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AboutDialog - Class in cytoscape.util.swing: About page for web service clients or other plugins.
AboutDialog(Frame, boolean) - Constructor for class cytoscape.util.swing.AboutDialog: Creates new form WSAboutDialog
AboutDialog(Frame, boolean, String, Icon, URL) - Constructor for class cytoscape.util.swing.AboutDialog: Creates a new AboutDialog object.
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor: DOCUMENT ME!
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor: DOCUMENT ME!
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.OboPanelDescriptor: DOCUMENT ME!
aboutToDisplayPanel() - Method in class cytoscape.data.servers.ui.SpeciesPanelDescriptor: DOCUMENT ME!
aboutToHidePanel() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor: DOCUMENT ME!
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: Deprecated. Will be removed 5/2008
AbstractCalculator(String, ObjectMapping, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.AbstractCalculator: Creates a new AbstractCalculator object.
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: Creates a new AbstractGraphReader object.
AbstractLayout - Class in cytoscape.layout: The AbstractLayout provides nice starting point for Layouts written for Cytoscape.
AbstractLayout() - Constructor for class cytoscape.layout.AbstractLayout: The Constructor is null
AbstractTreeTableModel - Class in cytoscape.util.swing
AbstractTreeTableModel(Object) - Constructor for class cytoscape.util.swing.AbstractTreeTableModel: Creates a new AbstractTreeTableModel object.
AbstractVisualProperty - Class in cytoscape.visual.properties
AbstractVisualProperty() - Constructor for class cytoscape.visual.properties.AbstractVisualProperty
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(URL, String) - Method in class cytoscape.util.CyFileFilter: Returns true if this class is capable of processing the specified URL
accept(File) - Method in class cytoscape.util.XGMMLFileFilter: Indicates which files the XGMMLFileFilter accepts.
ACTION_TITLE - Static variable in class cytoscape.actions.DeleteAction
actionHelp() - Method in class cytoscape.util.CytoscapeAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignHorizontalAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignVerticalAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlphabeticalSelectionAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AnimatedLayoutAction: Deprecated. DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BackgroundColorAction: Deprecated. Captures User Menu Selection.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BendSelectedEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BirdsEyeViewAction: Deprecated. DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BookmarkAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CloneGraphInNewWindowAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CreateNetworkViewAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CytoPanelAction: Toggles the cytopanel state.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeleteAction: Delete all selected nodes, edges, edges adjacent to the selected nodes, and any nodes/edges passed as arguments.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeselectAllAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkViewAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.EdgeManipulationAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExitAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAction: DOCUMENT ME!
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: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportEdgeAttributesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportNodeAttributesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportVizmapAction: Get file name and execute the saving task
actionPerformed(ActionEvent) - Method in class cytoscape.actions.FitContentAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.GraphObjectSelectionAction: This Should go away
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpAboutAction: Show about page.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpContactHelpDeskAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpContentsAction: Merely calls actionPerformed on the CSH.DisplayHelpFromSource object.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportBioDataServerAction: DOCUMENT ME!
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: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ListFromFileSelectionAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.MapOntologyAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewNetworkAction: create the new network and view
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewSessionAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesOnlyAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.OpenSessionAction: Clear current session and open the cys file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PluginManagerAction: Gets the lists of plugins and creates the ManagerDialog for users.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PluginUpdateAction
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PreferenceAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PrintAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ProxyServerAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.RotateSelectedNodesAction: DOCUMENT ME!
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.SelectAdjacentEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectConnectedNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectFirstNeighborsAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SetVisualPropertiesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowAllAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowGraphicsDetailsAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.StraightenSelectedEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ToggleVisualMapperAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedEdgesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedNodesAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.WebServiceNetworkImportAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomSelectedAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.data.annotation.AnnotationGui: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.data.servers.ui.OboPanelDescriptor: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.EditNetworkTitleDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ExpressionDataPopupTable.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GinyEdgeControlDialog.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GraphObjectSelection: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton: DOCUMENT ME!
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: DOCUMENT ME!
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.plugins.PluginManageDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.PopupTextArea.OKAction
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog.EditBookmarkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.ProxyServerDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ShrinkExpandGraph: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.URLimportAdvancedDialog.BookmarkDialog
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.LayoutSettingsDialog: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.SettingsAction
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.StaticLayoutMenu: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction: DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.util.undo.RedoAction: Tries to run redo() on the top edit of the edit stack.
actionPerformed(ActionEvent) - Method in class cytoscape.util.undo.UndoAction: Tries to run undo() on the top edit of the edit stack.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.continuous.AddPointListener: User Initiated Action.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.continuous.ContinuousUI: Deprecated. 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: DOCUMENT ME!
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: DOCUMENT ME!
add(CyLayoutAlgorithm) - Method in class cytoscape.layout.ui.LayoutMenu: DOCUMENT ME!
add(Tunable) - Method in interface cytoscape.util.ModuleProperties: This method is used to add a new Tunable to the LayoutProperties list.
add(Tunable) - Method in class cytoscape.util.ModulePropertiesImpl: This method is used to add a new Tunable to the LayoutProperties list.
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: DOCUMENT ME!
addAction(String, Action) - Method in class cytoscape.util.CytoscapeMenuBar: DOCUMENT ME!
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: Add the menu item.
addAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus: Add the menu item in a specific position
addActionListener(ActionListener) - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
addActionListener(ActionListener) - Method in class cytoscape.dialogs.ExportBitmapOptionsDialog: Add an action for when the "OK" button is pressed.
addAllAnnotationToNodes(AnnotationDescription, String) - Method in class cytoscape.data.annotation.OntologyMapperDialog: DOCUMENT ME!
addAlternateCommonName(String, String) - Method in class cytoscape.data.synonyms.Thesaurus: DOCUMENT ME!
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
addAnnotation(Annotation) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
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: DOCUMENT ME!
addAnnotationToNodes(AnnotationDescription, int, String) - Method in class cytoscape.data.annotation.OntologyMapperDialog: DOCUMENT ME!
addArguments(ArrayList<String>) - Method in class cytoscape.util.JnlpWriterUtil
addAuthor(String, String) - Method in class cytoscape.plugin.PluginInfo: Adds an author to the list of authors.
addButtonActionListener(ActionListener) - Method in class cytoscape.data.servers.ui.AnotationPanel: DOCUMENT ME!
addCalculator(Calculator) - Method in class cytoscape.visual.CalculatorCatalog: Add any calculator to the catalog.
addCategory(String, List<DownloadableInfo>, PluginManageDialog.PluginInstallStatus) - Method in class cytoscape.dialogs.plugins.PluginManageDialog: Adds a category and it's list of plugins to the appropriate tree (based on Status) in the dialog.
addCategory(String, DownloadableInfo, List<DownloadableInfo>) - Method in class cytoscape.dialogs.plugins.PluginUpdateDialog: DOCUMENT ME
addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor: DOCUMENT ME!
addChangeListener(ChangeListener, byte) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Will be removed 5/2008
addChangeListener(ChangeListener, VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
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.
addChild(TreeNode) - Method in class cytoscape.dialogs.plugins.TreeNode: Adds newChild to this node if children are allowed.
addChildren(TreeNode[]) - Method in class cytoscape.dialogs.plugins.TreeNode: Adds all children to the child list of this node if children are allowed.
addComponentToSouth(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Add a component to the CytoPanel just below the TabbedPane.
addContainer(int) - Method in class cytoscape.data.annotation.OntologyTerm: DOCUMENT ME!
addContentType(String) - Method in class cytoscape.util.CyFileFilter: Adds a content-type to filter against.
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
addCytoscapeVersion(String) - Method in class cytoscape.plugin.DownloadableInfo: Contains a list of all the Cytoscape versions this object is compatible with.
addCyWebServiceEventListener(CyWebServiceEventListener) - Method in class cytoscape.data.webservice.CyWebServiceEventSupport: DOCUMENT ME!
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
addEdgeContextMenuItems(EdgeView, JPopupMenu) - Method in class cytoscape.data.webservice.ui.WebServiceContextMenu: DOCUMENT ME!
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. DOCUMENT ME!
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView: DOCUMENT ME!
addEdit(UndoableEdit) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated. Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008.
addError(String) - Method in class cytoscape.dialogs.ErrorDialog
addError(Throwable) - Method in class cytoscape.dialogs.ErrorDialog
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.
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.
addGroupChangeListener(CyGroupChangeListener) - Static method in class cytoscape.groups.CyGroupManager: Add a new change listener to our list of listeners
addInnerEdge(CyEdge) - Method in interface cytoscape.groups.CyGroup: Add an inner edge to the map.
addInnerEdge(CyEdge) - Method in class cytoscape.groups.CyGroupImpl: Add an inner edge to the map.
addItem(Object) - Method in class cytoscape.util.swing.FilterHistoryJList: DOCUMENT ME!
addItems(String[]) - Method in class cytoscape.dialogs.plugins.PluginUrlDialog: DOCUMENT ME!
addJars(String, ArrayList<String>, String) - Method in class cytoscape.util.JnlpWriterUtil
addLayout(CyLayoutAlgorithm, String) - Static method in class cytoscape.layout.CyLayouts: Add a layout to the layout manager's list.
addListenerToOk(ActionListener) - Method in class cytoscape.dialogs.plugins.LicenseDialog
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: DOCUMENT ME!
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
addNode(CyNode) - Method in interface cytoscape.groups.CyGroup: Add a new node to this group
addNode(CyNode) - Method in class cytoscape.groups.CyGroupImpl: Add a new node to this group
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.
addNodeContextMenuItems(NodeView, JPopupMenu) - Method in class cytoscape.data.webservice.ui.WebServiceContextMenu: Add this menu to the node context menu.
addNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
addNodeContextMenuListener(NodeContextMenuListener) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. DOCUMENT ME!
addNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView: DOCUMENT ME!
addNodeToParent(TreeNode, TreeNode) - Method in class cytoscape.dialogs.plugins.ManagerModel: Adds node to given parent, fires event
addObject(DownloadableInfo) - Method in class cytoscape.dialogs.plugins.TreeNode: Adds a PluginInfo object to this node.
addOntology(Ontology) - Method in class cytoscape.data.servers.OntologyServer
addOntology(URL, OntologyServer.OntologyType, String, String) - Method in class cytoscape.data.servers.OntologyServer
addOuterEdge(CyEdge) - Method in interface cytoscape.groups.CyGroup: Add an outer edge to the map.
addOuterEdge(CyEdge) - Method in class cytoscape.groups.CyGroupImpl: Add an outer edge to the map.
addParent(int) - Method in class cytoscape.data.annotation.OntologyTerm: DOCUMENT ME!
addPlugin(DownloadableInfo) - Method in class cytoscape.dialogs.plugins.LicenseDialog
addPlugin(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated. DOCUMENT ME!
addPlugin(URL) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated. DOCUMENT ME!
addPlugin(PluginInfo) - Method in class cytoscape.plugin.ThemeInfo
addPluginToPropertyString(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel: Deprecated. DOCUMENT ME!
