Index (Cytoscape 2.3.1 API)

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV NEXT

FRAMES NO FRAMES

A B C D E F G H I J L M N O P R S T U V W X Z

A

ALIASES - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape: Deprecated. this event should not be used, it is not fired
AbstractCellEditor - class cytoscape.util.swing.AbstractCellEditor.
AbstractCellEditor() - Constructor for class cytoscape.util.swing.AbstractCellEditor
AbstractTreeTableModel - class cytoscape.util.swing.AbstractTreeTableModel.
AbstractTreeTableModel(Object) - Constructor for class cytoscape.util.swing.AbstractTreeTableModel
AttributeLayout - class cytoscape.layout.AttributeLayout.: This class provides methods for performing operations on a graph related to the values of a particular data attribute attached to the nodes of the graph.
AttributeLayout(CyNetworkView) - Constructor for class cytoscape.layout.AttributeLayout
accept(File) - Method in class cytoscape.util.CyFileFilter: Return true if this file should be shown in the directory pane, false if it shouldn't.
accept(File, String) - Method in class cytoscape.util.CyFileFilter: In order to implement the AWT version of this class "FileNameFilter", the following method must also be implemented.
accept(String) - Method in class cytoscape.util.CyFileFilter
actionHelp() - Method in class cytoscape.util.CytoscapeAction
actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction
activate() - Method in class cytoscape.plugin.CytoscapePlugin: If implemented, then this plugin will be activated after being initialized
add(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel.
add(Component, int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a component to the CytoPanel with specified title, icon, and tool tip.
add(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel.
add(Component, int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a component to the CytoPanel with specified title, icon, and tool tip.
addAction(Action) - Method in class cytoscape.util.CytoscapeMenuBar: If the given Action has a present and false inMenuBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredMenu property, or null if it does not have that property.
addAction(Action, int) - Method in class cytoscape.util.CytoscapeMenuBar
addAction(String, Action) - Method in class cytoscape.util.CytoscapeMenuBar
addAction(Action) - Method in class cytoscape.util.CytoscapeToolBar: If the given Action has an absent or false inToolBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredButtonGroup property, or null if it does not have that property.
addAction(String, Action) - Method in class cytoscape.util.CytoscapeToolBar: Note that this presently ignores the button group name.
addAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus
addAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServer
addAnnotation(Annotation) - Method in interface cytoscape.data.servers.BioDataServerInterface
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServerRmi: if the new annotation is to an already annotated species, curator and type, then simply add (with possible overwriting for identical
addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
addCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork: Registers the argument as a listener to this object.
addCytoPanelListener(CytoPanelListener) - Method in interface cytoscape.view.cytopanels.CytoPanel: Adds a CytoPanel listener.
addCytoPanelListener(CytoPanelListener) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Adds a CytoPanel listener.
addCytoscapeAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus: Takes a CytoscapeAction and will add it to the MenuBar or the Toolbar as is appropriate.
addCytoscapeAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus: Add the menu item in a specific position
addDataDefinitionListener(MultiHashMapDefinitionListener) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Registers a listener for receiving events having to do with attribute definitions being created and deleted.
addDataListener(MultiHashMapListener) - Method in interface cytoscape.data.attr.MultiHashMap: Registers a listener for receiving events having to do with attribute values being assigned and removed.
addEdge(int) - Method in interface cytoscape.CyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdge(Edge) - Method in interface cytoscape.CyNetwork: Add a edge to this Network that already exists in Cytoscape
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
addEdit(UndoableEdit) - Method in class cytoscape.util.UndoManager
addEdit(UndoableEdit) - Method in class cytoscape.view.CytoscapeDesktop
addExtension(String) - Method in class cytoscape.util.CyFileFilter: Adds a filetype "dot" extension to filter against.
addFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork: Adds a listener for FlagEvents to this CyNetwork
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
addNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
addSelectEventListener(SelectEventListener) - Method in interface cytoscape.CyNetwork: Adds a listener for SelectEvents to this CyNetwork
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServer
addThesaurus(String, Thesaurus) - Method in interface cytoscape.data.servers.BioDataServerInterface
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServerRmi
addTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
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.
appendNetwork(CyNetwork) - Method in interface cytoscape.CyNetwork: Appends all of the nodes and edges in the given Network to this Network
applyAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the node, edge, and global visual attributes.
applyEdgeAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the edge appearances.
applyEdgeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies all of the edge appearances.
applyGlobalAppearances() - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies the global visual attributes.
applyGlobalAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager: Recalculates and reapplies the global visual attributes.
applyLayout(LayoutAlgorithm) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView
applyLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(LayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLockedLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
applyLockedLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given NodeViews and EdgeViews in place
applyLockedLayout(LayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place
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.
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 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.
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.
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()).
attributeUndefined(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinitionListener: This method is called by a MultiHashMapDefinition implementation as a result of an attribute being undefined (MultiHashMapDefinition.undefineAttribute()).
attributeValueAssigned(String, String, Object[], Object, Object) - Method in interface cytoscape.data.attr.MultiHashMapListener
attributeValueRemoved(String, String, Object[], Object) - Method in interface cytoscape.data.attr.MultiHashMapListener: This listener method gets called as a result of MultiHashMap.removeAttributeValue(objectKey, attributeName, keyIntoValue), but only if an attribute value was found [and removed] for specified key.

B

BEGIN - Static variable in class cytoscape.CyNetworkEvent: Indicates that someone is beginning to work with the network.
BIOLOGICAL_PROCESS - Static variable in class cytoscape.data.Semantics
BiModalJSplitPane - class cytoscape.view.cytopanels.BiModalJSplitPane.: 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 cytoscape.data.servers.BioDataServer.
BioDataServer(String) - Constructor for class cytoscape.data.servers.BioDataServer: serverName is either an RMI URI, or a manifest file which says what files to load into an in-process server; the manifest, the annotations, and the ontologies, may be files on a filesystem, files in a jar, or files retrieved by HTTP Mod. by Kei (9/10/2005): 1.
BioDataServer() - Constructor for class cytoscape.data.servers.BioDataServer
BioDataServerInterface - interface cytoscape.data.servers.BioDataServerInterface.
BioDataServerRmi - class cytoscape.data.servers.BioDataServerRmi.: This is the actual class which implements BioDataServer Methods.
BioDataServerRmi() - Constructor for class cytoscape.data.servers.BioDataServerRmi
BioDataServerUtil - class cytoscape.util.BioDataServerUtil.
BioDataServerUtil() - Constructor for class cytoscape.util.BioDataServerUtil
beginActivity(String) - Method in interface cytoscape.CyNetwork: Deprecated.
buildValueMap(String) - Method in class cytoscape.layout.AttributeLayout: This function build a Map structure based on the unique values of the data attribute specified by the argument.

