Index (Cytoscape Swing App API (swing-app-api) 3.0.0-beta1 API)

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Cytoscape 3.0.0-beta1 API

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abortShutdown(String) - Method in class org.cytoscape.application.events.CyShutdownEvent: A callback to the firing class that allows a listener to abort the shutdown.
abortShutdownReason() - Method in class org.cytoscape.application.events.CyShutdownEvent: Returns the reason that the application should not be shut down.
AboutToRemoveEdgesEvent - Class in org.cytoscape.model.events: Fired before an edge is actually removed so that listeners have a chance to clean up before the edge object disappears.
AboutToRemoveEdgesEvent(CyNetwork, Collection<CyEdge>) - Constructor for class org.cytoscape.model.events.AboutToRemoveEdgesEvent: Constructs event.
AboutToRemoveEdgesListener - Interface in org.cytoscape.model.events: Listener for AboutToRemoveEdgeEvents.
AboutToRemoveEdgeViewsEvent - Class in org.cytoscape.view.model.events: When edge Views are about to be removed from a CyNetworkView, this event will be fired.
AboutToRemoveEdgeViewsEvent(CyNetworkView, Collection<View<CyEdge>>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveEdgeViewsEvent: Creates the event for about to be removed edge views.
AboutToRemoveEdgeViewsListener - Interface in org.cytoscape.view.model.events: Listener for AboutToRemoveEdgeViewsEvent.
AboutToRemoveNodesEvent - Class in org.cytoscape.model.events: Fired before a node is actually removed so that listeners have a chance to clean up before the node object disappears.
AboutToRemoveNodesEvent(CyNetwork, Collection<CyNode>) - Constructor for class org.cytoscape.model.events.AboutToRemoveNodesEvent: Constructs event.
AboutToRemoveNodesListener - Interface in org.cytoscape.model.events: Listener for AboutToRemoveNodeEvents.
AboutToRemoveNodeViewsEvent - Class in org.cytoscape.view.model.events: When node Views are about to be removed from a CyNetworkView, this event will be fired.
AboutToRemoveNodeViewsEvent(CyNetworkView, Collection<View<CyNode>>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveNodeViewsEvent: Creates the event for about to be removed node views.
AboutToRemoveNodeViewsListener - Interface in org.cytoscape.view.model.events: Listener for AboutToRemoveNodeViewsEvent.
AbstractBounded<N extends Comparable<N>> - Class in org.cytoscape.work.util: A bounded number object whose bounds values cannot be modified
AbstractBounded(N, N, N, boolean, boolean) - Constructor for class org.cytoscape.work.util.AbstractBounded: Creates a new Bounded object.
AbstractCellEditor - Class in org.cytoscape.util.swing: An abstract, convenience implementation of a Cell Editor that really only adds event listener support.
AbstractCellEditor() - Constructor for class org.cytoscape.util.swing.AbstractCellEditor
AbstractConfigDirPropsReader - Class in org.cytoscape.property: An abstract implementation of CyProperty<Properties> that attempts to read the specified properties file first from the jar file running this code and then appends any properties found in the local configuration directory to that properties object.
AbstractConfigDirPropsReader(String, String, CyProperty.SavePolicy) - Constructor for class org.cytoscape.property.AbstractConfigDirPropsReader: Creates a new AbstractConfigDirPropsReader object.
AbstractCyAction - Class in org.cytoscape.application.swing: An abstract implementation of the CyAction interface.
AbstractCyAction(String) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object.
AbstractCyAction(String, CyApplicationManager, String, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object.
AbstractCyActivator - Class in org.cytoscape.service.util: A simple BundleActivator with convenience methods for registering OSGi services and either getting references to single services or registering interest in all services of a specified type.
AbstractCyActivator() - Constructor for class org.cytoscape.service.util.AbstractCyActivator: Constructor.
AbstractCyApp - Class in org.cytoscape.app: The primary app interface for Cytoscape that all apps must extend.
AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp: The constructor that all apps must call using "super(adapter);" where the "adapter" is a CyAppAdapter reference provided as an argument to the constructor.
AbstractCyEdit - Class in org.cytoscape.work.undo: A small class used to create new undoable edits.
AbstractCyEdit(String) - Constructor for class org.cytoscape.work.undo.AbstractCyEdit: Constructor.
AbstractCyEvent<T> - Class in org.cytoscape.event: A base implementation of CyEvent that can be used by events.
AbstractCyEvent(T, Class<?>) - Constructor for class org.cytoscape.event.AbstractCyEvent: Constructor.
AbstractCyPayloadEvent<T,P> - Class in org.cytoscape.event: A base implementation of CyPayloadEvent that can be used by events.
AbstractCyPayloadEvent(T, Class<?>, Collection<P>) - Constructor for class org.cytoscape.event.AbstractCyPayloadEvent: Constructor.
AbstractCySwingApp - Class in org.cytoscape.app.swing: The primary Swing-based app interface for Cytoscape that all Swing-based apps must extend.
AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp: The constructor that all apps must call using "super(adapter);" where the "adapter" is a CySwingAppAdapter reference provided as an argument to the constructor.
AbstractEdgeViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on an edge view and possibly its associated network view.
AbstractEdgeViewTask(View<CyEdge>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractEdgeViewTask: Base constructor for all tasks that need an edge view to operate on.
AbstractEdgeViewTaskFactory - Class in org.cytoscape.task: An EdgeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractEdgeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractEdgeViewTaskFactory
AbstractFunction - Class in org.cytoscape.equations: Base class for all Function implementations.
AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction: Base class constructor for easy creation of Functions from function argument descriptors.
AbstractGUITunableHandler - Class in org.cytoscape.work.swing: Base class for the various Swing implementations of TunableHandler.
AbstractGUITunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractGUITunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractInputStreamTaskFactory - Class in org.cytoscape.io.read
AbstractInputStreamTaskFactory(CyFileFilter) - Constructor for class org.cytoscape.io.read.AbstractInputStreamTaskFactory
AbstractLayoutAlgorithm - Class in org.cytoscape.view.layout: The AbstractLayoutAlgorithm provides a basic implementation of a layout TaskFactory.