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: Deprecated. Will be removed 5/2008
AddPointListener(ContinuousMapping, Object) - Constructor for class cytoscape.visual.mappings.continuous.AddPointListener: Creates a new AddPointListener object.
addProperty(String, VisualPropertyType, String) - Method in class cytoscape.data.readers.VisualStyleBuilder: This method actually adds a property to be considered for inclusion into the resulting style.
addProperty(String[]) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel: DOCUMENT ME!
addSelectButtonActionListener(ActionListener) - Method in class cytoscape.data.servers.ui.ManifestfileSelectionPanel: DOCUMENT ME!
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: DOCUMENT ME!
addThesaurus(String, Thesaurus) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
addToGroup(CyGroup) - Method in class cytoscape.CyNode: Add this node to the specified group.
addTreeModelListener(TreeModelListener) - Method in class cytoscape.dialogs.plugins.ManagerModel: Adds given listener
addTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel: DOCUMENT ME!
addVisualStyle(VisualStyle) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
adjustColumnPreferredWidths(JTable) - Static method in class cytoscape.util.swing.ColumnResizer: DOCUMENT ME!
ALIAS - Static variable in class cytoscape.data.synonyms.Aliases: Name of the attribute for aliases
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: Creates a new AlignHorizontalAction object.
AlignVerticalAction - Class in cytoscape.actions
AlignVerticalAction(CyNetworkView) - Constructor for class cytoscape.actions.AlignVerticalAction: Creates a new AlignVerticalAction object.
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.
allAttributeValuesRemoved(String, String) - Method in class cytoscape.visual.ui.VizMapperMainPanel: DOCUMENT ME!
AlphabeticalSelectionAction - Class in cytoscape.actions
AlphabeticalSelectionAction() - Constructor for class cytoscape.actions.AlphabeticalSelectionAction: Creates a new AlphabeticalSelectionAction object.
AnimatedLayoutAction - Class in cytoscape.actions: Deprecated. Not apparently used. Shout if you are. Will be removed 5/2008.
AnimatedLayoutAction(CyNetworkView) - Constructor for class cytoscape.actions.AnimatedLayoutAction: Deprecated. Creates a new AnimatedLayoutAction object.
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: Creates a new Annotation object.
Annotation(String, String, String) - Constructor for class cytoscape.data.annotation.Annotation: Creates a new Annotation object.
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: Creates a new AnnotationFlatFileReader object.
AnnotationFlatFileReader(BufferedReader, Thesaurus, boolean) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader: Creates a new AnnotationFlatFileReader object.
AnnotationFlatFileReader(String, Thesaurus) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader: Creates a new AnnotationFlatFileReader object.
AnnotationGui - Class in cytoscape.data.annotation
AnnotationGui() - Constructor for class cytoscape.data.annotation.AnnotationGui: Creates a new AnnotationGui object.
AnnotationGui(boolean, ImageIcon) - Constructor for class cytoscape.data.annotation.AnnotationGui: Creates a new AnnotationGui object.
AnnotationXmlReader - Class in cytoscape.data.annotation.readers
AnnotationXmlReader(File) - Constructor for class cytoscape.data.annotation.readers.AnnotationXmlReader: Creates a new AnnotationXmlReader object.
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: Creates a new AnotationPanelDescriptor object.
Appearance - Class in cytoscape.visual: A class that holds the appearance information for NodeViews and EdgeViews.
Appearance() - Constructor for class cytoscape.visual.Appearance: Creates a new Appearance object.
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: Deprecated. DOCUMENT ME!
apply(Appearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator: DOCUMENT ME!
apply(Appearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator: DOCUMENT ME!
apply(Appearance, Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator: DOCUMENT ME!
apply(Appearance, Node, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator: DOCUMENT ME!
apply(Object, VisualPropertyType) - Static method in class cytoscape.visual.ui.VizMapperMainPanel
applyAppearance(NodeView) - Method in class cytoscape.visual.Appearance: Applies this appearance to the specified NodeView.
applyAppearance(EdgeView) - Method in class cytoscape.visual.Appearance: Applies this appearance to the specified EdgeView.
applyAppearance(EdgeView, boolean) - Method in class cytoscape.visual.EdgeAppearance: Deprecated. Use applyAppearance(edgeView) instead - now we always optimize. Will be removed 10/2007
applyAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the node, edge, and global visual attributes.
applyBypass(GraphObject) - Method in class cytoscape.visual.Appearance: Applies the visual bypass values specified in the node (edge) attributes for the specified node (edge) to the node (edge).
applyDefaultProperties(Properties, String) - Method in class cytoscape.visual.Appearance: Applies the specified properties as default values for this appearance.
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(CyLayoutAlgorithm) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLayout(CyLayoutAlgorithm) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to the entire CyNetworkView
applyLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given Nodes and Edges
applyLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(CyLayoutAlgorithm, int[], int[]) - Method in class cytoscape.giny.PhoebeNetworkView: Deprecated. Applies the given layout to only the given Nodes and Edges
applyLayout(CyLayoutAlgorithm) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView
applyLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(CyLayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLockedLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, 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(CyLayoutAlgorithm, 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(CyLayoutAlgorithm, 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(CyLayoutAlgorithm, 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(CyLayoutAlgorithm, 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(CyLayoutAlgorithm, 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: Deprecated. Don't use this. Gone 2/2009.
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: DOCUMENT ME!
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: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.AbstractVisualProperty: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeColorProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeFontFaceProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeFontSizeProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLabelColorProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLabelOpacityProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLabelProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLineStyleProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLineTypeProp
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeLineWidthProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeOpacityProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowColorProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowOpacityProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowShapeProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowColorProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowOpacityProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowShapeProp: DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.EdgeToolTipProp
applyToEdgeView(EdgeView, Object) - Method in interface cytoscape.visual.VisualProperty
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.AbstractVisualProperty: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeBorderColorProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeBorderOpacityProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeFillColorProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeFontFaceProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeFontSizeProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeHeightProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLabelColorProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLabelOpacityProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLabelPositionProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLabelProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLineStyleProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLineTypeProp
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeLineWidthProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeOpacityProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeShapeProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeSizeProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeToolTipProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.NodeWidthProp: DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in interface cytoscape.visual.VisualProperty
applyVizMap(CyEdge) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(EdgeView) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(CyNode) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(NodeView) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(CyEdge, VisualStyle) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(EdgeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(CyNode, VisualStyle) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
applyVizMap(NodeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView: DOCUMENT ME!
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: DOCUMENT ME!
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.
ArrangeAction - Class in cytoscape.actions
ArrangeAction() - Constructor for class cytoscape.actions.ArrangeAction
arrangeFrames(CyDesktopManager.Arrange) - Static method in class cytoscape.view.CyDesktopManager
Arrow - Class in cytoscape.visual: This class is a replacement for the yFiles Arrow class.
Arrow(ArrowShape, Color) - Constructor for class cytoscape.visual.Arrow: New constructor for 2.5 and later:
Arrow(String) - Constructor for class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
ARROW - Static variable in class cytoscape.visual.Arrow: DOCUMENT ME!
ARROW - Static variable in class cytoscape.visual.ui.ValueDisplayer: Deprecated. Display and get input for an arrowhead
ArrowIcon - Class in cytoscape.visual.ui.icon: Icon for arrow shape.
ArrowIcon(Shape) - Constructor for class cytoscape.visual.ui.icon.ArrowIcon: Creates a new ArrowIcon object.
ArrowIcon(Shape, int, int, String) - Constructor for class cytoscape.visual.ui.icon.ArrowIcon: Creates a new ArrowIcon object.
ArrowIcon(Shape, int, int, String, Color) - Constructor for class cytoscape.visual.ui.icon.ArrowIcon: Creates a new ArrowIcon object.
ArrowParser - Class in cytoscape.visual.parsers: Parses a String into a yFiles Arrow object.
ArrowParser() - Constructor for class cytoscape.visual.parsers.ArrowParser
ArrowShape - Enum in cytoscape.visual: Defines arrow shapes.
ArrowShapeParser - Class in cytoscape.visual.parsers
ArrowShapeParser() - Constructor for class cytoscape.visual.parsers.ArrowShapeParser
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().
AttributeImportPanel - Class in cytoscape.util.swing: General GUI component for importing attributes.
AttributeImportQuery - Class in cytoscape.data.webservice
AttributeImportQuery(Object, String, String) - Constructor for class cytoscape.data.webservice.AttributeImportQuery
ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape: This signals when new attributes have been loaded and a few other large scale changes to attributes have been made.
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
attributeValueAssigned(String, String, Object[], Object, Object) - Method in class cytoscape.visual.ui.VizMapperMainPanel: DOCUMENT ME!
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.
attributeValueRemoved(String, String, Object[], Object) - Method in class cytoscape.visual.ui.VizMapperMainPanel: DOCUMENT ME!
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: Deprecated. Use vizmapper gui to edit background color. Will be removed 5/2008
BackgroundColorAction() - Constructor for class cytoscape.actions.BackgroundColorAction: Deprecated. Constructor.
BasicCalculator - Class in cytoscape.visual.calculators: BasicCalculator implements some UI features for calculators lower in the object tree.
BasicCalculator(String, ObjectMapping, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.BasicCalculator: Creates a new BasicCalculator object.
BasicCalculator(String, Properties, String, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.BasicCalculator: Creates a new BasicCalculator object.
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.
BelowAndAbovePanel - Class in cytoscape.visual.ui.editors.continuous: Drawing and updating below & above values in Gradient Editor.
BelowAndAbovePanel(VisualPropertyType, Color, boolean) - Constructor for class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel: Creates a new BelowAndAbovePanel object.
