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A

ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape
AUTO_MANIFEST - Variable in class cytoscape.util.swing.BioDataServerPanel2Descriptor
AUTO_MANIFEST - Variable in class cytoscape.util.swing.BioDataServerPanel6Descriptor
AbstractCellEditor - class cytoscape.util.swing.AbstractCellEditor.
AbstractCellEditor() - Constructor for class cytoscape.util.swing.AbstractCellEditor
AbstractLayout - class cytoscape.layout.AbstractLayout.: The AbstractLayout provides nice starting point for Layouts written for Cytoscape.
AbstractLayout(CyNetworkView) - Constructor for class cytoscape.layout.AbstractLayout: The Constructor is null
AbstractPlugin - class cytoscape.plugin.AbstractPlugin.: Deprecated. This class relies on CyWindow, which has been deprecated. Instead, use CytoscapePlugin
AbstractPlugin is the class that all Cytoscape plugins must subclass. The plugin should provide a one-argument constructor where the argument is an instance of CyWindow.
It is encouraged, but not mandatory, for plugins to override the describe method to state what the plugin does and how it should be used.
AbstractPlugin() - Constructor for class cytoscape.plugin.AbstractPlugin: Deprecated. this method's presence is superfluous; it is only here so that you don't have to call super(cytoscapeWindow) in your ctor.
AbstractPlugin(CyWindow) - Constructor for class cytoscape.plugin.AbstractPlugin: Deprecated. Standard constructor with a single CyWindow argument.
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
aboutToDisplayPanel() - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
aboutToDisplayPanel() - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
aboutToDisplayPanel() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
aboutToDisplayPanel() - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
aboutToHidePanel() - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
aboutToHidePanel() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
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.
actionHelp() - Method in class cytoscape.util.CytoscapeAction
actionPerformed(ActionEvent) - Method in class cytoscape.task.ui.JTask: Capture All Action Events.
actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction
actionPerformed(ActionEvent) - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
actionPerformed(ActionEvent) - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
actionPerformed(ActionEvent) - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
actionPerformed(ActionEvent) - Method in class cytoscape.util.swing.BioDataServerPanel5Descriptor
actionPerformed(ActionEvent) - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
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(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
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
addButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
addButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
addCheckBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addCheckBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
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.
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
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
addFlipCheckBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addGaFile(String) - Method in class cytoscape.util.swing.BioDataServerPanel6
addGaListActionListener(ListSelectionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addGaTextFieldActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addGaTextFieldActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
addGaTextFieldDocumentListener(DocumentListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addGaTextFieldDocumentListener(DocumentListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
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
addOboTextFieldActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addOboTextFieldActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
addOboTextFieldActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addOboTextFieldDocumentListener(DocumentListener) - Method in class cytoscape.util.swing.BioDataServerPanel2
addOboTextFieldDocumentListener(DocumentListener) - Method in class cytoscape.util.swing.BioDataServerPanel5
addOboTextFieldDocumentListener(DocumentListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addOverwriteCheckBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addOverwriteComboBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel6
addRadioButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel3
addSelectButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel4
addSetButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel3
addSpButtonActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel3
addSpComboBoxActionListener(ActionListener) - Method in class cytoscape.util.swing.BioDataServerPanel3
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
advancePositions() - Method in class cytoscape.layout.AbstractLayout: Implementors must override this method in order to create a Layout.
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
appendSpecies(String) - Method in class cytoscape.util.swing.BioDataServerWizard
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() - Method in interface cytoscape.layout.Layout
applyLayout(LayoutAlgorithm) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to the entire CyNetworkView
applyLayout(LayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(LayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given NodeViews and EdgeViews
applyLayout(LayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView: Applies the given layout to only the given Nodes and Edges
applyLayout(GraphView) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
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.
applySelLayout() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
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
applyVizmapSettings() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
applyVizmapper(VisualStyle) - Method in interface cytoscape.view.CyNetworkView
areSynonyms(String, String, CyNetwork) - Static method in class cytoscape.data.Semantics: This method is used to determine if two, potentially different names really refer to the same thing; that is, the two names are synonyms.
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.
BioDataServer() - Constructor for class cytoscape.data.servers.BioDataServer
BioDataServerInterface - interface cytoscape.data.servers.BioDataServerInterface.
BioDataServerPanel1 - class cytoscape.util.swing.BioDataServerPanel1.
BioDataServerPanel1() - Constructor for class cytoscape.util.swing.BioDataServerPanel1
BioDataServerPanel1Descriptor - class cytoscape.util.swing.BioDataServerPanel1Descriptor.
BioDataServerPanel1Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel1Descriptor
BioDataServerPanel2 - class cytoscape.util.swing.BioDataServerPanel2.
BioDataServerPanel2() - Constructor for class cytoscape.util.swing.BioDataServerPanel2
BioDataServerPanel2Descriptor - class cytoscape.util.swing.BioDataServerPanel2Descriptor.
BioDataServerPanel2Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel2Descriptor
BioDataServerPanel3 - class cytoscape.util.swing.BioDataServerPanel3.
BioDataServerPanel3() - Constructor for class cytoscape.util.swing.BioDataServerPanel3
BioDataServerPanel3Descriptor - class cytoscape.util.swing.BioDataServerPanel3Descriptor.
BioDataServerPanel3Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel3Descriptor
BioDataServerPanel4 - class cytoscape.util.swing.BioDataServerPanel4.
BioDataServerPanel4() - Constructor for class cytoscape.util.swing.BioDataServerPanel4
BioDataServerPanel4Descriptor - class cytoscape.util.swing.BioDataServerPanel4Descriptor.
BioDataServerPanel4Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel4Descriptor
BioDataServerPanel5 - class cytoscape.util.swing.BioDataServerPanel5.
BioDataServerPanel5() - Constructor for class cytoscape.util.swing.BioDataServerPanel5
BioDataServerPanel5Descriptor - class cytoscape.util.swing.BioDataServerPanel5Descriptor.
BioDataServerPanel5Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel5Descriptor
BioDataServerPanel6 - class cytoscape.util.swing.BioDataServerPanel6.
BioDataServerPanel6() - Constructor for class cytoscape.util.swing.BioDataServerPanel6
BioDataServerPanel6(boolean) - Constructor for class cytoscape.util.swing.BioDataServerPanel6
BioDataServerPanel6(LayoutManager) - Constructor for class cytoscape.util.swing.BioDataServerPanel6
BioDataServerPanel6(LayoutManager, boolean) - Constructor for class cytoscape.util.swing.BioDataServerPanel6
BioDataServerPanel6Descriptor - class cytoscape.util.swing.BioDataServerPanel6Descriptor.
BioDataServerPanel6Descriptor() - Constructor for class cytoscape.util.swing.BioDataServerPanel6Descriptor
BioDataServerRmi - class cytoscape.data.servers.BioDataServerRmi.
BioDataServerRmi() - Constructor for class cytoscape.data.servers.BioDataServerRmi
BioDataServerUtil - class cytoscape.util.BioDataServerUtil.
BioDataServerUtil() - Constructor for class cytoscape.util.BioDataServerUtil
BioDataServerWizard - class cytoscape.util.swing.BioDataServerWizard.
BioDataServerWizard() - Constructor for class cytoscape.util.swing.BioDataServerWizard
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
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
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
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.
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.
CyMain - class cytoscape.CyMain.: This is the main startup class for Cytoscape.
CyMain(String[]) - Constructor for class cytoscape.CyMain: Primary Method for Starting Cytoscape.
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. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork firt need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.
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.

