key (including key itself.)
getImportHandler() - Static method in class cytoscape.Cytoscape
getIndexOfChild(Object, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
getInputListener() - Method in class cytoscape.visual.ui.ValueDisplayer: Returns the ActionListener that will pop up the input UI when triggered.
getInputStream(String) - Static method in class cytoscape.util.FileUtil
getInputStream(String, TaskMonitor) - Static method in class cytoscape.util.FileUtil
getInputStream(URL) - Static method in class cytoscape.util.URLUtil
getInputString(String) - Static method in class cytoscape.util.FileUtil
getInt() - Method in class cytoscape.dialogs.IntegerEntryField
getInt(String) - Method in class cytoscape.dialogs.JointIntegerEntry
getInt() - Method in class cytoscape.util.MutableInt
getInteger() - Method in class cytoscape.dialogs.IntegerEntryField
getInteger(String) - Method in class cytoscape.dialogs.JointIntegerEntry
getIntegerAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets an Integer value at the specified id/attributeName.
getIntegerAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getIntegerValue() - Method in class cytoscape.dialogs.NewSlider
getInteractionString(CyNetwork) - Static method in class cytoscape.data.writers.InteractionWriter: Returns a SIF formatted string of the specified network.
getInteractionString(CyNetwork, TaskMonitor) - Static method in class cytoscape.data.writers.InteractionWriter: Returns a SIF formatted string of the specified network.
getInteractionType(CyNetwork, Edge) - Static method in class cytoscape.data.Semantics: Returns the interaction type of the given edge.
getInteractionTypes(CyNetwork) - Static method in class cytoscape.data.Semantics: Returns an array containing all of the unique interaction types present in the network.
getInternalFrameComponent(CyNetworkView) - Method in class cytoscape.view.NetworkViewManager: Given a CyNetwork, returns the InternalFrameComponent that wraps it.
getInterpolator() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingReader: Gets Interpolator Object.
getInterpolator() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets the Mapping Interpolator.
getJustify() - Method in class cytoscape.visual.LabelPosition
getJustifyNames() - Static method in class cytoscape.visual.LabelPosition
getKey(String) - Method in class cytoscape.data.synonyms.Aliases: Returns true if the object with the alias wxists in the memory (rootGraph).
getKeyAttributeName() - Method in class cytoscape.dialogs.ImportAttributeMatrixDialog
getKeyCode() - Method in class cytoscape.util.CytoscapeAction
getKeyModifiers() - Method in class cytoscape.util.CytoscapeAction
getLabel() - Method in class cytoscape.dialogs.IconPopupButton
getLabel() - Method in class cytoscape.dialogs.IntegerEntryField
getLabel(String) - Method in class cytoscape.dialogs.JointIntegerEntry
getLabel() - Method in class cytoscape.visual.EdgeAppearance
getLabel() - Method in class cytoscape.visual.NodeAppearance
getLabelAnchor() - Method in class cytoscape.visual.LabelPosition
getLabelColor() - Method in class cytoscape.visual.EdgeAppearance
getLabelColor() - Method in class cytoscape.visual.NodeAppearance
getLabelPosition() - Method in class cytoscape.visual.NodeAppearance
getLabelPositionIcon(LabelPosition) - Static method in class cytoscape.visual.ui.IconSupport
getLastKeyModified() - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets the Last Modified Key.
getLayoutMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items realted to layout actions.
getLegend(String, byte) - Method in class cytoscape.visual.mappings.ContinuousMapping
getLegend(String, byte) - Method in class cytoscape.visual.mappings.DiscreteMapping: Returns a JPanel containing a legend for this mapping.
getLegend(String, byte) - Method in interface cytoscape.visual.mappings.ObjectMapping
getLegend(String, byte) - Method in class cytoscape.visual.mappings.PassThroughMapping
getLengthOfTask() - Method in interface cytoscape.util.MonitoredTask: Returns the lenghtOfTask parameter.
getLibJars() - Method in class cytoscape.util.JnlpWriterUtil
getLineType(int) - Static method in class cytoscape.data.readers.GMLReader
getLineType() - Method in class cytoscape.visual.EdgeAppearance
getLineTypeIcons() - Static method in class cytoscape.visual.ui.IconSupport
getLineTypeIcons() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getLineTypeToStringHashMap() - Static method in class cytoscape.visual.ui.IconSupport
getLineTypeToStringHashMap() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getList() - Method in class cytoscape.data.readers.GMLReader: Returns a list containing the gml object tree
getListAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a 'simple' list of attributes for the id/attributeName pair.
getListAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class cytoscape.visual.ui.FontRenderer
getLoadSubMenu() - Method in class cytoscape.view.CyMenus: Returns the submenu with items related to loading objects.
getLocationOfExternalFrame(Dimension, Rectangle, Dimension, int, boolean) - Static method in class cytoscape.view.cytopanels.CytoPanelUtil: Gets Location of External Frame, based on current UI Dimensions.
getLocationOnScreen() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the location of the applications mainframe.
getLocationOnScreen() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Gets Location of Container, in screen coordinates.
getMainClass(ArrayList<String>, String) - Method in class cytoscape.util.JnlpWriterUtil
getMainFrame() - Method in interface cytoscape.view.NetworkView: Deprecated. Return the frame in which the graph is displayed.
getManifestFile(boolean) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
getManifestFileName() - Method in class cytoscape.data.servers.ui.GeneOntologyWizard
getManifestFileName() - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
getManifestFileName() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
getManifestFileNameFromTextBox() - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
getManifestName() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
getMap() - Method in class cytoscape.data.annotation.Annotation
getMap() - Method in class cytoscape.visual.mappings.discrete.DiscreteMappingReader: Gets the Discrete Map.
getMapAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a 'simple' map of attribute values.
getMapAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getMapping(String) - Method in class cytoscape.data.readers.GMLNode: Return the data mapped by this key
getMapping(String) - Method in class cytoscape.visual.CalculatorCatalog
getMapping(int) - Method in class cytoscape.visual.calculators.AbstractCalculator: Get the mapping at a specific index in this calculator.
getMapping(int) - Method in interface cytoscape.visual.calculators.Calculator
getMappingNames() - Method in class cytoscape.visual.CalculatorCatalog: Returns the HashMap of mappers
getMappings() - Method in class cytoscape.visual.calculators.AbstractCalculator: Get all mappings contained by this calculator.
getMappings() - Method in interface cytoscape.visual.calculators.Calculator
getMapValue(Object) - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets Value for Specified Key.
getMax() - Method in class cytoscape.util.MinMaxDouble
getMax() - Method in class cytoscape.util.MinMaxInt
getMeasurement(String, String) - Method in class cytoscape.data.ExpressionData: Gets Single Measurement Value for the specified gene at the specified condition.
getMeasurements(String) - Method in class cytoscape.data.ExpressionData: Gets a Vector of all Measurements associated with the specified gene.
getMenu(String) - Method in class cytoscape.util.CytoscapeMenuBar
getMenu(String, int) - Method in class cytoscape.util.CytoscapeMenuBar
getMenuBar() - Method in class cytoscape.view.CyMenus: Returns the main menu bar constructed by this object.
getMessage() - Method in interface cytoscape.util.MonitoredTask: Returns a String, possibly the message to be printed on a dialog.
getMetadata() - Method in class cytoscape.data.readers.MetadataParser: Get metadata as an RDF object
getMetadataMap() - Method in class cytoscape.data.readers.MetadataParser: Get Network Metadata as Map object
getMetanodeList() - Method in class cytoscape.data.readers.XGMMLReader
getMin() - Method in class cytoscape.util.MinMaxDouble
getMin() - Method in class cytoscape.util.MinMaxInt
getMode() - Method in class cytoscape.CyMain: DOCUMENT ME!
getMode() - Method in interface cytoscape.init.CyInitParams
getMode() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the current mode.
getMRUD() - Static method in class cytoscape.CytoscapeInit
getMRUF() - Static method in class cytoscape.CytoscapeInit
getMultiHashMap() - Method in interface cytoscape.data.CyAttributes: Gets the MultiHashMap Object, where we store attribute values.
getMultiHashMap() - Method in class cytoscape.data.CyAttributesImpl
getMultiHashMapDefinition() - Method in interface cytoscape.data.CyAttributes: Gets the MultiHashMapDefinition Object, where we store attribute definitions.
getMultiHashMapDefinition() - Method in class cytoscape.data.CyAttributesImpl
getName() - Method in class cytoscape.data.annotation.OntologyTerm
getName() - Method in class cytoscape.data.ontology.Ontology: Returns name (actually, an ID).
getName() - Method in class cytoscape.data.ontology.OntologyTerm: Return name (ID) of this term.
getName() - Method in class cytoscape.data.ontology.Triple: Returns human-readable name of this triple.
getName() - Method in class cytoscape.util.CytoscapeAction
getName() - Method in class cytoscape.visual.Arrow
getName() - Method in class cytoscape.visual.LineType
getName(Interpolator) - Static method in class cytoscape.visual.mappings.InterpolatorFactory: Given an Interpolator, returns an identifying name as recognized by the newInterpolator method. null will be returned if the argument is null or of an unrecognized class type.
getName() - Method in class cytoscape.visual.VisualStyle: Returns the name of this object.
getNames() - Method in class cytoscape.data.annotation.Annotation: returns an array of all the names (usually ORFs) currently annotated
getNameSpace() - Method in class cytoscape.data.ontology.GOTerm
getNavigatorPanel() - Method in class cytoscape.view.NetworkPanel
getNetwork() - Method in class cytoscape.CyNetworkEvent
getNetwork(String) - Static method in class cytoscape.Cytoscape
getNetwork() - Method in class cytoscape.ding.DingNetworkView
getNetwork() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getNetwork() - Method in interface cytoscape.view.CyNetworkView: Returns the network displayed by this object.
getNetwork() - Method in interface cytoscape.view.NetworkView: Deprecated. Returns the network displayed by this object.
getNetwork() - Method in class cytoscape.visual.VisualMappingManager
getNetworkAliases() - Method in class cytoscape.data.servers.OntologyServer
getNetworkAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Network Attributes.
getNetworkID() - Method in class cytoscape.data.readers.XGMMLReader
getNetworkMetadata() - Method in class cytoscape.data.readers.XGMMLReader
getNetworkName() - Method in class cytoscape.data.readers.AbstractGraphReader
getNetworkName() - Method in interface cytoscape.data.readers.GraphReader: Gets the name of the network.
getNetworkName() - Method in class cytoscape.data.readers.XGMMLReader
getNetworkNode(String) - Method in class cytoscape.view.NetworkPanel
getNetworkPanel() - Method in class cytoscape.view.CytoscapeDesktop
getNetworkSet() - Static method in class cytoscape.Cytoscape: Return a List of all available CyNetworks
getNetworkView(String) - Static method in class cytoscape.Cytoscape
getNetworkView() - Method in class cytoscape.visual.VisualMappingManager
getNetworkViewManager() - Method in class cytoscape.view.CytoscapeDesktop: Gets the NetworkView Manager.
getNetworkViewMap() - Static method in class cytoscape.Cytoscape: This Map has keys that are Strings ( network_ids ) and values that are networkviews.
getNewNetworkMenu() - Method in class cytoscape.view.CyMenus: Returns the File.New.Network menu.
getNewNetworkTitle() - Method in class cytoscape.dialogs.EditNetworkTitleDialog
getNextPanelDescriptor() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
getNextPanelDescriptor() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
getNextPanelDescriptor() - Method in class cytoscape.data.servers.ui.OboPanelDescriptor
getNextPanelDescriptor() - Method in class cytoscape.data.servers.ui.SelectFormatPanelDescriptor
getNextPanelDescriptor() - Method in class cytoscape.data.servers.ui.SpeciesPanelDescriptor
getNode(String) - Method in class cytoscape.giny.CytoscapeFingRootGraph
getNode(String) - Method in interface cytoscape.giny.CytoscapeRootGraph
getNodeAliases() - Method in class cytoscape.data.servers.OntologyServer
getNodeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the NodeAppearanceCalculator for this visual style.
getNodeAttributeDoubleValue(Node, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeDoubleValue(int, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeFiles() - Method in class cytoscape.CyMain: DOCUMENT ME!
getNodeAttributeFiles() - Method in interface cytoscape.init.CyInitParams
getNodeAttributeID(String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeObjectValue(Node, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeObjectValue(int, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Node Attributes.
getNodeAttributes() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getNodeAttributes(int[]) - Static method in class cytoscape.data.NetworkData: Returns all Attributes that one or more of the given nodes have values for.
getNodeAttributes() - Method in class cytoscape.data.readers.AbstractGraphReader: Deprecated. Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006.
getNodeAttributes() - Method in interface cytoscape.data.readers.GraphReader: Deprecated. Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006.
getNodeAttributesList() - Method in class cytoscape.giny.FingCyNetwork: Return all availble Attributes for the Nodes in this CyNetwork
getNodeAttributesList(Node[]) - Method in class cytoscape.giny.FingCyNetwork: Return all available Attributes for the given Nodes
getNodeAttributesList(Edge[]) - Method in class cytoscape.giny.FingCyNetwork: Return all available Attributes for the given Edges
getNodeAttributeStringValue(Node, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeStringValue(int, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeType(String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeValue(Node, String) - Static method in class cytoscape.data.NetworkData
getNodeAttributeValue(int, int) - Static method in class cytoscape.data.NetworkData
getNodeAttributeValue(Node, String) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Node
getNodeAttributeValue(int, String) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Node
getNodeBorderColorCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeColorCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeFillColorCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeFontFaceCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeFontFaceCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeFontFaceCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeFontSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeFontSizeCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeFontSizeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeHeightCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeHeightIcon(Double) - Static method in class cytoscape.visual.ui.IconSupport
getNodeIndicesArray() - Method in class cytoscape.data.readers.AbstractGraphReader
getNodeIndicesArray() - Method in class cytoscape.data.readers.GMLReader: Part of interface contract
getNodeIndicesArray() - Method in interface cytoscape.data.readers.GraphReader: Gets an array of node indices that participate in the newly created graph.
getNodeIndicesArray() - Method in class cytoscape.data.readers.InteractionsReader
getNodeIndicesArray() - Method in class cytoscape.data.readers.XGMMLReader: Part of interace contract
getNodeLabel(String) - Method in class cytoscape.data.synonyms.Thesaurus
getNodeLabelCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeLabelCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeLabelCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeLabelColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeLabelColorCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeLabelColorCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeLineTypeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeLineTypeCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeLineTypeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
getNodeSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
getNodeShapeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeShapeCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeShapeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeShapeText(byte) - Static method in class cytoscape.visual.ShapeNodeRealizer
getNodeSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeSizeCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeSizeIcon(Double) - Static method in class cytoscape.visual.ui.IconSupport
getNodeSizeLocked() - Method in class cytoscape.visual.NodeAppearance
getNodeSizeLocked() - Method in class cytoscape.visual.NodeAppearanceCalculator
getNodeToolTipCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculator(type,name) instead. Will be removed 10/2007.
getNodeToolTipCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeToolTipCalculators() - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use getCalculators(type) instead. Will be removed 10/2007.
getNodeViewsList() - Method in class cytoscape.ding.DingNetworkView
getNodeWidthCalculator() - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getCalculator(type) instead. This method will be removed Sept 2007.
getNodeWidthIcon(Double) - Static method in class cytoscape.visual.ui.IconSupport
getNullNetwork() - Static method in class cytoscape.Cytoscape
getNullNetworkView() - Static method in class cytoscape.Cytoscape
getNumberOfConditions() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Experimental Conditions.
getNumberOfGenes() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Genes.
getObject() - Method in class cytoscape.data.ontology.DBReference
getObject() - Method in class cytoscape.data.ontology.Triple
getObjectKeys(String) - Method in interface cytoscape.data.attr.MultiHashMap: Returns all objectKeys that have at least one attribute value assigned in attributeName.
getOBOFile() - Method in class cytoscape.data.servers.ui.AnotationPanel
getOffsetX() - Method in class cytoscape.visual.LabelPosition
getOffsetY() - Method in class cytoscape.visual.LabelPosition
getOntologies() - Method in class cytoscape.data.servers.OntologyServer: Getter of the property ontologies
getOntology() - Method in class cytoscape.data.annotation.Annotation
getOntology() - Method in class cytoscape.data.annotation.readers.OntologyFlatFileReader
getOntology() - Method in class cytoscape.data.annotation.readers.OntologyXmlReader
getOntology() - Method in class cytoscape.data.ontology.OntologyTerm: Get ontology object which contains this term.
getOntology() - Method in class cytoscape.data.ontology.Triple: Returns ontology which this triple belongs to.
getOntologyAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Network Attributes.
getOntologyNames() - Method in class cytoscape.data.servers.OntologyServer
getOntologyRootID() - Static method in class cytoscape.Cytoscape
getOntologyServer() - Static method in class cytoscape.Cytoscape
getOntologySources() - Method in class cytoscape.data.servers.OntologyServer
getOntologyType() - Method in class cytoscape.data.annotation.Annotation
getOperationsMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items associated with plug-ins.
getOps() - Method in class cytoscape.data.ontology.Ontology
getOverwiteComboBox() - Method in class cytoscape.data.servers.ui.AnotationPanel
getPage(String) - Static method in class cytoscape.data.readers.TextHttpReader
getPage(URL) - Static method in class cytoscape.data.readers.TextHttpReader
getParents() - Method in class cytoscape.data.annotation.OntologyTerm
getParentsAndContainers() - Method in class cytoscape.data.annotation.OntologyTerm
getParser(Object) - Static method in class cytoscape.visual.parsers.ParserFactory
getParser(Class) - Static method in class cytoscape.visual.parsers.ParserFactory
getPluginJars() - Method in class cytoscape.util.JnlpWriterUtil
getPlugins() - Method in class cytoscape.CyMain: DOCUMENT ME!
getPlugins() - Method in interface cytoscape.init.CyInitParams
getPluginURLs() - Static method in class cytoscape.CytoscapeInit: DOCUMENT ME!
getPoint(int) - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets Specified Point.
getPointCount() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets Total Point Count.
getPoints() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingReader: Gets ArrayList of all Data Points.
getPredicate() - Method in class cytoscape.data.ontology.Triple
getPreferredButtonGroup() - Method in class cytoscape.util.CytoscapeAction: This method returns a ButtonGroup specification string.
getPreferredMenu() - Method in class cytoscape.util.CytoscapeAction: This method returns a Menu specification string.
getPrefferedIndex() - Method in class cytoscape.util.CytoscapeAction
getPrefix() - Static method in enum cytoscape.data.ontology.readers.OBOTags
getProperties() - Method in class cytoscape.CytoscapeConfig: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
getProperties() - Static method in class cytoscape.CytoscapeInit: Returns the properties used by Cytoscape, the result of cytoscape.props and command line options.
getProperties(CalculatorCatalog) - Static method in class cytoscape.visual.CalculatorIO: Given a CalculatorCatalog, assembles a Properties object representing all of the calculators contained in the catalog.
getProperties() - Method in class cytoscape.visual.calculators.AbstractCalculator: Returns a properties description of this calculator.
getProperties(String) - Method in class cytoscape.visual.calculators.AbstractCalculator: Deprecated. Just use getProperties() - baseKey is already known by the calculator. This will be removed 10/2007.
getProperties() - Method in interface cytoscape.visual.calculators.Calculator: Get a description of this calculator as a Properties object.
getProperties(String) - Method in class cytoscape.visual.EdgeAppearanceCalculator
getProperties(String) - Method in class cytoscape.visual.GlobalAppearanceCalculator: Returns a Properties description of this object, suitable for customization by the applyProperties method.
getProperties() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingWriter: Gets Newly Defined Properties Object.
getProperties(String) - Method in class cytoscape.visual.mappings.ContinuousMapping: Returns a Properties object with entries suitable for customizing this object via the applyProperties method.
getProperties() - Method in class cytoscape.visual.mappings.discrete.DiscreteMappingWriter: Return a Properties object with entries suitable for customizing this object via the applyProperties method.
getProperties(String) - Method in class cytoscape.visual.mappings.DiscreteMapping: Returns a Properties object with entries suitable for customizing this object via the applyProperties method.
getProperties(ObjectMapping, String) - Static method in class cytoscape.visual.mappings.MappingFactory: Gets a description of the supplied ObjectMapping as properties.
getProperties(String) - Method in interface cytoscape.visual.mappings.ObjectMapping
getProperties(String) - Method in class cytoscape.visual.mappings.PassThroughMapping: Return a Properties object with entries suitable for customizing this object via the applyProperties method.
getProperties(String) - Method in class cytoscape.visual.NodeAppearanceCalculator
getPropertiesLocation() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007.
getProperty(String) - Static method in class cytoscape.CytoscapeInit: Deprecated. Use getProperties().getProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
getProperty(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getProperty(String, String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getProperty(String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getProperty(String, String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getPropertyChangeSupport() - Static method in class cytoscape.Cytoscape
getPropertyLabel() - Method in interface cytoscape.visual.calculators.Calculator
getPropertyLabel(byte) - Static method in class cytoscape.visual.calculators.CalculatorFactory: Returns the property label for calculators of a given type.
getPropertyLabel() - Method in class cytoscape.visual.calculators.EdgeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeColorCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeLabelCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeFillColorCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeHeightCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeToolTipCalculator
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.GenericNodeWidthCalculator: DOCUMENT ME!
getPropertyLabel() - Method in class cytoscape.visual.calculators.NodeCalculator
getPropertyValues(Properties, String) - Static method in class cytoscape.util.Misc: return the (possibly multiple) value of the specified property as a vector.
getProps() - Method in class cytoscape.CyMain: DOCUMENT ME!
getProps() - Method in interface cytoscape.init.CyInitParams
getProxyServer() - Static method in class cytoscape.util.ProxyHandler
getPTM() - Method in class cytoscape.dialogs.preferences.PreferencesDialog
getPvalueFromLambda(double) - Static method in class cytoscape.data.ExpressionData: Gets a PValue of the specified lambda value.
getQueryURL(String) - Method in class cytoscape.data.ontology.DBReference
getRange() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Gets BoundaryRangeValues.
getRangeClass() - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets the Range Class.
getRangeClass() - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets the Range Class.
getRangeClass() - Method in interface cytoscape.visual.mappings.ObjectMapping
getRangeClass() - Method in class cytoscape.visual.mappings.PassThroughMapping
getRangeValue(Object, Object, Object, Object, Object) - Method in class cytoscape.visual.mappings.FlatInterpolator
getRangeValue(Object, Object, Object, Object, Object) - Method in interface cytoscape.visual.mappings.Interpolator
getRangeValue(double, Object, double, Object, double) - Method in class cytoscape.visual.mappings.LinearNumberInterpolator
getRangeValue(double, Object, Object) - Method in class cytoscape.visual.mappings.LinearNumberInterpolator
getRangeValue(double, Object, Object) - Method in class cytoscape.visual.mappings.LinearNumberToColorInterpolator
getRangeValue(double, Object, Object) - Method in class cytoscape.visual.mappings.LinearNumberToNumberInterpolator
getRangeValue(Object, Object, Object, Object, Object) - Method in class cytoscape.visual.mappings.NumberInterpolator
getRangeValue(double, Object, double, Object, double) - Method in class cytoscape.visual.mappings.NumberInterpolator
getRatio() - Method in class cytoscape.data.mRNAMeasurement
getReader(String) - Method in class cytoscape.data.ImportHandler: Gets the GraphReader that is capable of reading the specified file.
getReader(URL) - Method in class cytoscape.data.ImportHandler: Gets the GraphReader that is capable of reading URL.
getReader(String) - Method in class cytoscape.util.CyFileFilter: Returns the reader.
getReader(String) - Method in class cytoscape.util.GMLFileFilter: Gets GraphReader.