C

CANONICAL_NAME - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
CELLULAR_COMPONENT - Static variable in class cytoscape.data.Semantics
CLEAN - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
CLEAR_OBJECTS - Static variable in class cytoscape.layout.AttributeLayout
COMMON_NAME - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
CREATE_EDGES - Static variable in class cytoscape.layout.AttributeLayout
CUSTOM - Static variable in class cytoscape.util.FileUtil
CYTOSCAPE_EXIT - Static variable in class cytoscape.Cytoscape
CYTOSCAPE_INITIALIZED - Static variable in class cytoscape.Cytoscape
CountedIterator - interface cytoscape.data.attr.CountedIterator.: A java.util.Iterator with knowledge of how many elements are remaining.
CreditScreen - class cytoscape.util.CreditScreen.
CreditScreen() - Constructor for class cytoscape.util.CreditScreen
CyAttributes - interface cytoscape.data.CyAttributes.: CyAttributes provides access to node and edge attributes within Cytoscape.
CyColorChooser - class cytoscape.util.CyColorChooser.: This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColorChooser() - Constructor for class cytoscape.util.CyColorChooser
CyEdge - class cytoscape.CyEdge.
CyEdge(RootGraph, int) - Constructor for class cytoscape.CyEdge
CyFileFilter - class cytoscape.util.CyFileFilter.: 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.
CyMain - class cytoscape.CyMain.: This is the main startup class for Cytoscape.
CyMain(String[]) - Constructor for class cytoscape.CyMain
CyMenus - class cytoscape.view.CyMenus.: This class creates the menu and tool bars for a Cytoscape window object.
CyMenus() - Constructor for class cytoscape.view.CyMenus
CyNetwork - interface cytoscape.CyNetwork.: CyNetwork is the primary class for algorithm writing.
CyNetworkAdapter - class cytoscape.CyNetworkAdapter.: Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes.
CyNetworkAdapter() - Constructor for class cytoscape.CyNetworkAdapter
CyNetworkData - interface cytoscape.CyNetworkData.: This will be the interface where things like multi-dimensional data are accessed.
CyNetworkEvent - class cytoscape.CyNetworkEvent.: Events of this class are fired from a CyNetwork object when something happens to the network.
CyNetworkEvent(CyNetwork, int) - Constructor for class cytoscape.CyNetworkEvent
CyNetworkListener - interface cytoscape.CyNetworkListener.: Interface for listeners that respond to CyNetwork events.
CyNetworkNaming - class cytoscape.util.CyNetworkNaming.
CyNetworkNaming() - Constructor for class cytoscape.util.CyNetworkNaming
CyNetworkView - interface cytoscape.view.CyNetworkView.: CyNetworkView is responsible for actually getting a graph to show up on the screen.
CyNode - class cytoscape.CyNode.
CyNode(RootGraph, int) - Constructor for class cytoscape.CyNode
CyProject - class cytoscape.CyProject.: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
CyProject(String) - Constructor for class cytoscape.CyProject: Deprecated. Constructs a Project object by reading the file at the supplied location, by calling readProjectFile with the argument.
CytoPanel - interface cytoscape.view.cytopanels.CytoPanel.: Interface to a CytoPanel.
CytoPanelContainer - interface cytoscape.view.cytopanels.CytoPanelContainer.: Interface for Container of CytoPanel Objects.
CytoPanelImp - class cytoscape.view.cytopanels.CytoPanelImp.: 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 cytoscape.view.cytopanels.CytoPanelListener.: This listener interface provides the mechanism to respond to CytoPanel Events.
CytoPanelState - class cytoscape.view.cytopanels.CytoPanelState.: CytoPanelState Class.
CytoPanelUtil - class cytoscape.view.cytopanels.CytoPanelUtil.: Contains methods to assist with various tasks performed by the CytoPanel API.
CytoPanelUtil() - Constructor for class cytoscape.view.cytopanels.CytoPanelUtil
Cytoscape - class cytoscape.Cytoscape.: This class, Cytoscape is the primary class in the API.
Cytoscape() - Constructor for class cytoscape.Cytoscape
CytoscapeAction - class cytoscape.util.CytoscapeAction.
CytoscapeAction() - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeAction(String) - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeAction(String, Icon) - Constructor for class cytoscape.util.CytoscapeAction
CytoscapeConfig - class cytoscape.CytoscapeConfig.: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
CytoscapeConfig() - Constructor for class cytoscape.CytoscapeConfig: Deprecated.
CytoscapeDesktop - class cytoscape.view.CytoscapeDesktop.: The CytoscapeDesktop is the central Window for working with Cytoscape
CytoscapeDesktop() - Constructor for class cytoscape.view.CytoscapeDesktop: The Default constructor uses a TabbedView
CytoscapeDesktop(int) - Constructor for class cytoscape.view.CytoscapeDesktop: Create a CytoscapeDesktop that conforms the given view type.
CytoscapeInit - class cytoscape.CytoscapeInit.: Cytoscape Init is responsible for starting Cytoscape in a way that makes sense.
CytoscapeInit() - Constructor for class cytoscape.CytoscapeInit
CytoscapeMenuBar - class cytoscape.util.CytoscapeMenuBar.
CytoscapeMenuBar() - Constructor for class cytoscape.util.CytoscapeMenuBar: Default constructor.
CytoscapeModifiedNetworkManager - class cytoscape.CytoscapeModifiedNetworkManager.: CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents.
CytoscapeModifiedNetworkManager() - Constructor for class cytoscape.CytoscapeModifiedNetworkManager
CytoscapeObj - class cytoscape.CytoscapeObj.: Deprecated. Will be removed October 2006. Use static methods in Cytoscape.java instead.
CytoscapeObj() - Constructor for class cytoscape.CytoscapeObj: Deprecated.
CytoscapePlugin - class cytoscape.plugin.CytoscapePlugin.: 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 cytoscape.util.CytoscapeProgressMonitor.: CytoscapeProgressMonitor.
CytoscapeProgressMonitor(MonitoredTask) - Constructor for class cytoscape.util.CytoscapeProgressMonitor: Construtor.
CytoscapeProgressMonitor(MonitoredTask, Component) - Constructor for class cytoscape.util.CytoscapeProgressMonitor: Constructor.
CytoscapeToolBar - class cytoscape.util.CytoscapeToolBar.
CytoscapeToolBar() - Constructor for class cytoscape.util.CytoscapeToolBar: Default constructor delegates to the superclass void constructor and then calls #initializeCytoscapeToolBar().
CytoscapeVersion - class cytoscape.CytoscapeVersion.
CytoscapeVersion() - Constructor for class cytoscape.CytoscapeVersion
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
checkConflictingCalculator(Calculator) - Method in class cytoscape.visual.VisualStyle: Check if contained appearance calculators are using given calculator
checkSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
clear() - Method in class cytoscape.data.servers.BioDataServer
clear() - Method in interface cytoscape.data.servers.BioDataServerInterface
clear() - Method in class cytoscape.data.servers.BioDataServerRmi
clearCytoscape() - Static method in class cytoscape.Cytoscape: Deprecated. WARNING: this should only be used under special circumstances.
clearPreviousGraphObjects() - Method in class cytoscape.layout.AttributeLayout: Removes any nodes and edges that were created by a previously called method of this class.
clearStatusBar() - Method in class cytoscape.view.CytoscapeDesktop: Clears the Status Bar Message.
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.VisualStyle: Perform deep copy of this VisualStyle.
completions() - Method in class cytoscape.util.CytoscapeAction
compressFast(int, boolean) - Method in class cytoscape.util.ZipUtil: Faster version of compression method.
configure() - Method in class cytoscape.util.MacAppConfig: Configures the Info.plist list with all cytoscape/*.jar files.
construct() - Method in class cytoscape.util.SwingWorker: Compute the value to be returned by the get method.
convert() - Method in class cytoscape.util.Transform
convertLambdasToPvals() - Method in class cytoscape.data.ExpressionData: Converts all lambdas to p-values.
copyToAttribs(CyAttributes, TaskMonitor) - Method in class cytoscape.data.ExpressionData: Copies ExpressionData data structure into CyAttributes data structure.
createDifferenceGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils: Create a new graph which is the difference of multiple graphs.
createEdges(String) - Method in class cytoscape.layout.AttributeLayout: Adds edges between all nodes that share a value for the given node attribute.
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
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(int[], int[], String) - Static method in class cytoscape.Cytoscape: Creates a new Network.
createNetwork(Collection, Collection, String) - Static method in class cytoscape.Cytoscape: Creates a new Network.
createNetwork(int[], int[], String, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(int[], int[], String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork
createNetwork(Collection, Collection, String, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(Collection, Collection, String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape: Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(String, int, boolean, BioDataServer, String) - Static method in class cytoscape.Cytoscape: Deprecated. It will be removed in April 2007 Use CyNetwork createNetworkFromFile(String location, boolean create_view) instead. File type is no longer needed as ImportHandler now manages all file types.
createNetwork(GraphReader, boolean, CyNetwork) - Static method in class cytoscape.Cytoscape: Creates a cytoscape.data.CyNetwork from a reader.
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.
createNetworkFromProject(CyProject, BioDataServer) - Static method in class cytoscape.Cytoscape: Deprecated. Will be removed Oct 2006. This is not apparently used, so don't start. This functionality has been subsumed by Cytoscape Sessions.
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.
createNewSession() - Static method in class cytoscape.Cytoscape: Clear all networks and attributes and start a new session.
createUnionGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils: Create a new graph which is the union of multiple graphs.
cytoscape.data.attr - package cytoscape.data.attr
cytoscape.data.attr.util - package cytoscape.data.attr.util

D

DATASERVER_CHANGED - Static variable in class cytoscape.Cytoscape
DEFAULT_MENU_SPECIFIER - Static variable in class cytoscape.util.CytoscapeMenuBar
DEF_COMPRESSION_LEVEL - Static variable in class cytoscape.util.ZipUtil
DNA - Static variable in class cytoscape.data.Semantics
DOCK - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Dock state of a CytoPanel.
DO_LAYOUT - Static variable in class cytoscape.layout.AttributeLayout
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.
defineAttribute(String, byte, byte[]) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Creates an attribute definition.
deleteAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Deletes the id/attributeName pair.
deleteAttribute(String) - Method in interface cytoscape.data.CyAttributes: Deletes the specified attribute.
deleteEdgeAttribute(String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
deleteNodeAttribute(String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
describe() - Method in class cytoscape.data.servers.BioDataServer
describe() - Method in interface cytoscape.data.servers.BioDataServerInterface
describe() - Method in class cytoscape.data.servers.BioDataServerRmi
describe() - Method in class cytoscape.plugin.CytoscapePlugin: method returning a String description of the plugin.
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
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
disableSquiggle() - Static method in class cytoscape.Cytoscape: Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
discardAllEdits() - Method in class cytoscape.util.UndoManager: called when a network view switches
doCallback(String, int) - Method in class cytoscape.layout.AttributeLayout
doLayout(String) - Method in class cytoscape.layout.AttributeLayout: Performs a layout operation based on values of the given node attribute.
doLayout() - Method in interface cytoscape.layout.LayoutAlgorithm
done() - Method in interface cytoscape.util.MonitoredTask: Returns true if the task is done.

E

END - Static variable in class cytoscape.CyNetworkEvent: Indicates that someone is done working with the network.
EXPRESSION_DATA_LOADED - Static variable in class cytoscape.Cytoscape
EXTERNAL_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in JFrames, so each Network has its own window. ( like the GIMP )
Exec - class cytoscape.util.Exec.
Exec() - Constructor for class cytoscape.util.Exec
Exec(String[]) - Constructor for class cytoscape.util.Exec
ExpressionData - class cytoscape.data.ExpressionData.: 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.
ExtensibleMultiHashMapModel - class cytoscape.data.attr.util.ExtensibleMultiHashMapModel.: Deprecated. Use MultiHashMapFactory instead.
ExtensibleMultiHashMapModel() - Constructor for class cytoscape.data.attr.util.ExtensibleMultiHashMapModel: Deprecated.
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
enableSquiggle() - Static method in class cytoscape.Cytoscape: Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
endActivity(String) - Method in interface cytoscape.CyNetwork: Deprecated.
ensureCapacity(int, int) - Static method in class cytoscape.Cytoscape: Ensure the capacity of Cytoscapce.
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.
exit() - Static method in class cytoscape.Cytoscape: Deprecated. Use exit(returnVal) instead. This will be removed in Sept 2006.
exit(int) - Static method in class cytoscape.Cytoscape: Shuts down Cytoscape, after giving plugins time to react.