AbstractLayoutAlgorithm(String, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutAlgorithm: The Constructor.
AbstractLayoutTask - Class in org.cytoscape.view.layout: This is a basic implementation of a LayoutAlgorithm Task that does some bookkeeping, but primarily delegates to the doLayout() method.
AbstractLayoutTask(String, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutTask: Constructor.
AbstractNetworkCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyNetworks.
AbstractNetworkCollectionTask(Collection<CyNetwork>) - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTask: Base Constructor for a task that will operate on a collection of networks
AbstractNetworkCollectionTaskFactory - Class in org.cytoscape.task: An NetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTaskFactory
AbstractNetworkTask - Class in org.cytoscape.task: Base class for all tasks that need to operate on a CyNetwork.
AbstractNetworkTask(CyNetwork) - Constructor for class org.cytoscape.task.AbstractNetworkTask: Base class for tasks that need to operate on a CyNetwork
AbstractNetworkTaskFactory - Class in org.cytoscape.task: A NetworkTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkTaskFactory
AbstractNetworkViewCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyNetworkViews.
AbstractNetworkViewCollectionTask(Collection<CyNetworkView>) - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTask: Base class for any tasks that need to operate on a collection of network views.
AbstractNetworkViewCollectionTaskFactory - Class in org.cytoscape.task: A NetworkViewCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory
AbstractNetworkViewLocationTaskFactory - Class in org.cytoscape.task: A base class for task factories that need to add a functionality to the network view considering a given location (for example adding a node where a mouse was clicked).
AbstractNetworkViewLocationTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory
AbstractNetworkViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a network view.
AbstractNetworkViewTask(CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNetworkViewTask: A base class for tasks that need to operate on a network view.
AbstractNetworkViewTaskFactory - Class in org.cytoscape.task: A NetworkViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewTaskFactory
AbstractNode - Class in org.cytoscape.equations: A node in the parse tree.
AbstractNode(int) - Constructor for class org.cytoscape.equations.AbstractNode: Base class constructor for any Node type.
AbstractNodeViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTask(View<CyNode>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNodeViewTask: Base class constructor for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTaskFactory - Class in org.cytoscape.task: A NodeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNodeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNodeViewTaskFactory
AbstractPartitionLayoutTask - Class in org.cytoscape.view.layout: This is a more helpful implementation of a LayoutAlgorithm Task that extends AbstractBasicLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Creates a new AbstractPartitionLayoutTask object.
AbstractRowTask - Class in org.cytoscape.task: Base class for all tasks that need to operate on a CyRow.
AbstractRowTask(CyRow) - Constructor for class org.cytoscape.task.AbstractRowTask: Base class constructor for all tasks that need to be provisioned with a CyRow.
AbstractTableCellTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on a single CyTable cell.
AbstractTableCellTask(CyColumn, Object) - Constructor for class org.cytoscape.task.AbstractTableCellTask: Initializes a Task that needs to operate on a CyTable cell entry.
AbstractTableCellTaskFactory - Class in org.cytoscape.task: A TableCellTaskFactory that is always ready to produce a TaskIterator.
AbstractTableCellTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableCellTaskFactory
AbstractTableColumnTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on an entire CyTable column.
AbstractTableColumnTask(CyColumn) - Constructor for class org.cytoscape.task.AbstractTableColumnTask: Initializes a Task that needs to operate on a CyTable column.
AbstractTableColumnTaskFactory - Class in org.cytoscape.task: A TableColumnTaskFactory that is always ready to produce a TaskIterator.
AbstractTableColumnTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableColumnTaskFactory
AbstractTableTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on an entire CyTable.
AbstractTableTask(CyTable) - Constructor for class org.cytoscape.task.AbstractTableTask: Initializes a Task that needs to operate on a CyTable.
AbstractTableTaskFactory - Class in org.cytoscape.task: A TableTaskFactory that is always ready to produce a TaskIterator.
AbstractTableTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableTaskFactory
AbstractTask - Class in org.cytoscape.work: A base class for tasks that need to be able to access the TaskIterator that contains them.
AbstractTask() - Constructor for class org.cytoscape.work.AbstractTask
AbstractTaskFactory - Class in org.cytoscape.work: A TaskFactory that is always ready to produce a TaskIterator.
AbstractTaskFactory() - Constructor for class org.cytoscape.work.AbstractTaskFactory
AbstractTaskManager<T,C> - Class in org.cytoscape.work: Provides access to a TunableInterceptor to all derived classes and a utility method to determine if an object has been annotated with Tunables.
AbstractTaskManager(TunableMutator) - Constructor for class org.cytoscape.work.AbstractTaskManager: Initializes an AbstractTaskManager object by setting its TunableInterceptor.
AbstractToolBarComponent - Class in org.cytoscape.application.swing: An abstract, convenience implementation of ToolBarComponent.
AbstractToolBarComponent() - Constructor for class org.cytoscape.application.swing.AbstractToolBarComponent
AbstractTreeTableModel - Class in org.cytoscape.util.swing: An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class org.cytoscape.util.swing.AbstractTreeTableModel: Creates a new AbstractTreeTableModel object.
AbstractTunableHandler - Class in org.cytoscape.work: Provides the standard implementation for most of the methods declared by the TunableHandler interface.
AbstractTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractTunableInterceptor<T extends TunableHandler> - Class in org.cytoscape.work: An abstract base class for TunableRecorder and TunableMutator implementations.
AbstractTunableInterceptor() - Constructor for class org.cytoscape.work.AbstractTunableInterceptor: Creates a new AbstractTunableInterceptor object.
AbstractViewUpdater<S> - Class in org.cytoscape.application.swing: A utility class that provides an implementation of RowsSetListener for a particular column and VisualProperty.
AbstractViewUpdater(VisualProperty<S>, String, Map<CyRow, View<?>>) - Constructor for class org.cytoscape.application.swing.AbstractViewUpdater: Constructor.
AbstractVisualMappingFunction<K,V> - Class in org.cytoscape.view.vizmap.mappings: A base class for visual mapping functions where all fields are immutable.