BelowAndAbovePanel(VisualPropertyType, boolean) - Constructor for class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel: Creates a new BelowAndAbovePanel object.
BendSelectedEdgesAction - Class in cytoscape.actions
BendSelectedEdgesAction() - Constructor for class cytoscape.actions.BendSelectedEdgesAction: Creates a new BendSelectedEdgesAction object.
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: Creates a new BioDataServer object.
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: Creates a new BioDataServerRmi object.
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: Deprecated. This class is no longer used since the BirdsEyeView is now always part of the NetworkPanel. BirdsEyeView creation and event handling is done by the BirdsEyeViewHandler and initialized in This class will be removed 5/2008.
BirdsEyeViewAction() - Constructor for class cytoscape.actions.BirdsEyeViewAction: Deprecated. Creates a new BirdsEyeViewAction object.
BitmapExporter - Class in cytoscape.util.export: Bitmap exporter by the ImageIO class.
BitmapExporter(String, double) - Constructor for class cytoscape.util.export.BitmapExporter
BLACK_ARROW - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
BLACK_CIRCLE - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
BLACK_DELTA - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
BLACK_DIAMOND - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
BLACK_T - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
BOOKMARK_PACKAGE_NAME - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
BookmarkAction - Class in cytoscape.actions
BookmarkAction() - Constructor for class cytoscape.actions.BookmarkAction: Creates a new BookmarkAction object.
BookmarkDialog - Class in cytoscape.dialogs.preferences
BookmarkDialog(JFrame) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog: Creates new BookmarkDialog
BookmarkDialog(JFrame, String) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog: Creates new BookmarkDialog, set the selection on the given category
BookmarkDialog() - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog: Creates a new BookmarkDialog object.
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: Creates a new BookmarkReader object.
BookmarksUtil - Class in cytoscape.util: Utility methods for getting entries in the bookmark object.
BookmarksUtil() - Constructor for class cytoscape.util.BookmarksUtil
BOOLEAN - Static variable in class cytoscape.layout.Tunable
BORDER_COLOR - Static variable in interface cytoscape.visual.ui.editors.continuous.VizMapperTrackRenderer
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: Creates a new BoundaryRangeValues object.
BoundaryRangeValues(Object, Object, Object) - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
BoundaryRangeValues(BoundaryRangeValues) - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
buildOntologyServer() - Static method in class cytoscape.Cytoscape: This will replace the bioDataServer.
buildStyle() - Method in class cytoscape.data.readers.VisualStyleBuilder: Actually build the style using the provided properties

C

C2CMappingEditor - Class in cytoscape.visual.ui.editors.continuous: Continuous-Continuous mapping editor.
C2CMappingEditor(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.C2CMappingEditor: Creates a new C2CMappingEditor object.
C2DMappingEditor - Class in cytoscape.visual.ui.editors.continuous: Continuous Mapping editor for discrete values, such as Font, Shape, Label Position, etc.
C2DMappingEditor(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.C2DMappingEditor: Creates a new C2DMappingEditor object.
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
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: Deprecated. DOCUMENT ME!
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: Deprecated. DOCUMENT ME!
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: Deprecated. DOCUMENT ME!
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: Deprecated. DOCUMENT ME!
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: Deprecated. Will be removed 5/2008
calculateEdgeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: DOCUMENT ME!
calculateEdgeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: DOCUMENT ME!
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: Deprecated. DOCUMENT ME!
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.
calculateNodeColor(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeColorCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeFontFace(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeFontFaceCalculator: Deprecated. DOCUMENT ME!
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: Deprecated. DOCUMENT ME!
calculateNodeFontSize(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeFontSizeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLabel(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelCalculator: Deprecated. DOCUMENT ME!
calculateNodeLabel(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLabelCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLabelColor(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLabelColorCalculator: Deprecated. DOCUMENT ME!
calculateNodeLabelColor(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLabelColorCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeLineType(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeLineTypeCalculator: Deprecated. Will be removed 5/2008
calculateNodeLineType(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeLineTypeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
calculateNodeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: DOCUMENT ME!
calculateNodeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: DOCUMENT ME!
calculateNodeShape(Node, CyNetwork) - Method in class cytoscape.visual.calculators.GenericNodeShapeCalculator: Deprecated. DOCUMENT ME!
calculateNodeShape(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeShapeCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
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: Deprecated. DOCUMENT ME!
calculateNodeToolTip(Node, CyNetwork) - Method in interface cytoscape.visual.calculators.NodeToolTipCalculator: Deprecated. Use Calculator.apply() instead. Will be removed 10/2007
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: DOCUMENT ME!
calculateSloppySelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator: Deprecated. Will be removed 5/2008
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: Creates a new CalculatorCatalog object.
CalculatorCatalog(Properties) - Constructor for class cytoscape.visual.CalculatorCatalog: Creates a new CalculatorCatalog object.
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: DOCUMENT ME!
CANONICAL_NAME - Static variable in class cytoscape.data.Semantics: The name "CANONICAL_NAME" is an historical artifact.
Category - Enum in cytoscape.plugin
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: DOCUMENT ME!
centerWindowOnScreen(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities: DOCUMENT ME!
centerWindowSize(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities: DOCUMENT ME!
CheckBoxFileChooser - Class in cytoscape.actions: Deprecated. This isn't apparently used anywhere. If you are using it, let us know! If you need a file use FileUtil.getFile(). Will be removed 5/2008.
CheckBoxFileChooser(File, String) - Constructor for class cytoscape.actions.CheckBoxFileChooser: Deprecated. Creates a new CheckBoxFileChooser object.
CheckBoxJList - Class in cytoscape.util.swing: This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 By Joshua Marinacci, Chris Adamson Customized by Keiichiro Ono
CheckBoxJList() - Constructor for class cytoscape.util.swing.CheckBoxJList: Creates a new CheckBoxJList object.
checkCalculatorName(String, byte) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Will be removed 5/2008
checkCalculatorName(String, VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
checkCalculatorName(byte, String) - Method in class cytoscape.visual.CalculatorCatalog: Deprecated. Will be removed 5/2008
checkCalculatorName(VisualPropertyType, String) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
checkCalculatorUsage(Calculator) - Method in class cytoscape.visual.ui.VizMapUI: Deprecated. 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
checkMappingName(String) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
checkSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil: DOCUMENT ME!
checkVisualStyleName(String) - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
CIRCLE - Static variable in class cytoscape.visual.Arrow: DOCUMENT ME!
CLEAN - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
clear() - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
clear() - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
clear() - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
clear - Class in cytoscape.data.servers
clear() - Constructor for class cytoscape.data.servers.clear
clear() - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
clearAuthorList() - Method in class cytoscape.plugin.PluginInfo: Clears author list.
clearCorruptedElements() - Method in class cytoscape.plugin.PluginTracker: Clears the list of elements and sets the found flag to false.
clearErrorList() - Method in class cytoscape.plugin.PluginManager: Clears the loading error list.
clearFlag(int) - Method in class cytoscape.layout.Tunable: This method can be used to clear a flag for this Tunable
clearPluginList() - Method in class cytoscape.plugin.ThemeInfo
clearStatusBar() - Method in class cytoscape.view.CytoscapeDesktop: Clears the Status Bar Message.
clearVector() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel: DOCUMENT ME!
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.Appearance: Returns a clone of this Appearance.
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.
clone() - Method in class cytoscape.visual.EdgeAppearanceCalculator: Create deep copy of the object.
clone() - Method in class cytoscape.visual.GlobalAppearanceCalculator: Make deep copy of this object
clone() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint: Clones the object.
clone() - Method in class cytoscape.visual.mappings.ContinuousMapping: Create deep copy of the 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: DOCUMENT ME!
clone() - Method in class cytoscape.visual.NodeAppearance: Clone.
clone() - Method in class cytoscape.visual.NodeAppearanceCalculator: Create deep copy of the object.
clone() - Method in class cytoscape.visual.ui.icon.NodeIcon: DOCUMENT ME!
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: Creates a new CloneGraphInNewWindowAction object.
CLOSE_EVENT - Static variable in class cytoscape.util.swing.AttributeImportPanel: Will be caught by parent object (usually a dialog.)
closeAllWindows() - Method in class cytoscape.view.CyDesktopManager
COLOR - Static variable in class cytoscape.visual.ui.ValueDisplayer: Deprecated. Display and get input for a color
COLOR_ARROW - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
COLOR_CHANGED - Static variable in class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel: DOCUMENT ME!
COLOR_CIRCLE - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
COLOR_DELTA - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
COLOR_DIAMOND - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
COLOR_T - Static variable in class cytoscape.visual.Arrow: Deprecated. Will be removed 5/2008
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: Creates a new ColorScaleTable object.
ColumnResizer - Class in cytoscape.util.swing: Automatically resize column based on the objects in the cell.
ColumnResizer() - Constructor for class cytoscape.util.swing.ColumnResizer
compare(Object, Object) - Method in class cytoscape.data.readers.GMLNode: DOCUMENT ME!
completions() - Method in class cytoscape.util.CytoscapeAction: DOCUMENT ME!
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.layout.AbstractLayout: These abstract methods must be overridden.
construct() - Method in class cytoscape.layout.algorithms.GridNodeLayout: DOCUMENT ME!
construct() - Method in class cytoscape.util.SwingWorker: Compute the value to be returned by the get method.
contains(CyNode) - Method in interface cytoscape.groups.CyGroup: Determine if a node is a member of this group
contains(CyNode) - Method in class cytoscape.groups.CyGroupImpl: Determine if a node is a member of this group
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.
containsPlugin(PluginInfo) - Method in class cytoscape.plugin.ThemeInfo
containsTerm(int) - Method in class cytoscape.data.annotation.Ontology: DOCUMENT ME!
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.
containsVersion(String) - Method in class cytoscape.plugin.DownloadableInfo
ContinuousLegend - Class in cytoscape.visual.mappings.continuous
ContinuousLegend(String, String, List, Object, byte) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousLegend: Deprecated. Use constructor with VisualPropertyType instead. Gone 5/2008.
ContinuousLegend(String, List, Object, VisualPropertyType) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousLegend: Creates a new ContinuousLegend object.
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.
ContinuousMappingEditorPanel - Class in cytoscape.visual.ui.editors.continuous: Abstract class for all Continuous Mapping Editors.
ContinuousMappingEditorPanel(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel: Creates new form ContinuousMapperEditorPanel
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.