F

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_SBML - Static variable in class cytoscape.Cytoscape
FILE_SIF - Static variable in class cytoscape.Cytoscape
FILE_XGMML - Static variable in class cytoscape.Cytoscape
FLOAT - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Float state of a CytoPanel.
FileUtil - class cytoscape.util.FileUtil.: Provides a platform-dependent way to open files.
FileUtil() - Constructor for class cytoscape.util.FileUtil
finished() - Method in class cytoscape.util.SwingWorker: Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
firePropertyChange(String, Object, Object) - Static method in class cytoscape.Cytoscape
flagAllEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.selectAllEdges()
flagAllNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.selectAllNodes()
forceClear(String) - Method in interface cytoscape.CyNetwork: Deprecated.

G

GMLFileFilter - class cytoscape.util.GMLFileFilter.
GMLFileFilter() - Constructor for class cytoscape.util.GMLFileFilter
GO_ALIASES - Static variable in class cytoscape.data.Semantics
GO_COMMON_NAME - Static variable in class cytoscape.data.Semantics
GRAPH_REPLACED - Static variable in class cytoscape.CyNetworkEvent: Indicates that a new graph has been installed in the network.
GraphSetUtils - class cytoscape.util.GraphSetUtils.: Class contains various static methods to perform set-like operations on graph.
GraphSetUtils() - Constructor for class cytoscape.util.GraphSetUtils
get() - Method in class cytoscape.util.SwingWorker: Return the value created by the construct method.
getActionList() - Static method in class cytoscape.util.CytoscapeAction
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
getAllAnnotations(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAllAttributeKeys(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all key sequnces that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeKeysAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all key sequences having a given prefix that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeValues(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering all attribute values on an object in a given attribute definition; this method is only useful with attribute definitions that have nonzero key spaces.
getAllAttributeValuesAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers: Convenience method for discovering attribute values along a specified key prefix; this method is only useful with attribute definitions that have nonzero key spaces.
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServer
getAllCommonNames(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAllMeasurements() - Method in class cytoscape.data.ExpressionData: Gets all Measurements.
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.
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServer
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServer
getAnnotation(String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotation(AnnotationDescription) - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServer
getAnnotationCount() - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServerRmi
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServer
getAnnotationDescriptions() - Method in interface cytoscape.data.servers.BioDataServerInterface
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServerRmi
getArgs() - Method in class cytoscape.CyMain
getArgs() - Method in class cytoscape.CytoscapeConfig: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
getArgs() - Static method in class cytoscape.CytoscapeInit: Deprecated. Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007.
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: Gets a 'simple' list of attributes for the id/attributeName pair.
getAttributeMap(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a 'simple' map of attribute values.
getAttributeNames() - Method in interface cytoscape.data.CyAttributes: Gets an array of all attribute names.
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.
getBioDataDirectory() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getBioDataServer() - Static method in class cytoscape.Cytoscape
getBioDataServer() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getProperty("bioDataServer") instead.
getBioDataServer() - Method in class cytoscape.CytoscapeObj: Deprecated. Will be removed October 2006. Use static methods in Cytoscape.java instead.
getBool() - Method in class cytoscape.util.MutableBool
getBooleanAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a Boolean value at the specified id/attributeName.
getBounds() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the bounds of the applications mainframe.
getBounds() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Gets Bounds of Container, relative to parent component.
getBriefHistory() - Method in class cytoscape.CytoscapeVersion
getCalculatorCatalog() - Method in class cytoscape.visual.VisualMappingManager
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServer
getCanonicalName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getCanonicalize() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getCellEditorValue() - Method in class cytoscape.util.swing.AbstractCellEditor
getClassLoader() - Static method in class cytoscape.CytoscapeInit
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServer
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
getClassifications(String, String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getClassifications(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getClientData(String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientData(String) - Method in interface cytoscape.view.CyNetworkView: Get Some client data
getClientDataNames() - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientDataNames() - Method in interface cytoscape.view.CyNetworkView: Get a list of all currently available ClientData objects
getCmd() - Method in class cytoscape.util.Exec
getColor() - Method in class cytoscape.util.MutableColor: Deprecated.
getColumnClass(int) - Method in class cytoscape.util.swing.AbstractTreeTableModel
getColumnClass(int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the type for column number column.
getColumnClass(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getColumnCount() - Method in interface cytoscape.util.swing.TreeTableModel: Returns the number of availible columns.
getColumnCount() - Method in class cytoscape.util.swing.TreeTableModelAdapter
getColumnName(int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the name for column number column.
getColumnName(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServer
getCommonName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
getConditionIndex(String) - Method in class cytoscape.data.ExpressionData: Gets the index value of the specified experimenal conditon.
getConditionNames() - Method in class cytoscape.data.ExpressionData: Gets an Array of All Experimental Conditions.
getConfigDirectory() - Static method in class cytoscape.CytoscapeInit: If .cytoscape directory does not exist, it creates it and returns it
getConfigDirectoy() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method is only deprecated because it is misspelled. Just use the correctly spelled method: getConfigDirectory(). This method will be removed 12/2006.
getConfigFile(String) - Static method in class cytoscape.CytoscapeInit
getConfiguration() - Method in class cytoscape.CytoscapeObj: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit.java instead.
getCurrent() - Method in interface cytoscape.util.MonitoredTask: Returns the currentProgress parameter.
getCurrentNetwork() - Static method in class cytoscape.Cytoscape: Return the Network that currently has the Focus.
getCurrentNetworkView() - Static method in class cytoscape.Cytoscape: Return the CyNetworkView that currently has the focus.
getCurrentSessionFileName() - Static method in class cytoscape.Cytoscape: Get name of the current session file.
getCyEdge(Node, Node, String, Object, boolean) - Static method in class cytoscape.Cytoscape: Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.
getCyEdge(Node, Node, String, Object, boolean, boolean) - Static method in class cytoscape.Cytoscape: Gets the first CyEdge found between the two nodes that has the given value for the given attribute.
getCyEdge(String, String, String, String) - Static method in class cytoscape.Cytoscape
getCyEdgesList() - Static method in class cytoscape.Cytoscape
getCyInitParams() - Static method in class cytoscape.CytoscapeInit: Returns the CyInitParams object used to initialize Cytoscape.
getCyMenus() - Method in class cytoscape.view.CytoscapeDesktop
getCyNetworkListeners() - Method in interface cytoscape.CyNetwork: Returns the set of listeners registered with this object.
getCyNode(String) - Static method in class cytoscape.Cytoscape
getCyNode(String, boolean) - Static method in class cytoscape.Cytoscape
getCyNodesList() - Static method in class cytoscape.Cytoscape
getCytoPanel(int) - Method in class cytoscape.view.CytoscapeDesktop: Gets a cytoPanel given a Compass direction.
getCytoPanelComponentCount() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the number of components in the CytoPanel.
getCytoPanelComponentCount() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the number of components in the CytoPanel.
getCytoPanelMenu() - Method in class cytoscape.view.CyMenus: Returns the cytopanels menu.
getCytoscapeObj() - Static method in class cytoscape.Cytoscape: Deprecated.
getDefaultLayoutStrategy() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getDefaultMenuSpecifier() - Method in class cytoscape.util.CytoscapeMenuBar
getDefaultSpeciesName() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getDefaultSpeciesName() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead.
getDefaultVisualStyle() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead.
getDefinedAttributes() - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Returns all defined attributeNames.
getDescription() - Method in class cytoscape.data.ExpressionData: Returns a text description of this data object.
getDescription() - Method in class cytoscape.util.CyFileFilter: Returns the human readable description of this filter.
getDesktop() - Static method in class cytoscape.Cytoscape
getDoubleAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a Double value at the specified id/attributeName.
getDupeCount() - Method in class cytoscape.visual.VisualStyle: Get how many times this style has been cloned.
getEdgeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the EdgeAppearanceCalculator for this visual style.
getEdgeAttributeFilenames() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getEdgeAttributeFiles() - Method in class cytoscape.CyMain
getEdgeAttributeValue(Edge, String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getEdgeAttributeValue(int, String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getEdgeAttributeValue(Edge, String) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getEdgeAttributes() - Method in interface cytoscape.CyNetwork: Deprecated. Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.
getEdgeAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Edge Attributes
getEdgeAttributes() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getEdgeAttributesList() - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getEdgeAttributesList() - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getEdgeNetworkData() - Static method in class cytoscape.Cytoscape: Deprecated. Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.
getEditMenu() - Method in class cytoscape.view.CyMenus: returns the menu with items related to editing the graph.
getEditingRow() - Method in class cytoscape.util.swing.JTreeTable
getExpressionData() - Method in interface cytoscape.CyNetwork: Deprecated.
getExpressionData() - Static method in class cytoscape.Cytoscape
getExpressionFilename() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getExpressionFiles() - Method in class cytoscape.CyMain
getExpressionFiles() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getExtension(File) - Method in class cytoscape.util.CyFileFilter: Return the extension portion of the file's name.
getExtension(String) - Method in class cytoscape.util.CyFileFilter
getExtensionSet() - Method in class cytoscape.util.CyFileFilter: Returns the Set of file extension names.
getExtremeValues() - Method in class cytoscape.data.ExpressionData: Returns a 2D Matrix of Extreme Values.
getFile(String, int) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to file operations.
getFileName() - Method in class cytoscape.data.ExpressionData: Gets the Name of the Expression Data File.
getFileNature() - Method in class cytoscape.util.CyFileFilter: Returns the nature of the file.
getFiles(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil: Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String, boolean) - Static method in class cytoscape.util.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFlaggedEdgeIndicesArray() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedEdges()
getFlaggedEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedEdges()
getFlaggedNodeIndicesArray() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedNodes()
getFlaggedNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectedNodes()
getFlagger() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.getSelectFilter()
getFullPath() - Method in class cytoscape.data.ExpressionData: Gets the File representation of the Expression Data Object.
getGeneDescriptor(String) - Method in class cytoscape.data.ExpressionData: Gets the Gene Descriptor for the specified gene.
getGeneDescriptors() - Method in class cytoscape.data.ExpressionData: Gets an Array of GeneDescriptors.
getGeneDescriptorsVector() - Method in class cytoscape.data.ExpressionData: Gets a Vector Gene Descriptors.
getGeneNames() - Method in class cytoscape.data.ExpressionData: Gets a List of All Gene Names.
getGeneNamesVector() - Method in class cytoscape.data.ExpressionData: Gets a List of All Gene Names.
getGeometryFilename() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getGlobalAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the GlobalAppearanceCalculator for this visual style.
getGlobalPercent(int, int, int) - Method in class cytoscape.util.PercentUtil: Calculates Global Percent Based on Current Step, Current Value, and MaxValue.
getGraphFiles() - Method in class cytoscape.CyMain
getGraphFiles() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getGraphPerspective() - Method in interface cytoscape.CyNetwork: Deprecated.
getGraphPerspective() - Method in class cytoscape.CyNode
getGraphViewController() - Method in class cytoscape.view.CytoscapeDesktop: TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
getHelp() - Method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.
getHelpBroker() - Method in class cytoscape.view.CytoscapeDesktop
getHelpMenu() - Method in class cytoscape.view.CyMenus: Returns the help menu.
getHelpSet() - Method in class cytoscape.view.CytoscapeDesktop
getIdentifier() - Method in class cytoscape.CyEdge
getIdentifier() - Method in interface cytoscape.CyNetwork: Can't Change
getIdentifier() - Method in class cytoscape.CyNode