AbstractVisualMappingFunction(String, Class<K>, CyTable, VisualProperty<V>) - Constructor for class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: Constructs this AbstractVisualMappingFunction.
AbstractVisualProperty<T> - Class in org.cytoscape.view.model: An abstract implementation of VisualProperty that omits the methods dealing with serializing data.
AbstractVisualProperty(T, Range<T>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.model.AbstractVisualProperty: Constructor to set all immutable fields.
AbstractVisualPropertyEditor<T> - Class in org.cytoscape.view.vizmap.gui.editor: Abstract implementation of Visual Property Editor.
AbstractVisualPropertyEditor(Class<T>, PropertyEditor, ContinuousEditorType) - Constructor for class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor: Creates a new AbstractVisualPropertyEditor object.
AbstractVisualPropertyValue - Class in org.cytoscape.view.presentation.property.values: Base class for all VisualPropertyValue.
AbstractVisualPropertyValue(String, String) - Constructor for class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue: Constructs an AbstractVisualPropertyValue.
AbstractWebServiceClient - Class in org.cytoscape.io.webservice.client: Abstract class for all web service clients.
AbstractWebServiceClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.client.AbstractWebServiceClient: Constructs this AbstractWebServiceClient.
AbstractWebServiceGUIClient - Class in org.cytoscape.io.webservice.swing: Abstract base class for web service clients with Swing GUI.
AbstractWebServiceGUIClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient: Constructor.
ACCELERATOR - Static variable in interface org.cytoscape.work.ServiceProperties: Shortcut key combination for desktop app.
acceleratorKeyStroke - Variable in class org.cytoscape.application.swing.AbstractCyAction: The accelerator keystroke, if set.
acceleratorSet - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether accelerator keys have been set for the action.
accept(File) - Method in class org.cytoscape.util.swing.FileChooserFilter: Accept or not the file from JFileChooser.
accepts(URI, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter: A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
accepts(InputStream, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter: This method always returns false in this particular implementation.
accepts(URI, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter: A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
accepts(InputStream, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter: A method that attempts to determine whether the specified InputStream can be read by the Reader using this filter.
acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor: Returns true if this ArgDescriptor accepts multiple arguments, otherwise false.
acceptsMultipleArgs() - Method in enum org.cytoscape.equations.ArgType: Returns true if this type accepts multiple args.
ActionEnableSupport - Class in org.cytoscape.application.swing: A class that allows the enabled state of an Action of JMenuItem to managed in a consistent way.
ActionEnableSupport(DynamicSubmenuListener, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport: Constructor.
ActionEnableSupport(Action, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport: Constructor.
ActionEnableSupport(JMenuItem, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport: Constructor.
actuallyShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent: Returns true if no reason is provided to abort the shutdown and false if anyone processing this event wants to prevent shutdown.
adapter - Variable in class org.cytoscape.app.AbstractCyApp: Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.
add(URL) - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker: Adds "newURL" to the list of recently opened file names and trims the list if it has exceeded its maximum length.
add(Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: This method will not add components as might be expected, instead use the method getContentPane() which will return a panel, and you may use add() on that.
addAction(CyAction) - Method in interface org.cytoscape.application.swing.CySwingApplication: Add a CyAction to application.
addAggregator(Aggregator) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Add a new aggregator to the available aggregators.
addAppFiles(String, List<File>) - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent: A method that allows apps to specify a list of files that should be stored in the session.
addBasicVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Add a new basic visual property.
addBendFactory(BendFactory, Map) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
addCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
addChangeListener(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Adds the argument as a new dependency to this GUITunableHandler.
addChangeListener(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler: Adds a GUITunableHandler that listens to THIS tunable handler.
addDependent(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Adds the argument as a new dependency to this GUITunableHandler.
addDependent(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler: Adds a GUITunableHandler that depends on THIS tunable handler.
AddedEdgesEvent - Class in org.cytoscape.model.events: An event fired when an edge is added to a network.
AddedEdgesEvent(CyNetwork, Collection<CyEdge>) - Constructor for class org.cytoscape.model.events.AddedEdgesEvent: Constructs event.
AddedEdgesListener - Interface in org.cytoscape.model.events: Listener for AddedEdgesEvents.
AddedEdgeViewsEvent - Class in org.cytoscape.view.model.events: When edge View is added to a CyNetworkView, this event will be fired.
AddedEdgeViewsEvent(CyNetworkView, Collection<View<CyEdge>>) - Constructor for class org.cytoscape.view.model.events.AddedEdgeViewsEvent: Creates the event for new edge views.
AddedEdgeViewsListener - Interface in org.cytoscape.view.model.events: Listener for AddedEdgeViewsEvent.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.CyNetwork: This method is used to create and add an edge to this network.
addEdge(CyEdge) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Adds an edge to this CySubNetwork.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: A shortcut method that Creates a new CyEdge in both this subnetwork AND in the CyRootNetwork.
addEdge(CyEdge, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition: Add an edge to this partition assuming that the source and target nodes are not yet known.
addEdge(CyEdge, LayoutNode, LayoutNode, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition: Add an edge to this partition assuming that the source and target nodes are known.
addEdges(List<CyEdge>) - Method in interface org.cytoscape.group.CyGroup: Add a list of edges to a group.
AddedNodesEvent - Class in org.cytoscape.model.events: Event for upper layers.
AddedNodesEvent(CyNetwork, Collection<CyNode>) - Constructor for class org.cytoscape.model.events.AddedNodesEvent: Constructs event.
AddedNodesListener - Interface in org.cytoscape.model.events: Listener for AddedNodesEvents.
AddedNodeViewsEvent - Class in org.cytoscape.view.model.events: When node View is added to a CyNetworkView, this event will be fired.
AddedNodeViewsEvent(CyNetworkView, Collection<View<CyNode>>) - Constructor for class org.cytoscape.view.model.events.AddedNodeViewsEvent: Creates the event for a new node view.