getReader(String) - Method in class cytoscape.util.SIFFileFilter: Gets Graph Reader.
getReader(String) - Method in class cytoscape.util.XGMMLFileFilter: Gets Graph Reader.
getResourcePlugins() - Static method in class cytoscape.CytoscapeInit: DOCUMENT ME!
getResult() - Method in class cytoscape.data.annotation.FlattenIntVectors
getRGBText(Color) - Static method in class cytoscape.util.Misc
getRoot() - Method in class cytoscape.util.swing.AbstractTreeTableModel
getRootGraph() - Method in class cytoscape.CyEdge
getRootGraph() - Method in class cytoscape.CyNode
getRootGraph() - Static method in class cytoscape.Cytoscape: Return the CytoscapeRootGraph
getRootGraph() - Method in class cytoscape.data.readers.AbstractGraphReader: Deprecated. Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006.
getRootGraph() - Method in interface cytoscape.data.readers.GraphReader: Deprecated. Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006.
getRootGraphIndex() - Method in class cytoscape.CyEdge
getRootGraphIndex() - Method in class cytoscape.CyNode
getRowCount() - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
getRowCount() - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getRowCount() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getRowCount() - Method in class cytoscape.util.swing.TreeTableModelAdapter
getSaveSubMenu() - Method in class cytoscape.view.CyMenus: Returns the submenu with items related to saving objects.
getScriptName() - Method in class cytoscape.plugin.CytoscapePlugin: If this plugin is scriptable, then this will return a unique script name, that will come after the colon like: :name
getSecondaryViewThreshold() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead.
getSelectedComponent() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the currently selected component.
getSelectedComponent() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the currently selected component.
getSelectedEdges() - Method in interface cytoscape.CyNetwork: Returns the set of selected edges in this CyNetwork
getSelectedEdges() - Method in class cytoscape.data.SelectFilter: Returns the set of all selected edges in the referenced GraphPespective.
getSelectedEdges() - Method in class cytoscape.giny.FingCyNetwork: Returns the set of selected edges in this CyNetwork
getSelectedFont() - Method in class cytoscape.visual.ui.FontChooser
getSelectedIndex() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the currently selected index.
getSelectedIndex() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the currently selected index.
getSelectedItem() - Method in class cytoscape.visual.ui.ValueDisplayer: Provided for convenience.
getSelectedNodes() - Method in interface cytoscape.CyNetwork: Returns the set of selected nodes in this CyNetwork
getSelectedNodes() - Method in class cytoscape.data.SelectFilter: Returns the set of all selected nodes in the referenced GraphPespective.
getSelectedNodes() - Method in class cytoscape.giny.FingCyNetwork: Returns the set of selected nodes in this CyNetwork
getSelectEventListeners() - Method in class cytoscape.data.SelectFilter: Gets a List of All Registered Listeners.
getSelectFilter() - Method in interface cytoscape.CyNetwork
getSelectFilter() - Method in class cytoscape.giny.FingCyNetwork
getSelectionList() - Method in class cytoscape.dialogs.GraphObjectSelection
getSelectionMode() - Static method in class cytoscape.Cytoscape: Gets the selection mode value.
getSelectMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to selecting nodes and edges in the graph.
getSessionFile() - Method in class cytoscape.CyMain: DOCUMENT ME!
getSessionFile() - Method in interface cytoscape.init.CyInitParams
getSessionstate() - Static method in class cytoscape.Cytoscape
getShape() - Method in class cytoscape.visual.NodeAppearance
getShapeByteToStringHashMap() - Static method in class cytoscape.visual.ui.IconSupport
getShapeByteToStringHashMap() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getShapeIcons() - Static method in class cytoscape.visual.ui.IconSupport
getShapeIcons() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getSignificance() - Method in class cytoscape.data.mRNAMeasurement
getSignificanceType() - Method in class cytoscape.data.ExpressionData: Gets the Significance Type.
getSize() - Method in class cytoscape.visual.NodeAppearance
getSloppySelectionColor() - Method in class cytoscape.visual.GlobalAppearance
getSource() - Method in class cytoscape.CyEdge
getSource() - Method in class cytoscape.data.FlagEvent: Deprecated. Returns the source of this event.
getSource() - Method in class cytoscape.data.Interaction
getSource() - Method in class cytoscape.data.SelectEvent: Returns the source of this event.
getSourceArrow() - Method in class cytoscape.visual.EdgeAppearance
getSpecies() - Method in class cytoscape.data.annotation.Annotation
getSpecies() - Method in class cytoscape.data.annotation.AnnotationDescription
getSpecies() - Method in class cytoscape.data.synonyms.Thesaurus
getSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
getSpeciesInNetwork(CyNetwork) - Static method in class cytoscape.data.Semantics: Returns every unique species defined in the supplied network.
getState() - Method in interface cytoscape.view.cytopanels.CytoPanel: Gets the state of the CytoPanel.
getState() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Gets the state of the CytoPanel.
getStatus() - Method in class cytoscape.dialogs.ImportAttributeMatrixDialog
getStatus() - Method in class cytoscape.dialogs.ImportNetworkDialog
getStderr() - Method in class cytoscape.util.Exec
getStderrAsString() - Method in class cytoscape.util.Exec
getStdout() - Method in class cytoscape.util.Exec
getStdoutAsString() - Method in class cytoscape.util.Exec
getString() - Method in class cytoscape.dialogs.NewStringPopupDialog
getString() - Method in class cytoscape.util.JnlpWriterUtil
getString() - Method in class cytoscape.util.MutableString
getStringAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a String value at the specified id/attributeName.
getStringAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
getStringToArrowHashMap(int) - Static method in class cytoscape.visual.ui.IconSupport: arrow dialog functions: getStringToArrowHashMap(int nodeSize) getArrowToStringHashMap(int nodeSize) getArrowIcons() Note: with the move to Giny, I'm dropping support for the scalable arrow type; we can add this back later if desired.
getStringToArrowHashMap(int) - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getStringToLineTypeHashMap() - Static method in class cytoscape.visual.ui.IconSupport: line type dialog functions: getStringToLineTypeHashMap() getLineTypeToStringHashMap() getLineTypeIcons()
getStringToLineTypeHashMap() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getStringToShapeByteHashMap() - Static method in class cytoscape.visual.ui.IconSupport: shape dialog functions: getStringToShapeByteHashMap() getShapeByteToStringHashMap() getShapeIcons()
getStringToShapeByteHashMap() - Static method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getStringValue(Object) - Static method in class cytoscape.visual.parsers.ObjectToString: Constructs and returns a String representation of the given Object.
getStroke() - Method in class cytoscape.visual.LineType
getStyleName(VisualStyle) - Method in class cytoscape.visual.ui.VizMapUI.StyleSelector
getStyleSelector() - Method in class cytoscape.visual.ui.VizMapUI
getSubject() - Method in class cytoscape.data.ontology.Triple
getSuggestedNetworkTitle(String) - Static method in class cytoscape.util.CyNetworkNaming
getSuggestedSubnetworkTitle(CyNetwork) - Static method in class cytoscape.util.CyNetworkNaming
getSwingPropertyChangeSupport() - Static method in class cytoscape.Cytoscape: Bound events are: NETWORK_CREATED NETWORK_DESTROYED CYTOSCAPE_EXIT
getSwingPropertyChangeSupport() - Method in class cytoscape.view.CytoscapeDesktop
getSwingPropertyChangeSupport() - Method in class cytoscape.view.NetworkPanel
getSwingPropertyChangeSupport() - Method in class cytoscape.view.NetworkViewManager
getSynonyms() - Method in class cytoscape.data.ontology.DBReference
getSynonyms() - Method in class cytoscape.data.ontology.OntologyTerm: Return sysnonym attributes for this term.
getSynonyms() - Method in class cytoscape.data.ontology.Triple: Synonym is not supported.
getTabbedPane() - Method in class cytoscape.view.NetworkViewManager
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellEditor
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: TreeCellRenderer method.
getTarget() - Method in class cytoscape.CyEdge
getTarget() - Method in class cytoscape.data.FlagEvent: Deprecated. Returns an object references the target that was changed.
getTarget() - Method in class cytoscape.data.SelectEvent: Returns an object reference to the target that was changed.
getTargetAnchor() - Method in class cytoscape.visual.LabelPosition
getTargetArrow() - Method in class cytoscape.visual.EdgeAppearance
getTargets() - Method in class cytoscape.data.Interaction
getTargetType() - Method in class cytoscape.data.FlagEvent: Deprecated. Returns a static constant identifying the type of object; either SINGLE_NODE for a Node, SINGLE_EDGE for an Edge, NODE_SET for a Set of Nodes, or EDGE_SET for a Set of Edges.
getTargetType() - Method in class cytoscape.data.SelectEvent: Returns a static constant identifying the type of object; either SINGLE_NODE for a Node, SINGLE_EDGE for an Edge, NODE_SET for a Set of Nodes, or EDGE_SET for a Set of Edges.
getTaskName() - Method in interface cytoscape.util.MonitoredTask: Returns a String, possibly the message that describes the task being performed.
getTaxonMap(File) - Method in class cytoscape.util.BioDataServerUtil
getTaxonMap(BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
getTerm(int) - Method in class cytoscape.data.annotation.Ontology
getTerm(String) - Method in class cytoscape.data.ontology.Ontology: Fetch the term with the specified name.
getTerms() - Method in class cytoscape.data.annotation.Ontology
getTerms() - Method in class cytoscape.data.ontology.Ontology: Return all the terms in this ontology.
getTermsAttributes() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
getTermsInNamespace(String) - Method in class cytoscape.data.ontology.GeneOntology
getText() - Method in class cytoscape.data.readers.TextFileReader
getText() - Method in class cytoscape.data.readers.TextHttpReader
getText() - Method in class cytoscape.data.readers.TextJarReader
getThesaurus() - Method in class cytoscape.data.synonyms.readers.ThesaurusFlatFileReader
getTitle() - Method in class cytoscape.actions.LoadNetworkTask: Gets the Task Title.
getTitle() - Method in interface cytoscape.CyNetwork: Can Change
getTitle() - Method in class cytoscape.ding.DingNetworkView
getTitle() - Method in class cytoscape.giny.FingCyNetwork: Can Change
getTitle() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getTitle() - Method in interface cytoscape.view.CyNetworkView: Returns the Title of this View
getTitle() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the title of the CytoPanel.
getTitle() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the proper title based on our compass direction.
getToolBar() - Method in class cytoscape.view.CyMenus: Returns the toolbar object constructed by this class.
getToolbarComboBox() - Method in class cytoscape.visual.ui.VizMapUI.StyleSelector: Retrieve copy of style selection combo box for toolbar
getToolTip() - Method in class cytoscape.visual.EdgeAppearance
getToolTip() - Method in class cytoscape.visual.NodeAppearance
getToolTipText(MouseEvent) - Method in class cytoscape.util.swing.JTreeTable: The code in this method is copy and pasted from source code to the same method in javax.swing.JTable, except for one value change on one line.
getTree() - Method in class cytoscape.util.swing.JTreeTable: Returns the tree that is being shared between the model.
getTreeTable() - Method in class cytoscape.view.NetworkPanel: This is used by Session writer.
getTriples(Term, Term, Term) - Method in class cytoscape.data.ontology.Ontology: returns set of Triples.
getType() - Method in class cytoscape.CyNetworkEvent
getType() - Method in class cytoscape.data.annotation.Annotation
getType() - Method in class cytoscape.data.annotation.AnnotationDescription
getType() - Method in class cytoscape.data.annotation.Ontology
getType() - Method in class cytoscape.data.annotation.OntologyDescription
getType(String) - Method in interface cytoscape.data.CyAttributes: Gets the data type of the specified attribute.
getType(String) - Method in class cytoscape.data.CyAttributesImpl
getType() - Method in class cytoscape.data.Interaction
getType() - Method in class cytoscape.data.ontology.GOTerm
getType(Calculator) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use calc.getType() instead. Will be removed 10/2007.
getType() - Method in interface cytoscape.visual.calculators.Calculator
getType() - Method in class cytoscape.visual.calculators.EdgeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericEdgeColorCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeLabelCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeFillColorCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeHeightCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeToolTipCalculator
getType() - Method in class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.GenericNodeWidthCalculator: DOCUMENT ME!
getType() - Method in class cytoscape.visual.calculators.NodeCalculator
getType() - Method in class cytoscape.visual.ui.ValueDisplayer: Returns the type of input this ValueDisplayer displays/gets input for
getTypeName() - Method in class cytoscape.visual.calculators.AbstractCalculator
getTypeName() - Method in interface cytoscape.visual.calculators.Calculator
getTypeName(byte) - Static method in class cytoscape.visual.calculators.CalculatorFactory: Returns the type name for calculators of a given type.
getTypeName() - Method in class cytoscape.visual.calculators.EdgeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeColorCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeLabelCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericEdgeToolTipCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeFillColorCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeFontSizeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeHeightCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeToolTipCalculator
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.GenericNodeWidthCalculator: DOCUMENT ME!
getTypeName() - Method in class cytoscape.visual.calculators.NodeCalculator
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator: Get the UI for the calculator.
getUI(JDialog, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator: Get the UI for a calculator.
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.calculators.EdgeCalculator: Get the UI for edge calculators.
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.calculators.NodeCalculator: Get the UI for node calculators.
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.mappings.ContinuousMapping: Gets the UI Object Associated with the Mapper.
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.mappings.DiscreteMapping: Gets the UI Object Associated with the Mapper.
getUI(JDialog, CyNetwork) - Method in interface cytoscape.visual.mappings.ObjectMapping
getUI(JDialog, CyNetwork) - Method in class cytoscape.visual.mappings.PassThroughMapping
getURLStr() - Method in class cytoscape.dialogs.ImportNetworkDialog
getUserEditable(String) - Method in interface cytoscape.data.CyAttributes: Returns the boolean indicating whether this attribute should be editable by the end user or not.
getUserEditable(String) - Method in class cytoscape.data.CyAttributesImpl
getUserVisible(String) - Method in interface cytoscape.data.CyAttributes: Returns the boolean indicating whether the specified attribute should be made visible to the end user or not.
getUserVisible(String) - Method in class cytoscape.data.CyAttributesImpl
getValue() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Gets Point Value.
getValue() - Method in class cytoscape.visual.ui.ValueDisplayer: Returns an object representing the user input.
getValueAt(int, int) - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
getValueAt(int, int) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
getValueAt(int, int) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
getValueAt(Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the value to be displayed for node node, at column number column.
getValueAt(int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getVector(String, String, int) - Method in class cytoscape.data.readers.GMLTree: Deprecated. use anonymous String arrays instead
getVector(String[], int) - Method in class cytoscape.data.readers.GMLTree: Return a vector of information stored in gmlNodes
getVersion() - Method in class cytoscape.CytoscapeVersion
getView() - Method in class cytoscape.ding.DingNetworkView
getView() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getView() - Method in interface cytoscape.view.CyNetworkView
getView() - Method in interface cytoscape.view.NetworkView: Deprecated.
getViewMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to data operations.
getViewThreshold() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "viewThreshold" ) instead.
getViewType() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType"));
getViewType() - Method in class cytoscape.view.CytoscapeDesktop: Return the view type for this CytoscapeDesktop
getVisibleAttributeNames(CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
getVisualMapperEnabled() - Method in class cytoscape.ding.DingNetworkView
getVisualMapperEnabled() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getVisualMapperEnabled() - Method in interface cytoscape.view.CyNetworkView
getVisualMappingManager() - Static method in class cytoscape.Cytoscape
getVisualProperties() - Static method in class cytoscape.CytoscapeInit: DOCUMENT ME!
getVisualStyle() - Method in class cytoscape.ding.DingNetworkView
getVisualStyle() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getVisualStyle() - Method in interface cytoscape.view.CyNetworkView
getVisualStyle(String) - Method in class cytoscape.visual.CalculatorCatalog
getVisualStyle() - Method in class cytoscape.visual.VisualMappingManager
getVisualStyleNames() - Method in class cytoscape.visual.CalculatorCatalog
getVisualStyles() - Method in class cytoscape.visual.CalculatorCatalog
getVizMapManager() - Method in class cytoscape.ding.DingNetworkView
getVizMapManager() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getVizMapManager() - Method in interface cytoscape.view.CyNetworkView
getVizMapManager() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated. Use Cytoscape.getVisualMappingManager() instead. This will be removed at 03/2007 (possibly sooner).
getVizMapManager() - Method in interface cytoscape.view.NetworkView: Deprecated. Returns the visual mapper associated with this display.
getVizmapPropertiesLocation() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().getProperty( "TODO" ) instead.
getVizMapUI() - Method in class cytoscape.ding.DingNetworkView
getVizMapUI() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
getVizMapUI() - Method in interface cytoscape.view.CyNetworkView
getVizMapUI() - Method in class cytoscape.view.CytoscapeDesktop: returns the top-level UI object for the visual mapper.
getVizMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to visualiation.
getVizProps() - Method in class cytoscape.CyMain: DOCUMENT ME!
getVizProps() - Method in interface cytoscape.init.CyInitParams
getWhetherToCopyExpToAttribs() - Method in class cytoscape.actions.ExpFileChooser: method for accessing last state of JCheckBox jcb
getWidth() - Method in class cytoscape.visual.NodeAppearance
getXrefMap() - Method in class cytoscape.data.ontology.readers.DBCrossReferenceReader: Get the references as a map.
GinyEdgeControlDialog - Class in cytoscape.dialogs: present a JTree with edge attributes names as top level nodes, and attribute values as child nodes; any node/s, once selected, are operated on by buttons in the bottom of the dialog box.
GinyEdgeControlDialog(CyNetworkView, HashMap, String) - Constructor for class cytoscape.dialogs.GinyEdgeControlDialog
GinyEdgeControlDialog.OKAction - Class in cytoscape.dialogs
GinyUtils - Class in cytoscape.actions: Utility operations for selection and hiding/unhiding nodes and edges in a Giny GraphView.
GinyUtils() - Constructor for class cytoscape.actions.GinyUtils
GlobalAppearance - Class in cytoscape.visual: Objects of this class hold data describing global appearance attributes of the graph window.
GlobalAppearance() - Constructor for class cytoscape.visual.GlobalAppearance
GlobalAppearanceCalculator - Class in cytoscape.visual: This class calculates global visual attributes such as the background color of the graph window.
GlobalAppearanceCalculator() - Constructor for class cytoscape.visual.GlobalAppearanceCalculator
GlobalAppearanceCalculator(GlobalAppearanceCalculator) - Constructor for class cytoscape.visual.GlobalAppearanceCalculator: Copy constructor.
GlobalAppearanceCalculator(String, Properties, String, CalculatorCatalog) - Constructor for class cytoscape.visual.GlobalAppearanceCalculator: Creates a new GlobalAppearanceCalculator and immediately customizes it by calling applyProperties with the supplied arguments.
GMLException - Exception in cytoscape.data.readers: Exception for GML Reader.
GMLException(String) - Constructor for exception cytoscape.data.readers.GMLException
GMLFileFilter - Class in cytoscape.util: FileFilter for Reading in GML Files.
GMLFileFilter() - Constructor for class cytoscape.util.GMLFileFilter: Constructor.
GMLNode - Class in cytoscape.data.readers: This class represents a GMLNode.
GMLNode(String) - Constructor for class cytoscape.data.readers.GMLNode: This constructor create a terminal GMLNode.
GMLNode() - Constructor for class cytoscape.data.readers.GMLNode: This constructor creates a non-terminal GMLNode.
GMLParser - Class in cytoscape.data.readers: The purpose of hte class is to translate gml into an object tree, and print out an object treee into GML
GMLParser(StreamTokenizer) - Constructor for class cytoscape.data.readers.GMLParser: Constructor has to initialize the relevenat regular expression patterns
GMLParser(String) - Constructor for class cytoscape.data.readers.GMLParser: Make a stream tokenizer out of the given this file and read in the file
GMLReader - Class in cytoscape.data.readers: This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1.
GMLReader(String) - Constructor for class cytoscape.data.readers.GMLReader: Constructor.
GMLReader(String, TaskMonitor) - Constructor for class cytoscape.data.readers.GMLReader: Constructor.
GMLTree - Class in cytoscape.data.readers: This class wraps around GMLNode and provides various methods for constructing a tree structure given other data.
GMLTree() - Constructor for class cytoscape.data.readers.GMLTree: Create an empty GMLTree
GMLTree(GMLNode) - Constructor for class cytoscape.data.readers.GMLTree
GMLTree(CyNetworkView) - Constructor for class cytoscape.data.readers.GMLTree: Create a GMLTree from the information contained in this GraphView.
GMLTree(String) - Constructor for class cytoscape.data.readers.GMLTree: Create a GMLTree from data contained in a file
GMLTree(String, boolean) - Constructor for class cytoscape.data.readers.GMLTree
GMLTREE - Static variable in class cytoscape.data.readers.GMLTree: When getting a vector, used to specify the type for the contained objects
GMLWriter - Class in cytoscape.data.readers: The purpse of this class is to translate cytoscape data structures into a gml object tree, we can then use the gml parser to write this tree out into a file
GMLWriter() - Constructor for class cytoscape.data.readers.GMLWriter
go(boolean) - Method in interface cytoscape.util.MonitoredTask: Initializes currentProgress (generally to zero) and then spawns a SwingWorker to start doing the work.
GO_ALIASES - Static variable in class cytoscape.data.Semantics
GO_BIOLOGICAL_PROCESS - Static variable in class cytoscape.data.annotation.OntologyMapperDialog
GO_CELLULAR_COMPONENT - Static variable in class cytoscape.data.annotation.OntologyMapperDialog
GO_COMMON_NAME - Static variable in class cytoscape.data.Semantics
GO_MOLECULAR_FUNCTION - Static variable in class cytoscape.data.annotation.OntologyMapperDialog
GOTerm - Class in cytoscape.data.ontology: A Gene Ontology term.
GOTerm(String, String, String, String) - Constructor for class cytoscape.data.ontology.GOTerm
GRAPH_NATURE - Static variable in class cytoscape.data.ImportHandler: Filter Type: NETWORK.
GRAPH_REPLACED - Static variable in class cytoscape.CyNetworkEvent: Indicates that a new graph has been installed in the network.
GRAPH_VIEW_CENTER_X - Static variable in class cytoscape.data.writers.XGMMLWriter
GRAPH_VIEW_CENTER_Y - Static variable in class cytoscape.data.writers.XGMMLWriter
GRAPH_VIEW_ZOOM - Static variable in class cytoscape.data.writers.XGMMLWriter
GraphObjectSelection - Class in cytoscape.dialogs
GraphObjectSelection() - Constructor for class cytoscape.dialogs.GraphObjectSelection
GraphObjectSelectionAction - Class in cytoscape.actions
GraphObjectSelectionAction() - Constructor for class cytoscape.actions.GraphObjectSelectionAction
graphPerspectiveChanged(GraphPerspectiveChangeEvent) - Method in class cytoscape.data.FlagFilter: Deprecated. Implementation of the GraphPerspectiveChangeListener interface.
graphPerspectiveChanged(GraphPerspectiveChangeEvent) - Method in class cytoscape.data.SelectFilter: Implementation of the GraphPerspectiveChangeListener interface.
graphPerspectiveChanged(GraphPerspectiveChangeEvent) - Method in class cytoscape.view.GraphViewController: Invoked when a graph change to any of the giny.model.GraphPerspective objects accessed through giny.view.GraphView.getGraphPerspective() of this object's graphViews is made.
GraphReader - Interface in cytoscape.data.readers: Interface for Reading in Cytoscape Graphs.
GraphSetUtils - Class in cytoscape.util: Class contains various static methods to perform set-like operations on graph.
GraphSetUtils() - Constructor for class cytoscape.util.GraphSetUtils
graphViewChanged(GraphViewChangeEvent) - Method in class cytoscape.view.CyMenus: Update the UI menus and buttons.
graphViewChanged(GraphViewChangeEvent) - Method in class cytoscape.view.FlagAndSelectionHandler: Responds to selection events from the view by setting the matching flagged state in the FlagFilter object.
GraphViewController - Class in cytoscape.view
GraphViewController() - Constructor for class cytoscape.view.GraphViewController: Empty constructor, initializes class members to empty HashMaps.
GraphViewController(GraphView[]) - Constructor for class cytoscape.view.GraphViewController: Constructor, assigns GraphViewController.DEFAULT_GRAPH_VIEW_HANDLER to all the given giny.view.GraphView objects in the array.
GraphViewController(GraphView[], Map) - Constructor for class cytoscape.view.GraphViewController: Constructor, specifies the cytoscape.view.GraphViewHandler objects for the given giny.view.GraphView objects in the arrays.
GraphViewHandler - Interface in cytoscape.view: This interface represents an object that handles a change in a giny.mode.GraphPerspective by updating one of its giny.view.GraphViews.
GREATER - Static variable in class cytoscape.visual.mappings.continuous.ContinuousUI
greaterValue - Variable in class cytoscape.visual.mappings.BoundaryRangeValues
gridbag - Variable in class cytoscape.dialogs.GridBagGroup
GridBagGroup - Class in cytoscape.dialogs
GridBagGroup() - Constructor for class cytoscape.dialogs.GridBagGroup
GridBagGroup(JPanel) - Constructor for class cytoscape.dialogs.GridBagGroup
GridBagGroup(String) - Constructor for class cytoscape.dialogs.GridBagGroup
GUI - Static variable in interface cytoscape.init.CyInitParams