Cytoscape does not currently define specific classes for NodeViews and EdgeViews, the deafults from the GINY graph library ( namely phoebe.PNodeView and phoebe.PEdgeView ) are most commonly used.
CyNode - class cytoscape.CyNode.
CyNode(RootGraph, int) - Constructor for class cytoscape.CyNode
CyProject - class cytoscape.CyProject.: This class is constructed from a project file, and contains string values associated with various meaningful variable names that identify the component of a CyNetwork object or various customization options.
CyProject(String) - Constructor for class cytoscape.CyProject: 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.
CytoscapeConfig() - Constructor for class cytoscape.CytoscapeConfig
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: Calling the constructor sets up the CytoscapeInit Object to be a CYTOSCAPE_EXIT event listener, and will take care of saving all properties.
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.
CytoscapeObj() - Constructor for class cytoscape.CytoscapeObj
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 class cytoscape.layout.AbstractLayout: Gets called when the user clicks on the Cancel button of the progress monitor.
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
configure() - Method in class cytoscape.util.MacAppConfig: Configures the Info.plist list with all cytoscape/*.jar files.
construct() - Method in class cytoscape.layout.AbstractLayout
construct() - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
construct() - Method in class cytoscape.util.SwingWorker: Compute the value to be returned by the get method.
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.
createEdges(String) - Method in class cytoscape.layout.AttributeLayout: Adds edges between all nodes that share a value for the given node attribute.
createJMenu(String) - Method in class cytoscape.util.CytoscapeMenuBar: Factory method for instantiating objects of type JMenu
createManifest(File, File) - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
createManifest(File, File[]) - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
createManifestFileChooser() - Method in class cytoscape.util.swing.BioDataServerPanel4
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(Collection, Collection, String, CyNetwork) - 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: Creates a cytoscape.data.CyNetwork from a file.
createNetworkFromFile(String) - Static method in class cytoscape.Cytoscape: Creates a cytoscape.data.CyNetwork from a file.
createNetworkFromProject(CyProject, BioDataServer) - Static method in class cytoscape.Cytoscape: Constructs a network using information from a CyProject argument that contains information on the location of the graph file, any node/edge attribute files, and a possible expression data file.
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.
cytoscape.data.attr - package cytoscape.data.attr
cytoscape.data.attr.util - package cytoscape.data.attr.util
cytoscape.task - package cytoscape.task: Cytoscape Task Framework.
cytoscape.task.sample - package cytoscape.task.sample: Sample task, used to illustrate the Task framework.
cytoscape.task.ui - package cytoscape.task.ui: UI code related to task control.
cytoscape.task.util - package cytoscape.task.util: Utility manager for executing tasks.