AddedNodeViewsListener - Interface in org.cytoscape.view.model.events: Listener for AddedNodeViewsEvent.
addEventPayload(S, P, Class<E>) - Method in interface org.cytoscape.event.CyEventHelper: Adds a payload object to be accumulated in a CyPayloadEvent.
addGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager: Registers a group with the group manager.
addGroups(List<CyGroup>) - Method in interface org.cytoscape.group.CyGroupManager: Registers a list of groups with the group manager.
addGroupToNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Add a group to an additional network.
addIdentifierMapping(Class<?>, String, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon: #ASKMIKE
addMenu(JMenu, double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a new submenu into a position based on "gravity" of the new item.
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addMenuItem(JMenuItem, double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a new menu item into a position based on "gravity" of the new item.
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addMenuSeparator(double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a separator into a position based on "gravity" of the new item.
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addNeighbor(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Convenience function to keep track of neighbors of this node.
addNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager: Registers a network with the network manager.
addNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Registers a network view with the network view manager.
addNode() - Method in interface org.cytoscape.model.CyNetwork: This method is used to create and add a node to this network.
addNode(CyNode) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Adds a node to this CySubNetwork.
addNode() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: A shortcut method that Creates a new CyNode in both this subnetwork AND in the CyRootNetwork.
addNode(CyNetwork, View<CyNode>, boolean) - Method in class org.cytoscape.view.layout.LayoutPartition: Add a node to this partition.
addNodes(List<CyNode>) - Method in interface org.cytoscape.group.CyGroup: Add a list of nodes and their edges
addNodes(LayoutNode, LayoutNode) - Method in class org.cytoscape.view.layout.LayoutEdge: Set the nodes associated with this edge.
addPoint(K, BoundaryRangeValues<V>) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Adds a New Data Point.
addRangeValue(T) - Method in class org.cytoscape.view.model.DiscreteRange: Add a value to this DiscreteRange.
addRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Add new RenderingEngine to this manager.
addScalarArgumentTypes(List<Class>) - Static method in class org.cytoscape.equations.FunctionUtil: Adds the scalar types that equations use internally to the argument, i.e.
addSubNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Create an empty CySubNetwork.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Create a CySubNetwork containing the specified CyNodes and CyEdges.
addTable(CyTable) - Method in interface org.cytoscape.model.CyTableManager: Registers a new table with the manager and fires a TableAddedEvent event.
addTreeModelListener(TreeModelListener) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
addTunableHandlerFactory(TunableHandlerFactory<T>, Map) - Method in class org.cytoscape.work.AbstractTunableInterceptor: Allows TunableHandlerFactory services to be added to the list of factories used to process Tunables.
addTunableRecorder(TunableRecorder, Map) - Method in class org.cytoscape.work.AbstractTaskManager: Adds the specified TunableRecorder service to the task manager.
addValueEditor(ValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Add value editor OSGi services.
addVirtualColumn(String, String, CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable: Adds a "virtual" column to the the current table.
addVirtualColumns(CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable: Adds all columns in another table as "virtual" columns to the the current table.
addVisualMappingFunction(VisualMappingFunction<?, ?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Add a new VisualMappingFunction to this VisualStyle.
addVisualProperty(VisualProperty<?>, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Insert a VisualProperty to the tree.
addVisualPropertyDependency(VisualPropertyDependency<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Add a new VisualPropertyDependency.
addVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Add a new VisualStyle to this manager.
adjustColumnPreferredWidths(JTable) - Static method in class org.cytoscape.util.swing.ColumnResizer: Adjust the columns in the table to their preferred widths.
aggregate(CyTable, CyGroup, CyColumn) - Method in interface org.cytoscape.group.data.Aggregator: Aggregate the column for the members of the specified group into the group.
Aggregator<T> - Interface in org.cytoscape.group.data: The Aggregator interface acts as a service interface for different methods of aggregating attribute data for the nodes in a CyGroup.
ALL_NODE_VIEWS - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithm: A convenience declaration for an empty set signifying that all node views should be laid out when creating the task iterator.
append(Task) - Method in class org.cytoscape.work.TaskIterator: Adds the given task to the end of this iterator.
append(TaskIterator) - Method in class org.cytoscape.work.TaskIterator: Adds the tasks in the given TaskIterator to the end of this iterator.
appFileListMap(Map<String, List<File>>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified app file list map.
The app name should follow the java class namespace convention (e.g.
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Apply mapping to the view model.
apply(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Apply Visual Style to the entire network view.
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Apply Visual Property values only to the given View Object (node or edge).
ApplyPreferredLayoutTaskFactory - Interface in org.cytoscape.task.visualize: This interface provides a task iterator for applying the preferred layout.
ApplyVisualStyleTaskFactory - Interface in org.cytoscape.task.visualize: Marker interface which provides a task iterator for applying a visual style to views.
ARBITRARY_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
ARBITRARY_STRING_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
ArgDescriptor - Class in org.cytoscape.equations: A class describing a function argument.
ArgDescriptor(ArgType, String, String) - Constructor for class org.cytoscape.equations.ArgDescriptor
ArgType - Enum in org.cytoscape.equations: An enum specifying a function argument type.
argTypesAreValid(Class[]) - Method in class org.cytoscape.equations.AbstractFunction: Returns true of false if the args passed in had arity of a type mismatch.
ARROW - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Pointy triangle shaped arrow
ArrowShape - Interface in org.cytoscape.view.presentation.property.values: Marker interface representing edge end shape (arrow).
ArrowShapeVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for ArrowShape values.
ArrowShapeVisualProperty(ArrowShape, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Constructor.
attribNameAsReference(String) - Static method in class org.cytoscape.equations.EquationUtil: Converts a bare name to a variable reference.
Attribute - Class in org.cytoscape.property.bookmark: Java class for anonymous complex type.
Attribute() - Constructor for class org.cytoscape.property.bookmark.Attribute
attribute - Variable in class org.cytoscape.property.bookmark.DataSource
AttributeHandlingType - Enum in org.cytoscape.group.data: The AttributeHandlingType enum contains the list of all of the different ways that attributes can be aggregated.
attrName - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: Mapping attribute name.
attrType - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: Type of attribute.