H

halt() - Method in class cytoscape.actions.LoadNetworkTask: Halts the Task: Not Currently Implemented.
handleGraphPerspectiveEvent(GraphPerspectiveChangeEvent, GraphView) - Method in class cytoscape.view.BasicGraphViewHandler: Handles the event as desired by updating the given giny.view.GraphView.
handleGraphPerspectiveEvent(GraphPerspectiveChangeEvent, GraphView) - Method in interface cytoscape.view.GraphViewHandler: Handles the event as desired by updating the given giny.view.GraphView.
hasAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Determines if the specified id/attributeName pair exists.
hasAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
hashCode() - Method in class cytoscape.data.annotation.AnnotationDescription: redefine hashCode so that instances with the same contents have the same hashCode. this will make them identical when used as the keys in HashMaps, the purpose for which they were invented.
hasSignificanceValues() - Method in class cytoscape.data.ExpressionData: Indicates whether the expression data has significance values.
HelpAboutAction - Class in cytoscape.actions
HelpAboutAction() - Constructor for class cytoscape.actions.HelpAboutAction
HelpContactHelpDeskAction - Class in cytoscape.actions
HelpContactHelpDeskAction() - Constructor for class cytoscape.actions.HelpContactHelpDeskAction
HEXAGON - Static variable in class cytoscape.visual.ShapeNodeRealizer
HIDE - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Hide state of a CytoPanel.
hideAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
HideSelectedAction - Class in cytoscape.actions
HideSelectedAction() - Constructor for class cytoscape.actions.HideSelectedAction
HideSelectedAction(boolean) - Constructor for class cytoscape.actions.HideSelectedAction
hideSelectedEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
HideSelectedEdgesAction - Class in cytoscape.actions
HideSelectedEdgesAction() - Constructor for class cytoscape.actions.HideSelectedEdgesAction
hideSelectedNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
HideSelectedNodesAction - Class in cytoscape.actions
HideSelectedNodesAction() - Constructor for class cytoscape.actions.HideSelectedNodesAction
HideSelectedNodesAction(boolean) - Constructor for class cytoscape.actions.HideSelectedNodesAction
hideSplash() - Static method in class cytoscape.util.shadegrown.WindowUtilities

I

IconPopupButton - Class in cytoscape.dialogs
IconPopupButton(String, String, HashMap, HashMap, ImageIcon[], Object, JDialog) - Constructor for class cytoscape.dialogs.IconPopupButton
IconPopupButton.ApplyIconAction - Class in cytoscape.dialogs
IconPopupButton.ApplyIconAction() - Constructor for class cytoscape.dialogs.IconPopupButton.ApplyIconAction
IconPopupButton.CancelIconAction - Class in cytoscape.dialogs
IconSupport - Class in cytoscape.visual.ui: This used to be the MiscDialog class, but that was so poorly named, I had to change it.
IconSupport() - Constructor for class cytoscape.visual.ui.IconSupport
IconSupport(Object) - Constructor for class cytoscape.visual.ui.IconSupport
IconSupport(Object, byte) - Constructor for class cytoscape.visual.ui.IconSupport
ID - Static variable in class cytoscape.visual.calculators.AbstractCalculator: String literal used to refer to the generic "ID" attribute.
IDENTIFIER - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
IDENTIFIER - Static variable in class cytoscape.data.servers.ui.AnotationPanelDescriptor
IDENTIFIER - Static variable in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
IDENTIFIER - Static variable in class cytoscape.data.servers.ui.OboPanelDescriptor
IDENTIFIER - Static variable in class cytoscape.data.servers.ui.SelectFormatPanelDescriptor
IDENTIFIER - Static variable in class cytoscape.data.servers.ui.SpeciesPanelDescriptor
ImportAttributeMatrixDialog - Class in cytoscape.dialogs: This class prompts the user for data for entry of the attribute matrix, which includes expression data as a use case.
ImportAttributeMatrixDialog(Frame, boolean) - Constructor for class cytoscape.dialogs.ImportAttributeMatrixDialog: Creates new form AttributeMatrixImportDialog
ImportBioDataServerAction - Class in cytoscape.actions: Action allows the loading of a BioDataServer from the gui.
ImportBioDataServerAction() - Constructor for class cytoscape.actions.ImportBioDataServerAction
ImportEdgeAttributesAction - Class in cytoscape.actions
ImportEdgeAttributesAction() - Constructor for class cytoscape.actions.ImportEdgeAttributesAction: Constructor.
ImportExpressionMatrixAction - Class in cytoscape.actions: User has requested loading of an Expression Matrix File.
ImportExpressionMatrixAction() - Constructor for class cytoscape.actions.ImportExpressionMatrixAction: Constructor.
ImportGraphFileAction - Class in cytoscape.actions: Imports a graph of arbitrary type.
ImportGraphFileAction(CyMenus) - Constructor for class cytoscape.actions.ImportGraphFileAction: Constructor.
ImportGraphFileAction(CyMenus, boolean) - Constructor for class cytoscape.actions.ImportGraphFileAction: Constructor.
ImportHandler - Class in cytoscape.data: Central registry for all Cytoscape import classes.
ImportHandler() - Constructor for class cytoscape.data.ImportHandler: Constructor.
ImportNetworkDialog - Class in cytoscape.dialogs
ImportNetworkDialog(Frame, boolean) - Constructor for class cytoscape.dialogs.ImportNetworkDialog: Creates new form NetworkImportDialog
ImportNodeAttributesAction - Class in cytoscape.actions
ImportNodeAttributesAction() - Constructor for class cytoscape.actions.ImportNodeAttributesAction: Constructor.
importTerm(Term, String) - Method in class cytoscape.data.ontology.Ontology
ImportVizmapAction - Class in cytoscape.actions
ImportVizmapAction() - Constructor for class cytoscape.actions.ImportVizmapAction
includeAttribute(CyAttributes, String, String) - Method in interface cytoscape.data.AttributeFilter: Return true iff a given attribute should be included in some operation, such as CyAttributesUtils.copyAttributes().
incrementProgress() - Method in interface cytoscape.util.MonitoredTask: Increments the progress by one
IndeterminateProgressBar - Class in cytoscape.util: This class creates a dialog with a JProgressBar in indeterminate state.
IndeterminateProgressBar(String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with no owner, the given title and label.
IndeterminateProgressBar(Dialog, String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with the specified owner dialog, title and label.
IndeterminateProgressBar(Frame, String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with the specified owner frame, title and label.
indexOfComponent(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the index for the specified component.
indexOfComponent(String) - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the first Component index with given title.
indexOfComponent(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the index for the specified component.
indexOfComponent(String) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the first Component index with given title.
init(CyInitParams) - Method in class cytoscape.CytoscapeInit: Cytoscape Init must be initialized using the command line arguments.
initCytoPanelMenus() - Method in class cytoscape.view.CyMenus
initializeMenus() - Method in class cytoscape.view.CyMenus: This method should be called by the creator of this object after the constructor has finished.
INSANE_ATTRIBUTE_ID - Static variable in class cytoscape.data.NetworkData
INSANE_ATTRIBUTE_TYPE - Static variable in class cytoscape.data.NetworkData
insert(JPanel, Component, GridBagLayout, GridBagConstraints) - Static method in class cytoscape.dialogs.MiscGB
insert(GridBagGroup, Component, int, int) - Static method in class cytoscape.dialogs.MiscGB
insert(GridBagGroup, Component, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
insert(GridBagGroup, Component, int, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
insert(GridBagGroup, Component, int, int, int, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
insertCytoPanel(CytoPanelImp, int) - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Inserts CytoPanel at desired compass direction.
insertCytoPanel(CytoPanelImp, int) - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Inserts CytoPanel at Specified Compass Direction.
inset(GridBagConstraints, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
inset(GridBagConstraints, int) - Static method in class cytoscape.dialogs.MiscGB
instantiateDataModel() - Static method in class cytoscape.data.attr.util.MultiHashMapFactory: The return object implements both cytoscape.data.attr.MultiHashMapDefinition and cytoscape.data.attr.MultiHashMap.
INT - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for an int
INTEGER - Static variable in class cytoscape.data.readers.GMLTree: When getting a vector, used to specify the type for the contained objects
IntegerEntryField - Class in cytoscape.dialogs
IntegerEntryField(String, int, int) - Constructor for class cytoscape.dialogs.IntegerEntryField
IntegerEntryField.PositiveIntegerListener - Class in cytoscape.dialogs
IntegerEntryField.PositiveIntegerListener(int, int) - Constructor for class cytoscape.dialogs.IntegerEntryField.PositiveIntegerListener
integerValue() - Method in class cytoscape.data.readers.GMLNode: Get the value of this node as an Integer
Interaction - Class in cytoscape.data
Interaction(String, String, String) - Constructor for class cytoscape.data.Interaction
Interaction(String) - Constructor for class cytoscape.data.Interaction
Interaction(String, String) - Constructor for class cytoscape.data.Interaction
INTERACTION - Static variable in class cytoscape.data.Semantics
InteractionsReader - Class in cytoscape.data.readers: Reader for graphs in the interactions file format.
InteractionsReader(BioDataServer, String, String) - Constructor for class cytoscape.data.readers.InteractionsReader: Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.
InteractionsReader(BioDataServer, String, String, TaskMonitor) - Constructor for class cytoscape.data.readers.InteractionsReader: Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.
InteractionsReader(BioDataServer, String, String, boolean) - Constructor for class cytoscape.data.readers.InteractionsReader: Deprecated. Will be removed 12/2006. BioDataServer and species are no longer needed or used.
InteractionsReader(String, TaskMonitor, boolean) - Constructor for class cytoscape.data.readers.InteractionsReader: Creates an interaction reader based on a string consisting of data that has been read from a zip file.
InteractionsReader(String) - Constructor for class cytoscape.data.readers.InteractionsReader: Creates an interaction reader based on the string file name.
InteractionsReader(String, TaskMonitor) - Constructor for class cytoscape.data.readers.InteractionsReader: Creates an interaction reader based on the string file name.
InteractionWriter - Class in cytoscape.data.writers: A few utility methods to assist in writing SIF files.
InteractionWriter() - Constructor for class cytoscape.data.writers.InteractionWriter
INTERNAL_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in JInternalFrames, using the mock desktop interface. ( like MS Office )
internalFrameActivated(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager: For Internal Frames
internalFrameClosed(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
internalFrameClosing(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
InternalFrameComponent - Class in cytoscape.view: This class manages the JLayeredPane that resides in each internal frame of cytoscape.
InternalFrameComponent(JLayeredPane, DGraphView) - Constructor for class cytoscape.view.InternalFrameComponent: Constructor.
internalFrameDeactivated(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
internalFrameDeiconified(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
internalFrameIconified(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
internalFrameOpened(InternalFrameEvent) - Method in class cytoscape.view.NetworkViewManager
Interpolator - Interface in cytoscape.visual.mappings: This interface defines an interpolation function that takes two pairs of (domain,range) values plus a target domain value, and calculates an associated range value via some kind of interpolation.
InterpolatorFactory - Class in cytoscape.visual.mappings: Provides static factory methods for constructing known interpolators from a recognized name, for example from a properties object.
InterpolatorFactory() - Constructor for class cytoscape.visual.mappings.InterpolatorFactory
interpretScript(String[], CyNetwork) - Method in class cytoscape.plugin.CytoscapePlugin: Take a CyNetwork as input along with some arguments, and return a CyNetwork, which can be the same, or different, it doesn't really matter, and is up to the individual plugin.
interrupt() - Method in class cytoscape.util.SwingWorker: A new method that interrupts the worker thread.
invertSelectedEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
InvertSelectedEdgesAction - Class in cytoscape.actions
InvertSelectedEdgesAction() - Constructor for class cytoscape.actions.InvertSelectedEdgesAction
invertSelectedNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
InvertSelectedNodesAction - Class in cytoscape.actions
InvertSelectedNodesAction() - Constructor for class cytoscape.actions.InvertSelectedNodesAction
IS_ONTOLOGY - Static variable in class cytoscape.data.ontology.Ontology
isAccelerated() - Method in class cytoscape.util.CytoscapeAction
isAncestorOf(Ontology, OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isCellEditable(int, int) - Method in class cytoscape.dialogs.NetworkMetaDataTableModel: Determine which cell is editible or not.
isCellEditable(EventObject) - Method in class cytoscape.util.swing.AbstractCellEditor
isCellEditable(Object, int) - Method in class cytoscape.util.swing.AbstractTreeTableModel: By default, make the column with the Tree in it the only editable one.
isCellEditable(EventObject) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellEditor: Overridden to return false, and if the event is a mouse event it is forwarded to the tree.
isCellEditable(Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Indicates whether the the value for node node, at column number column is editable.
isCellEditable(int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
isChildOf(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isChildOfOrContainedIn(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isContainedIn(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isContainerOf(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isDirected() - Method in class cytoscape.CyEdge
isExtensionListInDescription() - Method in class cytoscape.util.CyFileFilter: Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFilesSelected() - Method in class cytoscape.data.servers.ui.AnotationPanel
isFlagged(Node) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.isSelected(Node)
isFlagged(Edge) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.isSelected(Edge)
isFlagged(Node) - Method in class cytoscape.data.FlagFilter: Deprecated. Returns true if the argument is a flagged Node in the referenced GraphPerspective, false otherwise.
isFlagged(Edge) - Method in class cytoscape.data.FlagFilter: Deprecated. Returns true if the argument is a flagged Edge in the referenced GraphPerspective, false otherwise.
isFlagged(Node) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.isSelected(Node)
isFlagged(Edge) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.isSelected(Edge)
isFlip() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor
isHeadless() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getMode() instead.
isInBookmarks(Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
isInBookmarks(URL, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
isInMenuBar() - Method in class cytoscape.util.CytoscapeAction: By default all CytoscapeActions wish to be included in CommunityMenuBars, but you may override if you wish.
isInToolBar() - Method in class cytoscape.util.CytoscapeAction: By default no CytoscapeActions wish to be included in CommunityToolBars, but you may override if you wish.
isLeaf(Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
isList(String, String, String, String) - Static method in class cytoscape.util.Misc: determine whether a string encodes a list
isModified(CyNetwork) - Static method in class cytoscape.CytoscapeModifiedNetworkManager
isParentOf(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isParentOrContainerOf(OntologyTerm) - Method in class cytoscape.data.annotation.OntologyTerm
isReidentificationEnabled() - Method in class cytoscape.util.CytoscapeMenuBar
isRemote() - Method in class cytoscape.dialogs.ImportNetworkDialog
isScriptable() - Method in class cytoscape.plugin.CytoscapePlugin: If true, this plugin is capable if accepting scripts, and we will find out what its script name is
isSelected(Node) - Method in interface cytoscape.CyNetwork: Returns the selected state of the given node.
isSelected(Edge) - Method in interface cytoscape.CyNetwork: Returns the selected state of the given edge.
isSelected(Node) - Method in class cytoscape.data.SelectFilter: Returns true if the argument is a selected Node in the referenced GraphPerspective, false otherwise.
isSelected(Edge) - Method in class cytoscape.data.SelectFilter: Returns true if the argument is a selected Edge in the referenced GraphPerspective, false otherwise.
isSelected(Node) - Method in class cytoscape.giny.FingCyNetwork: Returns the selected state of the given node.
isSelected(Edge) - Method in class cytoscape.giny.FingCyNetwork: Returns the selected state of the given edge.
isValidShape(byte) - Static method in class cytoscape.visual.parsers.NodeShapeParser
isValidShape(byte) - Method in class cytoscape.visual.ShapeNodeRealizer
isWindows() - Method in class cytoscape.view.cytopanels.CytoPanelUtil: Determines if we are running on Windows platform.
itemStateChanged(ItemEvent) - Method in class cytoscape.dialogs.JointIntegerEntry.LockedItemListener
itemStateChanged(ItemEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog
itemStateChanged(ItemEvent) - Method in class cytoscape.dialogs.preferences.ProxyServerDialog
itemStateChanged(ItemEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog
itemStateChanged(ItemEvent) - Method in class cytoscape.visual.mappings.continuous.ValueListener: Item State Change.
itemStateChanged(ItemEvent) - Method in class cytoscape.visual.mappings.discrete.ValueChangeListener: The ValueDisplayer being reflected by this listener was changed.

J

JnlpWriterUtil - Class in cytoscape.util
JnlpWriterUtil(String[]) - Constructor for class cytoscape.util.JnlpWriterUtil
JointIntegerEntry - Class in cytoscape.dialogs
JointIntegerEntry(String, String, String, int, int, int, int) - Constructor for class cytoscape.dialogs.JointIntegerEntry
JointIntegerEntry.CopyField1To2Listener - Class in cytoscape.dialogs
JointIntegerEntry.CopyField1To2Listener() - Constructor for class cytoscape.dialogs.JointIntegerEntry.CopyField1To2Listener
JointIntegerEntry.LockedItemListener - Class in cytoscape.dialogs
JointIntegerEntry.LockedItemListener() - Constructor for class cytoscape.dialogs.JointIntegerEntry.LockedItemListener
JStatusBar - Class in cytoscape.util.swing: Simple status bar with 3 fields.
JStatusBar() - Constructor for class cytoscape.util.swing.JStatusBar
JTreeTable - Class in cytoscape.util.swing: This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the JTable.
JTreeTable(TreeTableModel) - Constructor for class cytoscape.util.swing.JTreeTable
JTreeTable.TreeTableCellEditor - Class in cytoscape.util.swing: TreeTableCellEditor implementation.
JTreeTable.TreeTableCellEditor() - Constructor for class cytoscape.util.swing.JTreeTable.TreeTableCellEditor
JTreeTable.TreeTableCellRenderer - Class in cytoscape.util.swing: A TreeCellRenderer that displays a JTree.
JTreeTable.TreeTableCellRenderer(TreeModel) - Constructor for class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer
justifyCenterName - Static variable in class cytoscape.visual.LabelPosition
justifyLeftName - Static variable in class cytoscape.visual.LabelPosition
justifyRightName - Static variable in class cytoscape.visual.LabelPosition

K

key - Variable in class cytoscape.data.readers.KeyValue
KeyValue - Class in cytoscape.data.readers
KeyValue(String, Object) - Constructor for class cytoscape.data.readers.KeyValue

