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

A

ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape

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

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.

actionPerformed(ActionEvent) - Method in class cytoscape.task.ui.JTask

Capture All Action Events.

actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction

activate() - Method in class cytoscape.plugin.CytoscapePlugin

If implemented, then this plugin will be activated after being initialized

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

addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor

addCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork

Registers the argument as a listener to this object.

addCytoscapeAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus

Takes a CytoscapeAction and will add it to the MenuBar or the Toolbar as is appropriate.

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

addExtension(String) - Method in class cytoscape.util.CyFileFilter

Adds a filetype "dot" extension to filter against.

addFlagEventListener(FlagEventListener) - Method in interface cytoscape.CyNetwork

addNode(int) - Method in interface cytoscape.CyNetwork

Add a node to this Network that already exists in Cytoscape

addNode(Node) - Method in interface cytoscape.CyNetwork

Add a node to this Network that already exists in Cytoscape

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.

appendNetwork(CyNetwork) - Method in interface cytoscape.CyNetwork

Appends all of the nodes and edges in the given Network to this Network

applyAppearances() - Method in class cytoscape.visual.VisualMappingManager

Recalculates and reapplies all of the node, edge, and global visual attributes.

applyEdgeAppearances() - Method in class cytoscape.visual.VisualMappingManager

Recalculates and reapplies all of the edge appearances.

applyEdgeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager

Recalculates and reapplies all of the edge appearances.

applyGlobalAppearances() - Method in class cytoscape.visual.VisualMappingManager

Recalculates and reapplies the global visual attributes.

applyGlobalAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager

Recalculates and reapplies the global visual attributes.

applyLayout() - 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.

B

BEGIN - Static variable in class cytoscape.CyNetworkEvent

Indicates that someone is beginning to work with the network.

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

BioDataServer() - Constructor for class cytoscape.data.servers.BioDataServer

BioDataServerInterface - interface cytoscape.data.servers.BioDataServerInterface.

BioDataServerRmi - class cytoscape.data.servers.BioDataServerRmi.

BioDataServerRmi() - Constructor for class cytoscape.data.servers.BioDataServerRmi

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

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

CreditScreen - class cytoscape.util.CreditScreen.

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

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.

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.

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

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.

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.

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(GraphObjAttributes, TaskMonitor) - Method in class cytoscape.data.ExpressionData

Copies ExpressionData data structure into GraphObjAttributes 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

createNetwork(String) - 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.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

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.

deleteEdgeAttribute(String) - Method in interface cytoscape.CyNetwork

Deleted the attribute with the given name from edge attributes

deleteNodeAttribute(String) - Method in interface cytoscape.CyNetwork

Deletes the attribute with the given name from node attributes

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.

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.

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

ExpressionData(String) - Constructor for class cytoscape.data.ExpressionData

ExpressionData(String, TaskMonitor) - Constructor for class cytoscape.data.ExpressionData

enableDeleteSelectionMenuItem() - Method in class cytoscape.view.CyMenus

Called when the window switches to edit mode, enabling the menu option for deleting selected objects.

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

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

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.

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

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

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

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

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

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

getConditionNames() - Method in class cytoscape.data.ExpressionData

getConfigDirectoy() - Static method in class cytoscape.CytoscapeInit

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.

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

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

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

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

Return the requested Attribute for the given Edge

getEdgeAttributeValue(int, String) - Method in interface cytoscape.CyNetwork

Return the requested Attribute for the given Edge

getEdgeAttributeValue(Edge, String) - Static method in class cytoscape.Cytoscape

Return the requested Attribute for the given Edge

getEdgeAttributes() - Method in interface cytoscape.CyNetwork

Deprecated.

getEdgeAttributes() - Static method in class cytoscape.CytoscapeInit

getEdgeAttributesList() - Method in interface cytoscape.CyNetwork

Return all availble Attributes for the Edges in this CyNetwork

getEdgeAttributesList() - Static method in class cytoscape.Cytoscape

Return all availble Attributes for the Edges in this CyNetwork

getEdgeNetworkData() - Static method in class cytoscape.Cytoscape

Deprecated. This should not be used by any user-code

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 .

getExtremeValues() - Method in class cytoscape.data.ExpressionData

getFile(String, int) - Static method in class cytoscape.util.FileUtil

Returns a File object, this method should be used instead of rolling your own JFileChooser.

getFile(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil

Returns a File object, this method should be used instead of rolling your own JFileChooser.

getFile(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil

Returns a File object, this method should be used instead of rolling your own JFileChooser.

getFileMenu() - Method in class cytoscape.view.CyMenus

Returns the menu with items related to file operations.

getFileName() - Method in class cytoscape.data.ExpressionData

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

getFullPath() - Method in class cytoscape.data.ExpressionData

getGeneDescriptor(String) - Method in class cytoscape.data.ExpressionData

getGeneDescriptors() - Method in class cytoscape.data.ExpressionData

getGeneDescriptorsVector() - Method in class cytoscape.data.ExpressionData

getGeneNames() - Method in class cytoscape.data.ExpressionData

getGeneNamesVector() - Method in class cytoscape.data.ExpressionData

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

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.

getMRUD() - Static method in class cytoscape.CytoscapeInit

getMRUF() - Static method in class cytoscape.CytoscapeInit

getMainFrame() - Method in class cytoscape.view.CytoscapeDesktop

Deprecated.