ContinuousTrackRenderer - Class in cytoscape.visual.ui.editors.continuous
ContinuousTrackRenderer(VisualPropertyType, Number, Number) - Constructor for class cytoscape.visual.ui.editors.continuous.ContinuousTrackRenderer: Creates a new ContinuousTrackRenderer object.
ContinuousUI - Class in cytoscape.visual.mappings.continuous: Deprecated. Will be removed 5/2008
ContinuousUI(JDialog, Object, CyNetwork, ContinuousMapping) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousUI: Deprecated. Constructor.
convert() - Method in class cytoscape.util.Transform: DOCUMENT ME!
convert(int) - Static method in class cytoscape.visual.LabelPosition: DOCUMENT ME!
convert(String) - Static method in class cytoscape.visual.LabelPosition: DOCUMENT ME!
convertLambdasToPvals() - Method in class cytoscape.data.ExpressionData: Converts all lambdas to p-values.
copy(Appearance) - Method in class cytoscape.visual.Appearance: Copies the specified Appearance into this Appearance object.
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: DOCUMENT ME!
createBasicOntology(URL, String, String) - Method in class cytoscape.data.ontology.OntologyFactory: DOCUMENT ME!
createColorLabel(Color) - Static method in class cytoscape.dialogs.MiscGB: DOCUMENT ME!
createDefaultVisualStyle() - Method in class cytoscape.visual.CalculatorCatalog: DOCUMENT ME!
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: DOCUMENT ME!
createGroup(String, String) - Static method in class cytoscape.groups.CyGroupManager: Create a new, empty group.
createGroup(String, List, String) - Static method in class cytoscape.groups.CyGroupManager: Create a new group with a list of nodes as initial members.
createGroup(CyNode, List, String) - Static method in class cytoscape.groups.CyGroupManager: Create a new group with a list of nodes as initial members, and a precreated group node.
createHorizontalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createHorizontalAlignLeft() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createHorizontalAlignRight() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createHorizontalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
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: DOCUMENT ME!
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: DOCUMENT ME!
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(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: DOCUMENT ME!
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: DOCUMENT ME!
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.
createNetworkView(CyNetwork, String, CyLayoutAlgorithm) - Static method in class cytoscape.Cytoscape: Creates a CyNetworkView, but doesn't do anything with it.
createNetworkView(CyNetwork, String, CyLayoutAlgorithm, VisualStyle) - Static method in class cytoscape.Cytoscape: Creates a CyNetworkView that is placed placed in a given visual style and rendered with a given layout algorithm.
CreateNetworkViewAction - Class in cytoscape.actions
CreateNetworkViewAction() - Constructor for class cytoscape.actions.CreateNetworkViewAction: Creates a new CreateNetworkViewAction object.
CreateNetworkViewAction(boolean) - Constructor for class cytoscape.actions.CreateNetworkViewAction: Creates a new CreateNetworkViewAction object.
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: Deprecated. Generates the main UI Panel.
createResourcesTag() - Method in class cytoscape.util.JnlpWriterUtil: DOCUMENT ME!
createSettings() - Method in class cytoscape.layout.algorithms.GridNodeLayout: Returns a JPanel to be used as part of the Settings dialog for this layout algorithm.
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: DOCUMENT ME!
createTriple(Term, Term, Term, String, String) - Method in class cytoscape.data.ontology.Ontology: DOCUMENT ME!
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: DOCUMENT ME!
createVerticalAlignBottom() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createVerticalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createVerticalAlignTop() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createVerticalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl: DOCUMENT ME!
createViewFromCurrentNetwork(CyNetwork) - Static method in class cytoscape.actions.CreateNetworkViewAction: DOCUMENT ME!
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
CyAbstractEdit - Class in cytoscape.util.undo: A small convenience class that can be used to create new edits.
CyAbstractEdit(String) - Constructor for class cytoscape.util.undo.CyAbstractEdit
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: Creates a new CyAttributesImpl object.
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
CyAttributesUtils.AttributeType - Enum in cytoscape.data
CyAttributesWriter - Class in cytoscape.data.writers: CyAttributeWriter extracted from AttributeSaverDialog.
CyAttributesWriter(CyAttributes, String, Writer) - Constructor for class cytoscape.data.writers.CyAttributesWriter: Creates a new CyAttributesWriter2 object.
CyColorCellRenderer - Class in cytoscape.visual.ui.editors.discrete: CyColorCellRenderer.
CyColorCellRenderer() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer
CyColorCellRenderer.PaintIcon - Class in cytoscape.visual.ui.editors.discrete
CyColorCellRenderer.PaintIcon(Paint) - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
CyColorCellRenderer.PaintIcon(Paint, int, int) - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
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
CyColorPropertyEditor - Class in cytoscape.visual.ui.editors.discrete: ColorPropertyEditor.
CyColorPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor: Creates a new CyColorPropertyEditor object.
CyColorPropertyEditor.AsInt - Class in cytoscape.visual.ui.editors.discrete
CyColorPropertyEditor.AsInt() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor.AsInt
CyComboBoxPropertyEditor - Class in cytoscape.visual.ui.editors.discrete: ComboBoxPropertyEditor.
CyComboBoxPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor: Creates a new CyComboBoxPropertyEditor object.
CyComboBoxPropertyEditor.Renderer - Class in cytoscape.visual.ui.editors.discrete
CyComboBoxPropertyEditor.Renderer() - Constructor for class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Renderer
CyComboBoxPropertyEditor.Value - Class in cytoscape.visual.ui.editors.discrete
CyComboBoxPropertyEditor.Value(Object, Object) - Constructor for class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Value
CyDesktopManager - Class in cytoscape.view
CyDesktopManager.Arrange - Enum in cytoscape.view
CyDoublePropertyEditor - Class in cytoscape.visual.ui.editors.discrete
CyDoublePropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyDoublePropertyEditor: Creates a new CyStringPropertyEditor object.
CyEdge - Class in cytoscape
CyEdge(RootGraph, int) - Constructor for class cytoscape.CyEdge: Creates a new CyEdge object.
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.
CyFontPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
CyFontPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyFontPropertyEditor
CyGradientTrackRenderer - Class in cytoscape.visual.ui.editors.continuous: DOCUMENT ME!
CyGradientTrackRenderer(VisualPropertyType, Color, Color, String) - Constructor for class cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer: Creates a new GradientTrackRenderer object.
CyGraphAllLOD - Class in cytoscape.ding: CyGraphAllLOD is the level of detail (LOD) class used for the "Show Graphics Details" menu item.
CyGraphAllLOD() - Constructor for class cytoscape.ding.CyGraphAllLOD
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: Creates a new CyGraphLOD object.
CyGroup - Interface in cytoscape.groups: The CyGroup interface provides the methods for a group model that maintains the list of nodes belonging to a group, the parent of a particular group, and the node that represents the group.
CyGroupChangeListener - Interface in cytoscape.groups: The CyGroupChangeListener interface provides a mechanism for plugins that track group related information to get notified of changes to groups.
CyGroupChangeListener.ChangeType - Enum in cytoscape.groups: The types of notifications we pass to our listeners
CyGroupImpl - Class in cytoscape.groups: The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular group, and the node that represents the group.
CyGroupManager - Class in cytoscape.groups: The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular group, and the node that represents the group.
CyGroupManager() - Constructor for class cytoscape.groups.CyGroupManager
CyGroupViewer - Interface in cytoscape.groups: The CyGroupViewer interface provides a mechanism for group view implementations to register themselves and get notified of group creation and deletion.
CyGroupViewer.ChangeType - Enum in cytoscape.groups: The change values
CyHelpBroker - Class in cytoscape.view: This class creates the Cytoscape Help Broker for managing the JavaHelp system and help set access
CyInitParams - Interface in cytoscape.init: An interface that describes the initialization parameters needed by cytoscape.
CyLabelPositionPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
CyLabelPositionPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyLabelPositionPropertyEditor: Creates a new CyLabelPositionLabelEditor object.
CyLayoutAlgorithm - Interface in cytoscape.layout
CyLayouts - Class in cytoscape.layout: CyLayouts is a singleton class that is used to register all available layout algorithms.
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: Creates a new CyMenus object.
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: Creates a new CyNetworkEvent object.
CyNetworkListener - Interface in cytoscape: Interface for listeners that respond to CyNetwork events.
CyNetworkNaming - Class in cytoscape.util
CyNetworkNaming() - Constructor for class cytoscape.util.CyNetworkNaming
CyNetworkTitleChange - Class in cytoscape: Class used for passing along information about the network when the network title has changed (firing an event)
CyNetworkTitleChange(String, String) - Constructor for class cytoscape.CyNetworkTitleChange
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: Creates a new CyNode object.
CyNodeView - Interface in cytoscape.view
CYSESSION - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
CyStartupListener - Class in cytoscape: Implementation of StartupListener interface in install4j API.
CyStartupListener() - Constructor for class cytoscape.CyStartupListener
CyStringPropertyEditor - Class in cytoscape.visual.ui.editors.discrete: DOCUMENT ME!
CyStringPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyStringPropertyEditor: Creates a new CyStringPropertyEditor object.
CytoPanel - Interface in cytoscape.view.cytopanels: Interface to a CytoPanel.
CytoPanelAction - Class in cytoscape.actions
CytoPanelAction(JCheckBoxMenuItem, CytoPanel) - Constructor for class cytoscape.actions.CytoPanelAction: Deprecated. Use other constructor instead. Will be removed 4/2008.
CytoPanelAction(CytoPanelName, boolean) - Constructor for class cytoscape.actions.CytoPanelAction
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.
CytoPanelName - Enum in cytoscape.view.cytopanels: An enum that maps names to compass directions.
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.webservice - package cytoscape.data.webservice
cytoscape.data.webservice.ui - package cytoscape.data.webservice.ui
cytoscape.data.webservice.util - package cytoscape.data.webservice.util
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.plugins - package cytoscape.dialogs.plugins
cytoscape.dialogs.preferences - package cytoscape.dialogs.preferences
cytoscape.ding - package cytoscape.ding
cytoscape.giny - package cytoscape.giny
cytoscape.groups - package cytoscape.groups
cytoscape.init - package cytoscape.init
cytoscape.layout - package cytoscape.layout: Classes providing some kind of graph layout functionality.
cytoscape.layout.algorithms - package cytoscape.layout.algorithms
cytoscape.layout.ui - package cytoscape.layout.ui
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.export - package cytoscape.util.export
cytoscape.util.shadegrown - package cytoscape.util.shadegrown
cytoscape.util.swing - package cytoscape.util.swing
cytoscape.util.undo - package cytoscape.util.undo
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.properties - package cytoscape.visual.properties
cytoscape.visual.ui - package cytoscape.visual.ui: Top-level UI components for the cytoscape.visual package.
cytoscape.visual.ui.editors.continuous - package cytoscape.visual.ui.editors.continuous
cytoscape.visual.ui.editors.discrete - package cytoscape.visual.ui.editors.discrete
cytoscape.visual.ui.icon - package cytoscape.visual.ui.icon
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: Creates a new CytoscapeAction object.