L

LABEL - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
LABEL_POSITION - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for label position
LabelPosition - Class in cytoscape.visual
LabelPosition() - Constructor for class cytoscape.visual.LabelPosition
LabelPosition(LabelPosition) - Constructor for class cytoscape.visual.LabelPosition
LabelPosition(int, int, int, double, double) - Constructor for class cytoscape.visual.LabelPosition
LabelPositionParser - Class in cytoscape.visual.parsers: Parses a String into a LabelPosition object.
LabelPositionParser() - Constructor for class cytoscape.visual.parsers.LabelPositionParser
LabelTextPanel - Class in cytoscape.dialogs
LabelTextPanel(CyAttributes, MutableString) - Constructor for class cytoscape.dialogs.LabelTextPanel
LabelTextPanel.BoxAction - Class in cytoscape.dialogs
LabelTextPanel.BoxAction() - Constructor for class cytoscape.dialogs.LabelTextPanel.BoxAction
LAMBDA - Static variable in class cytoscape.data.ExpressionData: Significance value: LAMBA.
layout(GraphView) - Method in class cytoscape.data.readers.AbstractGraphReader
layout(GraphView) - Method in class cytoscape.data.readers.GMLReader
layout(GraphView) - Method in interface cytoscape.data.readers.GraphReader: Lays out the graph.
layout(GraphView) - Method in class cytoscape.data.readers.InteractionsReader
layout(GraphView) - Method in class cytoscape.data.readers.XGMMLReader: Based on the graphic attributes, layout the graph.
LayoutAlgorithm - Interface in cytoscape.layout
LegendDialog - Class in cytoscape.visual.ui
LegendDialog(Dialog, VisualStyle) - Constructor for class cytoscape.visual.ui.LegendDialog
LegendTable - Class in cytoscape.visual.mappings
LegendTable(Object[][], byte) - Constructor for class cytoscape.visual.mappings.LegendTable
LESSER - Static variable in class cytoscape.visual.mappings.continuous.ContinuousUI
lesserValue - Variable in class cytoscape.visual.mappings.BoundaryRangeValues
LibDir - Variable in class cytoscape.util.JnlpWriterUtil
LIBRARY - Static variable in interface cytoscape.init.CyInitParams
LINE_1 - Static variable in class cytoscape.visual.LineType
LINE_2 - Static variable in class cytoscape.visual.LineType
LINE_3 - Static variable in class cytoscape.visual.LineType
LINE_4 - Static variable in class cytoscape.visual.LineType
LINE_5 - Static variable in class cytoscape.visual.LineType
LINE_6 - Static variable in class cytoscape.visual.LineType
LINE_7 - Static variable in class cytoscape.visual.LineType
LinearNumberInterpolator - Class in cytoscape.visual.mappings: This subclass of NumberInterpolator further assumes a linear interpolation, and calculates the fractional distance of the target domain value from the lower boundary value for the convenience of subclasses.
LinearNumberInterpolator() - Constructor for class cytoscape.visual.mappings.LinearNumberInterpolator
LinearNumberToColorInterpolator - Class in cytoscape.visual.mappings: The class provides a linear interpolation between color values.
LinearNumberToColorInterpolator() - Constructor for class cytoscape.visual.mappings.LinearNumberToColorInterpolator
LinearNumberToNumberInterpolator - Class in cytoscape.visual.mappings: The class assumes that the supplied range objects are Numbers, and returns a linearly interplated value according to the value of frac.
LinearNumberToNumberInterpolator() - Constructor for class cytoscape.visual.mappings.LinearNumberToNumberInterpolator
LineType - Class in cytoscape.visual: This class is a replacement for the yFiles LineType class.
LineType(String) - Constructor for class cytoscape.visual.LineType
LINETYPE - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for a linetype
LineTypeParser - Class in cytoscape.visual.parsers: Parses a String into a yFiles LineType object.
LineTypeParser() - Constructor for class cytoscape.visual.parsers.LineTypeParser
ListFromFileSelectionAction - Class in cytoscape.actions
ListFromFileSelectionAction() - Constructor for class cytoscape.actions.ListFromFileSelectionAction
load() - Method in class cytoscape.data.ontology.DBCrossReferences
LOAD - Static variable in class cytoscape.util.FileUtil
loadAnnotation - Class in cytoscape.data.servers: load an annotation into an rmi biodata server.
loadAnnotation() - Constructor for class cytoscape.data.servers.loadAnnotation
loadAnnotationFiles(String[], String[]) - Method in class cytoscape.data.servers.BioDataServer
loadAnnotationFromFlatFiles - Class in cytoscape.data.servers: load an annotation into an rmi biodata server.
loadAnnotationFromFlatFiles() - Constructor for class cytoscape.data.servers.loadAnnotationFromFlatFiles
loadAttributes(String[], String[], boolean, BioDataServer, String) - Static method in class cytoscape.Cytoscape: Deprecated. Use loadAttributes(nodeAttrLocations,edgeAttrLocations) instead. BioDataServer, canonicalize, and species are no longer used. Will be removed 10/2007.
loadAttributes(String[], String[]) - Static method in class cytoscape.Cytoscape: Loads Node and Edge attribute data into Cytoscape from the given file locations.
loadAttributes(CyAttributes, Reader) - Static method in class cytoscape.data.readers.CyAttributesReader
loadBioDataServer(String) - Static method in class cytoscape.Cytoscape: A BioDataServer should be loadable from a file systems file or from a URL.
loadCalculatorCatalog() - Static method in class cytoscape.visual.CalculatorCatalogFactory
loadCalculatorCatalog(String) - Static method in class cytoscape.visual.CalculatorCatalogFactory: Deprecated. The vmName parameter is no longer used - just use loadCalculatorCatalog(). Will be removed 10/06.
loadCalculatorCatalog() - Method in class cytoscape.visual.VisualMappingManager: Attempts to load a CalculatorCatalog object, using the information from the CytoscapeConfig object.
loadCalculatorCatalog(String) - Method in class cytoscape.visual.VisualMappingManager
loadCalculators(Properties, CalculatorCatalog) - Static method in class cytoscape.visual.CalculatorIO: Equivalent to loadCalculators(props, catalog, true);
loadCalculators(Properties, CalculatorCatalog, boolean) - Static method in class cytoscape.visual.CalculatorIO: Loads calculators from their description in a Properties object into a supplied CalculatorCatalog object.
loadCalculators(Properties, CalculatorCatalog) - Static method in class cytoscape.visual.OldStyleCalculatorIO: Deprecated. Use CalculatorIO instead. Will be removed 10/2007
loadData(String, String) - Method in class cytoscape.data.ExpressionData: Loads the Specified File into memory.
loaded - Static variable in class cytoscape.visual.OldStyleCalculatorIO: Deprecated.
loadExpressionData(String, boolean) - Static method in class cytoscape.Cytoscape: Load Expression Data
loadFile(File, boolean) - Static method in class cytoscape.actions.LoadNetworkTask
LoadNetworkTask - Class in cytoscape.actions: Task to load a new network.
loadObo(String[], String[]) - Method in class cytoscape.data.servers.BioDataServer
loadPlugin(Class) - Method in class cytoscape.CytoscapeInit: DOCUMENT ME!
loadPlugin(Class) - Static method in class cytoscape.plugin.CytoscapePlugin: Attempts to instantiate a plugin of the class argument.
loadProperties() - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
loadProperties() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
loadThesaurus - Class in cytoscape.data.servers: load an thesaurus into an rmi biodata server.
loadThesaurus() - Constructor for class cytoscape.data.servers.loadThesaurus
loadThesaurusFiles(String[]) - Method in class cytoscape.data.servers.BioDataServer
loadThesaurusFiles2(String[]) - Method in class cytoscape.data.servers.BioDataServer
loadURL(URL, boolean) - Static method in class cytoscape.actions.LoadNetworkTask
lockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
lockNodes(NodeView[]) - Method in interface cytoscape.layout.LayoutAlgorithm
LOWER - Static variable in class cytoscape.visual.mappings.FlatInterpolator

M

MacAppConfig - Class in cytoscape.util: Configures the Mac OS X Info.plist file associated with Cytoscape.
MacAppConfig() - Constructor for class cytoscape.util.MacAppConfig
main(String[]) - Static method in class cytoscape.CyMain: DOCUMENT ME!
main(String[]) - Static method in class cytoscape.data.readers.GMLParser: A short test of the regeular expressio patterns
main(String[]) - Static method in class cytoscape.data.readers.TextFileReader
main(String[]) - Static method in class cytoscape.data.servers.BioDataServerRmi
main(String[]) - Static method in class cytoscape.data.servers.clear
main(String[]) - Static method in class cytoscape.data.servers.getCanonicalName
main(String[]) - Static method in class cytoscape.data.servers.getCommonName
main(String[]) - Static method in class cytoscape.data.servers.loadAnnotation
main(String[]) - Static method in class cytoscape.data.servers.loadAnnotationFromFlatFiles
main(String[]) - Static method in class cytoscape.data.servers.loadThesaurus
main(String[]) - Static method in class cytoscape.data.servers.status
main(String[]) - Static method in class cytoscape.dialogs.preferences.BookmarkDialog
main(String[]) - Static method in class cytoscape.dialogs.URLimportAdvancedDialog
main(String[]) - Static method in class cytoscape.util.JnlpWriterUtil
main(String[]) - Static method in class cytoscape.util.MacAppConfig: Main Method.
main(String[]) - Static method in class cytoscape.util.Transform
makeNewMetadataMap() - Method in class cytoscape.data.readers.MetadataParser: Build new metadata RDF structure based on given network information.
makeShrinkExpandGraphUI(CyMenus) - Static method in class cytoscape.dialogs.ShrinkExpandGraphUI
ManifestfileSelectionPanel - Class in cytoscape.data.servers.ui
ManifestfileSelectionPanel() - Constructor for class cytoscape.data.servers.ui.ManifestfileSelectionPanel
ManifestFileSelectionPanelDescriptor - Class in cytoscape.data.servers.ui
ManifestFileSelectionPanelDescriptor() - Constructor for class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor
MapOntologyAction - Class in cytoscape.actions
MapOntologyAction() - Constructor for class cytoscape.actions.MapOntologyAction
MapOntologyAction(boolean, ImageIcon) - Constructor for class cytoscape.actions.MapOntologyAction
MapperAndAttribute - Class in cytoscape.visual.ui
MapperAndAttribute() - Constructor for class cytoscape.visual.ui.MapperAndAttribute
MapperAndAttribute(Object, MutableString) - Constructor for class cytoscape.visual.ui.MapperAndAttribute
MappingFactory - Class in cytoscape.visual.mappings: This class provides a static factory method for constructing an instance of ObjectMapping as specified by a Properties object and other arguments.
MappingFactory() - Constructor for class cytoscape.visual.mappings.MappingFactory
MappingUtil - Class in cytoscape.visual.mappings: Provides simple utility methods for the Mapping classes.
MappingUtil() - Constructor for class cytoscape.visual.mappings.MappingUtil
MAX_LINE_SIZE - Static variable in class cytoscape.data.ExpressionData
maxDepth() - Method in class cytoscape.data.annotation.Annotation: get all of the full paths (as ints) from the ontology for all of the currently annotated entities. then traverse this (possibly large) list and return the longest path.
MENU_LABEL - Static variable in class cytoscape.actions.ExportAction
MENU_LABEL - Static variable in class cytoscape.actions.ExportAsGraphicsAction
MENU_LABEL - Static variable in class cytoscape.actions.PrintAction
MetadataEntries - Enum in cytoscape.data.readers: Entries in the network metadata.
MetadataParser - Class in cytoscape.data.readers: Manipulates network metadata for loading and saving.
MetadataParser(CyNetwork) - Constructor for class cytoscape.data.readers.MetadataParser: Constructor.
MetadataParser(CyNetwork, String) - Constructor for class cytoscape.data.readers.MetadataParser: Constructor.
MinMaxDouble - Class in cytoscape.util: find the min and max of a 1- or 2-d aarray of doubles.
MinMaxDouble(double[]) - Constructor for class cytoscape.util.MinMaxDouble
MinMaxDouble(double[][]) - Constructor for class cytoscape.util.MinMaxDouble
MinMaxInt - Class in cytoscape.util: find the min and max of a 1- or 2-d array of ints.
MinMaxInt(int[]) - Constructor for class cytoscape.util.MinMaxInt
MinMaxInt(int[][]) - Constructor for class cytoscape.util.MinMaxInt
Misc - Class in cytoscape.util
Misc() - Constructor for class cytoscape.util.Misc
MiscDialog - Class in cytoscape.visual.ui: Deprecated. This class has been enhanced and renamed to IconSupport. This will be removed 10/2007.
MiscDialog() - Constructor for class cytoscape.visual.ui.MiscDialog: Deprecated.
MiscGB - Class in cytoscape.dialogs: We DO need to replace this with swing-layout!
MiscGB() - Constructor for class cytoscape.dialogs.MiscGB
MODE_HIDE_SPLIT - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane
MODE_PROPERTY - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane: Property listener modes.
MODE_SHOW_SPLIT - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane: Available modes of the BiModalJSplitPane.
MODIFIED - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
MOLECULAR_FUNCTION - Static variable in class cytoscape.data.Semantics
MOLECULE_TYPE - Static variable in class cytoscape.data.Semantics
MonitoredTask - Interface in cytoscape.util
mRNAMeasurement - Class in cytoscape.data
mRNAMeasurement(String, String) - Constructor for class cytoscape.data.mRNAMeasurement
MultiHashMap - Interface in cytoscape.data.attr: This interface consists of the API specification to bind attribute values to objects.
MultiHashMapDefinition - Interface in cytoscape.data.attr: This interface contains the API specification for creating attribute definitions.
MultiHashMapDefinitionListener - Interface in cytoscape.data.attr: A hook to receive notification when attribute definitions are created and destroyed.
MultiHashMapFactory - Class in cytoscape.data.attr.util: This class provides access to implementations of MultiHashMap and MultiHashMapDefinition.
MultiHashMapHelpers - Class in cytoscape.data.attr.util: This class contains static utilitarian methods that return information pertaining to attributes.
MultiHashMapListener - Interface in cytoscape.data.attr: A hook to receive notification when attribute values are set and removed from objects.
MutableBool - Class in cytoscape.util
MutableBool(boolean) - Constructor for class cytoscape.util.MutableBool
MutableColor - Class in cytoscape.util: Deprecated. No one uses this, so don't start. Just use Color directly. This will be removed 12/2006.
MutableColor(Color) - Constructor for class cytoscape.util.MutableColor: Deprecated.
MutableInt - Class in cytoscape.util
MutableInt(int) - Constructor for class cytoscape.util.MutableInt
MutableString - Class in cytoscape.util
MutableString(String) - Constructor for class cytoscape.util.MutableString

N

NETWORK_CREATED - Static variable in class cytoscape.Cytoscape
NETWORK_DESTROYED - Static variable in class cytoscape.Cytoscape
NETWORK_LOADED - Static variable in class cytoscape.Cytoscape
NETWORK_MODIFIED - Static variable in class cytoscape.Cytoscape
NETWORK_SAVED - Static variable in class cytoscape.Cytoscape
NETWORK_VIEW_CREATED - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_DESTROYED - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_FOCUS - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_FOCUSED - Static variable in class cytoscape.view.CytoscapeDesktop
NetworkData - Class in cytoscape.data: There is an event fired anytime that a value is modified, you need to be listener to the attribute name though.
NetworkData() - Constructor for class cytoscape.data.NetworkData
NetworkMetaDataDialog - Class in cytoscape.dialogs: Dialog for editing network metadata in RDF.
NetworkMetaDataDialog(Frame, boolean, CyNetwork) - Constructor for class cytoscape.dialogs.NetworkMetaDataDialog: Creates new form MetadataDialog
NetworkMetaDataTableModel - Class in cytoscape.dialogs: Table model for the Network Metadata Dialog.
NetworkMetaDataTableModel(CyNetwork) - Constructor for class cytoscape.dialogs.NetworkMetaDataTableModel: Constructor for the network metadata table model.
NetworkPanel - Class in cytoscape.view
NetworkPanel(CytoscapeDesktop) - Constructor for class cytoscape.view.NetworkPanel: Constructor for the Network Panel.
NetworkPanel.NetworkTreeNode - Class in cytoscape.view
NetworkPanel.NetworkTreeNode(Object, String) - Constructor for class cytoscape.view.NetworkPanel.NetworkTreeNode
NetworkView - Interface in cytoscape.view: Deprecated. Will be removed April 2007. This interface defines methods for displaying a graph without specifying the details of the UI components surrounding the graph display.
NetworkViewManager - Class in cytoscape.view
NetworkViewManager(CytoscapeDesktop, int) - Constructor for class cytoscape.view.NetworkViewManager: Constructor for overiding the default Desktop view type
NetworkViewManager(CytoscapeDesktop) - Constructor for class cytoscape.view.NetworkViewManager
newCalculator(String, Properties, String, String) - Static method in class cytoscape.visual.calculators.CalculatorFactory: Deprecated. Use othe newCalculator - we don't need the base interface class name any more. Will be removed 10/2007.
newCalculator(String, Properties, String) - Static method in class cytoscape.visual.calculators.CalculatorFactory: Attempt to construct an instance of Calculator as defined by the supplied arguments.
newDefaultCalculator(byte, String, ObjectMapping) - Static method in class cytoscape.visual.calculators.CalculatorFactory: Creates a new default Calculator based on type.
newInterpolator(String) - Static method in class cytoscape.visual.mappings.InterpolatorFactory: Attempt to construct one of the standard interpolators.
newline - Static variable in class cytoscape.data.writers.CyAttributesWriter2
newMapping(Properties, String, ValueParser, Object, byte) - Static method in class cytoscape.visual.mappings.MappingFactory: Attempt to construct an instance of ObjectMapping as defined by the supplied arguments.
NewSessionAction - Class in cytoscape.actions
NewSessionAction() - Constructor for class cytoscape.actions.NewSessionAction
NewSlider - Class in cytoscape.dialogs
NewSlider() - Constructor for class cytoscape.dialogs.NewSlider
NewSlider(String, double, double, double) - Constructor for class cytoscape.dialogs.NewSlider
NewSlider(String, double, double, double, int) - Constructor for class cytoscape.dialogs.NewSlider
NewSlider(String, String, double, double, double) - Constructor for class cytoscape.dialogs.NewSlider
NewSlider(String, String, double, double, double, int) - Constructor for class cytoscape.dialogs.NewSlider
NewSlider.MJSlider - Class in cytoscape.dialogs
NewSlider.MJTextField - Class in cytoscape.dialogs
NewStringPopupDialog - Class in cytoscape.dialogs: NewStringPopupDialog: a dialog that is used for creating a new string.
NewStringPopupDialog(Frame, String) - Constructor for class cytoscape.dialogs.NewStringPopupDialog
NewStringPopupDialog.CancelAction - Class in cytoscape.dialogs
NewStringPopupDialog.OkAction - Class in cytoscape.dialogs
NewWindowSelectedNodesEdgesAction - Class in cytoscape.actions
NewWindowSelectedNodesEdgesAction() - Constructor for class cytoscape.actions.NewWindowSelectedNodesEdgesAction
NewWindowSelectedNodesOnlyAction - Class in cytoscape.actions
NewWindowSelectedNodesOnlyAction() - Constructor for class cytoscape.actions.NewWindowSelectedNodesOnlyAction
NO_SUCH_ATTRIBUTE - Static variable in class cytoscape.data.NetworkData
noCanonicalization() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead.
NODE - Static variable in class cytoscape.data.writers.CytoscapeSessionWriter
NODE_ATTRIBUTE_ADDED - Static variable in class cytoscape.data.NetworkData
NODE_ATTRIBUTE_REMOVED - Static variable in class cytoscape.data.NetworkData
NODE_BORDER_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_FONT_FACE - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_FONT_SIZE - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_HEIGHT - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_LABEL - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_LABEL_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_LABEL_FONT - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_LABEL_POSITION - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_LINETYPE - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_MAPPING - Static variable in interface cytoscape.visual.mappings.ObjectMapping
NODE_NATURE - Static variable in class cytoscape.data.ImportHandler: Filter Type: NODE.
NODE_SET - Static variable in class cytoscape.data.FlagEvent: Deprecated. Static constant indicating a change to a group of Nodes.
NODE_SET - Static variable in class cytoscape.data.SelectEvent: Static constant indicating a change to a group of Nodes.
NODE_SHAPE - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_SIZE - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_TOOLTIP - Static variable in class cytoscape.visual.ui.VizMapUI
NODE_WIDTH - Static variable in class cytoscape.visual.ui.VizMapUI
NodeAppearance - Class in cytoscape.visual: Objects of this class hold data describing the appearance of a Node.
NodeAppearance() - Constructor for class cytoscape.visual.NodeAppearance
NodeAppearanceCalculator - Class in cytoscape.visual: This class calculates the appearance of a Node.
NodeAppearanceCalculator() - Constructor for class cytoscape.visual.NodeAppearanceCalculator
NodeAppearanceCalculator(String, Properties, String, CalculatorCatalog) - Constructor for class cytoscape.visual.NodeAppearanceCalculator: Creates a new NodeAppearanceCalculator and immediately customizes it by calling applyProperties with the supplied arguments.
NodeAppearanceCalculator(NodeAppearanceCalculator) - Constructor for class cytoscape.visual.NodeAppearanceCalculator: Copy constructor.
nodeBorderColorBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
nodeBorders(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render node borders.
NodeCalculator - Class in cytoscape.visual.calculators: NodeCalculator implements some UI features for calculators lower in the object tree.
NodeCalculator(String, ObjectMapping, Class) - Constructor for class cytoscape.visual.calculators.NodeCalculator
NodeCalculator(String, Properties, String, ValueParser, Object) - Constructor for class cytoscape.visual.calculators.NodeCalculator: Constructor that calls MappingFactory to construct a new ObjectMapping based on the supplied arguments.
nodeColorBaseKey - Static variable in class cytoscape.visual.CalculatorIO
NodeColorCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeColorClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeFillColorBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
nodeFontBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
nodeFontFaceBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
NodeFontFaceCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeFontFaceClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeFontSizeBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
NodeFontSizeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeFontSizeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeHeightBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
nodeLabelBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
nodeLabelBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
NodeLabelCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeLabelClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeLabelColorBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
NodeLabelColorCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeLabelCount() - Method in class cytoscape.data.synonyms.Thesaurus
nodeLabels(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render node labels.
nodeLineTypeBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
nodeLineTypeBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
NodeLineTypeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeLineTypeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
NODES - Static variable in class cytoscape.data.AttributeSaverDialog: Constant ot specify nodes
NODESHAPE - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for node shape
nodeShapeBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
nodeShapeBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
NodeShapeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeShapeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
NodeShapeParser - Class in cytoscape.visual.parsers: Parses a String into a yFiles shape, which is represented by a byte identifier.
NodeShapeParser() - Constructor for class cytoscape.visual.parsers.NodeShapeParser
nodeSizeBaseKey - Static variable in class cytoscape.visual.CalculatorIO
NodeSizeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeSizeClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeToolTipBaseKey - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Use Calculator.getPropertyLabel(). Will be removed 10/2007
nodeToolTipBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
NodeToolTipCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
nodeToolTipClassName - Static variable in class cytoscape.visual.CalculatorIO: Deprecated. Implement this yourself. Will be removed 10/2007
nodeWidthBypass - Static variable in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use calculator.getAttrNameBypass() instead. Will be removed Sept 2007.
noName - Static variable in class cytoscape.visual.LabelPosition
NONE - Static variable in class cytoscape.data.ExpressionData: Significance value: NONE.
NONE - Static variable in class cytoscape.visual.Arrow
northEastName - Static variable in class cytoscape.visual.LabelPosition
northName - Static variable in class cytoscape.visual.LabelPosition
northWestName - Static variable in class cytoscape.visual.LabelPosition
NotAPluginException - Exception in cytoscape.plugin: Thrown to indicate that a class cannot be used as a plugin becuase it does not extend AbstractPlugin.
NotAPluginException(String) - Constructor for exception cytoscape.plugin.NotAPluginException: constructor.
NumberInterpolator - Class in cytoscape.visual.mappings: This partial implementation of Interpolator assumes that the domain values are some kind of number, and extracts the values into ordinary doubles for the convenience of subclasses.
NumberInterpolator() - Constructor for class cytoscape.visual.mappings.NumberInterpolator
numberOfContainers() - Method in class cytoscape.data.annotation.OntologyTerm
numberOfParents() - Method in class cytoscape.data.annotation.OntologyTerm
numberOfParentsAndContainers() - Method in class cytoscape.data.annotation.OntologyTerm
numberOfTargets() - Method in class cytoscape.data.Interaction
numRemaining() - Method in interface cytoscape.data.attr.CountedIterator: Returns a non-negative integer I such that next() will successfully return a value no more and no less than I times.