B

BasicCollapsiblePanel - Class in org.cytoscape.util.swing: A user-triggered collapsible panel containing the component (trigger) in the titled border
BasicCollapsiblePanel(JRadioButton) - Constructor for class org.cytoscape.util.swing.BasicCollapsiblePanel: Constructor for an option button controlled collapsible panel.
BasicCollapsiblePanel(String) - Constructor for class org.cytoscape.util.swing.BasicCollapsiblePanel: Constructor for a label/button controlled collapsible panel.
BasicCyFileFilter - Class in org.cytoscape.io: This is meant to be an basic implementation of CyFileFilter that can either be used directly or extended to provide different acceptance criteria.
BasicCyFileFilter(Set<String>, Set<String>, String, DataCategory, StreamUtil) - Constructor for class org.cytoscape.io.BasicCyFileFilter: Creates a file filter from the specified arguments.
BasicCyFileFilter(String[], String[], String, DataCategory, StreamUtil) - Constructor for class org.cytoscape.io.BasicCyFileFilter: Creates a file filter from the specified arguments.
BasicTunableHandlerFactory<T extends TunableHandler> - Class in org.cytoscape.work: A convenience implementation of TunableHandlerFactory that will construct a TunableHandler of the specified type given the TunableHandler in question has at least two constructors, one with Field, Object, Tunable parameters and the other with Method, Method, Object, Tunable parameters.
BasicTunableHandlerFactory(Class<T>, Class<?>...) - Constructor for class org.cytoscape.work.BasicTunableHandlerFactory: Constructor.
BasicVisualLexicon - Class in org.cytoscape.view.presentation.property: Basic Implementation of VisualLexicon.
BasicVisualLexicon(VisualProperty<NullDataType>) - Constructor for class org.cytoscape.view.presentation.property.BasicVisualLexicon: Constructor for VisualLexicon.
Bend - Interface in org.cytoscape.view.presentation.property.values: Definition of Edge Bends.
BendFactory - Interface in org.cytoscape.view.presentation.property.values: Factory to create an instance of Bend.
Bookmarks - Class in org.cytoscape.property.bookmark: Java class for anonymous complex type.
Bookmarks() - Constructor for class org.cytoscape.property.bookmark.Bookmarks
BookmarksUtil - Interface in org.cytoscape.property.bookmark: A set of utility methods to manipulate the bookmarks.
BooleanList - Class in org.cytoscape.equations: An convenience implementation of ArrayList<Boolean> that allows for strong type checking.
BooleanList(boolean...) - Constructor for class org.cytoscape.equations.BooleanList: Constructor.
BooleanVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Boolean values.
BooleanVisualProperty(Boolean, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.BooleanVisualProperty: Constructor.
BooleanVisualProperty(Boolean, String, String, Boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.BooleanVisualProperty: Constructor.
BoundaryRangeValues<T> - Class in org.cytoscape.view.vizmap.mappings: This class defines a data object representing the range values associated with a particular domain value, called a boundary value.
BoundaryRangeValues(T, T, T) - Constructor for class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
BoundaryRangeValues(BoundaryRangeValues<T>) - Constructor for class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
BoundedDouble - Class in org.cytoscape.work.util: A Double object which has low and up bounds
BoundedDouble(Double, Double, Double, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedDouble: Creates a new Bounded Double object.
BoundedFloat - Class in org.cytoscape.work.util: A Float object which has low and up bounds.
BoundedFloat(Float, Float, Float, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedFloat: Creates a new Bounded Float object.
BoundedInteger - Class in org.cytoscape.work.util: An Integer object which has low and up bounds.
BoundedInteger(Integer, Integer, Integer, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedInteger: Creates a new Bounded Integer object.
BoundedLong - Class in org.cytoscape.work.util: A Long object which has low and up bounds.
BoundedLong(Long, Long, Long, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedLong: Creates a new Bounded Long object.
build() - Method in class org.cytoscape.session.CySession.Builder: Returns a complete instance of CySession based upon the methods called on this instance of Builder.
buildConfiguration(Object) - Method in interface org.cytoscape.work.TunableMutator: Returns the configuration object used to mutate the tunables.
buildCyNetworkView(CyNetwork) - Method in interface org.cytoscape.io.read.CyNetworkReader: A method to build a CyNetworkView from one of the networks just read.

C

calcSampleVariance(double[]) - Static method in class org.cytoscape.equations.FunctionUtil: Calculates the sample variance of some numbers.
calculateEdgeWeights() - Method in class org.cytoscape.view.layout.LayoutPartition: Calculate and set the edge weights.
calculateHandleLocation(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.view.presentation.property.values.Handle: Calculate absolute position of this handle for the given edge view.
cancel() - Method in class org.cytoscape.work.AbstractTask: Calling this attempts to abort the current Task.
cancel() - Method in interface org.cytoscape.work.Task: This method is called by the TaskManager when the user chooses to cancel the Task.
cancelCellEditing() - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
cancelled - Variable in class org.cytoscape.work.AbstractTask: If this is true, we should abort whatever the Task is currently doing in the run() method.
category - Variable in class org.cytoscape.io.BasicCyFileFilter: Type of data that this filter applies to.
category - Variable in class org.cytoscape.property.bookmark.Bookmarks
Category - Class in org.cytoscape.property.bookmark: Java class for anonymous complex type.
Category() - Constructor for class org.cytoscape.property.bookmark.Category
categoryOrDataSource - Variable in class org.cytoscape.property.bookmark.Category
changeOccurred(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: This is called when a GUITunableHandler that this tunable handler listens to makes a change.
changeOccurred(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler: This is called when a GUITunableHandler that this tunable handler listens to makes a change.
CheckBoxJList - Class in org.cytoscape.util.swing: This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 By Joshua Marinacci, Chris Adamson
CheckBoxJList() - Constructor for class org.cytoscape.util.swing.CheckBoxJList: Creates a new CheckBoxJList object.
checkDependency(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: To check the dependencies of this GUITunableHandler with the others.
checkDependency(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler: To check the dependencies of this GUITunableHandler with the others.
CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Circle shaped arrow
clearValueLock(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View: Clear value lock for given VisualProperty.