D

DEFAULT_MENU_SPECIFIER - Static variable in class cytoscape.util.CytoscapeMenuBar
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.AbstractPlugin: Deprecated. method returning a String description of the plugin.
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
disableDeleteSelectionMenuItem() - Method in class cytoscape.view.CyMenus: Called when the window switches to read-only mode, disabling the menu option for deleting selected objects.
disableSquiggle() - Static method in class cytoscape.Cytoscape: Utility method to disable Squiggle function.
displayCancelButton(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Display of the Cancel Button.
displayCloseButton(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Display of the Close Button.
displayStatus(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Display of the Status Field.
displayTimeElapsed(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Display of the Time Elapsed Field.
displayTimeRemaining(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Display of the Time Remaining Field.
doCallback(String, int) - Method in class cytoscape.layout.AttributeLayout
doLayout() - Method in class cytoscape.layout.AbstractLayout
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 class cytoscape.layout.AbstractLayout
done() - Method in interface cytoscape.util.MonitoredTask: Returns true if the task is done.
dontMove(NodeView) - Method in class cytoscape.layout.AbstractLayout

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.
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, 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.
enableDeleteSelectionMenuItem() - Method in class cytoscape.view.CyMenus: Called when the window switches to edit mode, enabling the menu option for deleting selected objects.
enableSquiggle() - Static method in class cytoscape.Cytoscape: Utility method to enable Squiggle function.
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.
errorOccurred() - Method in class cytoscape.task.ui.JTask: Returns true if Task Has Encountered An Error.
executeTask(Task, JTaskConfig) - Static method in class cytoscape.task.util.TaskManager: Executes the specified task in a new thread, and automatically pops open a JTask UI Component for visually monitoring the task.
exit(int) - Static method in class cytoscape.CyMain
exit() - 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
FILE_GML - Static variable in class cytoscape.Cytoscape
FILE_SBML - Static variable in class cytoscape.Cytoscape
FILE_SIF - 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
flagAllNodes() - Method in interface cytoscape.CyNetwork
forceClear(String) - Method in interface cytoscape.CyNetwork: Deprecated.
forceMove(NodeView, double, double) - Method in class cytoscape.layout.AbstractLayout: Forcibly moves a vertex to the (x,y) location by setting its x and y locations to the inputted location.