O

OBJECT_TYPE - Static variable in class cytoscape.data.NetworkData
ObjectMapping - Interface in cytoscape.visual.mappings: Mappings should implement this interface.
ObjectToString - Class in cytoscape.visual.parsers: This class contains a method that does the reverse of the various parsing classes in this package, i.e. turns a Object back into a String representation.
ObjectToString() - Constructor for class cytoscape.visual.parsers.ObjectToString
OBO_PREFIX - Static variable in class cytoscape.data.ontology.readers.OBOFlatFileReader
OBOFlatFileReader - Class in cytoscape.data.ontology.readers: OBO file reader.
OBOFlatFileReader(String, String) - Constructor for class cytoscape.data.ontology.readers.OBOFlatFileReader
OBOFlatFileReader(URL, String) - Constructor for class cytoscape.data.ontology.readers.OBOFlatFileReader
OBOFlatFileReader(InputStream, String) - Constructor for class cytoscape.data.ontology.readers.OBOFlatFileReader
OBOHeaderTags - Enum in cytoscape.data.ontology.readers
OboPanel - Class in cytoscape.data.servers.ui
OboPanel() - Constructor for class cytoscape.data.servers.ui.OboPanel: Creates new OboPanel
OboPanelDescriptor - Class in cytoscape.data.servers.ui
OboPanelDescriptor() - Constructor for class cytoscape.data.servers.ui.OboPanelDescriptor
OBOTags - Enum in cytoscape.data.ontology.readers: Tags used in OBO file:
OBO This requirs JavaSE 5
OCTAGON - Static variable in class cytoscape.visual.ShapeNodeRealizer
OldStyleCalculatorIO - Class in cytoscape.visual: Deprecated. Use CalculatorIO instead. Will be removed 10/2007
OldStyleCalculatorIO() - Constructor for class cytoscape.visual.OldStyleCalculatorIO: Deprecated.
onComponentAdded(int) - Method in class cytoscape.actions.CytoPanelAction: Notifies the listener when a component is added to the CytoPanel.
onComponentAdded(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a component is added to the CytoPanel.
onComponentRemoved(int) - Method in class cytoscape.actions.CytoPanelAction: Notifies the listener when a component is removed from the CytoPanel.
onComponentRemoved(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a component is removed from the CytoPanel.
onComponentSelected(int) - Method in class cytoscape.actions.CytoPanelAction: Notifies the listener when a new component on the CytoPanel is selected.
onComponentSelected(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a new component on the CytoPanel is selected.
onCyNetworkEvent(CyNetworkEvent) - Method in class cytoscape.CyNetworkAdapter
onCyNetworkEvent(CyNetworkEvent) - Method in interface cytoscape.CyNetworkListener: This method is called when an event is fired by a CyNetwork.
onCyNetworkEvent(CyNetworkEvent) - Method in class cytoscape.visual.ui.VizMapUI: State of Underlying CyNework has Changed.
ONE_SECOND - Static variable in class cytoscape.util.CytoscapeProgressMonitor
onFlagEvent(FlagEvent) - Method in interface cytoscape.data.FlagEventListener
onFlagEvent(FlagEvent) - Method in class cytoscape.view.FlagAndSelectionHandler: Responds to events indicating a change in the flagged state of one or more nodes or edges.
onSelectEvent(SelectEvent) - Method in interface cytoscape.data.SelectEventListener
onSelectEvent(SelectEvent) - Method in class cytoscape.view.NetworkPanel
onStateChange(CytoPanelState) - Method in class cytoscape.actions.CytoPanelAction: Notifies the listener on a change in the CytoPanel state.
onStateChange(CytoPanelState) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener on a change in the CytoPanel state.
Ontology - Class in cytoscape.data.annotation: Contains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary.
Ontology(String, String) - Constructor for class cytoscape.data.annotation.Ontology
Ontology - Class in cytoscape.data.ontology: General Ontology class which implements Ontology interface from BioJava project.
Ontology(String) - Constructor for class cytoscape.data.ontology.Ontology: Constructor.
Ontology(String, String, String, CyNetwork) - Constructor for class cytoscape.data.ontology.Ontology: Constructor.
ONTOLOGY_DAG_ROOT - Static variable in class cytoscape.data.ontology.readers.OBOFlatFileReader
ONTOLOGY_ROOT - Static variable in class cytoscape.Cytoscape
ontologyCount() - Method in class cytoscape.data.servers.OntologyServer
OntologyDescription - Class in cytoscape.data.annotation: Distinguish among different ontologies, by curator and type.
OntologyDescription(String, String) - Constructor for class cytoscape.data.annotation.OntologyDescription
OntologyFactory - Class in cytoscape.data.ontology
OntologyFactory() - Constructor for class cytoscape.data.ontology.OntologyFactory
OntologyFlatFileReader - Class in cytoscape.data.annotation.readers
OntologyFlatFileReader(File) - Constructor for class cytoscape.data.annotation.readers.OntologyFlatFileReader
OntologyFlatFileReader(BufferedReader) - Constructor for class cytoscape.data.annotation.readers.OntologyFlatFileReader
OntologyFlatFileReader(String) - Constructor for class cytoscape.data.annotation.readers.OntologyFlatFileReader
OntologyMapperDialog - Class in cytoscape.data.annotation
OntologyMapperDialog() - Constructor for class cytoscape.data.annotation.OntologyMapperDialog
OntologyMapperDialog(Frame, boolean) - Constructor for class cytoscape.data.annotation.OntologyMapperDialog: Creates new form OntologyMapperDialog.
OntologyReader - Interface in cytoscape.data.ontology.readers: Interface for all ontology file readers.
OntologyServer - Class in cytoscape.data.servers: Ontology Server which manages ontologies, aliases, and bookmarks.
OntologyServer() - Constructor for class cytoscape.data.servers.OntologyServer: Constructor.
OntologyServer.OntologyType - Enum in cytoscape.data.servers
OntologyTerm - Class in cytoscape.data.annotation: Represents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary.
OntologyTerm(String, int) - Constructor for class cytoscape.data.annotation.OntologyTerm
OntologyTerm - Class in cytoscape.data.ontology: Simple in-memory implementation of an ontology term based on BioJava's interface.
OntologyTerm(String, String, String) - Constructor for class cytoscape.data.ontology.OntologyTerm: Constructor.
OntologyTerm.SynonymType - Enum in cytoscape.data.ontology
OntologyXmlReader - Class in cytoscape.data.annotation.readers
OntologyXmlReader(File) - Constructor for class cytoscape.data.annotation.readers.OntologyXmlReader
OpenBrowser - Class in cytoscape.util
OpenBrowser() - Constructor for class cytoscape.util.OpenBrowser
OpenSessionAction - Class in cytoscape.actions: Call the session reader and read everything in the zip archive.
OpenSessionAction() - Constructor for class cytoscape.actions.OpenSessionAction: Constructor.
OpenSessionAction(CyMenus, boolean) - Constructor for class cytoscape.actions.OpenSessionAction: Constructor for the Icon button on the toolbar.
openURL(String) - Static method in class cytoscape.util.OpenBrowser
Out - Variable in class cytoscape.util.JnlpWriterUtil

P

PACKAGE_NAME - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
packageHeader - Static variable in class cytoscape.visual.OldStyleCalculatorIO: Deprecated.
pad(GridBagConstraints, int, int) - Static method in class cytoscape.dialogs.MiscGB
paint(Graphics) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: Sublcassed to translate the graphics such that the last visible row will be drawn at 0,0.
panel - Variable in class cytoscape.dialogs.GridBagGroup
PARALLELOGRAM - Static variable in class cytoscape.visual.ShapeNodeRealizer
parse(String) - Static method in class cytoscape.visual.LabelPosition
parseArrow(String) - Method in class cytoscape.visual.parsers.ArrowParser
parseArrowText(String) - Static method in class cytoscape.visual.Arrow
parseColor(String) - Method in class cytoscape.visual.parsers.ColorParser
parseDouble(String) - Method in class cytoscape.visual.parsers.DoubleParser
parseFont(String) - Method in class cytoscape.visual.parsers.FontParser
parseHeader(String) - Method in class cytoscape.data.annotation.readers.AnnotationFlatFileReader
parseLabelPosition(String) - Method in class cytoscape.visual.parsers.LabelPositionParser
parseLineType(String) - Method in class cytoscape.visual.parsers.LineTypeParser
parseLineTypeText(String) - Static method in class cytoscape.visual.LineType: This method converts the names of linetypes, such as from a visual mappings properties file, to a LineType object.
parseList() - Method in class cytoscape.data.readers.GMLParser: A list consists of zero or more paris of keys and values
parseList(String, String, String, String) - Static method in class cytoscape.util.Misc: parse and return an array of strings
parseNodeShape(String) - Method in class cytoscape.visual.parsers.NodeShapeParser
parseNodeShapeText(String) - Static method in class cytoscape.visual.ShapeNodeRealizer
parseNodeShapeTextIntoByte(String) - Static method in class cytoscape.visual.ShapeNodeRealizer
parseObjectType(String, byte) - Static method in class cytoscape.visual.mappings.MappingUtil: This method returns an object of the specified type based on the string read from the props file.
ParserFactory - Class in cytoscape.visual.parsers
ParserFactory() - Constructor for class cytoscape.visual.parsers.ParserFactory
parseRGBText(String) - Static method in class cytoscape.util.Misc
parseString(String) - Method in class cytoscape.visual.parsers.StringParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.ArrowParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.ColorParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.DoubleParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.FontParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.LabelPositionParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.LineTypeParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.NodeShapeParser
parseStringValue(String) - Method in class cytoscape.visual.parsers.StringParser
parseStringValue(String) - Method in interface cytoscape.visual.parsers.ValueParser: Parse the argument into an onject.
parseViewType(String) - Static method in class cytoscape.view.CytoscapeDesktop
passesFilter(Object) - Method in class cytoscape.data.FlagFilter: Deprecated. Implementation of the Filter interface.
passesFilter(Object) - Method in class cytoscape.data.SelectFilter: Implementation of the Filter interface.
PassThroughMapping - Class in cytoscape.visual.mappings: Defines a mapping from a bundle of data attributes to a visual attribute.
PassThroughMapping(Object, byte) - Constructor for class cytoscape.visual.mappings.PassThroughMapping: Standard constructor for compatibility with new calculator creation in the UI.
PassThroughMapping(Object) - Constructor for class cytoscape.visual.mappings.PassThroughMapping
PassThroughMapping(Object, String) - Constructor for class cytoscape.visual.mappings.PassThroughMapping
PercentUtil - Class in cytoscape.util: Helper Class for Calculating Percentage of Multi-Step Processes.
PercentUtil(int) - Constructor for class cytoscape.util.PercentUtil: Constructor.
performSearch() - Method in class cytoscape.dialogs.GraphObjectSelection
PhoebeNetworkView - Class in cytoscape.giny: Deprecated. You should be using DingNetworkView instead. This will be removed in whatever major release follows 2.4.
PhoebeNetworkView(CyNetwork, String) - Constructor for class cytoscape.giny.PhoebeNetworkView: Deprecated.
PhoebeNodeControl - Class in cytoscape.dialogs: An Adobe style node organizer.
PhoebeNodeControl(GraphView) - Constructor for class cytoscape.dialogs.PhoebeNodeControl
PhoebeNodeControl.SliderListener - Class in cytoscape.dialogs
PhoebeNodeControl.SliderListener() - Constructor for class cytoscape.dialogs.PhoebeNodeControl.SliderListener
PluginDir - Variable in class cytoscape.util.JnlpWriterUtil
PluginsTableModel - Class in cytoscape.dialogs.preferences: Deprecated. This class is no longer used in cytoscape. If you are using it, let us know and we'll figure something out. Otherwise, this will be removed December 2007.
PluginsTableModel() - Constructor for class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
PointTextListener - Class in cytoscape.visual.mappings.continuous: Listens for a User Initiated Change in any of the JTextFields in the Continuous Mapper UI.
PointTextListener(JTextField, ContinuousMapping, JDialog, int) - Constructor for class cytoscape.visual.mappings.continuous.PointTextListener: Constructor.
popup() - Method in class cytoscape.dialogs.GeneralColorDialogListener: Deprecated.
PopupFontChooser - Class in cytoscape.visual.ui
PopupIconChooser - Class in cytoscape.visual.ui: PopupIconChooser borrows all of its functionality from IconPopupButton.
PopupIconChooser(String, String, ImageIcon[], ImageIcon, Frame) - Constructor for class cytoscape.visual.ui.PopupIconChooser: Create a PopupIconChooser with the supplied attributes.
PopupIconChooser(String, String, ImageIcon[], ImageIcon, Dialog) - Constructor for class cytoscape.visual.ui.PopupIconChooser
PopupIconChooser.ApplyIconAction - Class in cytoscape.visual.ui
PopupIconChooser.ApplyIconAction() - Constructor for class cytoscape.visual.ui.PopupIconChooser.ApplyIconAction
PopupIconChooser.CancelIconAction - Class in cytoscape.visual.ui
PopupLabelPositionChooser - Class in cytoscape.visual.ui
PopupStringChooser - Class in cytoscape.visual.ui: An input dialog for strings, ints, and doubles.
PopupStringChooser() - Constructor for class cytoscape.visual.ui.PopupStringChooser
PopupTextArea - Class in cytoscape.dialogs
PopupTextArea(JDialog, String, String) - Constructor for class cytoscape.dialogs.PopupTextArea
PopupTextArea(Frame, String, String) - Constructor for class cytoscape.dialogs.PopupTextArea
PopupTextArea.OKAction - Class in cytoscape.dialogs
positionToBarycenter(NodeView) - Static method in class cytoscape.view.BasicGraphViewHandler: If the node that node_view represents is a meta-node, then it positions it at the barycenter of its viewable children nodes.
PREFERENCE_MODIFIED - Static variable in class cytoscape.Cytoscape
PreferenceAction - Class in cytoscape.actions
PreferenceAction() - Constructor for class cytoscape.actions.PreferenceAction
PREFERENCES_UPDATED - Static variable in class cytoscape.Cytoscape
PreferencesDialog - Class in cytoscape.dialogs.preferences
PreferencesDialog(Frame) - Constructor for class cytoscape.dialogs.preferences.PreferencesDialog
PreferenceTableModel - Class in cytoscape.dialogs.preferences
PreferenceTableModel() - Constructor for class cytoscape.dialogs.preferences.PreferenceTableModel
PreferenceValueDialog - Class in cytoscape.dialogs.preferences
PreferenceValueDialog(Dialog, String, String, PreferencesDialog, TableModel, String, boolean) - Constructor for class cytoscape.dialogs.preferences.PreferenceValueDialog
prefsTM - Variable in class cytoscape.dialogs.preferences.PreferencesDialog
print(Graphics, PageFormat, int) - Method in class cytoscape.view.InternalFrameComponent: Our implementation of the Printable interface.
PrintAction - Class in cytoscape.actions
PrintAction() - Constructor for class cytoscape.actions.PrintAction
printList(List, Writer) - Static method in class cytoscape.data.readers.GMLParser: Public method to print out a given object tree(list) using the supplied filewriter
PROPERTIES_NATURE - Static variable in class cytoscape.data.ImportHandler: Filer Type: PROPERTIES.
propertyChange(PropertyChangeEvent) - Method in class cytoscape.actions.BirdsEyeViewAction
propertyChange(PropertyChangeEvent) - Method in class cytoscape.actions.CreateNetworkViewAction
propertyChange(PropertyChangeEvent) - Method in class cytoscape.actions.MapOntologyAction
propertyChange(PropertyChangeEvent) - Method in class cytoscape.CytoscapeModifiedNetworkManager
propertyChange(PropertyChangeEvent) - Method in class cytoscape.data.servers.OntologyServer
propertyChange(PropertyChangeEvent) - Method in class cytoscape.dialogs.preferences.PreferencesDialog
propertyChange(PropertyChangeEvent) - Method in class cytoscape.ding.CyGraphLOD
propertyChange(PropertyChangeEvent) - Method in class cytoscape.plugin.CytoscapePlugin
propertyChange(PropertyChangeEvent) - Method in class cytoscape.util.ProxyHandler
propertyChange(PropertyChangeEvent) - Method in class cytoscape.view.CytoscapeDesktop
propertyChange(PropertyChangeEvent) - Method in class cytoscape.view.NetworkPanel
propertyChange(PropertyChangeEvent) - Method in class cytoscape.view.NetworkViewManager: This handles all of the incoming PropertyChangeEvents.
propertyChange(PropertyChangeEvent) - Method in class cytoscape.visual.ui.PopupLabelPositionChooser: Handles all property changes that the panel listens for.
propertyChange(PropertyChangeEvent) - Method in class cytoscape.visual.ui.VizMapBypassNetworkListener: Listens for NETWORK_VIEW_CREATED events and if it hears one, it adds node and edge context menu listeners to the view.
PROTEIN - Static variable in class cytoscape.data.Semantics
ProxyHandler - Class in cytoscape.util
ProxyServerAction - Class in cytoscape.actions
ProxyServerAction() - Constructor for class cytoscape.actions.ProxyServerAction
ProxyServerDialog - Class in cytoscape.dialogs.preferences
ProxyServerDialog(JFrame) - Constructor for class cytoscape.dialogs.preferences.ProxyServerDialog: Creates new form URLimportAdvancedDialog
putAll(Map) - Method in class cytoscape.visual.mappings.DiscreteMapping: Adds All Members of Specified Map.
putClientData(String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
putClientData(String, Object) - Method in class cytoscape.ding.DingNetworkView
putClientData(String, Object) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. Networks can support client data.
putClientData(String, Object) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Networks can support client data.
putClientData(String, Object) - Method in interface cytoscape.view.CyNetworkView: Networks can support client data.
putMapValue(Object, Object) - Method in class cytoscape.visual.mappings.DiscreteMapping: Puts New Key/Value in Map.
PVAL - Static variable in class cytoscape.data.ExpressionData: Significance value: PVAL.