getIdentifier() - Method in class cytoscape.util.CytoscapeMenuBar
getImportHandler() - Static method in class cytoscape.Cytoscape
getIndexOfChild(Object, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
getInputStream(String) - Static method in class cytoscape.util.FileUtil
getInputStream(String, TaskMonitor) - Static method in class cytoscape.util.FileUtil
getInputString(String) - Static method in class cytoscape.util.FileUtil
getInt() - Method in class cytoscape.util.MutableInt
getIntegerAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets an Integer value at the specified id/attributeName.
getInteractionType(CyNetwork, Edge) - Static method in class cytoscape.data.Semantics: Returns the interaction type of the given edge.
getInteractionTypes(CyNetwork) - Static method in class cytoscape.data.Semantics: Returns an array containing all of the unique interaction types present in the network.
getInteractionsFilename() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getKeyCode() - Method in class cytoscape.util.CytoscapeAction
getKeyModifiers() - Method in class cytoscape.util.CytoscapeAction
getLayoutMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items realted to layout actions.
getLengthOfTask() - Method in interface cytoscape.util.MonitoredTask: Returns the lenghtOfTask parameter.
getLoadSubMenu() - Method in class cytoscape.view.CyMenus: Returns the submenu with items related to loading objects.
getLocationOfExternalFrame(Dimension, Rectangle, Dimension, int, boolean) - Static method in class cytoscape.view.cytopanels.CytoPanelUtil: Gets Location of External Frame, based on current UI Dimensions.
getLocationOnScreen() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the location of the applications mainframe.
getLocationOnScreen() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Gets Location of Container, in screen coordinates.
getMRUD() - Static method in class cytoscape.CytoscapeInit
getMRUF() - Static method in class cytoscape.CytoscapeInit
getMax() - Method in class cytoscape.util.MinMaxDouble
getMax() - Method in class cytoscape.util.MinMaxInt
getMeasurement(String, String) - Method in class cytoscape.data.ExpressionData: Gets Single Measurement Value for the specified gene at the specified condition.
getMeasurements(String) - Method in class cytoscape.data.ExpressionData: Gets a Vector of all Measurements associated with the specified gene.
getMenu(String) - Method in class cytoscape.util.CytoscapeMenuBar
getMenu(String, int) - Method in class cytoscape.util.CytoscapeMenuBar
getMenuBar() - Method in class cytoscape.view.CyMenus: Returns the main menu bar constructed by this object.
getMessage() - Method in interface cytoscape.util.MonitoredTask: Returns a String, possibly the message to be printed on a dialog.
getMin() - Method in class cytoscape.util.MinMaxDouble
getMin() - Method in class cytoscape.util.MinMaxInt
getMode() - Method in class cytoscape.CyMain
getMode() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Gets the current mode.
getMultiHashMap() - Method in interface cytoscape.data.CyAttributes: Gets the MultiHashMap Object, where we store attribute values.
getMultiHashMapDefinition() - Method in interface cytoscape.data.CyAttributes: Gets the MultiHashMapDefinition Object, where we store attribute definitions.
getName() - Method in class cytoscape.util.CytoscapeAction
getName() - Method in class cytoscape.visual.VisualStyle: Returns the name of this object.
getNetwork() - Method in class cytoscape.CyNetworkEvent
getNetwork(String) - Static method in class cytoscape.Cytoscape
getNetwork() - Method in interface cytoscape.view.CyNetworkView: Returns the network displayed by this object.
getNetwork() - Method in class cytoscape.visual.VisualMappingManager
getNetworkAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Network Attributes.
getNetworkPanel() - Method in class cytoscape.view.CytoscapeDesktop
getNetworkSet() - Static method in class cytoscape.Cytoscape: Return a List of all available CyNetworks
getNetworkView(String) - Static method in class cytoscape.Cytoscape
getNetworkView() - Method in class cytoscape.visual.VisualMappingManager
getNetworkViewManager() - Method in class cytoscape.view.CytoscapeDesktop: Gets the NetworkView Manager.
getNetworkViewMap() - Static method in class cytoscape.Cytoscape: This Map has keys that are Strings ( network_ids ) and values that are networkviews.
getNodeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the NodeAppearanceCalculator for this visual style.
getNodeAttributeFilenames() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getNodeAttributeFiles() - Method in class cytoscape.CyMain
getNodeAttributeValue(Node, String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributeValue(int, String) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributeValue(Node, String) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributes() - Method in interface cytoscape.CyNetwork: Deprecated. Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.
getNodeAttributes() - Static method in class cytoscape.Cytoscape: Gets Global Node Attributes.
getNodeAttributes() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. No one appears to be using this method, so don't start.
getNodeAttributesList() - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributesList(Node[]) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributesList(Edge[]) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributesList() - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributesList(Node[]) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeAttributesList(Edge[]) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
getNodeNetworkData() - Static method in class cytoscape.Cytoscape: Deprecated. Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.
getNullNetwork() - Static method in class cytoscape.Cytoscape
getNullNetworkView() - Static method in class cytoscape.Cytoscape
getNumberOfConditions() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Experimental Conditions.
getNumberOfEdgeAttributeFiles() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getNumberOfGenes() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Genes.
getNumberOfNodeAttributeFiles() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getObjectKeys(String) - Method in interface cytoscape.data.attr.MultiHashMap: Returns all objectKeys that have at least one attribute value assigned in attributeName.
getOperationsMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items associated with plug-ins.
getOtherArgs() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getPluginURLs() - Static method in class cytoscape.CytoscapeInit
getPlugins() - Method in class cytoscape.CyMain
getPreferredButtonGroup() - Method in class cytoscape.util.CytoscapeAction: This method returns a ButtonGroup specification string.
getPreferredMenu() - Method in class cytoscape.util.CytoscapeAction: This method returns a Menu specification string.
getPrefferedIndex() - Method in class cytoscape.util.CytoscapeAction
getProjectFilename() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getProjectPropsFileName() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getProjectVizmapPropsFileName() - Method in class cytoscape.CyProject: Deprecated. Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.
getProperties() - Method in class cytoscape.CytoscapeConfig: Deprecated. Will be removed October 2006. Use methods in CytoscapeInit instead.
getProperties() - Static method in class cytoscape.CytoscapeInit: Returns the properties used by Cytoscape, the result of cytoscape.props and command line options.
getPropertiesLocation() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007.
getProperty(String) - Static method in class cytoscape.CytoscapeInit: Deprecated. Use getProperties().getProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
getPropertyChangeSupport() - Static method in class cytoscape.Cytoscape
getPropertyValues(Properties, String) - Static method in class cytoscape.util.Misc: return the (possibly multiple) value of the specified property as a vector.
getProps() - Method in class cytoscape.CyMain
getPvalueFromLambda(double) - Static method in class cytoscape.data.ExpressionData: Gets a PValue of the specified lambda value.
getRGBText(Color) - Static method in class cytoscape.util.Misc
getReader(String) - Method in class cytoscape.util.CyFileFilter: Returns the reader.
getReader(String) - Method in class cytoscape.util.GMLFileFilter
getReader(String) - Method in class cytoscape.util.SIFFileFilter
getReader(String) - Method in class cytoscape.util.XGMMLFileFilter
getResourcePlugins() - Static method in class cytoscape.CytoscapeInit
getRoot() - Method in class cytoscape.util.swing.AbstractTreeTableModel
getRootGraph() - Method in class cytoscape.CyEdge
getRootGraph() - Method in class cytoscape.CyNode
getRootGraph() - Static method in class cytoscape.Cytoscape: Return the CytoscapeRootGraph
getRootGraphIndex() - Method in class cytoscape.CyEdge
getRootGraphIndex() - Method in class cytoscape.CyNode
getRowCount() - Method in class cytoscape.util.swing.TreeTableModelAdapter
getSaveSubMenu() - Method in class cytoscape.view.CyMenus: Returns the submenu with items related to saving objects.
getScriptName() - Method in class cytoscape.plugin.CytoscapePlugin: If this plugin is scriptable, then this will return a unique script name, that will come after the colon like: :name
getSecondaryViewThreshold() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead.
getSelectFilter() - Method in interface cytoscape.CyNetwork
getSelectMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to selecting nodes and edges in the graph.
getSelectedComponent() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the currently selected component.
getSelectedComponent() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the currently selected component.
getSelectedEdges() - Method in interface cytoscape.CyNetwork: Returns the set of selected edges in this CyNetwork
getSelectedIndex() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the currently selected index.
getSelectedIndex() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the currently selected index.
getSelectedNodes() - Method in interface cytoscape.CyNetwork: Returns the set of selected nodes in this CyNetwork
getSelectionMode() - Static method in class cytoscape.Cytoscape: Gets the selection mode value.
getSessionFile() - Method in class cytoscape.CyMain
getSessionstate() - Static method in class cytoscape.Cytoscape
getSignificanceType() - Method in class cytoscape.data.ExpressionData: Gets the Significance Type.
getSource() - Method in class cytoscape.CyEdge
getSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
getSpeciesInNetwork(CyNetwork) - Static method in class cytoscape.data.Semantics: Returns every unique species defined in the supplied network.
getState() - Method in interface cytoscape.view.cytopanels.CytoPanel: Gets the state of the CytoPanel.
getState() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Gets the state of the CytoPanel.
getStderr() - Method in class cytoscape.util.Exec
getStderrAsString() - Method in class cytoscape.util.Exec
getStdout() - Method in class cytoscape.util.Exec
getStdoutAsString() - Method in class cytoscape.util.Exec
getString() - Method in class cytoscape.util.MutableString
getStringAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Gets a String value at the specified id/attributeName.
getSuggestedNetworkTitle(String) - Static method in class cytoscape.util.CyNetworkNaming
getSuggestedSubnetworkTitle(CyNetwork) - Static method in class cytoscape.util.CyNetworkNaming
getSwingPropertyChangeSupport() - Static method in class cytoscape.Cytoscape: Bound events are: NETWORK_CREATED NETWORK_DESTROYED CYTOSCAPE_EXIT
getSwingPropertyChangeSupport() - Method in class cytoscape.view.CytoscapeDesktop
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellEditor
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: TreeCellRenderer method.
getTarget() - Method in class cytoscape.CyEdge
getTaskName() - Method in interface cytoscape.util.MonitoredTask: Returns a String, possibly the message that describes the task being performed.
getTaxonMap(File) - Method in class cytoscape.util.BioDataServerUtil
getTaxonMap(BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
getTitle() - Method in interface cytoscape.CyNetwork: Can Change
getTitle() - Method in interface cytoscape.view.CyNetworkView: Returns the Title of this View
getTitle() - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the title of the CytoPanel.
getTitle() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the proper title based on our compass direction.
getToolBar() - Method in class cytoscape.view.CyMenus: Returns the toolbar object constructed by this class.
getToolTipText(MouseEvent) - Method in class cytoscape.util.swing.JTreeTable: The code in this method is copy and pasted from source code to the same method in javax.swing.JTable, except for one value change on one line.
getTree() - Method in class cytoscape.util.swing.JTreeTable: Returns the tree that is being shared between the model.
getType() - Method in class cytoscape.CyNetworkEvent
getType(String) - Method in interface cytoscape.data.CyAttributes: Gets the data type of the specified attribute.
getValueAt(Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Returns the value to be displayed for node node, at column number column.
getValueAt(int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
getVersion() - Method in class cytoscape.CytoscapeVersion
getView() - Method in interface cytoscape.view.CyNetworkView
getViewMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to data operations.
getViewThreshold() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "viewThreshold" ) instead.
getViewType() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType"));
getViewType() - Method in class cytoscape.view.CytoscapeDesktop: Return the view type for this CytoscapeDesktop
getVisualMapperEnabled() - Method in interface cytoscape.view.CyNetworkView
getVisualMappingManager() - Static method in class cytoscape.Cytoscape
getVisualProperties() - Static method in class cytoscape.CytoscapeInit
getVisualStyle() - Method in interface cytoscape.view.CyNetworkView
getVisualStyle() - Method in class cytoscape.visual.VisualMappingManager
getVizMapManager() - Method in interface cytoscape.view.CyNetworkView
getVizMapManager() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated. Use Cytoscape.getVisualMappingManager() instead. This will be removed at 03/2007 (possibly sooner).
getVizMapUI() - Method in interface cytoscape.view.CyNetworkView
getVizMapUI() - Method in class cytoscape.view.CytoscapeDesktop: returns the top-level UI object for the visual mapper.
getVizMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to visualiation.
getVizProps() - Method in class cytoscape.CyMain
getVizmapPropertiesLocation() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().getProperty( "TODO" ) instead.
go(boolean) - Method in interface cytoscape.util.MonitoredTask: Initializes currentProgress (generally to zero) and then spawns a SwingWorker to start doing the work.
graphViewChanged(GraphViewChangeEvent) - Method in class cytoscape.view.CyMenus: Update the UI menus and buttons.