G

GA_BUTTON - Variable in class cytoscape.util.swing.BioDataServerPanel2Descriptor
GA_BUTTON - Variable in class cytoscape.util.swing.BioDataServerPanel6Descriptor
GRAPH_REPLACED - Static variable in class cytoscape.CyNetworkEvent: Indicates that a new graph has been installed in the network.
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.CytoscapeConfig
getArgs() - Static method in class cytoscape.CytoscapeInit
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.
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel1Descriptor
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel5Descriptor
getBackPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
getBioDataDirectory() - Method in class cytoscape.CyProject
getBioDataServer() - Static method in class cytoscape.Cytoscape
getBioDataServer() - Static method in class cytoscape.CytoscapeInit
getBioDataServer() - Method in class cytoscape.CytoscapeObj: Returns the (possibly null) bioDataServer.
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
getCellEditorValue() - Method in class cytoscape.util.swing.AbstractCellEditor
getCheckBoxStatus() - Method in class cytoscape.util.swing.BioDataServerPanel2
getCheckBoxStatus() - Method in class cytoscape.util.swing.BioDataServerPanel5
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: Get Some client data
getClientData(String) - Method in interface cytoscape.view.CyNetworkView: Get Some client data
getClientDataNames() - Method in interface cytoscape.CyNetwork: Get a list of all currently available ClientData objects
getClientDataNames() - Method in interface cytoscape.view.CyNetworkView: Get a list of all currently available ClientData objects
getCmd() - Method in class cytoscape.util.Exec
getColor() - Method in class cytoscape.util.MutableColor
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 ofs availible column.
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.
getConfigDirectoy() - Static method in class cytoscape.CytoscapeInit: If .cytoscape directory does not exist, it creates it and returns it
getConfigFile(String) - Static method in class cytoscape.CytoscapeInit
getConfiguration() - Method in class cytoscape.CytoscapeObj
getCurrent() - Method in class cytoscape.layout.AbstractLayout
getCurrent() - Method in interface cytoscape.util.MonitoredTask: Returns the currentProgress parameter.
getCurrentDirectory() - Method in class cytoscape.CytoscapeObj: Deprecated. As of Cytoscape 2.1, replaced by CytoscapeInit.getMRUD();
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.
getCurrentSize() - Method in class cytoscape.layout.AbstractLayout: Returns the current size of the visualization space, accoring to the last call to resize().
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(String, String, String, String) - Static method in class cytoscape.Cytoscape
getCyEdgesList() - Static method in class cytoscape.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.
getDataMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items related to data operations.
getDefaultLayoutStrategy() - Method in class cytoscape.CyProject
getDefaultMenuSpecifier() - Method in class cytoscape.util.CytoscapeMenuBar
getDefaultSpeciesName() - Method in class cytoscape.CyProject
getDefaultSpeciesName() - Static method in class cytoscape.CytoscapeInit
getDefaultVisualStyle() - Static method in class cytoscape.CytoscapeInit
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
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
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. @see{getNetworkData} Returns the expression data object associated with this network.
getExpressionData() - Static method in class cytoscape.Cytoscape
getExpressionFilename() - Method in class cytoscape.CyProject
getExpressionFiles() - Static method in class cytoscape.CytoscapeInit
getExtension(File) - Method in class cytoscape.util.CyFileFilter: Return the extension portion of the file's name .
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.
getFileFormatRadioButtonSelected() - Method in class cytoscape.util.swing.BioDataServerPanel1
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.
getFinalState() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
getFlaggedEdgeIndicesArray() - Method in interface cytoscape.CyNetwork
getFlaggedEdges() - Method in interface cytoscape.CyNetwork
getFlaggedNodeIndicesArray() - Method in interface cytoscape.CyNetwork
getFlaggedNodes() - Method in interface cytoscape.CyNetwork
getFlagger() - Method in interface cytoscape.CyNetwork
getFlip() - Method in class cytoscape.util.swing.BioDataServerWizard
getFlipCheckBoxStatus() - Method in class cytoscape.util.swing.BioDataServerPanel6
getFullPath() - Method in class cytoscape.data.ExpressionData: Gets the File representation of the Expression Data Object.
getGAFileList() - Method in class cytoscape.util.swing.BioDataServerPanel6
getGaTextField() - Method in class cytoscape.util.swing.BioDataServerPanel2
getGaTextField() - Method in class cytoscape.util.swing.BioDataServerPanel5
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
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() - Static method in class cytoscape.CytoscapeInit
getGraphPerspective() - Method in interface cytoscape.CyNetwork: Deprecated.
getGraphPerspective() - Method in class cytoscape.CyNode
getGraphView() - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
getGraphViewController() - Method in class cytoscape.view.CytoscapeDesktop: TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
getHelp() - Method in class cytoscape.CytoscapeInit
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
getIndexOfChild(Object, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
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
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 class cytoscape.layout.AbstractLayout
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
getMainFrame() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
getManifestFile(boolean) - Method in class cytoscape.util.swing.BioDataServerPanel4
getManifestFileName() - Method in class cytoscape.util.swing.BioDataServerPanel4
getManifestFileName() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
getManifestFileName() - Method in class cytoscape.util.swing.BioDataServerWizard
getManifestFileNameFromTextBox() - Method in class cytoscape.util.swing.BioDataServerPanel4
getManifestName() - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
getManifestName() - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
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
getMenuBar() - Method in class cytoscape.view.CyMenus: Returns the main menu bar constructed by this object.
getMessage() - Method in class cytoscape.layout.AbstractLayout
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.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.layout.AbstractLayout
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.view.CytoscapeDesktop: Deprecated.
getNetwork() - Method in class cytoscape.visual.VisualMappingManager
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 interface cytoscape.layout.Layout
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.
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel1Descriptor
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel4Descriptor