CytoscapeAction(String, Icon) - Constructor for class cytoscape.util.CytoscapeAction: Creates a new CytoscapeAction object.
CytoscapeDesktop - Class in cytoscape.view: The CytoscapeDesktop is the central Window for working with Cytoscape
CytoscapeDesktop(int) - Constructor for class cytoscape.view.CytoscapeDesktop: Deprecated. view_type is no longer used. Use the other CytoscapeDesktop() instead. Will be gone August 1008.
CytoscapeDesktop() - Constructor for class cytoscape.view.CytoscapeDesktop: Creates a new CytoscapeDesktop object.
CytoscapeFingRootGraph - Class in cytoscape.giny
CytoscapeFingRootGraph() - Constructor for class cytoscape.giny.CytoscapeFingRootGraph: Creates a new CytoscapeFingRootGraph object.
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: Reader to load CYtoscape Session file (.cys).
CytoscapeSessionReader(URL, TaskMonitor) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Constructor for remote file (specified by an URL)
CytoscapeSessionReader(String, TaskMonitor) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Creates a new CytoscapeSessionReader object.
CytoscapeSessionReader(String) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Constructor.
CytoscapeSessionReader(URL) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader: Creates a new CytoscapeSessionReader object.
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
CyUndo - Class in cytoscape.util.undo: A tiny class for supporting undo in the Cytoscape context.
CyUndo() - Constructor for class cytoscape.util.undo.CyUndo
CyWebServiceEvent<P> - Class in cytoscape.data.webservice: Event object used by Web Service Clients and the core.
CyWebServiceEvent(String, CyWebServiceEvent.WSEventType, P) - Constructor for class cytoscape.data.webservice.CyWebServiceEvent
CyWebServiceEvent(String, CyWebServiceEvent.WSEventType, P, CyWebServiceEvent.WSEventType) - Constructor for class cytoscape.data.webservice.CyWebServiceEvent
CyWebServiceEvent.WSEventType - Enum in cytoscape.data.webservice
CyWebServiceEvent.WSResponseType - Enum in cytoscape.data.webservice: Will be used to catch the signal from WS.
CyWebServiceEventListener - Interface in cytoscape.data.webservice: Listener for Web Service Event handling.
CyWebServiceEventSupport - Class in cytoscape.data.webservice
CyWebServiceEventSupport() - Constructor for class cytoscape.data.webservice.CyWebServiceEventSupport: Creates a new CyWebServiceEventSupport object.
CyWebServiceException - Exception in cytoscape.data.webservice
CyWebServiceException(CyWebServiceException.WSErrorCode) - Constructor for exception cytoscape.data.webservice.CyWebServiceException
CyWebServiceException.WSErrorCode - Enum in cytoscape.data.webservice

D

DASHED_1 - Static variable in class cytoscape.visual.LineType: Deprecated.
DASHED_2 - Static variable in class cytoscape.visual.LineType: Deprecated.
DASHED_3 - Static variable in class cytoscape.visual.LineType: Deprecated.
DASHED_4 - Static variable in class cytoscape.visual.LineType: Deprecated.
DASHED_5 - Static variable in class cytoscape.visual.LineType: Deprecated.
dashedEdges(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to honor dashed edges.
DatabaseSearchResult<R> - Class in cytoscape.data.webservice
DatabaseSearchResult(Integer, R, CyWebServiceEvent.WSEventType) - Constructor for class cytoscape.data.webservice.DatabaseSearchResult
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: Creates a new DBCrossReferences object.
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: Creates a new DBReference object.
DBReference(String, String, String, String, String) - Constructor for class cytoscape.data.ontology.DBReference: Creates a new DBReference object.
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_ICON_COLOR - Static variable in class cytoscape.visual.ui.icon.VisualPropertyIcon: Default icon color.
DEFAULT_ICON_SIZE - Static variable in class cytoscape.visual.ui.icon.VisualPropertyIcon
DEFAULT_MENU_SPECIFIER - Static variable in class cytoscape.util.CytoscapeMenuBar
DEFAULT_NETWORK_METADATA_LABEL - Static variable in class cytoscape.data.readers.MetadataParser
DefaultAppearenceBuilder - Class in cytoscape.visual.ui: Dialog for editing default visual property values.
DefaultAppearenceBuilder(Frame, boolean) - Constructor for class cytoscape.visual.ui.DefaultAppearenceBuilder: Creates a new DefaultAppearenceBuilder object.
DefaultPanel - Class in cytoscape.visual.ui: Deprecated. Will be removed 5/2008
DefaultPanel(VizMapUI, VisualMappingManager) - Constructor for class cytoscape.visual.ui.DefaultPanel: Deprecated. Constructor.
DefaultViewPanel - Class in cytoscape.visual.ui: Panel to show the default properties visually (as graphics).
defineAttribute(String, byte, byte[]) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Creates an attribute definition.
delete(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager: Marks the given object for deletion the next time Cytoscape is restarted.
delete() - Method in class cytoscape.plugin.PluginManager: Takes all objects on the "to-delete" list and deletes them.
DeleteAction - Class in cytoscape.actions: action for deleting selected Cytoscape nodes and edges
DeleteAction() - Constructor for class cytoscape.actions.DeleteAction: action for deleting selected Cytoscape nodes and edges
DeleteAction(GraphObject) - Constructor for class cytoscape.actions.DeleteAction: perform deletion on the input object. if object is a Node, then this will result in also deleting the edges adjacent to the node
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: DOCUMENT ME!
deleteAttribute(String) - Method in class cytoscape.data.CyAttributesImpl: DOCUMENT ME!
deleteBookmark(String, Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil: DOCUMENT ME!
deleteBookmark(Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil: DOCUMENT ME!
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. DOCUMENT ME!
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: Deprecated. Will be removed 5/2008
DeletePointListener(ContinuousMapping) - Constructor for class cytoscape.visual.mappings.continuous.DeletePointListener: Creates a new DeletePointListener object.
deleteProperty(String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel: DOCUMENT ME!
deleteTerm(Term) - Method in class cytoscape.data.ontology.Ontology: Delete a term from DAG (CyNetwork)
DELTA - Static variable in class cytoscape.visual.Arrow: DOCUMENT ME!
describe() - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
describe() - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
describe() - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
describe() - Method in class cytoscape.plugin.CytoscapePlugin: Deprecated.
DeselectAllAction - Class in cytoscape.actions
DeselectAllAction() - Constructor for class cytoscape.actions.DeselectAllAction: Creates a new DeselectAllAction object.
deselectAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils: DOCUMENT ME!
DeSelectAllEdgesAction - Class in cytoscape.actions
DeSelectAllEdgesAction() - Constructor for class cytoscape.actions.DeSelectAllEdgesAction: Creates a new DeSelectAllEdgesAction object.
deselectAllNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils: DOCUMENT ME!
DeSelectAllNodesAction - Class in cytoscape.actions
DeSelectAllNodesAction() - Constructor for class cytoscape.actions.DeSelectAllNodesAction: Creates a new DeSelectAllNodesAction object.
destroyCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkAction: Deprecated. Use Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork()) instead. Will be gone 11/2008.
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: Creates a new DestroyNetworkAction object.
DestroyNetworkAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkAction: Creates a new DestroyNetworkAction object.
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: Creates a new DestroyNetworkViewAction object.
DestroyNetworkViewAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkViewAction: Creates a new DestroyNetworkViewAction object.
destroyViewFromCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkViewAction: Deprecated. Use Cytoscape.destroyNetworkView() instead. Will go 11/2008.
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.Arrow: DOCUMENT ME!
DIAMOND - Static variable in class cytoscape.visual.ShapeNodeRealizer: Deprecated.
DingNetworkView - Class in cytoscape.ding
DingNetworkView(CyNetwork, String) - Constructor for class cytoscape.ding.DingNetworkView: Creates a new DingNetworkView object.
DiscreteLegend - Class in cytoscape.visual.mappings.discrete
DiscreteLegend(Map, String, String, byte) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteLegend: Deprecated. Use VisualPropertyType constructor instead. Gone 5/2008.
DiscreteLegend(Map, String, VisualPropertyType) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteLegend: Creates a new DiscreteLegend object.
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.
DiscreteTrackRenderer - Class in cytoscape.visual.ui.editors.continuous: DOCUMENT ME!
DiscreteTrackRenderer(VisualPropertyType, Object, Object) - Constructor for class cytoscape.visual.ui.editors.continuous.DiscreteTrackRenderer: Creates a new DiscreteTrackRenderer object.
DiscreteTrackRenderer(Object, ContinuousMapping) - Constructor for class cytoscape.visual.ui.editors.continuous.DiscreteTrackRenderer: Creates a new DiscreteTrackRenderer object.
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
DOCK - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Dock state of a CytoPanel.
document - Variable in class cytoscape.util.JnlpWriterUtil
doLayout() - Method in class cytoscape.layout.AbstractLayout: doLayout on current network view.
doLayout(CyNetworkView) - Method in class cytoscape.layout.AbstractLayout: doLayout on specified network view.
doLayout(CyNetworkView, TaskMonitor) - Method in class cytoscape.layout.AbstractLayout: doLayout on specified network view with specified monitor.
doLayout() - Method in interface cytoscape.layout.CyLayoutAlgorithm: This method performs the layout on the current network using the current network view.
doLayout(CyNetworkView) - Method in interface cytoscape.layout.CyLayoutAlgorithm: This method performs the layout on the current network.
doLayout(CyNetworkView, TaskMonitor) - Method in interface cytoscape.layout.CyLayoutAlgorithm: This method performs the layout on the current network, but assumes that the layout is part of an existing monitored task
doLayout() - Method in class cytoscape.layout.LayoutAdapter: This method performs the layout on the current network using the current network view.
doLayout(CyNetworkView) - Method in class cytoscape.layout.LayoutAdapter: This method performs the layout on the current network.
doLayout(CyNetworkView, TaskMonitor) - Method in class cytoscape.layout.LayoutAdapter: This method performs the layout on the current network, but assumes that the layout is part of an existing monitored task
doLayout() - Method in interface cytoscape.layout.LayoutAlgorithm: Deprecated.