getMax() - Method in class cytoscape.util.MinMaxDouble

getMax() - Method in class cytoscape.util.MinMaxInt

getMeasurement(String, String) - Method in class cytoscape.data.ExpressionData

getMeasurements(String) - Method in class cytoscape.data.ExpressionData

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

getName() - Method in class cytoscape.layout.AbstractLayout

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

getNetworkViewMap() - Static method in class cytoscape.Cytoscape

This Map has keys that are Strings ( network_ids ) and values that are networkviews.

getNodeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle

Get the NodeAppearanceCalculator for this visual style.

getNodeAttributeFilenames() - Method in class cytoscape.CyProject

getNodeAttributeValue(Node, String) - Method in interface cytoscape.CyNetwork

Return the requested Attribute for the given Node

getNodeAttributeValue(int, String) - Method in interface cytoscape.CyNetwork

Return the requested Attribute for the given Node

getNodeAttributeValue(Node, String) - Static method in class cytoscape.Cytoscape

Return the requested Attribute for the given Node

getNodeAttributes() - Method in interface cytoscape.CyNetwork

Deprecated.

getNodeAttributes() - Static method in class cytoscape.CytoscapeInit

getNodeAttributesList() - Method in interface cytoscape.CyNetwork

Return all availble Attributes for the Nodes in this CyNetwork

getNodeAttributesList(Node[]) - Method in interface cytoscape.CyNetwork

Return all available Attributes for the given Nodes

getNodeAttributesList(Edge[]) - Method in interface cytoscape.CyNetwork

Return all available Attributes for the given Edges

getNodeAttributesList() - Static method in class cytoscape.Cytoscape

Return all availble Attributes for the Nodes in this CyNetwork

getNodeAttributesList(Node[]) - Static method in class cytoscape.Cytoscape

Return all available Attributes for the given Nodes

getNodeAttributesList(Edge[]) - Static method in class cytoscape.Cytoscape

Return all available Attributes for the given Edges

getNodeNetworkData() - Static method in class cytoscape.Cytoscape

Deprecated. This should not be used by any user-code

getNodeView(double, double) - Method in class cytoscape.layout.AbstractLayout

getNumberOfConditions() - Method in class cytoscape.data.ExpressionData

getNumberOfEdgeAttributeFiles() - Method in class cytoscape.CyProject

getNumberOfGenes() - Method in class cytoscape.data.ExpressionData

getNumberOfNodeAttributeFiles() - Method in class cytoscape.CyProject

getOperationsMenu() - Method in class cytoscape.view.CyMenus

Returns the menu with items associated with plug-ins.

getOtherArgs() - Method in class cytoscape.CyProject

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

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

getRGBText(Color) - Static method in class cytoscape.util.Misc

getRoot() - Method in class cytoscape.util.swing.AbstractTreeTableModel

getRootGraph() - Method in class cytoscape.CyEdge

getRootGraph() - Method in class cytoscape.CyNode

getRootGraph() - Static method in class cytoscape.Cytoscape

Return the CytoscapeRootGraph

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.

getSignificanceType() - Method in class cytoscape.data.ExpressionData

getSource() - Method in class cytoscape.CyEdge

getSourceNode() - Method in class cytoscape.CyEdge

Deprecated.

getSpeciesInNetwork(CyNetwork) - Static method in class cytoscape.data.Semantics

Returns every unique species defined in the supplied network.

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

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.

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

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

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

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.

hasSignificanceValues() - Method in class cytoscape.data.ExpressionData

I

IDENTIFIER - Static variable in class cytoscape.data.Semantics

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

init(String[]) - Method in class cytoscape.CytoscapeInit

Cytoscape Init must be initialized using the command line arguments.

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.

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

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

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

isStateClear() - Method in interface cytoscape.CyNetwork

Deprecated.

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

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

loadExpressionData(String, boolean) - Static method in class cytoscape.Cytoscape

Load Expression Data

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

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

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.

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_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

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

O

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

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.

openURL(String) - Static method in class cytoscape.util.OpenBrowser

P

PROTEIN - Static variable in class cytoscape.data.Semantics

PVAL - Static variable in class cytoscape.data.ExpressionData

Kinds of significance values

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.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

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.

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.

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.

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

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

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

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.

setDefaultMenuSpecifier(String) - Method in class cytoscape.util.CytoscapeMenuBar

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

Return the requested Attribute for the given Edge

setEdgeAttributeValue(int, String, Object) - Method in interface cytoscape.CyNetwork

Return the requested Attribute for the given Edge

setEdgeAttributeValue(Edge, String, Object) - Static method in class cytoscape.Cytoscape

Return the requested Attribute for the given Edge

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

setGeneDescriptors(Vector) - Method in class cytoscape.data.ExpressionData

setGeneNames(Vector) - Method in class cytoscape.data.ExpressionData

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

setModal(boolean) - Method in class cytoscape.task.ui.JTaskConfig

Enables modality of the JTask Dialog box.

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

Return the requested Attribute for the given Node

setNodeAttributeValue(int, String, Object) - Method in interface cytoscape.CyNetwork

Return the requested Attribute for the given Node

setNodeAttributeValue(Node, String, Object) - Static method in class cytoscape.Cytoscape

Return the requested Attribute for the given Node

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.

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

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

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

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.

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.

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

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.

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 )

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

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.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

unFlagAllEdges() - Method in interface cytoscape.CyNetwork

unFlagAllNodes() - Method in interface cytoscape.CyNetwork

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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