H

HIDE - Static variable in class cytoscape.view.cytopanels.CytoPanelState: Hide state of a CytoPanel.
hasAttribute(String, String) - Method in interface cytoscape.data.CyAttributes: Determines if the specified id/attributeName pair exists.
hasSignificanceValues() - Method in class cytoscape.data.ExpressionData: Indicates whether the expression data has significance values.

I

IDENTIFIER - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
INTERACTION - Static variable in class cytoscape.data.Semantics
INTERNAL_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in JInternalFrames, using the mock desktop interface. ( like MS Office )
IndeterminateProgressBar - class cytoscape.util.IndeterminateProgressBar.: This class creates a dialog with a JProgressBar in indeterminate state.
IndeterminateProgressBar(String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with no owner, the given title and label.
IndeterminateProgressBar(Dialog, String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with the specified owner dialog, title and label.
IndeterminateProgressBar(Frame, String, String) - Constructor for class cytoscape.util.IndeterminateProgressBar: Constructs an initially invisible, non-modal Dialog with the specified owner frame, title and label.
incrementProgress() - Method in interface cytoscape.util.MonitoredTask: Increments the progress by one
indexOfComponent(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the index for the specified component.
indexOfComponent(String) - Method in interface cytoscape.view.cytopanels.CytoPanel: Returns the first Component index with given title.
indexOfComponent(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the index for the specified component.
indexOfComponent(String) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Returns the first Component index with given title.
init(CyInitParams) - Method in class cytoscape.CytoscapeInit: Cytoscape Init must be initialized using the command line arguments.
initCytoPanelMenus() - Method in class cytoscape.view.CyMenus
initializeMenus() - Method in class cytoscape.view.CyMenus: This method should be called by the creator of this object after the constructor has finished.
insertCytoPanel(CytoPanelImp, int) - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Inserts CytoPanel at desired compass direction.
insertCytoPanel(CytoPanelImp, int) - Method in interface cytoscape.view.cytopanels.CytoPanelContainer: Inserts CytoPanel at Specified Compass Direction.
instantiateDataModel() - Static method in class cytoscape.data.attr.util.MultiHashMapFactory: The return object implements both cytoscape.data.attr.MultiHashMapDefinition and cytoscape.data.attr.MultiHashMap.
interpretScript(String[], CyNetwork) - Method in class cytoscape.plugin.CytoscapePlugin: Take a CyNetwork as input along with some arguments, and return a CyNetwork, which can be the same, or different, it doesn't really matter, and is up to the individual plugin.
interrupt() - Method in class cytoscape.util.SwingWorker: A new method that interrupts the worker thread.
isAccelerated() - Method in class cytoscape.util.CytoscapeAction
isCellEditable(EventObject) - Method in class cytoscape.util.swing.AbstractCellEditor
isCellEditable(Object, int) - Method in class cytoscape.util.swing.AbstractTreeTableModel: By default, make the column with the Tree in it the only editable one.
isCellEditable(EventObject) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellEditor: Overridden to return false, and if the event is a mouse event it is forwarded to the tree.
isCellEditable(Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Indicates whether the the value for node node, at column number column is editable.
isCellEditable(int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
isDirected() - Method in class cytoscape.CyEdge
isExtensionListInDescription() - Method in class cytoscape.util.CyFileFilter: Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFlagged(Node) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.isSelected(Node)
isFlagged(Edge) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.isSelected(Edge)
isHeadless() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getMode() instead.
isInMenuBar() - Method in class cytoscape.util.CytoscapeAction: By default all CytoscapeActions wish to be included in CommunityMenuBars, but you may override if you wish.
isInToolBar() - Method in class cytoscape.util.CytoscapeAction: By default no CytoscapeActions wish to be included in CommunityToolBars, but you may override if you wish.
isLeaf(Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
isList(String, String, String, String) - Static method in class cytoscape.util.Misc: determine whether a string encodes a list
isModified(CyNetwork) - Static method in class cytoscape.CytoscapeModifiedNetworkManager
isReidentificationEnabled() - Method in class cytoscape.util.CytoscapeMenuBar
isScriptable() - Method in class cytoscape.plugin.CytoscapePlugin: If true, this plugin is capable if accepting scripts, and we will find out what its script name is
isSelected(Node) - Method in interface cytoscape.CyNetwork: Returns the selected state of the given node.
isSelected(Edge) - Method in interface cytoscape.CyNetwork: Returns the selected state of the given edge.
isSquiggleEnabled() - Static method in class cytoscape.Cytoscape: Deprecated. Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.
isStateClear() - Method in interface cytoscape.CyNetwork: Deprecated.
isWindows() - Method in class cytoscape.view.cytopanels.CytoPanelUtil: Determines if we are running on Windows platform.