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: DOCUMENT ME!
doPostProcessing(CyNetwork) - Method in interface cytoscape.data.readers.GraphReader: Execute whatever post-processing is required.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.InteractionsReader
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.XGMMLReader: DOCUMENT ME!
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.layout.Tunable
DOUBLE - Static variable in class cytoscape.visual.ui.ValueDisplayer: Deprecated. 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
download(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager: Downloads given object to the temporary directory.
download(DownloadableInfo, TaskMonitor) - Method in class cytoscape.plugin.PluginManager: Downloads given object to the temporary directory.
download(String, File, TaskMonitor) - Static method in class cytoscape.util.URLUtil: Download the file specified by the url string to the given File object
download(URL) - Static method in class cytoscape.util.URLUtil: Get the the contents of the given URL as a string.
DownloadableInfo - Class in cytoscape.plugin
DownloadableInfo() - Constructor for class cytoscape.plugin.DownloadableInfo
DownloadableInfo(String) - Constructor for class cytoscape.plugin.DownloadableInfo
DownloadableInfo(String, DownloadableInfo) - Constructor for class cytoscape.plugin.DownloadableInfo
DownloadableType - Enum in cytoscape.plugin
downloadFromURL(URL, TaskMonitor) - Method in class cytoscape.data.ImportHandler: Download a temporary file from the given URL.
DropDownMenuButton - Class in cytoscape.util.swing: Button with drop down menu.
DropDownMenuButton(AbstractAction) - Constructor for class cytoscape.util.swing.DropDownMenuButton: Creates a new DropDownMenuButton object.
dump() - Method in class cytoscape.data.synonyms.Thesaurus: DOCUMENT ME!
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: Creates a new DuplicateCalculatorNameException object.
DuplicatePluginClassException - Exception in cytoscape.plugin
DuplicatePluginClassException() - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
DuplicatePluginClassException(String) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
DuplicatePluginClassException(Throwable) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
DuplicatePluginClassException(String, Throwable) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
DynamicLayoutMenu - Class in cytoscape.layout.ui: A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu items on-the-fly based on the capabilities of the layout algorithm and environment factors such as whether or not nodes are selected, the presence of node or edge attributes, etc.
DynamicLayoutMenu(CyLayoutAlgorithm, boolean) - Constructor for class cytoscape.layout.ui.DynamicLayoutMenu: Creates a new DynamicLayoutMenu object.

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: Deprecated.
EDGE_FONT_FACE - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_FONT_SIZE - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_LABEL - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_LABEL_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_LABEL_FONT - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_LABEL_POSITION - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_LINETYPE - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
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.SelectEvent: Static constant indicating a change to a group of Edges.
EDGE_SRCARROW - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_SRCARROW_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_TGTARROW - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_TGTARROW_COLOR - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
EDGE_TOOLTIP - Static variable in class cytoscape.visual.ui.VizMapUI: Deprecated.
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: Creates a new EdgeAppearance object.
EdgeAppearanceCalculator - Class in cytoscape.visual: This class calculates the appearance of an Edge.
EdgeAppearanceCalculator() - Constructor for class cytoscape.visual.EdgeAppearanceCalculator: Creates a new EdgeAppearanceCalculator object.
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.
EdgeArrowCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
edgeArrows(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render edge arrows.
EDGEATTRIBUTE - Static variable in class cytoscape.layout.Tunable
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: Creates a new EdgeAttributesPopupDetails object.
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: Deprecated. Will be removed 5/2008
EdgeCalculator(String, ObjectMapping, Class, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.EdgeCalculator: Creates a new EdgeCalculator object.
EdgeCalculator(String, Properties, String, ValueParser, Object) - Constructor for class cytoscape.visual.calculators.EdgeCalculator: Deprecated. Will be removed 5/2008
EdgeCalculator(String, Properties, String, ValueParser, Object, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.EdgeCalculator: Creates a new EdgeCalculator object.
EdgeColorCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeColorProp - Class in cytoscape.visual.properties
EdgeColorProp() - Constructor for class cytoscape.visual.properties.EdgeColorProp
EdgeFontFaceCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeFontFaceProp - Class in cytoscape.visual.properties
EdgeFontFaceProp() - Constructor for class cytoscape.visual.properties.EdgeFontFaceProp
EdgeFontSizeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeFontSizeProp - Class in cytoscape.visual.properties
EdgeFontSizeProp() - Constructor for class cytoscape.visual.properties.EdgeFontSizeProp
EdgeLabelCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeLabelColorProp - Class in cytoscape.visual.properties
EdgeLabelColorProp() - Constructor for class cytoscape.visual.properties.EdgeLabelColorProp
EdgeLabelOpacityProp - Class in cytoscape.visual.properties
EdgeLabelOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeLabelOpacityProp
EdgeLabelPositionProp - Class in cytoscape.visual.properties
EdgeLabelPositionProp() - Constructor for class cytoscape.visual.properties.EdgeLabelPositionProp
EdgeLabelProp - Class in cytoscape.visual.properties
EdgeLabelProp() - Constructor for class cytoscape.visual.properties.EdgeLabelProp
edgeLabels(int, int) - Method in class cytoscape.ding.CyGraphLOD: Determines whether or not to render edge labels.
EdgeLineStyleProp - Class in cytoscape.visual.properties
EdgeLineStyleProp() - Constructor for class cytoscape.visual.properties.EdgeLineStyleProp
EdgeLineTypeCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeLineTypeProp - Class in cytoscape.visual.properties
EdgeLineTypeProp() - Constructor for class cytoscape.visual.properties.EdgeLineTypeProp
EdgeLineWidthProp - Class in cytoscape.visual.properties
EdgeLineWidthProp() - Constructor for class cytoscape.visual.properties.EdgeLineWidthProp
EdgeManipulationAction - Class in cytoscape.actions
EdgeManipulationAction(CyNetworkView) - Constructor for class cytoscape.actions.EdgeManipulationAction: Creates a new EdgeManipulationAction object.
EdgeOpacityProp - Class in cytoscape.visual.properties
EdgeOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeOpacityProp
EDGES - Static variable in class cytoscape.data.AttributeSaverDialog: Constant to specify edges
EdgeSourceArrowColorProp - Class in cytoscape.visual.properties
EdgeSourceArrowColorProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowColorProp
EdgeSourceArrowOpacityProp - Class in cytoscape.visual.properties
EdgeSourceArrowOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
EdgeSourceArrowProp - Class in cytoscape.visual.properties
EdgeSourceArrowProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowProp
EdgeSourceArrowShapeProp - Class in cytoscape.visual.properties
EdgeSourceArrowShapeProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowShapeProp
EdgeTargetArrowColorProp - Class in cytoscape.visual.properties
EdgeTargetArrowColorProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowColorProp
EdgeTargetArrowOpacityProp - Class in cytoscape.visual.properties
EdgeTargetArrowOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
EdgeTargetArrowProp - Class in cytoscape.visual.properties
EdgeTargetArrowProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowProp
EdgeTargetArrowShapeProp - Class in cytoscape.visual.properties
EdgeTargetArrowShapeProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowShapeProp
EdgeToolTipCalculator - Interface in cytoscape.visual.calculators: Deprecated. Use Calculator instead. Will be removed 10/2007
EdgeToolTipProp - Class in cytoscape.visual.properties
EdgeToolTipProp() - Constructor for class cytoscape.visual.properties.EdgeToolTipProp
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: Creates a new EditNetworkTitleDialog object.
EDITOR_WINDOW_CLOSED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel: DOCUMENT ME!
EDITOR_WINDOW_OPENED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel: DOCUMENT ME!
EditorDisplayer - Enum in cytoscape.visual.ui: Managing value editors in for each data types.
EditorDisplayer.EditorType - Enum in cytoscape.visual.ui: Defines editor type.
EditorValueRangeTracer - Class in cytoscape.visual.ui.editors.continuous
ELLIPSE - Static variable in class cytoscape.visual.ShapeNodeRealizer: Deprecated.
EMBEDDED_WINDOW - Static variable in interface cytoscape.init.CyInitParams: A gui mode, but where cytoscape is embedded within a different application meaning the usual menus and/or toolbars may not be present.
enableListeners(boolean) - Method in class cytoscape.visual.ui.VizMapperMainPanel: On/Off listeners.
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: Deprecated.
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.plugin.DownloadableInfo: Compare the two info objects.
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: DOCUMENT ME!
equals(Object) - Method in class cytoscape.visual.LineType: Deprecated. DOCUMENT ME!
equals(Object) - Method in class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Value
equalsDifferentObjectVersion(Object) - Method in class cytoscape.plugin.DownloadableInfo: Compares the ID and download URL of the two objects.
equalValue - Variable in class cytoscape.visual.mappings.BoundaryRangeValues
ERROR - Static variable in interface cytoscape.init.CyInitParams: Error.
ErrorDialog - Class in cytoscape.dialogs
ErrorDialog() - Constructor for class cytoscape.dialogs.ErrorDialog: Creates new form ErrorDialog
ErrorDialog(JDialog) - Constructor for class cytoscape.dialogs.ErrorDialog
ErrorDialog(JDialog, String) - Constructor for class cytoscape.dialogs.ErrorDialog
ErrorDialog(JFrame, String) - Constructor for class cytoscape.dialogs.ErrorDialog
ErrorDialog(JFrame) - Constructor for class cytoscape.dialogs.ErrorDialog
Exec - Class in cytoscape.util
Exec() - Constructor for class cytoscape.util.Exec: Creates a new Exec object.
Exec(String[]) - Constructor for class cytoscape.util.Exec: Creates a new Exec object.
executeService(CyWebServiceEvent) - Method in interface cytoscape.data.webservice.CyWebServiceEventListener: Execute the service specified in the event object.
executeService(CyWebServiceEvent) - Method in class cytoscape.data.webservice.WebServiceClientImpl: Execute the service through event handling system.
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: Creates a new ExitAction object.
ExpFileChooser - Class in cytoscape.actions: Deprecated. Not apparently used anywhere. Shout if you are. Will be removed 5/2008.