CloneNetworkTaskFactory - Interface in org.cytoscape.task.create: This interface provides a task iterator for network cloning.
CodeAndSourceLocation - Class in org.cytoscape.equations: Encapsulates compiled code with the location in the original source equation.
CodeAndSourceLocation(Object, int) - Constructor for class org.cytoscape.equations.CodeAndSourceLocation
collapse(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Collapse this group in the designated network.
collapsed() - Method in class org.cytoscape.group.events.GroupCollapsedEvent: Is the group collapsed or expanded?
CollapseGroupTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator collapsing selection of nodes from a node view.
collapsing() - Method in class org.cytoscape.group.events.GroupAboutToCollapseEvent: Is the group collapsed or expanded?
column - Variable in class org.cytoscape.task.AbstractTableCellTask: The CyColumn of the CyTable cell
column - Variable in class org.cytoscape.task.AbstractTableColumnTask: The CyColumn that descendants will operate on.
ColumnCreatedEvent - Class in org.cytoscape.model.events: This event signals that a column has been created.
ColumnCreatedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnCreatedEvent: Constructs event.
ColumnCreatedListener - Interface in org.cytoscape.model.events: Listener for ColumnCreatedEvents.
ColumnDeletedEvent - Class in org.cytoscape.model.events: This event signals that a column has been deleted.
ColumnDeletedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnDeletedEvent: Constructs event.
ColumnDeletedListener - Interface in org.cytoscape.model.events: Listener for ColumnDeletedEvents.
columnName - Variable in class org.cytoscape.application.swing.AbstractViewUpdater: The name of the column that the RowsSetListener is provided for.
ColumnNameChangedEvent - Class in org.cytoscape.model.events: This event signals that a columns name has been changed.
ColumnNameChangedEvent(CyTable, String, String) - Constructor for class org.cytoscape.model.events.ColumnNameChangedEvent: Constructs event.
ColumnNameChangedListener - Interface in org.cytoscape.model.events: Listener for ColumnNameChangedEvents.
ColumnResizer - Class in org.cytoscape.util.swing: Automatically resize column based on the objects in the cell.
COMMAND - Static variable in interface org.cytoscape.work.ServiceProperties: Name of command used by Command Executor
COMMAND_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties: Name space for a command
compile(String, Map<String, Class<?>>) - Method in interface org.cytoscape.equations.EquationCompiler: Compiles a string to byte code plus some metadata as encapsulated by the Equation class
ConnectSelectedNodesTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for connecting selected nodes.
containsBookmarks(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Check if a bookmark is in the bookmarks.
containsEdge(CyEdge) - Method in interface org.cytoscape.model.CyNetwork: Determine if this CyNetwork contains a particular edge.
containsEdge(CyNode, CyNode) - Method in interface org.cytoscape.model.CyNetwork: Determine if this CyNetwork contains an edge between two nodes.
containsNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns true if the network to be checked is a subnetwork of this root network and returns false otherwise.
containsNode(CyNode) - Method in interface org.cytoscape.model.CyNetwork: Determine if this CyNetwork contains a particular node.
ContainsTunables - Annotation Type in org.cytoscape.work: An annotation designed to signal that the annotated field contains fields and methods that are annotated with the Tunable annotation.
content - Variable in class org.cytoscape.property.bookmark.Attribute
contentTypes - Variable in class org.cytoscape.io.BasicCyFileFilter
CONTINUOUS - Static variable in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: A label string for this mapping.
ContinuousEditorType - Enum in org.cytoscape.view.vizmap.gui.editor: An enum describing the possible types of continuous editors.
ContinuousMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings: An interface describing a continuous mapping from attribute value to visual property.
ContinuousMappingEditor<K extends Number,V> - Interface in org.cytoscape.view.vizmap.gui.editor: A basic interface used to display continuous mapping editors.
ContinuousMappingPoint<K,V> - Class in org.cytoscape.view.vizmap.mappings: Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(K, BoundaryRangeValues<V>) - Constructor for class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Constructor.
ContinuousRange<T> - Class in org.cytoscape.view.model: Defines a continuous range of values for VisualPropertys.
ContinuousRange(Class<T>, T, T, Boolean, Boolean) - Constructor for class org.cytoscape.view.model.ContinuousRange: Constructs this ContinuousRange.
continuousTableCellRenderer - Variable in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor: The cell renderer for continuous mappings.
controlsMutuallyExclusiveNestedChildren() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
controlsMutuallyExclusiveNestedChildren() - Method in interface org.cytoscape.work.TunableHandler: Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
CORE_PROPRERTY_NAME - Static variable in class org.cytoscape.property.SimpleCyProperty: Core Cytoscape Property (Cytoscape System Property)
countMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable: Returns the number of rows with the in the specified column with the specified value.
createAttribute() - Method in class org.cytoscape.property.bookmark.ObjectFactory: Create an instance of Attribute
createBend() - Method in interface org.cytoscape.view.presentation.property.values.BendFactory: Creates an instance of edge bend.
createBookmarks() - Method in class org.cytoscape.property.bookmark.ObjectFactory: Create an instance of Bookmarks
createCategory() - Method in class org.cytoscape.property.bookmark.ObjectFactory: Create an instance of Category
createColumn(String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type.
createColumn(String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type.
createDataSource() - Method in class org.cytoscape.property.bookmark.ObjectFactory: Create an instance of DataSource
createDescription(String) - Method in class org.cytoscape.property.bookmark.ObjectFactory: Create an instance of JAXBElement<String>}
createGroup(CyNetwork, boolean) - Method in interface org.cytoscape.group.CyGroupFactory: Creates a CyGroup object in the referenced network.
createGroup(CyNetwork, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory: Creates a CyGroup object in the referenced network initially populated with the supplied nodes.
createGroup(CyNetwork, CyNode, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory: Creates a CyGroup object in the referenced network from an existing CyNode.
createGroup(CyNetwork, CyNode, boolean) - Method in interface org.cytoscape.group.CyGroupFactory: Creates a CyGroup object in the referenced network from an existing CyNode.