R

RandomColorListener - Class in cytoscape.visual.mappings.discrete: User wants to Seed the Discrete Mapper with Random Color Values.
RandomColorListener(DiscreteMapping, TreeSet) - Constructor for class cytoscape.visual.mappings.discrete.RandomColorListener: Constructs a ValueChangeListener.
read() - Method in class cytoscape.data.readers.AbstractGraphReader
read(boolean) - Method in class cytoscape.data.readers.AbstractGraphReader: Deprecated. Use read() instead. Will be removed Dec 2006.
read() - Method in class cytoscape.data.readers.CytoscapeSessionReader: Read a session file.
read() - Method in class cytoscape.data.readers.GMLReader
read() - Method in interface cytoscape.data.readers.GraphReader: Reads/imports the graph.
read(boolean) - Method in interface cytoscape.data.readers.GraphReader: Deprecated. Use read() instead. Will be removed Dec 2006.
read(boolean) - Method in class cytoscape.data.readers.InteractionsReader
read() - Method in class cytoscape.data.readers.InteractionsReader: Calls read(false)
read() - Method in class cytoscape.data.readers.TextFileReader
read() - Method in class cytoscape.data.readers.TextHttpReader
read() - Method in class cytoscape.data.readers.TextJarReader
read() - Method in class cytoscape.data.readers.XGMMLReader
readBookmarks() - Method in class cytoscape.data.readers.BookmarkReader: Read bookmark from resource.
readBookmarks(URL) - Method in class cytoscape.data.readers.BookmarkReader: Read bookmarks from the specified location.
READER_CLIENT_KEY - Static variable in class cytoscape.Cytoscape
readFile(String, String) - Static method in class cytoscape.util.ZipUtil: Reads a file contained within a zip file and returns an InputStream.
readOntology() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
readOntology() - Method in interface cytoscape.data.ontology.readers.OntologyReader
readOntologyFlatFiles(String[]) - Method in class cytoscape.data.servers.BioDataServer
readOntologyFlatFiles2(String[]) - Method in class cytoscape.data.servers.BioDataServer
readResourceFile() - Method in class cytoscape.data.ontology.readers.DBCrossReferenceReader: Read the resource file in the jar.
RECT - Static variable in class cytoscape.visual.ShapeNodeRealizer
RECT_3D - Static variable in class cytoscape.visual.ShapeNodeRealizer
redrawGraph(boolean, boolean) - Method in class cytoscape.ding.DingNetworkView
redrawGraph(boolean, boolean) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
redrawGraph() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
redrawGraph(boolean, boolean) - Method in interface cytoscape.view.CyNetworkView
redrawGraph(boolean, boolean) - Method in interface cytoscape.view.NetworkView: Deprecated. Redraws the graph.
refresh() - Method in class cytoscape.dialogs.preferences.PreferencesDialog
refreshUI() - Method in class cytoscape.visual.ui.VizMapAttrTab: Refreshes the panel that displays the UI for the currently selected calculator.
refreshUI() - Method in class cytoscape.visual.ui.VizMapFontTab
refreshUI() - Method in class cytoscape.visual.ui.VizMapSizeTab
refreshUI() - Method in class cytoscape.visual.ui.VizMapTab: When the data structures underlying the visualization system change, (eg.
refreshUI() - Method in class cytoscape.visual.ui.VizMapUI: When the data structures (eg.
remove(String, String) - Method in class cytoscape.data.synonyms.Aliases: Remove an alias.
remove(String, String) - Method in class cytoscape.data.synonyms.Thesaurus
remove(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes specified component from the CytoPanel.
remove(int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes the component from the CytoPanel at the specified index.
remove(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes specified component from the CytoPanel.
remove(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes the component from the CytoPanel at the specified index.
removeAction(Action) - Method in class cytoscape.util.CytoscapeMenuBar: If the given Action has a present and false inMenuBar property, return; otherwise if there's a menu item for the action, remove it.
removeAction(Action) - Method in class cytoscape.util.CytoscapeToolBar: If the given Action has an absent or false inToolBar property, return; otherwise if there's a button for the action, remove it.
removeAll() - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes all the components from the CytoPanel.
removeAll() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes all the components from the CytoPanel.
removeAllAttributeValues(String, String) - Method in interface cytoscape.data.attr.MultiHashMap: Removes all values bound to objectKey in attributeName.
removeAllGraphViews() - Method in class cytoscape.view.GraphViewController: Removes all of the current giny.view.GraphView objects that this GraphViewController keeps synchronized to their corresponding giny.model.GraphPerspective members.
removeAttributeValue(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: This method is the same as getAttributeValue(), only the retrieved attribute value is also deleted.
removeCalculator(Calculator) - Method in class cytoscape.visual.CalculatorCatalog: Remove a calculator.
removeCalculator(byte, String) - Method in class cytoscape.visual.CalculatorCatalog
removeCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
removeChangeListener(ChangeListener) - Method in class cytoscape.visual.calculators.AbstractCalculator: Remove a ChangeListener from the calcaultor.
removeChangeListener(ChangeListener) - Method in interface cytoscape.visual.calculators.Calculator: Remove a ChangeListener from the calcaultor.
removeChangeListener(ChangeListener) - Method in interface cytoscape.visual.mappings.ObjectMapping: Remove a ChangeListener from the mapping.
removeChangeListener(ChangeListener) - Method in class cytoscape.visual.mappings.PassThroughMapping: Empty implementation because PassThroughMapping has no UI.
removeChangeListener(ChangeListener) - Method in class cytoscape.visual.SubjectBase: Remove a ChangeListener from the calcaultor.
removeCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork: Removes the argument from the set of listeners for this object.
removeCyNetworkListener(CyNetworkListener) - Method in class cytoscape.giny.FingCyNetwork: Removes the argument from the set of listeners for this object.
removeCytoPanelListener(CytoPanelListener) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes a CytoPanel listener.
removeCytoPanelListener(CytoPanelListener) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes a CytoPanel listener.
removeDataDefinitionListener(MultiHashMapDefinitionListener) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Unregisters a listener; this method has the opposite effect as addDataDefinitionListener(listener).
removeDataListener(MultiHashMapListener) - Method in interface cytoscape.data.attr.MultiHashMap: Unregisters a listener; this method has the opposite effect as addDataListener(listener).
removeDuplicate(Calculator, CalculatorCatalog) - Static method in class cytoscape.visual.CalculatorIO: Deprecated. WTF? Use CalculatorCatalog.removeCalculator() Will be removed 10/2007
removeEdge(int, boolean) - Method in interface cytoscape.CyNetwork: This will remove this edge from the Network.
removeEdge(int, boolean) - Method in class cytoscape.giny.FingCyNetwork: This will remove this edge from the Network.
removeEdgeArrowCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView
removeEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
removeEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
removeEdgeFontFaceCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeFontSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeLabelCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeLineTypeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeEdgeToolTipCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.removeSelectEventListener(SelectEventListener)
removeFlagEventListener(FlagEventListener) - Method in class cytoscape.data.FlagFilter: Deprecated. If the argument is a listener to this object, removes it from the list of listeners.
removeFlagEventListener(FlagEventListener) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.removeSelectEventListener(SelectEventListener)
removeGraphView(GraphView) - Method in class cytoscape.view.GraphViewController: If this GraphViewController contains the given giny.view.GraphView, then it is removed from it, and it no longer listens for change events from the removed giny.view.GraphView's giny.model.GraphPerspective.
removeGraphViewEdges(GraphView, Edge[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It removes the views of the edges in the array from the given giny.view.GraphView object.
removeGraphViewEdges(GraphView, int[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It removes the views of the edges in the array from the given giny.view.GraphView object.
removeGraphViewNodes(GraphView, Node[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It removes the nodes in the array from the given giny.view.GraphView object, it also removes the connected edges to these nodes (an edge without a connecting node makes no mathematical sense).
removeGraphViewNodes(GraphView, int[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It removes the views of the nodes with the given indices that are contained in the given giny.view.GraphView object, it also removes the connected edges to these nodes (an edge without a connecting node makes no mathematical sense).
removeMapping(String) - Method in class cytoscape.visual.CalculatorCatalog
removeNetwork(String) - Method in class cytoscape.view.NetworkPanel: Remove a network from the panel.
removeNode(int, boolean) - Method in interface cytoscape.CyNetwork: This will remove this node from the Network.
removeNode(int, boolean) - Method in class cytoscape.giny.FingCyNetwork: This will remove this node from the Network.
removeNodeColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView
removeNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
removeNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
removeNodeFontFaceCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeFontSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeLabelCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeLabelColorCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeLineTypeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeShapeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeSizeCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removeNodeToolTipCalculator(String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Use removeCalculator(type,name) instead. Will be removed 10/2007.
removePoint(int) - Method in class cytoscape.visual.mappings.ContinuousMapping: Removes a Point from the List.
removeSelectEventListener(SelectEventListener) - Method in interface cytoscape.CyNetwork: Removes a listener for SelectEvents from this CyNetwork
removeSelectEventListener(SelectEventListener) - Method in class cytoscape.data.SelectFilter: If the argument is a listener to this object, removes it from the list of listeners.
removeSelectEventListener(SelectEventListener) - Method in class cytoscape.giny.FingCyNetwork: Removes a listener for SelectEvents from this CyNetwork
removeSynonym(Object) - Method in class cytoscape.data.ontology.OntologyTerm: Remove a synonym for this term.
removeSynonym(Object) - Method in class cytoscape.data.ontology.Triple: Not supported.
removeTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
removeVisualStyle(String) - Method in class cytoscape.visual.CalculatorCatalog
renameAsNeeded(Calculator, CalculatorCatalog) - Static method in class cytoscape.visual.CalculatorIO: Given a Calculator of a given type and a CalculatorCatalog, checks for an existing catalog with the same name and type.
renameCalculator(Calculator, String) - Method in class cytoscape.visual.CalculatorCatalog: Renames a calculator.
renderEdges(int, int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render all edges in a graph, no edges, or only those edges which touch a visible node.
resetImportHandler() - Method in class cytoscape.data.ImportHandler: Unregisters all registered File Filters (except default file filters.)
resetStyles() - Method in class cytoscape.visual.ui.VizMapUI.StyleSelector: Reset the style selection controls.
resetStyles(String) - Method in class cytoscape.visual.ui.VizMapUI.StyleSelector
resetUI() - Method in class cytoscape.visual.mappings.continuous.ContinuousUI: Resets the UI and Updates the Continuous Mapper.
restore(Properties) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
restore(Properties) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
RESTORE_PLUGIN_STATE - Static variable in class cytoscape.Cytoscape
restoreGraphViewEdges(GraphView, Edge[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It restores the views of the edges in the array in the given giny.view.GraphView object
restoreGraphViewEdges(GraphView, int[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It restores the views of the edges with the given indices in the given giny.view.GraphView object
restoreGraphViewNodes(GraphView, Node[], boolean) - Static method in class cytoscape.view.BasicGraphViewHandler: It restores the views of the nodes in the array in the given giny.view.GraphView object
restoreGraphViewNodes(GraphView, int[], boolean) - Static method in class cytoscape.view.BasicGraphViewHandler: It restores the views of the nodes with the given indices in the given giny.view.GraphView object
restoreSessionState(List<File>) - Method in class cytoscape.plugin.CytoscapePlugin
resumeListening() - Method in class cytoscape.view.GraphViewController: It adds this GraphViewController as a listener for all giny.model.GraphPerspective that were temporarily "removed" by calling stopListening(), it updates the GraphViews of the GraphPerspectives so that they are synchronized to reflect changes that may have occured while not listening.
resumeListening(GraphView) - Method in class cytoscape.view.GraphViewController: It adds this GraphViewController listener to the giny.model.GraphPerspective of the given giny.view.GraphView that was temporarily "removed" by a call to stopListening(GraphView), it updates graph_view so that it's synchronized to its GraphPerspective due to changes that may have occured while not listening.
RNA - Static variable in class cytoscape.data.Semantics
Root - Variable in class cytoscape.util.JnlpWriterUtil
RotateSelectedNodesAction - Class in cytoscape.actions: Rotates the given selection by the specified amount.
RotateSelectedNodesAction(CyNetworkView) - Constructor for class cytoscape.actions.RotateSelectedNodesAction
ROUND_RECT - Static variable in class cytoscape.visual.ShapeNodeRealizer
run() - Method in class cytoscape.actions.LoadNetworkTask: Executes Task.
run() - Method in class cytoscape.util.CytoscapeProgressMonitor: Implementes Runnable.run()
run() - Method in class cytoscape.util.Exec
runThreaded() - Method in class cytoscape.util.Exec