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel5Descriptor
getNextPanelDescriptor() - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
getNodeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle: Get the NodeAppearanceCalculator for this visual style.
getNodeAttributeFilenames() - Method in class cytoscape.CyProject
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
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.
getNodeView(double, double) - Method in class cytoscape.layout.AbstractLayout
getNumberOfConditions() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Experimental Conditions.
getNumberOfEdgeAttributeFiles() - Method in class cytoscape.CyProject
getNumberOfGenes() - Method in class cytoscape.data.ExpressionData: Gets Total Number of Genes.
getNumberOfNodeAttributeFiles() - Method in class cytoscape.CyProject
getObjectKeys(String) - Method in interface cytoscape.data.attr.MultiHashMap: Returns all objectKeys that have at least one attribute value assigned in attributeName.
getOboTextField() - Method in class cytoscape.util.swing.BioDataServerPanel2
getOboTextField() - Method in class cytoscape.util.swing.BioDataServerPanel5
getOboTextField() - Method in class cytoscape.util.swing.BioDataServerPanel6
getOperationsMenu() - Method in class cytoscape.view.CyMenus: Returns the menu with items associated with plug-ins.
getOtherArgs() - Method in class cytoscape.CyProject
getOverwiteComboBox() - Method in class cytoscape.util.swing.BioDataServerPanel6
getPluginURLs() - Static method in class cytoscape.CytoscapeInit
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
getProjectPropsFileName() - Method in class cytoscape.CyProject
getProjectVizmapPropsFileName() - Method in class cytoscape.CyProject
getProperties() - Method in class cytoscape.CytoscapeConfig
getProperties() - Static method in class cytoscape.CytoscapeInit
getPropertiesLocation() - Static method in class cytoscape.CytoscapeInit
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.
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
getRadioButtonSelected() - Method in class cytoscape.util.swing.BioDataServerPanel3
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: Gets the Secondary View Threshold.
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.
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.
getSelectionMode() - Static method in class cytoscape.Cytoscape: Gets the selection mode value.
getSignificanceType() - Method in class cytoscape.data.ExpressionData: Gets the Significance Type.
getSource() - Method in class cytoscape.CyEdge
getSourceNode() - Method in class cytoscape.CyEdge: Deprecated.
getSpNameFromComboBox() - Method in class cytoscape.util.swing.BioDataServerPanel3
getSpNameFromTextBox() - Method in class cytoscape.util.swing.BioDataServerPanel3
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.
getSpeciesName() - Method in class cytoscape.util.swing.BioDataServerPanel3Descriptor
getState() - Method in interface cytoscape.view.cytopanels.CytoPanel: Gets the state of the CytoPanel.
getState() - Method in class cytoscape.view.cytopanels.CytoPanelImp: Gets the state of the CytoPanel.
getStatus() - Method in class cytoscape.layout.AbstractLayout: {@inheritDoc} By default, an AbstractLayout returns null for its status.
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 ATTRIBUTES_ADDED 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
getTargetNode() - Method in class cytoscape.CyEdge: Deprecated.
getTaskName() - Method in class cytoscape.layout.AbstractLayout
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
getTimeString(long) - Static method in class cytoscape.task.ui.StringUtils: Given a time value in milliseconds, this method returns a human readable representation.
getTitle() - Method in interface cytoscape.CyNetwork: Can Change
getTitle() - Method in interface cytoscape.task.Task: Gets a Human Readable Title of this Task.
getTitle() - Method in class cytoscape.task.sample.SampleTask: Gets the Task Title.
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
getView() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
getViewThreshold() - Static method in class cytoscape.CytoscapeInit: Gets the ViewThreshold.
getViewThreshold() - Method in class cytoscape.CytoscapeObj: Deprecated. As of Cytoscape 2.1, replaced by CytoscapeInit.getViewThreshold();
getViewType() - Static method in class cytoscape.CytoscapeInit
getVisualMapperEnabled() - 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: Returns the visual mapping manager that controls the appearance of nodes and edges in this display.
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.
getVizmapPropertiesLocation() - Static method in class cytoscape.CytoscapeInit
getWindowTitle() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
go(boolean) - Method in class cytoscape.layout.AbstractLayout: Initializes currentProgress (generally to zero) and then spawns a SwingWorker to start doing the work.
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.
Haltable - interface cytoscape.task.Haltable.: A hook for requesting that a running process be halted.
halt() - Method in interface cytoscape.task.Haltable: Requests that a running process be aborted.
halt() - Method in interface cytoscape.task.Task: halt() is a non-blocking request to halt the task, and is called by an external entity.
halt() - Method in class cytoscape.task.sample.SampleTask: Non-blocking call to interrupt the task.
haltRequested() - Method in class cytoscape.task.ui.JTask: Returns true if User Has Requested to Halt the Task.
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
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel1Descriptor
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel2Descriptor
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel3Descriptor
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel4Descriptor
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel5Descriptor
IDENTIFIER - Static variable in class cytoscape.util.swing.BioDataServerPanel6Descriptor
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.
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 class cytoscape.layout.AbstractLayout
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(String[]) - Method in class cytoscape.CytoscapeInit: Cytoscape Init must be initialized using the command line arguments.
initCytoPanelMenus() - Method in class cytoscape.view.CyMenus
initialize() - Method in class cytoscape.layout.AbstractLayout: Initializer, calls intialize_local and initializeLocations to start construction process.
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
isFlagged(Edge) - Method in interface cytoscape.CyNetwork
isFlip() - Method in class cytoscape.util.swing.BioDataServerPanel2Descriptor
isFlip() - Method in class cytoscape.util.swing.BioDataServerPanel6Descriptor
isHeadless() - Static method in class cytoscape.CytoscapeInit
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
isSquiggleEnabled() - Static method in class cytoscape.Cytoscape: Returns the value of the global flag to indicate whether the Squiggle function is enabled.
isStateClear() - Method in interface cytoscape.CyNetwork: Deprecated.
isWindows() - Method in class cytoscape.view.cytopanels.CytoPanelUtil: Determines if we are running on Windows platform.