createHandle(double, double) - Method in interface org.cytoscape.view.presentation.property.values.HandleFactory: Creates a new instance of the Handle.
createIcon(VisualProperty<V>, V, int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine: Create Icon object for the given VisualProperty value.
createImage(int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine: Render an Image object from current visualization.
createLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
createLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns a new layout context object.
createListColumn(String, Class<T>, boolean) - Method in interface org.cytoscape.model.CyTable: Create a column of Lists with the specified name and the specified element type.
createListColumn(String, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable: Create a column of Lists with the specified name and the specified element type.
createMenuItem(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.application.swing.CyEdgeViewContextMenuFactory: This method should return a CyMenuItem to be added to the context menu of the specified edge view.
createMenuItem(CyNetworkView, View<CyNode>) - Method in interface org.cytoscape.application.swing.CyNodeViewContextMenuFactory: This method should return a CyMenuItem to be added to the context menu of the specified node view.
createNetwork() - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object.
createNetworkView(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewFactory: Create a CyNetworkView from a CyNetwork object.
createNetworkView(CyNetwork, Boolean) - Method in interface org.cytoscape.view.model.CyNetworkViewFactory: Creates view with or without using viewThreshold property.
CreateNetworkViewTaskFactory - Interface in org.cytoscape.task.create: This interface provides a task iterator for creating network views.
createNetworkWithPrivateTables() - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object where the associated default tables are private.
createNewEmptyNetworkView() - Method in interface org.cytoscape.task.create.NewEmptyNetworkViewFactory: Returns a new, empty CyNetworkView.
createPrintable() - Method in interface org.cytoscape.view.presentation.RenderingEngine: For export image function.
createRenderingEngine(Object, View<T>) - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory: A view model can have multiple presentations.
createTable(String, String, Class<?>, boolean, boolean, CyTableFactory.InitialTableSize) - Method in interface org.cytoscape.model.CyTableFactory: Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTable(String, String, Class<?>, boolean, boolean) - Method in interface org.cytoscape.model.CyTableFactory: Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTaskIterator(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory: Sets the input stream that will be read by the Reader created from this factory.
createTaskIterator(Object) - Method in interface org.cytoscape.io.webservice.WebServiceClient: Set query for the tasks to be executed.
createTaskIterator(boolean) - Method in interface org.cytoscape.task.create.NewSessionTaskFactory: Creates a task iterator for creating a new session and destroying the current session based on the input.
createTaskIterator(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory: Creates a new TaskIterator using the given edge view and network view.
createTaskIterator(CyNetwork, String) - Method in interface org.cytoscape.task.edit.EditNetworkTitleTaskFactory: Creates a task iterator for editing a network's title.
createTaskIterator(CyTable, CyTable) - Method in interface org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory: Creates a task iterator for mapping a selected global table to a selected local table.
createTaskIterator(CyTable, String) - Method in interface org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory
createTaskIterator(CyColumn, String) - Method in interface org.cytoscape.task.edit.RenameColumnTaskFactory: Create a task iterator for renaming a selected column.
createTaskIterator(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory: Provisions this factory with the collection of networks that will be passed into any task created by it.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory: Provisions this factory with the CyNetwork that will be passed into any task created by it.
createTaskIterator(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory: Provisions this factory with the collection of network views that will be passed into any task created by it.
createTaskIterator(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory: Creates a task iterator using the specified network view and points.
createTaskIterator(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory: Creates a new TaskIterator using the given CyNetworkView
createTaskIterator(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory: Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadTableFileTaskFactory: Creates the task iterator for loading an attribute file to a table.
createTaskIterator(URL) - Method in interface org.cytoscape.task.read.LoadTableURLTaskFactory: Creates a task iterator for loading an attribute URL to the global table.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory: Creates a task iterator for loading files into visual styles.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory: Creates a task iterator for loading a session from a file.
createTaskIterator(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory: Provisions this factory with the CyRow that will be passed into any task created by it.
createTaskIterator(CyNetwork, File) - Method in interface org.cytoscape.task.select.SelectFromFileListTaskFactory: Creates a task iterator for selecting items of a network based on a file.
createTaskIterator(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory: Used to provision this factory with a CyColumn and a primary key that will be used to create tasks.
createTaskIterator(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory: Used to provision this factory with a CyColumn that will be used to create tasks.
createTaskIterator(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory: Used to provision this factory with a CyTable that will be used to create tasks.
createTaskIterator(CyNetworkView, File) - Method in interface org.cytoscape.task.write.ExportNetworkViewTaskFactory: Creates the task iterator for exporting network views.
createTaskIterator(CyTable, File) - Method in interface org.cytoscape.task.write.ExportTableTaskFactory: Returns a task factory that write the specified table to the specified file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.SaveSessionAsTaskFactory: Creates a task iterator for saving the session in a specified file.
createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Creates a task iterator containing the layout tasks.
createTaskIterator() - Method in interface org.cytoscape.work.TaskFactory: Returns an iterator returning a sequence of Tasks.
createTaskIterator(TaskIterator, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter: This method takes as input a TaskIterator and a map of tunable names to tunable values and applies those values to any tunables found in the Tasks found in the TaskIterator.
createTunableHandler(Field, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
createTunableHandler(Method, Method, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
createTunableHandler(Field, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory: This method returns a TunableHandler for a Field annotated as a Tunable if this factory can produce an appropriate handler for this type of field.
createTunableHandler(Method, Method, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory: This method returns a TunableHandler for a Method annotated as a Tunable if this factory can produce an appropriate handler for this type of field.
createVisualMappingFunction(String, Class<K>, CyTable, VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory: Create a new VisualMappingFunction.
createVisualPropertyDependency() - Method in interface org.cytoscape.view.vizmap.VisualPropertyDependencyFactory
createVisualStyle(String) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory: Create a new VisualStyle.
createVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory: Create a copy of given VisualStyle.
createWriter(OutputStream, CyNetworkView) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory: Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, CyNetwork) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory: Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, Object) - Method in interface org.cytoscape.io.write.CyPropertyWriterFactory: Creates a single Task that will write the specified property object to the specified OutputStream.