S

save(Properties) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
save(Properties) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
SAVE - Static variable in class cytoscape.util.FileUtil
SAVE_PLUGIN_STATE - Static variable in class cytoscape.Cytoscape
SAVE_VIZMAP_PROPS - Static variable in class cytoscape.Cytoscape
saveBookmark(Bookmarks, String, DataSource, FileOutputStream) - Static method in class cytoscape.util.BookmarksUtil
saveBookmark(URL, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
saveBookmark(Bookmarks, File) - Static method in class cytoscape.util.BookmarksUtil
saveBookmark(Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
saveSelectedNodeNames(CyNetworkView, CyNetwork, String) - Static method in class cytoscape.data.CyNetworkUtilities: Saves all selected nodes in the current view to a file with the given name.
SaveSessionAction - Class in cytoscape.actions: Save Session action.
SaveSessionAction(String) - Constructor for class cytoscape.actions.SaveSessionAction: Constructor.
SaveSessionAction() - Constructor for class cytoscape.actions.SaveSessionAction: Constructor.
SaveSessionAsAction - Class in cytoscape.actions: Same as SaveSessionAction, but always opens file chooser.
SaveSessionAsAction(String) - Constructor for class cytoscape.actions.SaveSessionAsAction: Constructor.
SaveSessionAsAction() - Constructor for class cytoscape.actions.SaveSessionAsAction
saveSessionStateFiles(List<File>) - Method in class cytoscape.plugin.CytoscapePlugin
saveVisibleNodeNames(CyNetwork, String) - Static method in class cytoscape.data.CyNetworkUtilities: Saves all nodes in the given network to a file with the given name.
SELECT_EDGES_ONLY - Static variable in class cytoscape.Cytoscape
SELECT_NODES_AND_EDGES - Static variable in class cytoscape.Cytoscape
SELECT_NODES_ONLY - Static variable in class cytoscape.Cytoscape
SelectAllAction - Class in cytoscape.actions
SelectAllAction() - Constructor for class cytoscape.actions.SelectAllAction
selectAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
selectAllEdges() - Method in interface cytoscape.CyNetwork: Sets the selected state of all edges in this CyNetwork to true
selectAllEdges() - Method in class cytoscape.data.SelectFilter: Sets the selected state to true for all Edges in the GraphPerspective.
selectAllEdges() - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of all edges in this CyNetwork to true
SelectAllEdgesAction - Class in cytoscape.actions
SelectAllEdgesAction() - Constructor for class cytoscape.actions.SelectAllEdgesAction
selectAllNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
selectAllNodes() - Method in interface cytoscape.CyNetwork: Sets the selected state of all nodes in this CyNetwork to true
selectAllNodes() - Method in class cytoscape.data.SelectFilter: Sets the selected state to true for all Nodes in the GraphPerspective.
selectAllNodes() - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of all nodes in this CyNetwork to true
SelectAllNodesAction - Class in cytoscape.actions
SelectAllNodesAction() - Constructor for class cytoscape.actions.SelectAllNodesAction
SelectEvent - Class in cytoscape.data: Events that are fired when the selected state of a Node or Edge, or a group of Nodes or Edges, is changed.
SelectEvent(SelectFilter, Object, boolean) - Constructor for class cytoscape.data.SelectEvent: Standard constructor.
SelectEventListener - Interface in cytoscape.data: Listener for SelectEvents fired by a SelectFilter object.
SelectFilter - Class in cytoscape.data: This class implements the ability to set the selected state of every node or edge in a GraphPerspective.
SelectFilter(GraphPerspective) - Constructor for class cytoscape.data.SelectFilter: Standard Constructor.
selectFirstNeighbors(GraphView) - Static method in class cytoscape.actions.GinyUtils
SelectFirstNeighborsAction - Class in cytoscape.actions: select every first neighbor (directly connected nodes) of the currently selected nodes.
SelectFirstNeighborsAction() - Constructor for class cytoscape.actions.SelectFirstNeighborsAction
SelectFormatPanel - Class in cytoscape.data.servers.ui: Start panel
SelectFormatPanel() - Constructor for class cytoscape.data.servers.ui.SelectFormatPanel: Creates new form NewBioDataServerPanel
SelectFormatPanelDescriptor - Class in cytoscape.data.servers.ui: First panel for the Gene Ontology Wizard
SelectFormatPanelDescriptor() - Constructor for class cytoscape.data.servers.ui.SelectFormatPanelDescriptor
selectGraphViewEdges(GraphView, Edge[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It selects the edges in the array in the given giny.view.GraphView object.
selectGraphViewNodes(GraphView, Node[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It selects the nodes in the array in the given giny.view.GraphView object.
SelectionModeAction - Class in cytoscape.actions
SelectionModeAction() - Constructor for class cytoscape.actions.SelectionModeAction
selectNodesStartingWith(CyNetwork, String, CyNetworkView) - Static method in class cytoscape.data.CyNetworkUtilities: Selects every node in the current view whose canonical name, label, or any known synonym starts with the string specified by the second argument.
Semantics - Class in cytoscape.data: This class defines names for certain data attributes that are commonly used within Cytoscape.
Semantics() - Constructor for class cytoscape.data.Semantics
SESSION_CHANGED - Static variable in class cytoscape.Cytoscape
SESSION_CLOSED - Static variable in class cytoscape.Cytoscape
SESSION_EXT - Static variable in class cytoscape.actions.OpenSessionAction
SESSION_EXT - Static variable in class cytoscape.actions.SaveSessionAction
SESSION_EXT - Static variable in class cytoscape.actions.SaveSessionAsAction
SESSION_LOADED - Static variable in class cytoscape.Cytoscape
SESSION_NEW - Static variable in class cytoscape.Cytoscape
SESSION_OPENED - Static variable in class cytoscape.Cytoscape
SESSION_SAVED - Static variable in class cytoscape.Cytoscape
set(GridBagConstraints, int, int, int, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
set(GridBagConstraints, int, int, int, int) - Static method in class cytoscape.dialogs.MiscGB
set(GridBagConstraints, int, int) - Static method in class cytoscape.dialogs.MiscGB
set(byte, String, String) - Method in interface cytoscape.visual.calculators.EdgeArrowCalculator: Deprecated. DON'T USE. Only exists to support deprecated code. Will be removed 10/2007
set(byte, String, String) - Method in interface cytoscape.visual.calculators.NodeColorCalculator: Deprecated. DON'T USE. Only exists to support deprecated code. Will be removed 10/2007
set(byte, String, String) - Method in interface cytoscape.visual.calculators.NodeSizeCalculator: Deprecated. DON'T USE. Only exists to support deprecated code. Will be removed 10/2007
set(byte, Object) - Method in class cytoscape.visual.EdgeAppearance
set(byte, Object) - Method in class cytoscape.visual.NodeAppearance
setAcceleratorCombo(int, int) - Method in class cytoscape.util.CytoscapeAction
setAttribute(String, String, Boolean) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Boolean.
setAttribute(String, String, Integer) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Integer.
setAttribute(String, String, Double) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Double.
setAttribute(String, String, String) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type String.
setAttribute(String, String, Boolean) - Method in class cytoscape.data.CyAttributesImpl
setAttribute(String, String, Integer) - Method in class cytoscape.data.CyAttributesImpl
setAttribute(String, String, Double) - Method in class cytoscape.data.CyAttributesImpl
setAttribute(String, String, String) - Method in class cytoscape.data.CyAttributesImpl
setAttributeDescription(String, String) - Method in interface cytoscape.data.CyAttributes: Sets a human readable description of a specific attribute.
setAttributeDescription(String, String) - Method in class cytoscape.data.CyAttributesImpl
setAttributeList(String, String, List) - Method in interface cytoscape.data.CyAttributes: Deprecated. Use setListAttribute() instead. Will be removed 11/2007.
setAttributeList(String, String, List) - Method in class cytoscape.data.CyAttributesImpl
setAttributeMap(String, String, Map) - Method in interface cytoscape.data.CyAttributes: Deprecated. Use setMapAttribute() instead. Will be removed 11/2007.
setAttributeMap(String, String, Map) - Method in class cytoscape.data.CyAttributesImpl
setAttributeValue(String, String, Object, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: Binds an attribute value to an object.
setBackgroundColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setBookmarks(Bookmarks) - Static method in class cytoscape.Cytoscape
setBool(boolean) - Method in class cytoscape.util.MutableBool
setBorderColor(Color) - Method in class cytoscape.visual.NodeAppearance
setBorderLineType(LineType) - Method in class cytoscape.visual.NodeAppearance
setBounds(int, int, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: This is overridden to set the height to match that of the JTable.
setBounds(int, int, int, int) - Method in class cytoscape.view.InternalFrameComponent: Our implementation of Component setBounds().
setCenterLabel(String) - Method in class cytoscape.util.swing.JStatusBar
setColor(Color) - Method in class cytoscape.util.MutableColor: Deprecated.
setColor(Color) - Method in class cytoscape.visual.EdgeAppearance
setComboBoxState(boolean) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
setControllingAttributeName(String, CyNetwork, boolean) - Method in class cytoscape.visual.mappings.ContinuousMapping: Sets the Name of the Controlling Attribte.
setControllingAttributeName(String, CyNetwork, boolean) - Method in class cytoscape.visual.mappings.DiscreteMapping: Call whenever the controlling attribute changes.
setControllingAttributeName(String, CyNetwork, boolean) - Method in interface cytoscape.visual.mappings.ObjectMapping: Set the controlling attribute name.
setControllingAttributeName(String, CyNetwork, boolean) - Method in class cytoscape.visual.mappings.PassThroughMapping
setCurrentNetwork(String) - Static method in class cytoscape.Cytoscape: Deprecated. This will be removed Feb 2007.
setCurrentNetworkView(String) - Static method in class cytoscape.Cytoscape: Deprecated. This will be removed Feb 2007.
setCurrentSessionFileName(String) - Static method in class cytoscape.Cytoscape: Set the current session name.
setCytoPanelContainer(CytoPanelContainer) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets CytoPanelContainer interface reference.
setDBReference(DBReference) - Method in class cytoscape.data.ontology.DBCrossReferences: Add a database reference object
setDefaultAppearance(EdgeAppearance) - Method in class cytoscape.visual.EdgeAppearanceCalculator
setDefaultAppearance(NodeAppearance) - Method in class cytoscape.visual.NodeAppearanceCalculator
setDefaultBackgroundColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultEdgeColor(Color) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeFont(Font) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeFontFace(Font) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeFontSize(float) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeLabel(String) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeLineType(LineType) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeReverseSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultEdgeSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultEdgeSourceArrow(Arrow) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeTargetArrow(Arrow) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultEdgeToolTip(String) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setDefaultAppearance() instead. This method will be removed Sept. 2007.
setDefaultMenuSpecifier(String) - Method in class cytoscape.util.CytoscapeMenuBar
setDefaultNodeBorderColor(Color) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeFillColor(Color) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeFont(Font) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeFontFace(Font) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeFontSize(float) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeHeight(double) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeLabel(String) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeLabelColor(Color) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeLineType(LineType) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeReverseSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultNodeSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultNodeShape(byte) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeToolTip(String) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultNodeWidth(double) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use getDefaultAppearance() and then set that. This method will be removed Sept 2007.
setDefaultSloppySelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearanceCalculator
setDefaultSpeciesName() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. This doesn't do anything. To set the default species name use getProperties().setProperty("defaultSpeciesName", newName), which you were presumably doing already.
setDescription(String) - Method in class cytoscape.util.CyFileFilter: Sets the human readable description of this filter.
setEdgeAppearanceCalculator(EdgeAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the EdgeAppearanceCalculator for this visual style.
setEdgeAttributeValue(Edge, String, Object) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Edge
setEdgeAttributeValue(int, String, Object) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Edge
setEdgeColorCalculator(EdgeColorCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeFontFaceCalculator(EdgeFontFaceCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeFontSizeCalculator(EdgeFontSizeCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeIdentifier(String, int) - Method in class cytoscape.giny.CytoscapeFingRootGraph
setEdgeIdentifier(String, int) - Method in interface cytoscape.giny.CytoscapeRootGraph
setEdgeLabelCalculator(EdgeLabelCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeLineTypeCalculator(EdgeLineTypeCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeMaps(VisualMappingManager) - Method in class cytoscape.data.readers.GMLReader
setEdgeReverseSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setEdgeSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setEdgeSourceArrowCalculator(EdgeArrowCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeTargetArrowCalculator(EdgeArrowCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEdgeToolTipCalculator(EdgeToolTipCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept. 2007.
setEnabled(boolean) - Method in class cytoscape.visual.mappings.continuous.ContinuousUI: Enables or disables all components of the panel.
setEnabled(boolean) - Method in class cytoscape.visual.ui.ValueDisplayer: Set the ValueDisplayer active/inactive.
setExpressionData(ExpressionData) - Static method in class cytoscape.Cytoscape
setExpressionData(ExpressionData) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. Sets the expression data object associated with this network. Will be removed Feb 2007.
setExtensionListInDescription(boolean) - Method in class cytoscape.util.CyFileFilter: Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setFileNature(String) - Method in class cytoscape.util.CyFileFilter: Sets the nature of the files for this filter.
setFillColor(Color) - Method in class cytoscape.visual.NodeAppearance
setFlagged(Node, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Node,boolean)
setFlagged(Edge, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Edge,boolean)
setFlagged(Node, boolean) - Method in class cytoscape.data.FlagFilter: Deprecated. If the first argument is a Node in the referenced GraphPerspective, sets its flagged state to the value of the second argument.
setFlagged(Edge, boolean) - Method in class cytoscape.data.FlagFilter: Deprecated. If the first argument is an Edge in the referenced GraphPerspective, sets its flagged state to the value of the second argument.
setFlagged(Node, boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean)
setFlagged(Edge, boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(Collection, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(int[], boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(Collection, boolean) - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state defined by the second argument for all Edges contained in the first argument, which should be a Collection of Edge objects contained in the referenced GraphPerspective.
setFlaggedEdges(Collection, boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(int[], boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedNodes(Collection, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)
setFlaggedNodes(int[], boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)
setFlaggedNodes(Collection, boolean) - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state defined by the second argument for all Nodes contained in the first argument, which should be a Collection of Node objects contained in the referenced GraphPerspective.
setFlaggedNodes(Collection, boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean)
setFlaggedNodes(int[], boolean) - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean)
setFocus(String) - Method in class cytoscape.view.CytoscapeDesktop
setFont(Font) - Method in class cytoscape.visual.EdgeAppearance
setFont(Font) - Method in class cytoscape.visual.NodeAppearance
setFontSize(float) - Method in class cytoscape.visual.EdgeAppearance
setFontSize(float) - Method in class cytoscape.visual.NodeAppearance
setGeneDescriptors(Vector) - Method in class cytoscape.data.ExpressionData: Sets a List of Gene Descriptors.
setGeneNames(Vector) - Method in class cytoscape.data.ExpressionData: Sets a List of Gene Names.
setGlobalAppearanceCalculator(GlobalAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the GlobalAppearanceCalculator for this visual style.
setGraphPerspective(GraphPerspective) - Method in class cytoscape.CyNode
setGraphViewHandler(GraphView, GraphViewHandler) - Method in class cytoscape.view.GraphViewController: If the given giny.view.GraphView object belongs to this GraphViewController, then its GraphViewHandler is set to the given one.
setGraphViews(GraphView[]) - Method in class cytoscape.view.GraphViewController: Sets the array of giny.view.GraphView objects that this GraphViewController will keep synchronized with their corresponding giny.model.GraphPerspective objects available through their getGraphPerspective() method, the DEFAULT_GRAPH_VIEW_HANDLER is set for all the views.
setGraphViews(GraphView[], Map) - Method in class cytoscape.view.GraphViewController: Sets the array of giny.view.GraphView objects that this GraphViewController will keep synchronized with their corresponding giny.model.GraphPerspective objects available through their getGraphPerspective() method, the cytoscape.view.GraphViewHandler objects for the GraphViews are obtained from the given Map, if a GraphView in the array is not a key in the Map then DEFAULT_GRAPH_VIEW_HANDLER is used.
setHeight(double) - Method in class cytoscape.visual.NodeAppearance: Sets the height variable, but also the size variable if the node size is locked.
setIconName(String) - Method in class cytoscape.dialogs.IconPopupButton
setIconObject(Object) - Method in class cytoscape.dialogs.IconPopupButton
setIdentifier(String) - Method in class cytoscape.CyEdge
setIdentifier(String) - Method in interface cytoscape.CyNetwork: Can't Change
setIdentifier(String) - Method in class cytoscape.CyNode
setIdentifier(String) - Method in class cytoscape.giny.FingCyNetwork
setIdentifier(String) - Method in class cytoscape.util.CytoscapeMenuBar
setInt(int) - Method in class cytoscape.dialogs.IntegerEntryField
setInt(String, int) - Method in class cytoscape.dialogs.JointIntegerEntry
setInt(int) - Method in class cytoscape.util.MutableInt
setInteger(Integer) - Method in class cytoscape.dialogs.IntegerEntryField
setInteger(String, Integer) - Method in class cytoscape.dialogs.JointIntegerEntry
setInterpolator(Interpolator) - Method in class cytoscape.visual.mappings.ContinuousMapping: Sets the Mapping Interpolator.
setJustHeight(double) - Method in class cytoscape.visual.NodeAppearance: Sets only the height variable.
setJustify(int) - Method in class cytoscape.visual.LabelPosition
setJustWidth(double) - Method in class cytoscape.visual.NodeAppearance: Sets only the height variable.
setLabel(String) - Method in class cytoscape.visual.EdgeAppearance
setLabel(String) - Method in class cytoscape.visual.NodeAppearance
setLabelAnchor(int) - Method in class cytoscape.visual.LabelPosition
setLabelColor(Color) - Method in class cytoscape.visual.EdgeAppearance
setLabelColor(Color) - Method in class cytoscape.visual.NodeAppearance
setLabelPosition(LabelPosition) - Method in class cytoscape.visual.NodeAppearance
setLabelText(String) - Method in class cytoscape.util.IndeterminateProgressBar
setLeftLabel(String) - Method in class cytoscape.util.swing.JStatusBar
setLineType(LineType) - Method in class cytoscape.visual.EdgeAppearance
setListAttribute(String, String, List) - Method in interface cytoscape.data.CyAttributes: Sets a simple list of attributes.
setListAttribute(String, String, List) - Method in class cytoscape.data.CyAttributesImpl
setManifestFileName(String) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
setMapAttribute(String, String, Map) - Method in interface cytoscape.data.CyAttributes: Sets a 'simple' map of attribute values.
setMapAttribute(String, String, Map) - Method in class cytoscape.data.CyAttributesImpl
setMetadata(MetadataEntries, String) - Method in class cytoscape.data.readers.MetadataParser
setMetadata(RdfRDF) - Method in class cytoscape.data.readers.MetadataParser: Set Network Attribute called "Network Metadata" as a Map by using given JAXB object.
setMode(CytoPanelState, int) - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Sets the BiModalJSplitframe mode.
setModel(ListModel) - Method in class cytoscape.util.swing.FilterHistoryJList
setModified(CyNetwork, String) - Static method in class cytoscape.CytoscapeModifiedNetworkManager: set the state of the network
setMRUD(File) - Static method in class cytoscape.CytoscapeInit
setMRUF(File) - Static method in class cytoscape.CytoscapeInit
setName(String) - Method in class cytoscape.util.CytoscapeAction
setName(String) - Method in class cytoscape.visual.calculators.AbstractCalculator: Set the name of this calculator.
setName(String) - Method in interface cytoscape.visual.calculators.Calculator: Set calculator name.
setName(String) - Method in class cytoscape.visual.VisualStyle: Set the name of this visual style.
setNavigator(Component) - Method in class cytoscape.view.NetworkPanel
setNetworkAttributes(CyNetwork) - Method in class cytoscape.data.readers.XGMMLReader: This should be called after other classes actually creates CyNetwork object.
setNetworkView(CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
setNewNetwork(CyNetwork) - Method in class cytoscape.view.CytoscapeDesktop
setNewNetwork(CyNetwork) - Method in interface cytoscape.view.NetworkView: Deprecated.
setNodeAppearanceCalculator(NodeAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the NodeAppearanceCalculator for this visual style.
setNodeAttributeDoubleValue(int, String, double) - Static method in class cytoscape.data.NetworkData
setNodeAttributeDoubleValue(Node, String, double) - Static method in class cytoscape.data.NetworkData
setNodeAttributeDoubleValue(int, int, double) - Static method in class cytoscape.data.NetworkData
setNodeAttributeObjectValue(int, String, Object) - Static method in class cytoscape.data.NetworkData
setNodeAttributeObjectValue(Node, String, Object) - Static method in class cytoscape.data.NetworkData
setNodeAttributeObjectValue(int, int, Object) - Static method in class cytoscape.data.NetworkData
setNodeAttributeStringValue(int, String, String) - Static method in class cytoscape.data.NetworkData
setNodeAttributeStringValue(Node, String, String) - Static method in class cytoscape.data.NetworkData
setNodeAttributeStringValue(int, int, String) - Static method in class cytoscape.data.NetworkData
setNodeAttributeValue(Node, String, Object) - Static method in class cytoscape.data.NetworkData
setNodeAttributeValue(Node, String, Object, int) - Static method in class cytoscape.data.NetworkData: Attempts to set the value for a node, for a given attribute.
setNodeAttributeValue(Node, String, Object) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Node
setNodeAttributeValue(int, String, Object) - Method in class cytoscape.giny.FingCyNetwork: Return the requested Attribute for the given Node
setNodeBorderColorCalculator(NodeColorCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeFillColorCalculator(NodeColorCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeFontFaceCalculator(NodeFontFaceCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeFontSizeCalculator(NodeFontSizeCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeHeightCalculator(NodeSizeCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeIdentifier(String, int) - Method in class cytoscape.giny.CytoscapeFingRootGraph
setNodeIdentifier(String, int) - Method in interface cytoscape.giny.CytoscapeRootGraph
setNodeLabelCalculator(NodeLabelCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeLabelColorCalculator(NodeLabelColorCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeLineTypeCalculator(NodeLineTypeCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeMaps(VisualMappingManager) - Method in class cytoscape.data.readers.GMLReader
setNodeReverseSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setNodeSelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setNodeShapeCalculator(NodeShapeCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeSizeLocked(boolean) - Method in class cytoscape.visual.NodeAppearance
setNodeSizeLocked(boolean) - Method in class cytoscape.visual.NodeAppearanceCalculator
setNodesRequiredItemsEnabled() - Method in class cytoscape.view.CyMenus: Enables or disables save, print, and display nodes in new window GUI functions, based on the number of nodes in this window's graph perspective.
setNodeToolTipCalculator(NodeToolTipCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setNodeWidthCalculator(NodeSizeCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator: Deprecated. Use setCalculator(calc) instead. This method will be removed Sept 2007.
setObject(Object) - Method in class cytoscape.visual.ui.ValueDisplayer: Externally sets the object displayed.
setOffsetX(double) - Method in class cytoscape.visual.LabelPosition
setOffsetY(double) - Method in class cytoscape.visual.LabelPosition
setOntology(Ontology) - Method in class cytoscape.data.annotation.Annotation
setOntology(Ontology) - Method in class cytoscape.data.servers.OntologyServer
setOntologyRootID(String) - Static method in class cytoscape.Cytoscape
setOntologySources(Map<String, URL>) - Method in class cytoscape.data.servers.OntologyServer
setOverviewEnabled(boolean) - Method in class cytoscape.view.CyMenus
setParameter(TableModel, String, String) - Method in class cytoscape.dialogs.preferences.PreferencesDialog
setPluginFileMap(HashMap) - Method in class cytoscape.util.ZipUtil
setPreferredButtonGroup(String) - Method in class cytoscape.util.CytoscapeAction
setPreferredIndex(int) - Method in class cytoscape.util.CytoscapeAction
setPreferredMenu(String) - Method in class cytoscape.util.CytoscapeAction
setProperty(String, String) - Static method in class cytoscape.CytoscapeInit: Deprecated. Use getProperties().setProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
setProperty(String, String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
setProperty(String, String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
setRange(BoundaryRangeValues) - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Sets BoundaryRangeValues.
setRatio(double) - Method in class cytoscape.data.mRNAMeasurement
setRightLabel(String) - Method in class cytoscape.util.swing.JStatusBar
setRowHeight(int) - Method in class cytoscape.util.swing.JTreeTable: Overridden to pass the new rowHeight to the tree.
setRowHeight(int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: Sets the row height of the tree, and forwards the row height to the table.
setRunInBackground(boolean) - Method in class cytoscape.util.Exec
setSecondaryViewThreshold(int) - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().setProperty( "secondaryViewThreshold", thresh ) instead.
setSelected(Node, boolean) - Method in class cytoscape.data.SelectFilter: If the first argument is a Node in the referenced GraphPerspective, sets its selected state to the value of the second argument.
setSelected(Edge, boolean) - Method in class cytoscape.data.SelectFilter: If the first argument is an Edge in the referenced GraphPerspective, sets its selected state to the value of the second argument.
setSelected(CyNode[]) - Method in class cytoscape.ding.DingNetworkView
setSelected(NodeView[]) - Method in class cytoscape.ding.DingNetworkView
setSelected(CyEdge[]) - Method in class cytoscape.ding.DingNetworkView
setSelected(EdgeView[]) - Method in class cytoscape.ding.DingNetworkView
setSelected(CyNode[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Sets the Given nodes Selected
setSelected(NodeView[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Sets the Given nodes Selected
setSelected(CyEdge[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Sets the Given edges Selected
setSelected(EdgeView[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Sets the Given edges Selected
setSelected(CyNode[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
setSelected(NodeView[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
setSelected(CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)
setSelected(EdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)
setSelectedEdges(Collection<Edge>, boolean) - Method in class cytoscape.data.SelectFilter: Sets the selected state defined by the second argument for all Edges contained in the first argument, which should be a Collection of Edge objects contained in the referenced GraphPerspective.
setSelectedEdgeState(Collection, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a collection of edges.
setSelectedEdgeState(Edge, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a single edge.
setSelectedEdgeState(Collection, boolean) - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of a collection of edges.
setSelectedEdgeState(Edge, boolean) - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of an edge.
setSelectedIndex(int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Sets the selected index on the CytoPanel.
setSelectedIndex(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets the selected index on the CytoPanel.
setSelectedNodes(Collection<Node>, boolean) - Method in class cytoscape.data.SelectFilter: Sets the selected state defined by the second argument for all Nodes contained in the first argument, which should be a Collection of Node objects contained in the referenced GraphPerspective.
setSelectedNodeState(Collection, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a collection of nodes.
setSelectedNodeState(Node, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a single node.
setSelectedNodeState(Collection, boolean) - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of a collection of nodes.
setSelectedNodeState(Node, boolean) - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of a node.
setSelectionMode(int) - Static method in class cytoscape.Cytoscape: Sets the specified selection mode on all views.
setSelectionMode(int, GraphView) - Static method in class cytoscape.Cytoscape: Utility method to set the selection mode on the specified GraphView.
setSessionNote(String) - Method in class cytoscape.data.writers.CytoscapeSessionWriter: Set session note.
setSessionState(int) - Static method in class cytoscape.Cytoscape
setShape(byte) - Method in class cytoscape.visual.NodeAppearance
setSignificance(double) - Method in class cytoscape.data.mRNAMeasurement
setSize(double) - Method in class cytoscape.visual.NodeAppearance
setSloppySelectionColor(Color) - Method in class cytoscape.visual.GlobalAppearance
setSourceArrow(Arrow) - Method in class cytoscape.visual.EdgeAppearance
setSpecies() - Static method in class cytoscape.Cytoscape: Deprecated. This will be removed Feb 2007.
setStandardInput(String) - Method in class cytoscape.util.Exec
setState(CytoPanelState) - Method in interface cytoscape.view.cytopanels.CytoPanel: Sets the state of the CytoPanel.
setState(CytoPanelState) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets the state of the CytoPanel.
setStatusBarMsg(String) - Method in class cytoscape.view.CytoscapeDesktop: Sets the Status Bar Message.
setString(String) - Method in class cytoscape.util.MutableString
setSynonym(List<String>) - Method in class cytoscape.data.ontology.DBReference
setTargetAnchor(int) - Method in class cytoscape.visual.LabelPosition
setTargetArrow(Arrow) - Method in class cytoscape.visual.EdgeAppearance
setTaskMonitor(TaskMonitor) - Method in class cytoscape.actions.LoadNetworkTask: Sets the Task Monitor.
setTextBoxState(boolean) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel
setTitle(String) - Method in interface cytoscape.CyNetwork: Can Change
setTitle(String) - Method in class cytoscape.ding.DingNetworkView
setTitle(String) - Method in class cytoscape.giny.FingCyNetwork: Can Change
setTitle(String) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
setTitle(String) - Method in interface cytoscape.view.CyNetworkView: Sets the Title of this View
setToolTip(String) - Method in class cytoscape.visual.EdgeAppearance
setToolTip(String) - Method in class cytoscape.visual.NodeAppearance
setup() - Method in class cytoscape.dialogs.NewSlider
setupVizMapper() - Method in class cytoscape.view.CytoscapeDesktop: Create the VizMapper and the UI for it.
setUserEditable(String, boolean) - Method in interface cytoscape.data.CyAttributes: Sets the specified boolean to indicate whether or not the specified attribute should be editable by the end user.
setUserEditable(String, boolean) - Method in class cytoscape.data.CyAttributesImpl
setUserVisible(String, boolean) - Method in interface cytoscape.data.CyAttributes: Sets the specified boolean to indicate whether or not the specified attribute should be made visible to the end user.
setUserVisible(String, boolean) - Method in class cytoscape.data.CyAttributesImpl
setValue(double) - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Sets Point Value.
setValueAt(Object, int, int) - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
setValueAt(Object, Object, int) - Method in class cytoscape.util.swing.AbstractTreeTableModel
setValueAt(Object, Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Sets the value for node node, at column number column.
setValueAt(Object, int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
setViewThreshold(int) - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use setProperty( "viewThreshold", thresh ) instead.
setVisualMapperEnabled(boolean) - Method in class cytoscape.ding.DingNetworkView
setVisualMapperEnabled(boolean) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
setVisualMapperEnabled(boolean) - Method in interface cytoscape.view.CyNetworkView
setVisualMapperItemsEnabled(boolean) - Method in class cytoscape.view.CyMenus: Enables the menu items related to the visual mapper if the argument is true, else disables them.
SetVisualPropertiesAction - Class in cytoscape.actions
SetVisualPropertiesAction(ImageIcon) - Constructor for class cytoscape.actions.SetVisualPropertiesAction
SetVisualPropertiesAction(boolean) - Constructor for class cytoscape.actions.SetVisualPropertiesAction: The constructor that takes a boolean shows no label, no matter what the value of the boolean actually is.
setVisualStyle(String) - Method in class cytoscape.ding.DingNetworkView
setVisualStyle(String) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
setVisualStyle(String) - Method in interface cytoscape.view.CyNetworkView
setVisualStyle(VisualStyle) - Method in class cytoscape.view.CytoscapeDesktop
setVisualStyle(VisualStyle) - Method in class cytoscape.visual.VisualMappingManager: Sets a new visual style, and returns the old style.
setVisualStyle(String) - Method in class cytoscape.visual.VisualMappingManager: Sets a new visual style.
setWidth(double) - Method in class cytoscape.visual.NodeAppearance: Sets the width variable, but also the size variable if the node size is locked.
setWindowTitle(String) - Method in interface cytoscape.view.NetworkView: Deprecated.
ShapeNodeRealizer - Class in cytoscape.visual: This class is a replacement for the yFiles ShapeNodeRealizer class.
ShapeNodeRealizer() - Constructor for class cytoscape.visual.ShapeNodeRealizer
shortString() - Method in class cytoscape.visual.LabelPosition
shouldSelectCell(EventObject) - Method in class cytoscape.util.swing.AbstractCellEditor
show() - Method in class cytoscape.data.servers.ui.GeneOntologyWizard
ShowAllAction - Class in cytoscape.actions
ShowAllAction() - Constructor for class cytoscape.actions.ShowAllAction
showCredits(URL, String) - Static method in class cytoscape.util.CreditScreen
showDialog(Component, String, Color) - Static method in class cytoscape.util.CyColorChooser
showDialog(Frame, Font) - Static method in class cytoscape.visual.ui.PopupFontChooser
showDialog(Dialog, Font) - Static method in class cytoscape.visual.ui.PopupFontChooser
showDialog() - Method in class cytoscape.visual.ui.PopupIconChooser
showDialog(Dialog, LabelPosition) - Static method in class cytoscape.visual.ui.PopupLabelPositionChooser
showDialog(Frame, LabelPosition) - Static method in class cytoscape.visual.ui.PopupLabelPositionChooser
showDialog(Component, String, String, Object, byte) - Static method in class cytoscape.visual.ui.PopupStringChooser
showEdgeDialog() - Static method in class cytoscape.data.AttributeSaverDialog: Show a dialog box to save edge attributes
showMaps() - Method in class cytoscape.data.readers.GMLReader
showNodeDialog() - Static method in class cytoscape.data.AttributeSaverDialog: Show a dialog box to save node attributes
showSplash(ImageIcon, int) - Static method in class cytoscape.util.shadegrown.WindowUtilities
showSplash(ImageIcon, int, boolean) - Static method in class cytoscape.util.shadegrown.WindowUtilities
showSplash(JComponent, int) - Static method in class cytoscape.util.shadegrown.WindowUtilities
showSplash(JComponent, int, boolean) - Static method in class cytoscape.util.shadegrown.WindowUtilities
ShrinkExpandGraph - Class in cytoscape.dialogs: This class shifts the nodes to shrink or expand the graph: it averages the coordinates of all the nodes to find the center it translates the graph to a center at (0,0) it multiplies each node coordinate by a factor m it translates the graph back to the original center
ShrinkExpandGraphUI - Class in cytoscape.dialogs
ShrinkExpandGraphUI() - Constructor for class cytoscape.dialogs.ShrinkExpandGraphUI
SIFFileFilter - Class in cytoscape.util: FileFilter for Reading in Cytoscape SIF Files.
SIFFileFilter() - Constructor for class cytoscape.util.SIFFileFilter: Constructor.
SINGLE_EDGE - Static variable in class cytoscape.data.FlagEvent: Deprecated. Static constant indicating a change to a single Edge.
SINGLE_EDGE - Static variable in class cytoscape.data.SelectEvent: Static constant indicating a change to a single Edge.
SINGLE_NODE - Static variable in class cytoscape.data.FlagEvent: Deprecated. Static constant indicating a change to a single Node.
SINGLE_NODE - Static variable in class cytoscape.data.SelectEvent: Static constant indicating a change to a single Node.
size() - Method in class cytoscape.data.annotation.Annotation: total number of classifications. this will usually be larget than count (), since entities are frequently given two or more classifications, reflecting the multiple roles of many biological entities.
size() - Method in class cytoscape.data.annotation.Ontology
size() - Method in class cytoscape.data.ontology.Ontology
sort() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
southEastName - Static variable in class cytoscape.visual.LabelPosition
southName - Static variable in class cytoscape.visual.LabelPosition
southWestName - Static variable in class cytoscape.visual.LabelPosition
SPECIES - Static variable in class cytoscape.data.Semantics
SpeciesPanel - Class in cytoscape.data.servers.ui
SpeciesPanel() - Constructor for class cytoscape.data.servers.ui.SpeciesPanel: Creates new form SpeciesPanel
SpeciesPanelDescriptor - Class in cytoscape.data.servers.ui
SpeciesPanelDescriptor() - Constructor for class cytoscape.data.servers.ui.SpeciesPanelDescriptor
start() - Method in class cytoscape.util.SwingWorker: Start the worker thread.
startMonitor(boolean) - Method in class cytoscape.util.CytoscapeProgressMonitor: Starts the monitor by running the monitoredTask.
stateChanged(ChangeEvent) - Method in class cytoscape.dialogs.NewSlider.MJSlider
stateChanged(ChangeEvent) - Method in class cytoscape.dialogs.PhoebeNodeControl.SliderListener
stateChanged(ChangeEvent) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Our implementation of the ChangeListener interface, to determine when new tab has been selected
stateChanged(ChangeEvent) - Method in class cytoscape.view.NetworkViewManager: For Tabbed Panes
stateChanged(ChangeEvent) - Method in class cytoscape.visual.mappings.discrete.DiscreteUI: Underlying DiscreteMapping State has changed.
stateChanged(ChangeEvent) - Method in class cytoscape.visual.ui.DefaultPanel
stateChanged(ChangeEvent) - Method in class cytoscape.visual.ui.VizMapUI.StyleSelector: Called when the underlying VisualMappingManger object changes
status - Class in cytoscape.data.servers
status() - Constructor for class cytoscape.data.servers.status
stop() - Method in interface cytoscape.util.MonitoredTask: Stops the task by simply setting currentProgress to lengthOfTask, or if a boolean "done" variable is used, setting it to true.
stopCellEditing() - Method in class cytoscape.util.swing.AbstractCellEditor
stopListening() - Method in class cytoscape.view.GraphViewController: It temporarily removes this GraphViewController as a listener for all giny.model.GraphPerspective objects that it currently listens to
stopListening(GraphView) - Method in class cytoscape.view.GraphViewController: It temporarily removes this GraphViewController listener from the giny.model.GraphPerspective object that the given giny.view.GraphView views.
storeCatalog(CalculatorCatalog, File) - Static method in class cytoscape.visual.CalculatorIO: Writes the contents of a CalculatorCatalog to the specified file as a properties file.
StraightenSelectedEdgesAction - Class in cytoscape.actions
StraightenSelectedEdgesAction() - Constructor for class cytoscape.actions.StraightenSelectedEdgesAction
STRING - Static variable in class cytoscape.data.readers.GMLTree: When getting a vector, used to specify the type for the contained objects
STRING - Static variable in class cytoscape.visual.ui.ValueDisplayer: Display and get input for a string
STRING_TYPE - Static variable in class cytoscape.data.NetworkData
StringParser - Class in cytoscape.visual.parsers: Implements the ValueParser interface for String return values, by simply returning the supplied argument.
StringParser() - Constructor for class cytoscape.visual.parsers.StringParser
stringValue() - Method in class cytoscape.data.readers.GMLNode: Get the value of this node as a String
SubjectBase - Class in cytoscape.visual: Abstract Base Class for Subject in the Subject / Observer Pattern.
SubjectBase() - Constructor for class cytoscape.visual.SubjectBase
suppressView() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.
SwingWorker - Class in cytoscape.util: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class cytoscape.util.SwingWorker: Start a thread that will call the construct method and then exit.