J

JErrorPanel - class cytoscape.task.ui.JErrorPanel.: Common UI element for displaying errors and stack traces.
JTask - class cytoscape.task.ui.JTask.: Common UI element for visually monitoring task progress.
JTask(Task, JTaskConfig) - Constructor for class cytoscape.task.ui.JTask: Constructor.
JTaskConfig - class cytoscape.task.ui.JTaskConfig.: Used to configure the JTask UI component.
JTaskConfig() - Constructor for class cytoscape.task.ui.JTaskConfig
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

LAMBDA - Static variable in class cytoscape.data.ExpressionData: Significance value: LAMBA.
LOAD - Static variable in class cytoscape.util.FileUtil
Layout - interface cytoscape.layout.Layout.: A Layout can be applied to a CyNetworkView
LayoutAlgorithm - interface cytoscape.layout.LayoutAlgorithm.
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.
loadData(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, CyWindow) - Static method in class cytoscape.plugin.AbstractPlugin: Deprecated. Attempts to instantiate a plugin of the class defined by the first argument.
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 class cytoscape.layout.AbstractLayout: Adds the NodeView to the DontMove list
lockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
lockNode(NodeView) - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
lockNodes(NodeView[]) - Method in class cytoscape.layout.AbstractLayout
lockNodes(NodeView[]) - Method in interface cytoscape.layout.LayoutAlgorithm
lockNodes(NodeView[]) - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.

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.
MutableColor(Color) - Constructor for class cytoscape.util.MutableColor
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.task.sample.RunBareBones: Executes the Sample Task.
main(String[]) - Static method in class cytoscape.task.sample.RunSampleTask: Main Method, used to testing purposes only.
main(String[]) - Static method in class cytoscape.util.MacAppConfig: Main Method.
move(double, double) - Method in class cytoscape.layout.AbstractLayout
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.
NOT_AVAILABLE_STR - Static variable in class cytoscape.task.ui.StringUtils: Not Available String.
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
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

OBO_BUTTON - Variable in class cytoscape.util.swing.BioDataServerPanel2Descriptor
OBO_BUTTON - Variable in class cytoscape.util.swing.BioDataServerPanel6Descriptor
ONE_SECOND - Static variable in class cytoscape.util.CytoscapeProgressMonitor
OpenBrowser - class cytoscape.util.OpenBrowser.
OpenBrowser() - Constructor for class cytoscape.util.OpenBrowser
oldLoadData(String) - Method in class cytoscape.data.ExpressionData
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

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
propertyChange(PropertyChangeEvent) - Method in class cytoscape.CytoscapeInit
propertyChange(PropertyChangeEvent) - Method in class cytoscape.CytoscapeModifiedNetworkManager
propertyChange(PropertyChangeEvent) - Method in class cytoscape.view.CytoscapeDesktop
putClientData(String, Object) - Method in interface cytoscape.CyNetwork: Networks can support client data.
putClientData(String, Object) - Method in interface cytoscape.view.CyNetworkView: Networks can support client data.

R

RNA - Static variable in class cytoscape.data.Semantics
RunBareBones - class cytoscape.task.sample.RunBareBones.: Illustrates how to execute a sample task via the TaskManager.
RunBareBones() - Constructor for class cytoscape.task.sample.RunBareBones
RunSampleTask - class cytoscape.task.sample.RunSampleTask.: Runs the Sample Task and demonstrate various UI options.
RunSampleTask() - Constructor for class cytoscape.task.sample.RunSampleTask
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
redrawGraph() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
redrawGraph(boolean) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
redrawGraph(boolean, boolean) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
refreshOperationsMenu() - Method in class cytoscape.view.CyMenus: Deprecated. This method is no longer needed now that we don't use the NO_OPERATIONS menu placeholder. This method does nothing.
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.
removeFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork
removeNode(int, boolean) - Method in interface cytoscape.CyNetwork: This will remove this node from the Network.
removeTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
resize(Dimension) - Method in class cytoscape.layout.AbstractLayout: When a visualizetion is resized, it presumably wants to fix the locations of the vertices and possibly to reinitialize its data.
restart() - Method in class cytoscape.layout.AbstractLayout: Restarts the visualization entirely, as if the the user had pressed the "scramble" button.
rotateNode(PNode) - Static method in class cytoscape.util.CreditScreen
run() - Method in interface cytoscape.task.Task: run() executes the task, and is called by an external entity.
run() - Method in class cytoscape.task.sample.SampleTask: Run the Task.
run() - Method in class cytoscape.util.CytoscapeProgressMonitor: Implementes Runnable.run()
run() - Method in class cytoscape.util.Exec
runThreaded() - Method in class cytoscape.util.Exec