J

JTreeTable - class cytoscape.util.swing.JTreeTable.: This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the JTable.
JTreeTable(TreeTableModel) - Constructor for class cytoscape.util.swing.JTreeTable
JTreeTable.TreeTableCellEditor - class cytoscape.util.swing.JTreeTable.TreeTableCellEditor.: TreeTableCellEditor implementation.
JTreeTable.TreeTableCellEditor() - Constructor for class cytoscape.util.swing.JTreeTable.TreeTableCellEditor
JTreeTable.TreeTableCellRenderer - class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer.: A TreeCellRenderer that displays a JTree.
JTreeTable.TreeTableCellRenderer(TreeModel) - Constructor for class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer

L

LABEL - Static variable in class cytoscape.data.Semantics: Deprecated. Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.
LAMBDA - Static variable in class cytoscape.data.ExpressionData: Significance value: LAMBA.
LOAD - Static variable in class cytoscape.util.FileUtil
LayoutAlgorithm - interface cytoscape.layout.LayoutAlgorithm.
LayoutUtils - class cytoscape.layout.LayoutUtils.: A class with easy to call static methods for layout purposes.
LayoutUtils() - Constructor for class cytoscape.layout.LayoutUtils
layoutNodesInAStack(CyNetworkView, Collection, double, double) - Static method in class cytoscape.layout.LayoutUtils: Layouts a collection of nodes in a "stack" (one node on top of the other, vertically)
loadAnnotationFiles(String[], String[]) - Method in class cytoscape.data.servers.BioDataServer
loadAttributes(String[], String[], boolean, BioDataServer, String) - Static method in class cytoscape.Cytoscape: Loads Node and Edge attribute data into Cytoscape from the given file locations.
loadAttributes(String[], String[]) - Static method in class cytoscape.Cytoscape: Loads Node and Edge attribute data into Cytoscape from the given file locations.
loadBioDataServer(String) - Static method in class cytoscape.Cytoscape: A BioDataServer should be loadable from a file systems file or from a URL.
loadCalculatorCatalog() - Method in class cytoscape.visual.VisualMappingManager: Attempts to load a CalculatorCatalog object, using the information from the CytoscapeConfig object.
loadCalculatorCatalog(String) - Method in class cytoscape.visual.VisualMappingManager
loadData(String, String) - Method in class cytoscape.data.ExpressionData: Loads the Specified File into memory.
loadExpressionData(String, boolean) - Static method in class cytoscape.Cytoscape: Load Expression Data
loadObo(String[], String[]) - Method in class cytoscape.data.servers.BioDataServer
loadPlugin(Class) - Method in class cytoscape.CytoscapeInit
loadPlugin(Class) - Static method in class cytoscape.plugin.CytoscapePlugin: Attempts to instantiate a plugin of the class argument.
loadThesaurusFiles(String[]) - Method in class cytoscape.data.servers.BioDataServer
loadThesaurusFiles2(String[]) - Method in class cytoscape.data.servers.BioDataServer
lockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
lockNodes(NodeView[]) - Method in interface cytoscape.layout.LayoutAlgorithm

M

MAX_LINE_SIZE - Static variable in class cytoscape.data.ExpressionData
MODE_HIDE_SPLIT - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane
MODE_PROPERTY - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane: Property listener modes.
MODE_SHOW_SPLIT - Static variable in class cytoscape.view.cytopanels.BiModalJSplitPane: Available modes of the BiModalJSplitPane.
MODIFIED - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
MOLECULAR_FUNCTION - Static variable in class cytoscape.data.Semantics
MOLECULE_TYPE - Static variable in class cytoscape.data.Semantics
MacAppConfig - class cytoscape.util.MacAppConfig.: Configures the Mac OS X Info.plist file associated with Cytoscape.
MacAppConfig() - Constructor for class cytoscape.util.MacAppConfig
MinMaxDouble - class cytoscape.util.MinMaxDouble.: find the min and max of a 1- or 2-d aarray of doubles.
MinMaxDouble(double[]) - Constructor for class cytoscape.util.MinMaxDouble
MinMaxDouble(double[][]) - Constructor for class cytoscape.util.MinMaxDouble
MinMaxInt - class cytoscape.util.MinMaxInt.: find the min and max of a 1- or 2-d array of ints.
MinMaxInt(int[]) - Constructor for class cytoscape.util.MinMaxInt
MinMaxInt(int[][]) - Constructor for class cytoscape.util.MinMaxInt
Misc - class cytoscape.util.Misc.
Misc() - Constructor for class cytoscape.util.Misc
MonitoredTask - interface cytoscape.util.MonitoredTask.
MultiHashMap - interface cytoscape.data.attr.MultiHashMap.: This interface consists of the API specification to bind attribute values to objects.
MultiHashMapDefinition - interface cytoscape.data.attr.MultiHashMapDefinition.: This interface contains the API specification for creating attribute definitions.
MultiHashMapDefinitionListener - interface cytoscape.data.attr.MultiHashMapDefinitionListener.: A hook to receive notification when attribute definitions are created and destroyed.
MultiHashMapFactory - class cytoscape.data.attr.util.MultiHashMapFactory.: This class provides access to implementations of MultiHashMap and MultiHashMapDefinition.
MultiHashMapHelpers - class cytoscape.data.attr.util.MultiHashMapHelpers.: This class contains static utilitarian methods that return information pertaining to attributes.
MultiHashMapListener - interface cytoscape.data.attr.MultiHashMapListener.: A hook to receive notification when attribute values are set and removed from objects.
MutableBool - class cytoscape.util.MutableBool.
MutableBool(boolean) - Constructor for class cytoscape.util.MutableBool
MutableColor - class cytoscape.util.MutableColor.: Deprecated. No one uses this, so don't start. Just use Color directly. This will be removed 12/2006.
MutableColor(Color) - Constructor for class cytoscape.util.MutableColor: Deprecated.
MutableInt - class cytoscape.util.MutableInt.
MutableInt(int) - Constructor for class cytoscape.util.MutableInt
MutableString - class cytoscape.util.MutableString.
MutableString(String) - Constructor for class cytoscape.util.MutableString
main(String[]) - Static method in class cytoscape.CyMain
main(String[]) - Static method in class cytoscape.CytoscapeVersion
main(String[]) - Static method in class cytoscape.data.servers.BioDataServerRmi
main(String[]) - Static method in class cytoscape.util.MacAppConfig: Main Method.
main(String[]) - Static method in class cytoscape.util.Transform
moveCredits(PNode) - Static method in class cytoscape.util.CreditScreen

N

NETWORK_CREATED - Static variable in class cytoscape.Cytoscape
NETWORK_DESTROYED - Static variable in class cytoscape.Cytoscape
NETWORK_LOADED - Static variable in class cytoscape.Cytoscape
NETWORK_MODIFIED - Static variable in class cytoscape.Cytoscape
NETWORK_SAVED - Static variable in class cytoscape.Cytoscape
NETWORK_VIEW_CREATED - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_DESTROYED - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_FOCUS - Static variable in class cytoscape.view.CytoscapeDesktop
NETWORK_VIEW_FOCUSED - Static variable in class cytoscape.view.CytoscapeDesktop
NONE - Static variable in class cytoscape.data.ExpressionData: Significance value: NONE.
NotAPluginException - exception cytoscape.plugin.NotAPluginException.: Thrown to indicate that a class cannot be used as a plugin becuase it does not extend AbstractPlugin.
NotAPluginException(String) - Constructor for class cytoscape.plugin.NotAPluginException: constructor.
noCanonicalization() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead.
numRemaining() - Method in interface cytoscape.data.attr.CountedIterator: Returns a non-negative integer I such that next() will successfully return a value no more and no less than I times.

O

ONE_SECOND - Static variable in class cytoscape.util.CytoscapeProgressMonitor
OpenBrowser - class cytoscape.util.OpenBrowser.
OpenBrowser() - Constructor for class cytoscape.util.OpenBrowser
onComponentAdded(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a component is added to the CytoPanel.
onComponentRemoved(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a component is removed from the CytoPanel.
onComponentSelected(int) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener when a new component on the CytoPanel is selected.
onCyNetworkEvent(CyNetworkEvent) - Method in class cytoscape.CyNetworkAdapter
onCyNetworkEvent(CyNetworkEvent) - Method in interface cytoscape.CyNetworkListener: This method is called when an event is fired by a CyNetwork.
onStateChange(CytoPanelState) - Method in interface cytoscape.view.cytopanels.CytoPanelListener: Notifies the listener on a change in the CytoPanel state.
openURL(String) - Static method in class cytoscape.util.OpenBrowser

P

PREFERENCES_UPDATED - Static variable in class cytoscape.Cytoscape
PREFERENCE_MODIFIED - Static variable in class cytoscape.Cytoscape
PROTEIN - Static variable in class cytoscape.data.Semantics
PVAL - Static variable in class cytoscape.data.ExpressionData: Significance value: PVAL.
PercentUtil - class cytoscape.util.PercentUtil.: Helper Class for Calculating Percentage of Multi-Step Processes.
PercentUtil(int) - Constructor for class cytoscape.util.PercentUtil: Constructor.
paint(Graphics) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: Sublcassed to translate the graphics such that the last visible row will be drawn at 0,0.
parseList(String, String, String, String) - Static method in class cytoscape.util.Misc: parse and return an array of strings
parseRGBText(String) - Static method in class cytoscape.util.Misc
parseViewType(String) - Static method in class cytoscape.view.CytoscapeDesktop
propertyChange(PropertyChangeEvent) - Method in class cytoscape.CytoscapeModifiedNetworkManager
propertyChange(PropertyChangeEvent) - Method in class cytoscape.view.CytoscapeDesktop
putClientData(String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
putClientData(String, Object) - Method in interface cytoscape.view.CyNetworkView: Networks can support client data.