T

TABBED_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in TabbedPanes ( like Mozilla )
tableChanged(TableModelEvent) - Method in class cytoscape.dialogs.NetworkMetaDataDialog
takeArgs(String[]) - Method in class cytoscape.util.CytoscapeAction
taxIdToName(String, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
terminal - Variable in class cytoscape.data.readers.GMLNode: True if this node is a terminal.
TEXT - Static variable in interface cytoscape.init.CyInitParams
textAsShape(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to draw text as shape when rendering node and edge labels.
TextFileReader - Class in cytoscape.data.readers
TextFileReader(String) - Constructor for class cytoscape.data.readers.TextFileReader
TextHttpReader - Class in cytoscape.data.readers
TextHttpReader(String) - Constructor for class cytoscape.data.readers.TextHttpReader
TextJarReader - Class in cytoscape.data.readers
TextJarReader(String) - Constructor for class cytoscape.data.readers.TextJarReader
Thesaurus - Class in cytoscape.data.synonyms: todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name. a good example is from the d16s3098 marker region studied in the ISB's JDRF project: PHEMX -> NM_005705 PHEMX -> NM_139022 PHEMX -> NM_139023 PHEMX -> NM_139024 these are (I believe) mRNA splice variants. what to do?
Thesaurus(String) - Constructor for class cytoscape.data.synonyms.Thesaurus
ThesaurusFlatFileReader - Class in cytoscape.data.synonyms.readers: Read synonyms from flat file.
ThesaurusFlatFileReader(String) - Constructor for class cytoscape.data.synonyms.readers.ThesaurusFlatFileReader
ThesaurusFlatFileReader(BufferedReader, boolean) - Constructor for class cytoscape.data.synonyms.readers.ThesaurusFlatFileReader
ToggleVisualMapperAction - Class in cytoscape.actions: This class implements two menu items that allow enabling and disabling the visual mapper.
ToggleVisualMapperAction() - Constructor for class cytoscape.actions.ToggleVisualMapperAction
toggleVisualMapperEnabled() - Method in class cytoscape.ding.DingNetworkView
toggleVisualMapperEnabled() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated.
toggleVisualMapperEnabled() - Method in interface cytoscape.view.CyNetworkView
toString() - Method in class cytoscape.CytoscapeVersion
toString() - Method in class cytoscape.data.annotation.Annotation
toString() - Method in class cytoscape.data.annotation.AnnotationDescription
toString() - Method in class cytoscape.data.annotation.Ontology
toString() - Method in class cytoscape.data.annotation.OntologyDescription
toString() - Method in class cytoscape.data.annotation.OntologyTerm
toString(byte) - Static method in class cytoscape.data.CyAttributesUtils: Return a String representation of the various CyAttributes types returned by methods like CyAttributes.getType() and MultiHashMapDefinition.getAttributeKeysapceDimensionTypes().
toString() - Method in class cytoscape.data.FlagEvent: Deprecated. Returns a String representation of this object's data.
toString() - Method in class cytoscape.data.Interaction
toString() - Method in class cytoscape.data.mRNAMeasurement
toString() - Method in enum cytoscape.data.ontology.GeneOntology.GOAspect
toString() - Method in class cytoscape.data.ontology.Ontology
toString() - Method in enum cytoscape.data.ontology.OntologyTerm.SynonymType
toString() - Method in enum cytoscape.data.ontology.readers.DBXrefKeywords
toString() - Method in enum cytoscape.data.ontology.readers.OBOHeaderTags
toString() - Method in enum cytoscape.data.ontology.readers.OBOTags
toString() - Method in class cytoscape.data.ontology.Triple
toString() - Method in class cytoscape.data.readers.GMLNode: Return the string representation of this GMLNode.
toString() - Method in class cytoscape.data.readers.GMLTree: Get string representation
toString() - Method in enum cytoscape.data.readers.MetadataEntries
toString() - Method in class cytoscape.data.SelectEvent: Returns a String representation of this object's data.
toString() - Method in class cytoscape.data.synonyms.Thesaurus
toString() - Method in class cytoscape.util.CytoscapeMenuBar: Delegates to CytoscapeMenuBar.getIdentifier().
toString() - Method in class cytoscape.util.MinMaxDouble
toString() - Method in class cytoscape.util.MinMaxInt
toString() - Method in class cytoscape.view.cytopanels.CytoPanelState
toString() - Method in class cytoscape.visual.Arrow
toString() - Method in class cytoscape.visual.calculators.AbstractCalculator: Get the name of this calculator.
toString() - Method in interface cytoscape.visual.calculators.Calculator: Gets calculator name.
toString() - Method in class cytoscape.visual.LabelPosition
toString() - Method in class cytoscape.visual.LineType
toString() - Method in class cytoscape.visual.mappings.BoundaryRangeValues
toString() - Method in class cytoscape.visual.VisualStyle: Returns the name of this object, as returned by getName.
Transform - Class in cytoscape.util: Apply XSLT to an XML document
Transform(String, String, String) - Constructor for class cytoscape.util.Transform
TRAPEZOID - Static variable in class cytoscape.visual.ShapeNodeRealizer
TRAPEZOID_2 - Static variable in class cytoscape.visual.ShapeNodeRealizer
traverseAttributeValues(String, String, CyAttributes, AttributeValueVisitor) - Static method in class cytoscape.data.CyAttributesUtils: Traverse all the values of a given attribute applying an AttributeValueVisitor to each value.
TreeTableModel - Interface in cytoscape.util.swing: TreeTableModel is the model used by a JTreeTable.
TreeTableModelAdapter - Class in cytoscape.util.swing: This is a wrapper class takes a TreeTableModel and implements the table model interface.
TreeTableModelAdapter(TreeTableModel, JTree) - Constructor for class cytoscape.util.swing.TreeTableModelAdapter
TRIANGLE - Static variable in class cytoscape.visual.ShapeNodeRealizer
Triple - Class in cytoscape.data.ontology: Extract partial graph structure.
Triple(Term, Term, Term, String, String) - Constructor for class cytoscape.data.ontology.Triple
TYPE_BOOLEAN - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Boolean.
TYPE_BOOLEAN - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Boolean.
TYPE_COMPLEX - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a data structure of arbitrary complexity, e.g. anything more complex than a 'simple' list or a 'simple' map.
TYPE_FLOATING - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Double.
TYPE_FLOATING_POINT - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Double.
TYPE_INTEGER - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Integer.
TYPE_INTEGER - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Integer.
TYPE_SIMPLE_LIST - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a 'simple' list.
TYPE_SIMPLE_MAP - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a 'simple' hash map.
TYPE_STRING - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.String.
TYPE_STRING - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.String.
TYPE_UNDEFINED - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to an attribute which has not been defined.

U

undefineAttribute(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: WARNING: All bound attribute values on objects will go away in this attribute namespace when this method is called.
undo - Static variable in class cytoscape.view.CytoscapeDesktop: Cytoscape UndoManager
UndoManager - Class in cytoscape.util
UndoManager(CyMenus) - Constructor for class cytoscape.util.UndoManager
unFlagAllEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.unselectAllEdges()
unflagAllEdges() - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state to false for all Edges in the GraphPerspective.
unFlagAllEdges() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.unselectAllEdges()
unFlagAllNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.unselectAllNodes()
unflagAllNodes() - Method in class cytoscape.data.FlagFilter: Deprecated. Sets the flagged state to false for all Nodes in the GraphPerspective.
unFlagAllNodes() - Method in class cytoscape.giny.FingCyNetwork: Deprecated. As of 2.3, replaced by FingCyNetwork.unselectAllNodes()
unHideAll(GraphView) - Static method in class cytoscape.actions.GinyUtils
unHideAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
unHideNodesAndInterconnectingEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
UnHideSelectedAction - Class in cytoscape.actions
UnHideSelectedAction(CyNetworkView) - Constructor for class cytoscape.actions.UnHideSelectedAction
unHideSelectedEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
UnHideSelectedEdgesAction - Class in cytoscape.actions
UnHideSelectedEdgesAction() - Constructor for class cytoscape.actions.UnHideSelectedEdgesAction
unHideSelectedNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
UnHideSelectedNodesAction - Class in cytoscape.actions
UnHideSelectedNodesAction() - Constructor for class cytoscape.actions.UnHideSelectedNodesAction
UNKNOWN - Static variable in class cytoscape.CyNetworkEvent: This type is used when the requested type is unknown to this class.
UNKNOWN - Static variable in class cytoscape.data.ExpressionData: Significance value: UNKNOWN.
unlockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
unselectAllEdges() - Method in interface cytoscape.CyNetwork: Sets the selected state of all edges in this CyNetwork to false
unselectAllEdges() - Method in class cytoscape.data.SelectFilter: Sets the selected state to false for all Edges in the GraphPerspective.
unselectAllEdges() - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of all edges in this CyNetwork to false
unselectAllNodes() - Method in interface cytoscape.CyNetwork: Sets the selected state of all nodes in this CyNetwork to false
unselectAllNodes() - Method in class cytoscape.data.SelectFilter: Sets the selected state to false for all Nodes in the GraphPerspective.
unselectAllNodes() - Method in class cytoscape.giny.FingCyNetwork: Sets the selected state of all nodes in this CyNetwork to false
unselectGraphViewEdges(GraphView, Edge[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It unselects the edges in the array in the given giny.view.GraphView object
unselectGraphViewNodes(GraphView, Node[]) - Static method in class cytoscape.view.BasicGraphViewHandler: It unselects the nodes in the array in the given giny.view.GraphView object
updateGraphView(GraphView) - Method in class cytoscape.view.BasicGraphViewHandler: Updates the given graph_view to contain node and edge visual representations of only nodes and edges that are in its GraphPerspective
updateGraphView(GraphView) - Method in interface cytoscape.view.GraphViewHandler: Updates graph_view so that it is synchronized with its giny.model.GraphPerspective Useful if GraphPerspectiveChangeEvents haven't been handled, and a graph_view must be made synchronized with its GraphPerspective.
updateNetworkTitle(CyNetwork) - Method in class cytoscape.view.NetworkViewManager
updateStatusLabel() - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Resets the info label status bar text with the current number of nodes, edges, selected nodes, and selected edges.
updateTitle(CyNetwork) - Method in class cytoscape.view.NetworkPanel: update a network title
updateUI() - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: updateUI is overridden to set the colors of the Tree's renderer to match that of the table.
updateUI() - Method in class cytoscape.util.swing.JTreeTable: Overridden to message super and forward the method to the tree.
UPPER - Static variable in class cytoscape.visual.mappings.FlatInterpolator
URLimportAdvancedDialog - Class in cytoscape.dialogs
URLimportAdvancedDialog(JDialog, boolean, String, Bookmarks) - Constructor for class cytoscape.dialogs.URLimportAdvancedDialog: Creates new form URLimportAdvancedDialog
URLimportAdvancedDialog() - Constructor for class cytoscape.dialogs.URLimportAdvancedDialog
URLimportAdvancedDialog.BookmarkDialog - Class in cytoscape.dialogs
URLimportAdvancedDialog.BookmarkDialog(JDialog, boolean, Bookmarks, String, String, DataSource) - Constructor for class cytoscape.dialogs.URLimportAdvancedDialog.BookmarkDialog: Creates new form NewBookmarkDialog
urlPattern - Static variable in class cytoscape.util.FileUtil: A string that defines a simplified java regular expression for a URL.
URLUtil - Class in cytoscape.util
URLUtil() - Constructor for class cytoscape.util.URLUtil
useView() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getMode() instead.

V

validatedPluginData(Component, String) - Method in class cytoscape.dialogs.preferences.PreferenceValueDialog: Deprecated. no longer used by anyting. Will leave this world Dec 2007.
validateNewPlugins(String, Vector, Vector) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated.
value - Variable in class cytoscape.data.readers.KeyValue
VALUE_NOT_A_DOUBLE - Static variable in class cytoscape.data.NetworkData
valueChanged(ListSelectionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog: Called by ListSelectionListener interface when a table item is selected.
valueChanged(ListSelectionEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog: Called by ListSelectionListener interface when a table item is selected.
valueChanged(TreeSelectionEvent) - Method in class cytoscape.view.NetworkPanel
ValueChangeListener - Class in cytoscape.visual.mappings.discrete: Listens to a ValueDisplayer and updates the underlying DiscreteMapping class.
ValueChangeListener(DiscreteMapping, Object) - Constructor for class cytoscape.visual.mappings.discrete.ValueChangeListener: Constructs a ValueChangeListener.
ValueDisplayer - Class in cytoscape.visual.ui: Given an Object, figures out the class of the object and creates a JButton suitable for displaying the value of that object.
valueForPathChanged(TreePath, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
ValueListener - Class in cytoscape.visual.mappings.continuous: Listens for User Value Selection.
ValueListener(ContinuousUI, ContinuousMapping, int, int) - Constructor for class cytoscape.visual.mappings.continuous.ValueListener: Constructor.
valueOf(String) - Static method in enum cytoscape.data.ontology.GeneOntology.GOAspect: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.ontology.OntologyTerm.SynonymType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.ontology.readers.DBXrefKeywords: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.ontology.readers.OBOHeaderTags: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.ontology.readers.OBOTags: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.readers.MetadataEntries: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.servers.OntologyServer.OntologyType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum cytoscape.data.synonyms.AliasType: Returns the enum constant of this type with the specified name.
ValueParser - Interface in cytoscape.visual.parsers: Interface to classes that parse a String value into a particular class of object.
values() - Static method in enum cytoscape.data.ontology.GeneOntology.GOAspect: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.ontology.OntologyTerm.SynonymType: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.ontology.readers.DBXrefKeywords: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.ontology.readers.OBOHeaderTags: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.ontology.readers.OBOTags: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.readers.MetadataEntries: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.servers.OntologyServer.OntologyType: Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum cytoscape.data.synonyms.AliasType: Returns an array containing the constants of this enum type, in the order they're declared.
version - Static variable in class cytoscape.CytoscapeVersion
viewExists(String) - Static method in class cytoscape.Cytoscape
visitingAttributeValue(String, String, CyAttributes, Object[], Object) - Method in interface cytoscape.data.AttributeValueVisitor: Perform whatever operations are desired on the given attribute value.
VISUAL_STYLE - Static variable in class cytoscape.view.CytoscapeDesktop
VisualMappingManager - Class in cytoscape.visual: Top-level class for controlling the visual appearance of nodes and edges according to data attributes, as well as some global visual attributes.
VisualMappingManager(CyNetworkView) - Constructor for class cytoscape.visual.VisualMappingManager
VisualStyle - Class in cytoscape.visual: This class encapsulates a full set of visual mapping specifications for Cytoscape.
VisualStyle(String) - Constructor for class cytoscape.visual.VisualStyle: Simple constructor, creates default node/edge/global appearance calculators.
VisualStyle(String, NodeAppearanceCalculator, EdgeAppearanceCalculator, GlobalAppearanceCalculator) - Constructor for class cytoscape.visual.VisualStyle: Full constructor.
VisualStyle(VisualStyle) - Constructor for class cytoscape.visual.VisualStyle: Copy constructor.
VisualStyle(VisualStyle, String) - Constructor for class cytoscape.visual.VisualStyle: Copy constructor with new name.
VisualStyleBuilder - Class in cytoscape.data.readers: Based on the graph/node/edge view information, build new Visual Style.
VisualStyleBuilder() - Constructor for class cytoscape.data.readers.VisualStyleBuilder
VisualStyleBuilder(String, Map, Map, Map) - Constructor for class cytoscape.data.readers.VisualStyleBuilder: Accept List of JAXB graphics objects
VisualStyleBuilderDialog - Class in cytoscape.dialogs
VisualStyleBuilderDialog(String, GraphReader, Frame, boolean) - Constructor for class cytoscape.dialogs.VisualStyleBuilderDialog: Creates new form VisualStyleBuilderDialog
visualStyleChanged() - Method in class cytoscape.visual.ui.VizMapAttrTab: Alert the VizMapAttrTab that the relevant visual style has changed.
visualStyleChanged() - Method in class cytoscape.visual.ui.VizMapFontTab
visualStyleChanged() - Method in class cytoscape.visual.ui.VizMapSizeTab
visualStyleChanged() - Method in class cytoscape.visual.ui.VizMapTab: When the currently selected visual styles changed, a new set of calculators with their corresponding interfaces must be switched into the UI.
visualStyleChanged() - Method in class cytoscape.visual.ui.VizMapUI: When the currently selected visual styles changed, a new set of calculators with their corresponding interfaces must be switched into the UI.
VIZMAP_ENABLED - Static variable in class cytoscape.view.CytoscapeDesktop
VIZMAP_LOADED - Static variable in class cytoscape.Cytoscape
VIZMAP_PROPS - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
VIZMAP_RESTORED - Static variable in class cytoscape.Cytoscape
VizMapAttrTab - Class in cytoscape.visual.ui: VizMapAttrTab implements a tab for each mappable attribute of the graph except the size tab, which is a special case.
VizMapAttrTab(VizMapUI, JTabbedPane, int, VisualMappingManager, byte) - Constructor for class cytoscape.visual.ui.VizMapAttrTab: create a new tab representing the underlying type.
VizMapBypassNetworkListener - Class in cytoscape.visual.ui: Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created.
VizMapBypassNetworkListener() - Constructor for class cytoscape.visual.ui.VizMapBypassNetworkListener
vizmapEdge(EdgeView, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
VizMapFontTab - Class in cytoscape.visual.ui: Create a tab for the Set Visual Properties dialog for Node and Edge Font.
VizMapFontTab(VizMapUI, JTabbedPane, int, VisualMappingManager, byte) - Constructor for class cytoscape.visual.ui.VizMapFontTab: create a new tab for font face and size.
vizmapNode(NodeView, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
VizMapSizeTab - Class in cytoscape.visual.ui: Create a tab for the Set Visual Properties dialog for Node Size.
VizMapSizeTab(VizMapUI, JTabbedPane, int, VisualMappingManager, byte) - Constructor for class cytoscape.visual.ui.VizMapSizeTab: create a new tab representing the node size.
VizMapSizeTab(VizMapUI, JTabbedPane, int, VisualMappingManager, byte, boolean) - Constructor for class cytoscape.visual.ui.VizMapSizeTab: create a new tab representing the node size.
VizMapTab - Class in cytoscape.visual.ui: VizMapTab defines an organizational abstract class for tabs in the Set Visual Properties dialog.
VizMapUI - Class in cytoscape.visual.ui: Primary UI class for the Set Visual Properties dialog box.
VizMapUI(VisualMappingManager, JFrame) - Constructor for class cytoscape.visual.ui.VizMapUI: Make and display the Set Visual Properties UI.
VizMapUI.StyleSelector - Class in cytoscape.visual.ui: StyleSelector implements the style selection control.
VizUIUtilities - Class in cytoscape.visual.ui: This class provides utility functions for the UI package.
VizUIUtilities() - Constructor for class cytoscape.visual.ui.VizUIUtilities

W

wasCanceled() - Method in interface cytoscape.util.MonitoredTask
westName - Static variable in class cytoscape.visual.LabelPosition
whetherField2IsEnabled() - Method in class cytoscape.dialogs.JointIntegerEntry
WHITE_ARROW - Static variable in class cytoscape.visual.Arrow
WHITE_CIRCLE - Static variable in class cytoscape.visual.Arrow
WHITE_DELTA - Static variable in class cytoscape.visual.Arrow
WHITE_DIAMOND - Static variable in class cytoscape.visual.Arrow
WHITE_T - Static variable in class cytoscape.visual.Arrow
windowGainedFocus(WindowEvent) - Method in class cytoscape.view.NetworkViewManager: For Exteernal Frames
windowLostFocus(WindowEvent) - Method in class cytoscape.view.NetworkViewManager
WindowUtilities - Class in cytoscape.util.shadegrown: WindowUtilities keeps track of open windows and may close down the JVM when all primary windows are closed (see #setExitJVMWhenAllWindowsClose and #addPrimaryWindow( Window )).
WindowUtilities() - Constructor for class cytoscape.util.shadegrown.WindowUtilities
write(Writer) - Method in class cytoscape.data.writers.XGMMLWriter: Write the XGMML file.
writeAttributes(CyAttributes, String, Writer) - Static method in class cytoscape.data.writers.CyAttributesWriter
writeAttributes() - Method in class cytoscape.data.writers.CyAttributesWriter2: Write out the state for the given attributes
writeGML(CyNetwork, CyNetworkView, List) - Method in class cytoscape.data.readers.GMLWriter: Given an object tree given in oldList, update it with the information provided in network and optionall view (if view is not null).
writeInteractions(CyNetwork, Writer, TaskMonitor) - Static method in class cytoscape.data.writers.InteractionWriter: Writes a SIF formatted string of the specified network to the specified writer.
writeInteractions(CyNetwork, Writer) - Static method in class cytoscape.data.writers.InteractionWriter: Writes a SIF formatted string of the specified network to the specified writer.
writeSessionToDisk() - Method in class cytoscape.data.writers.CytoscapeSessionWriter: Write current session to a local .cys file.
writeToFile() - Method in class cytoscape.util.JnlpWriterUtil
WRONG_ATTRIBUTE_TYPE - Static variable in class cytoscape.data.NetworkData

X

XGMML_EXT - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
XGMMLException - Exception in cytoscape.data.readers: Exception for XGMML Reader.
XGMMLException(String) - Constructor for exception cytoscape.data.readers.XGMMLException
XGMMLFileFilter - Class in cytoscape.util: FileFilter for Reading in XGMML Files.
XGMMLFileFilter() - Constructor for class cytoscape.util.XGMMLFileFilter: Constructor.
XGMMLReader - Class in cytoscape.data.readers: XGMML file reader.
XGMMLReader(String) - Constructor for class cytoscape.data.readers.XGMMLReader: Constructor.
XGMMLReader(InputStream) - Constructor for class cytoscape.data.readers.XGMMLReader: Constructor.
XGMMLReader(String, TaskMonitor) - Constructor for class cytoscape.data.readers.XGMMLReader
XGMMLWriter - Class in cytoscape.data.writers: Write network and attributes in XGMML format and
marshall it in a streme.
XGMMLWriter(CyNetwork, CyNetworkView) - Constructor for class cytoscape.data.writers.XGMMLWriter: Constructor.

Z

ZipUtil - Class in cytoscape.util: Compression-related methods mainly for Session Writer.
ZipUtil(String, String[], String) - Constructor for class cytoscape.util.ZipUtil: Constructor.
ZipUtil(String, String[], String, String) - Constructor for class cytoscape.util.ZipUtil: Constructor.
zoom() - Method in class cytoscape.actions.ZoomAction
ZoomAction - Class in cytoscape.actions
ZoomAction(double) - Constructor for class cytoscape.actions.ZoomAction
ZoomSelectedAction - Class in cytoscape.actions
ZoomSelectedAction() - Constructor for class cytoscape.actions.ZoomSelectedAction

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