S

SAVE - Static variable in class cytoscape.util.FileUtil
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
SPECIES - Static variable in class cytoscape.data.Semantics
STR_LENGTH - Static variable in class cytoscape.task.ui.StringUtils: String Length.
SampleTask - class cytoscape.task.sample.SampleTask.: Sample Task, used to illustrate the Task Framework.
SampleTask(int, long) - Constructor for class cytoscape.task.sample.SampleTask: Constructor.
SampleTask(int, long, int) - Constructor for class cytoscape.task.sample.SampleTask: Constructor.
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
SpringEmbeddedLayouter - class cytoscape.layout.SpringEmbeddedLayouter.: Deprecated. Please avoid looking at or using this code -- this code is going away in the next Cytoscape release (the one after 2.1).
SpringEmbeddedLayouter(CyNetworkView) - Constructor for class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
StringUtils - class cytoscape.task.ui.StringUtils.: Misc Utilities for Formatting Times and Strings.
StringUtils() - Constructor for class cytoscape.task.ui.StringUtils
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.
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.
setAutoDispose(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables/Disables Auto-Dispose Feature.
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
setComboBoxState(boolean) - Method in class cytoscape.util.swing.BioDataServerPanel3
setComboBoxState(boolean) - Method in class cytoscape.util.swing.BioDataServerPanel4
setCurrentDirectory(File) - Method in class cytoscape.CytoscapeObj: Deprecated. As of Cytoscape 2.1, replaced by CytoscapeInit.getMRUD();
setCurrentNetwork(String) - Static method in class cytoscape.Cytoscape: Deprecated.
setCurrentNetworkView(String) - Static method in class cytoscape.Cytoscape: Deprecated.
setCurrentSpBox(String) - Method in class cytoscape.util.swing.BioDataServerPanel3
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
setDescription(String) - Method in class cytoscape.util.CyFileFilter: Sets the human readable description of this filter.
setDone() - Method in class cytoscape.task.ui.JTask: Indicates that the worker task is done processing.
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.
setEstimatedTimeRemaining(long) - Method in interface cytoscape.task.TaskMonitor: This is a hook for a child process to report to its parent application estimated time until task completion.
setEstimatedTimeRemaining(long) - Method in class cytoscape.task.ui.JTask: Sets Estimated Time Remaining.
setException(Throwable, String) - Method in interface cytoscape.task.TaskMonitor: Indicates to a parent application that a task has encountered an error while processing.
setException(Throwable, String) - Method in class cytoscape.task.ui.JTask: Reports an Error in Task Processing.
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.
setFlagged(Node, boolean) - Method in interface cytoscape.CyNetwork: Flags a node
setFlagged(Edge, boolean) - Method in interface cytoscape.CyNetwork: Flags a edge
setFlaggedEdges(Collection, boolean) - Method in interface cytoscape.CyNetwork: Flag a group of edge
setFlaggedEdges(int[], boolean) - Method in interface cytoscape.CyNetwork: Flag a group of edges using their indices
setFlaggedNodes(Collection, boolean) - Method in interface cytoscape.CyNetwork: Flag a group of node
setFlaggedNodes(int[], boolean) - Method in interface cytoscape.CyNetwork: Flag a group of nodes using their indices
setFocus(String) - Method in class cytoscape.view.CytoscapeDesktop
setGaFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel2
setGaFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel5
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
setGraphView(CyNetworkView) - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
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
setInteractivity(boolean) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
setLabelText(String) - Method in class cytoscape.util.IndeterminateProgressBar
setMRUD(File) - Static method in class cytoscape.CytoscapeInit
setMRUF(File) - Static method in class cytoscape.CytoscapeInit
setManifestFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel4
setModal(boolean) - Method in class cytoscape.task.ui.JTaskConfig: Enables modality of the JTask Dialog box.
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 interface cytoscape.layout.Layout: This could have unexpected consequences
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.
setOboFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel2
setOboFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel5
setOboFileName(String) - Method in class cytoscape.util.swing.BioDataServerPanel6
setOverwriteState() - Method in class cytoscape.util.swing.BioDataServerPanel6
setOwner(Container) - Method in class cytoscape.task.ui.JTaskConfig: Specifies the Owner of the JTask.
setPercentCompleted(int) - Method in interface cytoscape.task.TaskMonitor: This is a hook for a child process to report to its parent application what percentage of a task it has completed.
setPercentCompleted(int) - Method in class cytoscape.task.ui.JTask: Sets Percentage Complete.
setPreferredButtonGroup(String) - Method in class cytoscape.util.CytoscapeAction
setPreferredIndex(int) - Method in class cytoscape.util.CytoscapeAction
setPreferredMenu(String) - Method in class cytoscape.util.CytoscapeAction
setProgressText(String) - Method in class cytoscape.util.swing.BioDataServerPanel3
setProgressValue(int) - Method in class cytoscape.util.swing.BioDataServerPanel3
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: Sets the Secondary View Threshold.
setSelected(CyNode[]) - Method in interface cytoscape.view.CyNetworkView: Sets the Given nodes Selected
setSelected(NodeView[]) - Method in interface cytoscape.view.CyNetworkView: Sets the Given nodes Selected
setSelected(CyEdge[]) - Method in interface cytoscape.view.CyNetworkView: Sets the Given edges Selected
setSelected(EdgeView[]) - Method in interface cytoscape.view.CyNetworkView: Sets the Given edges Selected
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.
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.
setSingle(double, double) - Method in class cytoscape.layout.AbstractLayout
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.
setStatus(String) - Method in interface cytoscape.task.TaskMonitor: This is a hook for a child process to report to its parent application a short one-line text description (not exceeding, say, 60 characters, even though that is not enforced) of the current phase of processing.
setStatus(String) - Method in class cytoscape.task.ui.JTask: Sets the Status Message.
setStatusBarMsg(String) - Method in class cytoscape.view.CytoscapeDesktop: Sets the Status Bar Message.
setString(String) - Method in class cytoscape.util.MutableString
setTaskMonitor(TaskMonitor) - Method in interface cytoscape.task.Task: Lets this Task know who it should report to regarding task progress, errors, status description, etc.
setTaskMonitor(TaskMonitor) - Method in class cytoscape.task.sample.SampleTask: Sets the Task Monitor.
setTaxonomyTable() - Method in class cytoscape.util.swing.BioDataServerPanel6
setTextBoxState(boolean) - Method in class cytoscape.util.swing.BioDataServerPanel3
setTextBoxState(boolean) - Method in class cytoscape.util.swing.BioDataServerPanel4
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: Sets the ViewThreshold.
setViewThreshold(int) - Method in class cytoscape.CytoscapeObj: Deprecated. As of Cytoscape 2.1, replaced by CytoscapeInit.setViewThreshold(int);
setVisualMapperEnabled(boolean) - Method in interface cytoscape.view.CyNetworkView
setVisualMapperEnabled(boolean) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
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(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.
setWindowTitle(String) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
shouldSelectCell(EventObject) - Method in class cytoscape.util.swing.AbstractCellEditor
show() - Method in class cytoscape.util.swing.BioDataServerWizard
showCredits(URL, String) - Static method in class cytoscape.util.CreditScreen
showWindow(int, int) - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
showWindow() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
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 class cytoscape.layout.AbstractLayout
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
switchToEditMode() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
switchToReadOnlyMode() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.