R

READER_CLIENT_KEY - Static variable in class cytoscape.Cytoscape
RNA - Static variable in class cytoscape.data.Semantics
readFile(String, String) - Static method in class cytoscape.util.ZipUtil: Reads a file contained within a zip file and returns an InputStream.
readOntologyFlatFiles(String[]) - Method in class cytoscape.data.servers.BioDataServer
readOntologyFlatFiles2(String[]) - Method in class cytoscape.data.servers.BioDataServer
redrawGraph(boolean, boolean) - Method in interface cytoscape.view.CyNetworkView
remove(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes specified component from the CytoPanel.
remove(int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes the component from the CytoPanel at the specified index.
remove(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes specified component from the CytoPanel.
remove(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes the component from the CytoPanel at the specified index.
removeAction(Action) - Method in class cytoscape.util.CytoscapeMenuBar: If the given Action has a present and false inMenuBar property, return; otherwise if there's a menu item for the action, remove it.
removeAction(Action) - Method in class cytoscape.util.CytoscapeToolBar: If the given Action has an absent or false inToolBar property, return; otherwise if there's a button for the action, remove it.
removeAll() - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes all the components from the CytoPanel.
removeAll() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes all the components from the CytoPanel.
removeAllAttributeValues(String, String) - Method in interface cytoscape.data.attr.MultiHashMap: Removes all values bound to objectKey in attributeName.
removeAttributeValue(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: This method is the same as getAttributeValue(), only the retrieved attribute value is also deleted.
removeCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
removeCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork: Removes the argument from the set of listeners for this object.
removeCytoPanelListener(CytoPanelListener) - Method in interface cytoscape.view.cytopanels.CytoPanel: Removes a CytoPanel listener.
removeCytoPanelListener(CytoPanelListener) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Removes a CytoPanel listener.
removeDataDefinitionListener(MultiHashMapDefinitionListener) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: Unregisters a listener; this method has the opposite effect as addDataDefinitionListener(listener).
removeDataListener(MultiHashMapListener) - Method in interface cytoscape.data.attr.MultiHashMap: Unregisters a listener; this method has the opposite effect as addDataListener(listener).
removeEdge(int, boolean) - Method in interface cytoscape.CyNetwork: This will remove this edge from the Network.
removeEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
removeFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.removeSelectEventListener(SelectEventListener)
removeNode(int, boolean) - Method in interface cytoscape.CyNetwork: This will remove this node from the Network.
removeNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
removeSelectEventListener(SelectEventListener) - Method in interface cytoscape.CyNetwork: Removes a listener for SelectEvents from this CyNetwork
removeTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
rotateNode(PNode) - Static method in class cytoscape.util.CreditScreen
run() - Method in class cytoscape.util.CytoscapeProgressMonitor: Implementes Runnable.run()
run() - Method in class cytoscape.util.Exec
runThreaded() - Method in class cytoscape.util.Exec

S

SAVE - Static variable in class cytoscape.util.FileUtil
SAVE_VIZMAP_PROPS - Static variable in class cytoscape.Cytoscape
SELECT_EDGES_ONLY - Static variable in class cytoscape.Cytoscape
SELECT_NODES_AND_EDGES - Static variable in class cytoscape.Cytoscape
SELECT_NODES_ONLY - Static variable in class cytoscape.Cytoscape
SESSION_CHANGED - Static variable in class cytoscape.Cytoscape
SESSION_CLOSED - Static variable in class cytoscape.Cytoscape
SESSION_LOADED - Static variable in class cytoscape.Cytoscape
SESSION_NEW - Static variable in class cytoscape.Cytoscape
SESSION_OPENED - Static variable in class cytoscape.Cytoscape
SESSION_SAVED - Static variable in class cytoscape.Cytoscape
SIFFileFilter - class cytoscape.util.SIFFileFilter.
SIFFileFilter() - Constructor for class cytoscape.util.SIFFileFilter
SPECIES - Static variable in class cytoscape.data.Semantics
Semantics - class cytoscape.data.Semantics.: This class defines names for certain data attributes that are commonly used within Cytoscape.
Semantics() - Constructor for class cytoscape.data.Semantics
SwingWorker - class cytoscape.util.SwingWorker.: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class cytoscape.util.SwingWorker: Start a thread that will call the construct method and then exit.
selectAllEdges() - Method in interface cytoscape.CyNetwork: Sets the selected state of all edges in this CyNetwork to true
selectAllNodes() - Method in interface cytoscape.CyNetwork: Sets the selected state of all nodes in this CyNetwork to true
setAcceleratorCombo(int, int) - Method in class cytoscape.util.CytoscapeAction
setAttribute(String, String, Boolean) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Boolean.
setAttribute(String, String, Integer) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Integer.
setAttribute(String, String, Double) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type Double.
setAttribute(String, String, String) - Method in interface cytoscape.data.CyAttributes: Sets an id/attributeName pair of type String.
setAttributeList(String, String, List) - Method in interface cytoscape.data.CyAttributes: Sets a simple list of attributes.
setAttributeMap(String, String, Map) - Method in interface cytoscape.data.CyAttributes: Sets a 'simple' map of attribute values.
setAttributeValue(String, String, Object, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap: Binds an attribute value to an object.
setBool(boolean) - Method in class cytoscape.util.MutableBool
setBounds(int, int, int, int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: This is overridden to set the height to match that of the JTable.
setColor(Color) - Method in class cytoscape.util.MutableColor: Deprecated.
setCurrentNetwork(String) - Static method in class cytoscape.Cytoscape: Deprecated.
setCurrentNetworkView(String) - Static method in class cytoscape.Cytoscape: Deprecated.
setCurrentSessionFileName(String) - Static method in class cytoscape.Cytoscape: Set the current session name.
setCytoPanelContainer(CytoPanelContainer) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets CytoPanelContainer interface reference.
setDefaultMenuSpecifier(String) - Method in class cytoscape.util.CytoscapeMenuBar
setDefaultSpeciesName() - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. This doesn't do anything. To set the default species name use getProperties().setProperty("defaultSpeciesName", newName), which you were presumably doing already.
setDescription(String) - Method in class cytoscape.util.CyFileFilter: Sets the human readable description of this filter.
setEdgeAppearanceCalculator(EdgeAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the EdgeAppearanceCalculator for this visual style.
setEdgeAttributeValue(Edge, String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setEdgeAttributeValue(int, String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setEdgeAttributeValue(Edge, String, Object) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setExpressionData(ExpressionData) - Method in interface cytoscape.CyNetwork: Deprecated. Sets the expression data object associated with this network.
setExpressionData(ExpressionData) - Static method in class cytoscape.Cytoscape
setExtensionListInDescription(boolean) - Method in class cytoscape.util.CyFileFilter: Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setFileNature(String) - Method in class cytoscape.util.CyFileFilter: Sets the nature of the files for this filter.
setFlagged(Node, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)
setFlagged(Edge, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(Collection, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedEdges(int[], boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)
setFlaggedNodes(Collection, boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)
setFlaggedNodes(int[], boolean) - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)
setFocus(String) - Method in class cytoscape.view.CytoscapeDesktop
setGeneDescriptors(Vector) - Method in class cytoscape.data.ExpressionData: Sets a List of Gene Descriptors.
setGeneNames(Vector) - Method in class cytoscape.data.ExpressionData: Sets a List of Gene Names.
setGlobalAppearanceCalculator(GlobalAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the GlobalAppearanceCalculator for this visual style.
setGraphPerspective(GraphPerspective) - Method in class cytoscape.CyNode
setIdentifier(String) - Method in class cytoscape.CyEdge
setIdentifier(String) - Method in interface cytoscape.CyNetwork: Can't Change
setIdentifier(String) - Method in class cytoscape.CyNode
setIdentifier(String) - Method in class cytoscape.util.CytoscapeMenuBar
setInt(int) - Method in class cytoscape.util.MutableInt
setLabelText(String) - Method in class cytoscape.util.IndeterminateProgressBar
setMRUD(File) - Static method in class cytoscape.CytoscapeInit
setMRUF(File) - Static method in class cytoscape.CytoscapeInit
setMode(CytoPanelState, int) - Method in class cytoscape.view.cytopanels.BiModalJSplitPane: Sets the BiModalJSplitframe mode.
setModified(CyNetwork, String) - Static method in class cytoscape.CytoscapeModifiedNetworkManager: set the state of the network
setName(String) - Method in class cytoscape.util.CytoscapeAction
setName(String) - Method in class cytoscape.visual.VisualStyle: Set the name of this visual style.
setNetworkView(CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
setNewGraphFrom(CyNetwork, boolean) - Method in interface cytoscape.CyNetwork: Deprecated.
setNewNetwork(CyNetwork) - Method in class cytoscape.view.CytoscapeDesktop
setNodeAppearanceCalculator(NodeAppearanceCalculator) - Method in class cytoscape.visual.VisualStyle: Set the NodeAppearanceCalculator for this visual style.
setNodeAttributeValue(Node, String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setNodeAttributeValue(int, String, Object) - Method in interface cytoscape.CyNetwork: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setNodeAttributeValue(Node, String, Object) - Static method in class cytoscape.Cytoscape: Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
setNodesRequiredItemsEnabled() - Method in class cytoscape.view.CyMenus: Enables or disables save, print, and display nodes in new window GUI functions, based on the number of nodes in this window's graph perspective.
setOverviewEnabled(boolean) - Method in class cytoscape.view.CyMenus
setPreferredButtonGroup(String) - Method in class cytoscape.util.CytoscapeAction
setPreferredIndex(int) - Method in class cytoscape.util.CytoscapeAction
setPreferredMenu(String) - Method in class cytoscape.util.CytoscapeAction
setProperty(String, String) - Static method in class cytoscape.CytoscapeInit: Deprecated. Use getProperties().setProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.
setRowHeight(int) - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: Sets the row height of the tree, and forwards the row height to the table.
setRowHeight(int) - Method in class cytoscape.util.swing.JTreeTable: Overridden to pass the new rowHeight to the tree.
setRunInBackground(boolean) - Method in class cytoscape.util.Exec
setSecondaryViewThreshold(int) - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use getProperties().setProperty( "secondaryViewThreshold", thresh ) instead.
setSelected(CyNode[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
setSelected(NodeView[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
setSelected(CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)
setSelected(EdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Deprecated. this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)
setSelectedEdgeState(Collection, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a collection of edges.
setSelectedIndex(int) - Method in interface cytoscape.view.cytopanels.CytoPanel: Sets the selected index on the CytoPanel.
setSelectedIndex(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets the selected index on the CytoPanel.
setSelectedNodeState(Collection, boolean) - Method in interface cytoscape.CyNetwork: Sets the selected state of a collection of nodes.
setSelectionMode(int) - Static method in class cytoscape.Cytoscape: Sets the specified selection mode on all views.
setSelectionMode(int, GraphView) - Static method in class cytoscape.Cytoscape: Utility method to set the selection mode on the specified GraphView.
setSessionState(int) - Static method in class cytoscape.Cytoscape
setSpecies() - Static method in class cytoscape.Cytoscape: Deprecated. argh!...
setStandardInput(String) - Method in class cytoscape.util.Exec
setState(CytoPanelState) - Method in interface cytoscape.view.cytopanels.CytoPanel: Sets the state of the CytoPanel.
setState(CytoPanelState) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Sets the state of the CytoPanel.
setStatusBarMsg(String) - Method in class cytoscape.view.CytoscapeDesktop: Sets the Status Bar Message.
setString(String) - Method in class cytoscape.util.MutableString
setTitle(String) - Method in interface cytoscape.CyNetwork: Can Change
setTitle(String) - Method in interface cytoscape.view.CyNetworkView: Sets the Title of this View
setValueAt(Object, Object, int) - Method in class cytoscape.util.swing.AbstractTreeTableModel
setValueAt(Object, Object, int) - Method in interface cytoscape.util.swing.TreeTableModel: Sets the value for node node, at column number column.
setValueAt(Object, int, int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
setViewThreshold(int) - Static method in class cytoscape.CytoscapeInit: Deprecated. Will be removed April 2007. Use setProperty( "viewThreshold", thresh ) instead.
setVisualMapperEnabled(boolean) - Method in interface cytoscape.view.CyNetworkView
setVisualMapperItemsEnabled(boolean) - Method in class cytoscape.view.CyMenus: Enables the menu items related to the visual mapper if the argument is true, else disables them.
setVisualStyle(String) - Method in interface cytoscape.view.CyNetworkView
setVisualStyle(VisualStyle) - Method in class cytoscape.view.CytoscapeDesktop
setVisualStyle(VisualStyle) - Method in class cytoscape.visual.VisualMappingManager: Sets a new visual style, and returns the old style.
setVisualStyle(String) - Method in class cytoscape.visual.VisualMappingManager: Sets a new visual style.
setupVizMapper() - Method in class cytoscape.view.CytoscapeDesktop: Create the VizMapper and the UI for it.
shouldSelectCell(EventObject) - Method in class cytoscape.util.swing.AbstractCellEditor
showCredits(URL, String) - Static method in class cytoscape.util.CreditScreen
showDialog(Component, String, Color) - Static method in class cytoscape.util.CyColorChooser
start() - Method in class cytoscape.util.SwingWorker: Start the worker thread.
startMonitor(boolean) - Method in class cytoscape.util.CytoscapeProgressMonitor: Starts the monitor by running the monitoredTask.
stateChanged(ChangeEvent) - Method in class cytoscape.view.cytopanels.CytoPanelImp: Our implementation of the ChangeListener interface, to determine when new tab has been selected
stop() - Method in interface cytoscape.util.MonitoredTask: Stops the task by simply setting currentProgress to lengthOfTask, or if a boolean "done" variable is used, setting it to true.
stopCellEditing() - Method in class cytoscape.util.swing.AbstractCellEditor
suppressView() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. No one appears to use this method, so don't start.