ExpFileChooser(File) - Constructor for class cytoscape.actions.ExpFileChooser: Deprecated. Creates a new ExpFileChooser object.
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.BitmapExporter
export(CyNetworkView, FileOutputStream) - Method in interface cytoscape.util.export.Exporter: Export a view as graphics to a stream.
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.PDFExporter
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.PSExporter
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.SVGExporter
ExportAction - Class in cytoscape.actions
ExportAction() - Constructor for class cytoscape.actions.ExportAction: Creates a new ExportAction object.
ExportAsGMLAction - Class in cytoscape.actions
ExportAsGMLAction() - Constructor for class cytoscape.actions.ExportAsGMLAction: Creates a new ExportAsGMLAction object.
ExportAsGMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsGMLAction: Creates a new ExportAsGMLAction object.
ExportAsGraphicsAction - Class in cytoscape.actions: Action for exporting a network view to bitmap or vector graphics.
ExportAsGraphicsAction() - Constructor for class cytoscape.actions.ExportAsGraphicsAction
ExportAsGraphicsFileChooser - Class in cytoscape.dialogs: Dialog that chooses file to export to.
ExportAsGraphicsFileChooser(CyFileFilter[]) - Constructor for class cytoscape.dialogs.ExportAsGraphicsFileChooser
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: Creates a new ExportAsXGMMLAction object.
ExportAsXGMMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsXGMMLAction: Creates a new ExportAsXGMMLAction object.
ExportBitmapOptionsDialog - Class in cytoscape.dialogs: Options dialog for exporting to bitmap images.
ExportBitmapOptionsDialog(int, int) - Constructor for class cytoscape.dialogs.ExportBitmapOptionsDialog: Creates the options dialog.
ExportEdgeAttributesAction - Class in cytoscape.actions
ExportEdgeAttributesAction() - Constructor for class cytoscape.actions.ExportEdgeAttributesAction: Creates a new ExportEdgeAttributesAction object.
Exporter - Interface in cytoscape.util.export: Interface for exporting a network view to a graphics file.
ExportNodeAttributesAction - Class in cytoscape.actions
ExportNodeAttributesAction() - Constructor for class cytoscape.actions.ExportNodeAttributesAction: Creates a new ExportNodeAttributesAction object.
ExportVizmapAction - Class in cytoscape.actions: Export visual styles as a vizmap.props file
ExportVizmapAction() - Constructor for class cytoscape.actions.ExportVizmapAction: Creates a new ExportVizmapAction object.
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: Creates a new ExpressionDataPopupTable object.
ExpressionDataPopupTable(Frame, String, String[], ExpressionData) - Constructor for class cytoscape.dialogs.ExpressionDataPopupTable: Creates a new ExpressionDataPopupTable object.
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: Deprecated. View types are no longer support so stop using this. Will be removed August 2008.
extract() - Method in class cytoscape.data.readers.GMLReader: DOCUMENT ME!
extractLineStyle(Stroke) - Static method in enum cytoscape.visual.LineStyle: A method that attempts to figure out if a stroke is dashed or not.

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
fillPluginInfoObject(DownloadableInfo) - Method in class cytoscape.plugin.PluginProperties: Takes a PluginInfo object (can be null) and fills it in with information that would not come from a properties file like the unique identifier and download url.
FilterHistoryJList - Class in cytoscape.util.swing: JList with incremntal search & search history.
FilterHistoryJList() - Constructor for class cytoscape.util.swing.FilterHistoryJList: Creates a new FilterHistoryJList object.
findGroup(String) - Static method in class cytoscape.groups.CyGroupManager: Search all groups for the group named 'groupName'
findUpdates() - Method in interface cytoscape.plugin.Installable
findUpdates() - Method in class cytoscape.plugin.InstallablePlugin
findUpdates() - Method in class cytoscape.plugin.InstallableTheme
findUpdates(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager: Get list of plugins that would update the given plugin.
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.
fireCyWebServiceEvent(CyWebServiceEvent) - Method in class cytoscape.data.webservice.CyWebServiceEventSupport: DOCUMENT ME!
fireFocus(String) - Method in class cytoscape.view.NetworkPanel: Deprecated. No longer used. If you need to fire focus, call CytoscapeDesktop.setFocus(). will be removed 11/2008.
firePropertyChange(String, Object, Object) - Static method in class cytoscape.Cytoscape: DOCUMENT ME!
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: Creates a new FitContentAction object.
FlagAndSelectionHandler - Class in cytoscape.view: This class synchronizes the flagged status of nodes and edges as held by a SelectFilter object of a network with the selection status of the corresponding node and edge views in a GraphView.
FlagAndSelectionHandler(SelectFilter, GraphView) - Constructor for class cytoscape.view.FlagAndSelectionHandler: Standard constructor takes the flag filter and the view that should be synchronized.
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: Creates a new FlattenIntVectors object.
FLOAT - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Float state of a CytoPanel.
FloatParser - Class in cytoscape.visual.parsers: DOCUMENT ME!
FloatParser() - Constructor for class cytoscape.visual.parsers.FloatParser
focusGained(FocusEvent) - Method in class cytoscape.dialogs.ImportNetworkDialog: Listen for focus events in the text field.
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.ImportNetworkDialog: Listen for focus lost events in the text field.
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: DOCUMENT ME!
FONT - Static variable in class cytoscape.visual.ui.ValueDisplayer: Deprecated. Display and get input for a font
FontCellRenderer - Class in cytoscape.visual.ui.editors.discrete: DOCUMENT ME!
FontCellRenderer() - Constructor for class cytoscape.visual.ui.editors.discrete.FontCellRenderer
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: Creates a new FontChooser object.
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: Deprecated. 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: Deprecated. will be removed in May 2008
GeneOntologyWizard() - Constructor for class cytoscape.data.servers.ui.GeneOntologyWizard: Deprecated. Creates a new GeneOntologyWizard object.
generateLegendPanel(VisualStyle) - Static method in class cytoscape.visual.ui.LegendDialog: DOCUMENT ME!
GenericEdgeArrowCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. Will be removed 5/2008
GenericEdgeArrowCalculator(String, ObjectMapping, VisualPropertyType) - 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.
GenericEdgeArrowCalculator(String, Properties, String, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.GenericEdgeArrowCalculator: Deprecated. Creates a new GenericEdgeArrowCalculator object.
GenericEdgeColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeColorCalculator: Deprecated. Creates a new GenericEdgeColorCalculator object.
GenericEdgeColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeColorCalculator: Deprecated. Creates a new GenericEdgeColorCalculator object.
GenericEdgeFontFaceCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeFontFaceCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator: Deprecated. Creates a new GenericEdgeFontFaceCalculator object.
GenericEdgeFontFaceCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontFaceCalculator: Deprecated. Creates a new GenericEdgeFontFaceCalculator object.
GenericEdgeFontSizeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeFontSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator: Deprecated. Creates a new GenericEdgeFontSizeCalculator object.
GenericEdgeFontSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeFontSizeCalculator: Deprecated. Creates a new GenericEdgeFontSizeCalculator object.
GenericEdgeLabelCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeLabelCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelCalculator: Deprecated. Creates a new GenericEdgeLabelCalculator object.
GenericEdgeLabelCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelCalculator: Deprecated. Creates a new GenericEdgeLabelCalculator object.
GenericEdgeLabelColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeLabelColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator: Deprecated. Creates a new GenericEdgeLabelColorCalculator object.
GenericEdgeLabelColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLabelColorCalculator: Deprecated. Creates a new GenericEdgeLabelColorCalculator object.
GenericEdgeLineStyleCalculator - Class in cytoscape.visual.calculators: Deprecated. Will be removed 5/2008
GenericEdgeLineStyleCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineStyleCalculator: Deprecated. Creates a new GenericEdgeLineWidthCalculator object.
GenericEdgeLineStyleCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineStyleCalculator: Deprecated. Creates a new GenericEdgeLineWidthCalculator object.
GenericEdgeLineTypeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeLineTypeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator: Deprecated. Creates a new GenericEdgeLineTypeCalculator object.
GenericEdgeLineTypeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineTypeCalculator: Deprecated. Creates a new GenericEdgeLineTypeCalculator object.
GenericEdgeLineWidthCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeLineWidthCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineWidthCalculator: Deprecated. Creates a new GenericEdgeLineWidthCalculator object.
GenericEdgeLineWidthCalculator(String, ObjectMapping, Class) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineWidthCalculator: Deprecated. Creates a new GenericEdgeLineWidthCalculator object.
GenericEdgeLineWidthCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeLineWidthCalculator: Deprecated. Creates a new GenericEdgeLineWidthCalculator object.
GenericEdgeSourceArrowCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeSourceArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: Deprecated. Creates a new GenericEdgeSourceArrowCalculator object.
GenericEdgeSourceArrowCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator: Deprecated. Creates a new GenericEdgeSourceArrowCalculator object.
GenericEdgeSourceArrowColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeSourceArrowColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowColorCalculator: Deprecated. Creates a new GenericEdgeSourceArrowColorCalculator object.
GenericEdgeSourceArrowColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowColorCalculator: Deprecated. Creates a new GenericEdgeSourceArrowColorCalculator object.
GenericEdgeSourceArrowShapeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeSourceArrowShapeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator: Deprecated. Creates a new GenericEdgeSourceArrowShapeCalculator object.
GenericEdgeSourceArrowShapeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator: Deprecated. Creates a new GenericEdgeSourceArrowShapeCalculator object.
GenericEdgeTargetArrowCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeTargetArrowCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: Deprecated. Creates a new GenericEdgeTargetArrowCalculator object.
GenericEdgeTargetArrowCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator: Deprecated. Creates a new GenericEdgeTargetArrowCalculator object.
GenericEdgeTargetArrowColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeTargetArrowColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowColorCalculator: Deprecated. Creates a new GenericEdgeTargetArrowColorCalculator object.
GenericEdgeTargetArrowColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowColorCalculator: Deprecated. Creates a new GenericEdgeTargetArrowColorCalculator object.
GenericEdgeTargetArrowShapeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeTargetArrowShapeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator: Deprecated. Creates a new GenericEdgeTargetArrowShapeCalculator object.
GenericEdgeTargetArrowShapeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator: Deprecated. Creates a new GenericEdgeTargetArrowShapeCalculator object.
GenericEdgeToolTipCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericEdgeToolTipCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericEdgeToolTipCalculator: Deprecated. Creates a new GenericEdgeToolTipCalculator object.
GenericEdgeToolTipCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericEdgeToolTipCalculator: Deprecated. Creates a new GenericEdgeToolTipCalculator object.
GenericNodeBorderColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeBorderColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: Deprecated. Creates a new GenericNodeBorderColorCalculator object.
GenericNodeBorderColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeBorderColorCalculator: Deprecated. Creates a new GenericNodeBorderColorCalculator object.
GenericNodeColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be removed 5/2008. Will be hidden, although probably not removed, in 5/2008.
GenericNodeColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. Will be removed 5/2008
GenericNodeColorCalculator(String, ObjectMapping, VisualPropertyType) - 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. Will be removed 5/2008
GenericNodeColorCalculator(String, Properties, String, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.GenericNodeColorCalculator: Deprecated. Creates a new GenericNodeColorCalculator object.
GenericNodeFillColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeFillColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFillColorCalculator: Deprecated. Creates a new GenericNodeFillColorCalculator object.
GenericNodeFillColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFillColorCalculator: Deprecated. Creates a new GenericNodeFillColorCalculator object.
GenericNodeFontFaceCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeFontFaceCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFontFaceCalculator: Deprecated. Creates a new GenericNodeFontFaceCalculator object.
GenericNodeFontFaceCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFontFaceCalculator: Deprecated. Creates a new GenericNodeFontFaceCalculator object.
GenericNodeFontSizeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeFontSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeFontSizeCalculator: Deprecated. Creates a new GenericNodeFontSizeCalculator object.
GenericNodeFontSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeFontSizeCalculator: Deprecated. Creates a new GenericNodeFontSizeCalculator object.
GenericNodeHeightCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeHeightCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeHeightCalculator: Deprecated. Creates a new GenericNodeHeightCalculator object.
GenericNodeHeightCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeHeightCalculator: Deprecated. Creates a new GenericNodeHeightCalculator object.
GenericNodeLabelCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeLabelCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelCalculator: Deprecated. Creates a new GenericNodeLabelCalculator object.
GenericNodeLabelCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelCalculator: Deprecated. Creates a new GenericNodeLabelCalculator object.
GenericNodeLabelColorCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeLabelColorCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelColorCalculator: Deprecated. Creates a new GenericNodeLabelColorCalculator object.
GenericNodeLabelColorCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelColorCalculator: Deprecated. Creates a new GenericNodeLabelColorCalculator object.
GenericNodeLabelPositionCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeLabelPositionCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator: Deprecated. Creates a new GenericNodeLabelPositionCalculator object.
GenericNodeLabelPositionCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLabelPositionCalculator: Deprecated. Creates a new GenericNodeLabelPositionCalculator object.
GenericNodeLineStyleCalculator - Class in cytoscape.visual.calculators: Deprecated. Will be removed 5/2008
GenericNodeLineStyleCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLineStyleCalculator: Deprecated. Creates a new GenericNodeLineWidthCalculator object.
GenericNodeLineStyleCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLineStyleCalculator: Deprecated. Creates a new GenericNodeLineWidthCalculator object.
GenericNodeLineTypeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeLineTypeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLineTypeCalculator: Deprecated. Creates a new GenericNodeLineTypeCalculator object.
GenericNodeLineTypeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLineTypeCalculator: Deprecated. Creates a new GenericNodeLineTypeCalculator object.
GenericNodeLineWidthCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeLineWidthCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeLineWidthCalculator: Deprecated. Creates a new GenericNodeLineWidthCalculator object.
GenericNodeLineWidthCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeLineWidthCalculator: Deprecated. Creates a new GenericNodeLineWidthCalculator object.
GenericNodeShapeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeShapeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeShapeCalculator: Deprecated. Creates a new GenericNodeShapeCalculator object.
GenericNodeShapeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeShapeCalculator: Deprecated. Creates a new GenericNodeShapeCalculator object.
GenericNodeSizeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. Will be removed 5/2008
GenericNodeSizeCalculator(String, ObjectMapping, VisualPropertyType) - 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.
GenericNodeSizeCalculator(String, Properties, String, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.GenericNodeSizeCalculator: Deprecated. Creates a new GenericNodeSizeCalculator object.
GenericNodeToolTipCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeToolTipCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeToolTipCalculator: Deprecated. Creates a new GenericNodeToolTipCalculator object.
GenericNodeToolTipCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeToolTipCalculator: Deprecated. Creates a new GenericNodeToolTipCalculator object.
GenericNodeUniformSizeCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeUniformSizeCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: Deprecated. Creates a new GenericNodeUniformSizeCalculator object.
GenericNodeUniformSizeCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeUniformSizeCalculator: Deprecated. Creates a new GenericNodeUniformSizeCalculator object.
GenericNodeWidthCalculator - Class in cytoscape.visual.calculators: Deprecated. Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008.
GenericNodeWidthCalculator(String, ObjectMapping) - Constructor for class cytoscape.visual.calculators.GenericNodeWidthCalculator: Deprecated. Creates a new GenericNodeWidthCalculator object.
GenericNodeWidthCalculator(String, Properties, String) - Constructor for class cytoscape.visual.calculators.GenericNodeWidthCalculator: Deprecated. Creates a new GenericNodeWidthCalculator object.
get(String) - Method in interface cytoscape.util.ModuleProperties: This method is used to get the Tunable named name from this LayoutProperties.
get(String) - Method in class cytoscape.util.ModulePropertiesImpl: This method is used to get the Tunable named name from this LayoutProperties.
get() - Method in class cytoscape.util.SwingWorker: Return the value created by the construct method.
get(VisualPropertyType) - Method in class cytoscape.visual.Appearance: Gets the appearance for the specified VisualPropertyType.
get(byte) - Method in class cytoscape.visual.EdgeAppearance: Deprecated. Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008.
get(byte) - Method in class cytoscape.visual.NodeAppearance: Deprecated. Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008.
getAbbreviation() - Method in class cytoscape.data.ontology.DBReference: DOCUMENT ME!
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: DOCUMENT ME!
getAccessibleMethods() - Method in interface cytoscape.data.webservice.WebServiceClient: Returns all available methods accessible through client stub.
getAccessibleMethods() - Method in class cytoscape.data.webservice.WebServiceClientImpl: DOCUMENT ME!
getActionClass() - Method in enum cytoscape.visual.ui.EditorDisplayer: DOCUMENT ME!
getActionList() - Static method in class cytoscape.util.CytoscapeAction: DOCUMENT ME!
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: DOCUMENT ME!
getAllAnnotations(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
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.
getAllClients() - Static method in class cytoscape.data.webservice.WebServiceClientManager: DOCUMENT ME!
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
getAllCommonNames(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
getAllCommonNames(String) - Method in class cytoscape.data.synonyms.Thesaurus: DOCUMENT ME!
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.
getAllFiles(String, String) - Static method in class cytoscape.util.ZipUtil: Reads zip file, returns a list of all entries that match the given regular expression
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: DOCUMENT ME!
getAllHierarchyPathsAsNames(int) - Method in class cytoscape.data.annotation.Ontology: DOCUMENT ME!
getAllInteractions() - Method in class cytoscape.data.readers.InteractionsReader: DOCUMENT ME!
getAllLayouts() - Static method in class cytoscape.layout.CyLayouts: Get all of the available layouts.
getAllMeasurements() - Method in class cytoscape.data.ExpressionData: Gets all Measurements.
getAllNamesInGroup(String) - Method in class cytoscape.data.synonyms.Thesaurus: DOCUMENT ME!
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: DOCUMENT ME!
getAnchorNames() - Static method in class cytoscape.visual.LabelPosition: DOCUMENT ME!
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationFlatFileReader: DOCUMENT ME!
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationXmlReader: DOCUMENT ME!
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: DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
getAnnotation(String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
getAnnotationCount() - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServer: DOCUMENT ME!
getAnnotationDescriptions() - Method in interface cytoscape.data.servers.BioDataServerInterface: DOCUMENT ME!
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServerRmi: DOCUMENT ME!
getAnotationFiles() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor: DOCUMENT ME!
getArgs() - Method in class cytoscape.CyMain: DOCUMENT ME!
getArgs() - Method in interface cytoscape.init.CyInitParams: Returns the arguments used to trigger the initialization.
getArrowIcons() - Static method in class cytoscape.visual.ui.IconSupport: Deprecated. DOCUMENT ME!
getArrowIcons() - Method in class cytoscape.visual.ui.MiscDialog: Deprecated. Use IconSupport instead. This will be removed 10/2007.
getArrowShape(int) - Static method in enum cytoscape.visual.ArrowShape: DOCUMENT ME!
getArrowToStringHashMap(int) - Static method in class cytoscape.visual.ui.IconSupport: Deprecated. DOCUMENT ME!
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, String) - Method in interface cytoscape.data.CyAttributes: Gets an Object value at the specified id/attributeName.
getAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl: Gets an Object value at the specified id/attributeName.
getAttribute(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils: DOCUMENT ME!
getAttribute(DataSource, String) - Static method in class cytoscape.util.BookmarksUtil: DOCUMENT ME!
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: DOCUMENT ME!
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: DOCUMENT ME!
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: DOCUMENT ME!
getAttributeNames() - Method in interface cytoscape.data.CyAttributes: Gets an array of all attribute names.
getAttributeNames() - Method in class cytoscape.data.CyAttributesImpl: DOCUMENT ME!
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: DOCUMENT ME!
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.
getAuthor() - Method in class cytoscape.plugin.PluginInfo.AuthorInfo
getAuthors() - Method in class cytoscape.plugin.PluginInfo
getBackgroundColor() - Method in class cytoscape.visual.GlobalAppearance: DOCUMENT ME!
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.AnotationPanelDescriptor: DOCUMENT ME!
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.ManifestFileSelectionPanelDescriptor: DOCUMENT ME!
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.OboPanelDescriptor: DOCUMENT ME!
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.SelectFormatPanelDescriptor: DOCUMENT ME!
getBackPanelDescriptor() - Method in class cytoscape.data.servers.ui.SpeciesPanelDescriptor: DOCUMENT ME!
getBaseKey() - Method in enum cytoscape.visual.mappings.MappingType: DOCUMENT ME!
getBasicInputStream(URL) - Static method in class cytoscape.util.URLUtil