T

TABBED_VIEW - Static variable in class cytoscape.view.CytoscapeDesktop: Displays all network views in TabbedPanes ( like Mozilla )
TAXON_FILE - Variable in class cytoscape.util.swing.BioDataServerPanel3
TAXON_FILE - Variable in class cytoscape.util.swing.BioDataServerPanel5
TAXON_FILE - Variable in class cytoscape.util.swing.BioDataServerPanel6
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.
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.
Task - interface cytoscape.task.Task.: Represents a task that can be terminated prematurely by the same entity that started the task - tasks are started with Task.run() and tasks are terminated prematurely [and asynchronously] with Task.halt().
TaskManager - class cytoscape.task.util.TaskManager.: Utility class used to execute tasks and visually monitor their progress.
TaskManager() - Constructor for class cytoscape.task.util.TaskManager
TaskMonitor - interface cytoscape.task.TaskMonitor.: Interface for monitoring the progress of a task.
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
toggleVisualMapperEnabled() - Method in class cytoscape.view.CytoscapeDesktop: Deprecated.
truncateOrPadString(String) - Static method in class cytoscape.task.ui.StringUtils: Truncates a String to a specific length or pads it with extra spaces.

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
unFlagAllNodes() - Method in interface cytoscape.CyNetwork
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 class cytoscape.layout.AbstractLayout: Removes the NodeView from the DontMove list
unlockNode(NodeView) - Method in interface cytoscape.layout.LayoutAlgorithm
unlockNode(NodeView) - Method in class cytoscape.layout.SpringEmbeddedLayouter: Deprecated.
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.
useView() - Static method in class cytoscape.CytoscapeInit

V

VISUAL_STYLE - Static variable in class cytoscape.view.CytoscapeDesktop
VIZMAP_ENABLED - Static variable in class cytoscape.view.CytoscapeDesktop
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 class cytoscape.layout.AbstractLayout
wasCanceled() - Method in interface cytoscape.util.MonitoredTask
windowActivated(WindowEvent) - Method in class cytoscape.CyMain
windowClosed(WindowEvent) - Method in class cytoscape.CyMain
windowClosing(WindowEvent) - Method in class cytoscape.CyMain: on linux (at least) a killed window generates a 'windowClosed' event; trap that here
windowDeactivated(WindowEvent) - Method in class cytoscape.CyMain
windowDeiconified(WindowEvent) - Method in class cytoscape.CyMain
windowIconified(WindowEvent) - Method in class cytoscape.CyMain
windowOpened(WindowEvent) - Method in class cytoscape.CyMain

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