T

TABBED_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in TabbedPanes ( like Mozilla )
TYPE_BOOLEAN - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Boolean.
TYPE_BOOLEAN - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Boolean.
TYPE_COMPLEX - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a data structure of arbitrary complexity, e.g. anything more complex than a 'simple' list or a 'simple' map.
TYPE_FLOATING - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Double.
TYPE_FLOATING_POINT - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Double.
TYPE_INTEGER - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.Integer.
TYPE_INTEGER - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.Integer.
TYPE_SIMPLE_LIST - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a 'simple' list.
TYPE_SIMPLE_MAP - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to a 'simple' hash map.
TYPE_STRING - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to java.lang.String.
TYPE_STRING - Static variable in interface cytoscape.data.attr.MultiHashMapDefinition: This type corresponds to java.lang.String.
TYPE_UNDEFINED - Static variable in interface cytoscape.data.CyAttributes: This type corresponds to an attribute which has not been defined.
Transform - class cytoscape.util.Transform.: Apply XSLT to an XML document
Transform(String, String, String) - Constructor for class cytoscape.util.Transform
TreeTableModel - interface cytoscape.util.swing.TreeTableModel.: TreeTableModel is the model used by a JTreeTable.
TreeTableModelAdapter - class cytoscape.util.swing.TreeTableModelAdapter.: This is a wrapper class takes a TreeTableModel and implements the table model interface.
TreeTableModelAdapter(TreeTableModel, JTree) - Constructor for class cytoscape.util.swing.TreeTableModelAdapter
takeArgs(String[]) - Method in class cytoscape.util.CytoscapeAction
taxIdToName(String, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
toString() - Method in class cytoscape.CytoscapeVersion
toString() - Method in class cytoscape.util.CytoscapeMenuBar: Delegates to CytoscapeMenuBar.getIdentifier().
toString() - Method in class cytoscape.util.MinMaxDouble
toString() - Method in class cytoscape.util.MinMaxInt
toString() - Method in class cytoscape.view.cytopanels.CytoPanelState
toString() - Method in class cytoscape.visual.VisualStyle: Returns the name of this object, as returned by getName.
toggleVisualMapperEnabled() - Method in interface cytoscape.view.CyNetworkView

U

UNKNOWN - Static variable in class cytoscape.CyNetworkEvent: This type is used when the requested type is unknown to this class.
UNKNOWN - Static variable in class cytoscape.data.ExpressionData: Significance value: UNKNOWN.
UndoManager - class cytoscape.util.UndoManager.
UndoManager(CyMenus) - Constructor for class cytoscape.util.UndoManager
unFlagAllEdges() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.unselectAllEdges()
unFlagAllNodes() - Method in interface cytoscape.CyNetwork: Deprecated. As of 2.3, replaced by CyNetwork.unselectAllNodes()
undefineAttribute(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition: WARNING: All bound attribute values on objects will go away in this attribute namespace when this method is called.
undo - Static variable in class cytoscape.view.CytoscapeDesktop: Cytoscape UndoManager
unlockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
unselectAllEdges() - Method in interface cytoscape.CyNetwork: Sets the selected state of all edges in this CyNetwork to false
unselectAllNodes() - Method in interface cytoscape.CyNetwork: Sets the selected state of all nodes in this CyNetwork to false
updateUI() - Method in class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer: updateUI is overridden to set the colors of the Tree's renderer to match that of the table.
updateUI() - Method in class cytoscape.util.swing.JTreeTable: Overridden to message super and forward the method to the tree.
urlPattern - Static variable in class cytoscape.util.FileUtil: A string that defines a simplified java regular expression for a URL.
useView() - Static method in class cytoscape.CytoscapeInit: Deprecated. This method will be removed April 2007. Use getMode() instead.

V

VISUAL_STYLE - Static variable in class cytoscape.view.CytoscapeDesktop
VIZMAP_ENABLED - Static variable in class cytoscape.view.CytoscapeDesktop
VIZMAP_LOADED - Static variable in class cytoscape.Cytoscape
VIZMAP_RESTORED - Static variable in class cytoscape.Cytoscape
VisualMappingManager - class cytoscape.visual.VisualMappingManager.: Top-level class for controlling the visual appearance of nodes and edges according to data attributes, as well as some global visual attributes.
VisualMappingManager(CyNetworkView) - Constructor for class cytoscape.visual.VisualMappingManager
VisualStyle - class cytoscape.visual.VisualStyle.: This class encapsulates a full set of visual mapping specifications for Cytoscape.
VisualStyle(String) - Constructor for class cytoscape.visual.VisualStyle: Simple constructor, creates default node/edge/global appearance calculators.
VisualStyle(String, NodeAppearanceCalculator, EdgeAppearanceCalculator, GlobalAppearanceCalculator) - Constructor for class cytoscape.visual.VisualStyle: Full constructor.
VisualStyle(VisualStyle) - Constructor for class cytoscape.visual.VisualStyle: Copy constructor.
VisualStyle(VisualStyle, String) - Constructor for class cytoscape.visual.VisualStyle: Copy constructor with new name.
valueForPathChanged(TreePath, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
version - Static variable in class cytoscape.CytoscapeVersion
viewExists(String) - Static method in class cytoscape.Cytoscape
vizmapEdge(EdgeView, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
vizmapNode(NodeView, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager

W

wasCanceled() - Method in interface cytoscape.util.MonitoredTask

X

XGMMLFileFilter - class cytoscape.util.XGMMLFileFilter.
XGMMLFileFilter() - Constructor for class cytoscape.util.XGMMLFileFilter

Z

ZipUtil - class cytoscape.util.ZipUtil.: Compression-related methods mainly for Session Writer.
ZipUtil(String, String[], String) - Constructor for class cytoscape.util.ZipUtil: Constructor.

A B C D E F G H I J L M N O P R S T U V W X Z

Overview

Package

Class

Tree

Deprecated

Index

Help

www.cytoscape.org

PREV NEXT

FRAMES NO FRAMES