createWriter(OutputStream, CySession) - Method in interface org.cytoscape.io.write.CySessionWriterFactory: Creates a single Task that will write the specified CySession object to the specified OutputStream.
createWriter(OutputStream, CyTable) - Method in interface org.cytoscape.io.write.CyTableWriterFactory: Creates a single Task that will write the specified CyTable object to the specified OutputStream.
createWriter(OutputStream, RenderingEngine<?>) - Method in interface org.cytoscape.io.write.PresentationWriterFactory: Creates a single Task that will write the contents of the specified RenderingEngine object to the specified OutputStream.
createWriter(OutputStream, Set<VisualStyle>) - Method in interface org.cytoscape.io.write.VizmapWriterFactory: Creates a single Task that will write the specified set of VisualStyle objects to the specified OutputStream.
creatTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory: Create a task iterator for loading a network from a file.
creatTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportVizmapTaskFactory: Creates a task iterator for exporting the vizmap file.
current_size - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Partition size used for taskMonitor.
current_start - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Starting node number used for taskMonitor.
CUSTOM - Static variable in interface org.cytoscape.util.swing.FileUtil: Equal to FileDialog.LOAD + FileDialog.SAVE.
CyAction - Interface in org.cytoscape.application.swing: An interface that describes how an action should be placed within the menus and/or toolbars of the Swing application.
CyAppAdapter - Interface in org.cytoscape.app: A Java-only api providing access to Cytoscape functionality.
CyApplicationConfiguration - Interface in org.cytoscape.application: Application-wide setting will be accessible through this interface.
CyApplicationManager - Interface in org.cytoscape.application: Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.
CyColorChooser - Class in org.cytoscape.util.swing: This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColumn - Interface in org.cytoscape.model: This class describes a column in a CyTable.
CyEdge - Interface in org.cytoscape.model: An object that represents an edge within a network of nodes (vertices) and edges.
CyEdge.Type - Enum in org.cytoscape.model: The Type enum is used by methods in CyNetwork to restrict the edges that match a query.
CyEdgeViewContextMenuFactory - Interface in org.cytoscape.application.swing: A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified edge view.
CyEvent<T> - Interface in org.cytoscape.event: All Cytoscape events should extend this interface.
CyEventHelper - Interface in org.cytoscape.event: The basic event handling interface for Cytoscape.
CyFileFilter - Interface in org.cytoscape.io: An interface that captures the metadata description of a file type so that files of the specified type can be handled correctly by the application and the user interface.
CyFileFilterProvider - Interface in org.cytoscape.io: An interface extended by various reader and writer factories.
CyGroup - Interface in org.cytoscape.group: An object that represents a group of nodes and edges.
CyGroupAggregationManager - Interface in org.cytoscape.group.data: The CyGroupAggregationManager provides a mechanism to add new Aggregators to the group aggregation mechanism.
CyGroupFactory - Interface in org.cytoscape.group: An interface describing a factory used for creating CyGroup objects.
CyGroupManager - Interface in org.cytoscape.group: The CyGroupManager maintains information about all of the groups an instance of Cytoscape.
CyHelpBroker - Interface in org.cytoscape.application.swing: This interface provides access to the Cytoscape Help Broker and Help Set for managing the JavaHelp system.
CyIdentifiable - Interface in org.cytoscape.model: CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyLayoutAlgorithm - Interface in org.cytoscape.view.layout: A task factory specifically for layout algorithms.
CyLayoutAlgorithmManager - Interface in org.cytoscape.view.layout: This class provides access to the available layout algorithms.
CyListener - Interface in org.cytoscape.event: The basic interface that any class interested in a particular type of event should implement.
CyMenuItem - Class in org.cytoscape.application.swing: A simple wrapper class that allows a JMenuItem to be associated with a gravity value which defines where in a menu the item should fall.
CyMenuItem(JMenuItem, float) - Constructor for class org.cytoscape.application.swing.CyMenuItem: Constructor.
CyNetwork - Interface in org.cytoscape.model: CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNetworkFactory - Interface in org.cytoscape.model: A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager - Interface in org.cytoscape.model: Basic access to networks and view in an instance of Cytoscape.
CyNetworkNaming - Interface in org.cytoscape.session: A utility that helps with the creation of unique network names.
CyNetworkReader - Interface in org.cytoscape.io.read: An extension of the Task interface that returns an array of CyNetwork objects that are read as part of the Task.
CyNetworkReaderManager - Interface in org.cytoscape.io.read: An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyNetworkReader for the input.
CyNetworkTableManager - Interface in org.cytoscape.model: Provides access to all network-table relationships.
CyNetworkView - Interface in org.cytoscape.view.model: Additional methods for CyNetworkView.
CyNetworkViewFactory - Interface in org.cytoscape.view.model: Factory for CyNetworkView objects.
CyNetworkViewManager - Interface in org.cytoscape.view.model: Basic access to network views in an instance of Cytoscape.
CyNetworkViewWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a CyNetworkView or CyNetwork to be specified and written to an OutputStream.
CyNetworkViewWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing CyNetworkView objects.
CyNode - Interface in org.cytoscape.model: An object that represents a node (vertex) within a network of nodes and edges.
CyNodeViewContextMenuFactory - Interface in org.cytoscape.application.swing: A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified node view.
CyPayloadEvent<S,P> - Interface in org.cytoscape.event: An extension of CyEvent specifically for payload events.
CyProperty<P> - Interface in org.cytoscape.property: A general property service interface for providing access to different types of property objects as OSGi services.
CyProperty.SavePolicy - Enum in org.cytoscape.property: SavePolicy specifies how the CyProperty will be saved, or if it will not be saved.
CyPropertyReader - Interface in org.cytoscape.io.read: An extension of the Task interface that returns a property object.
CyPropertyReaderManager - Interface in org.cytoscape.io.read: An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyPropertyReader for the input.
CyPropertyWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a property Object to be specified and written.
CyPropertyWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing property objects.
CyRootNetwork - Interface in org.cytoscape.model.subnetwork: CyRootNetwork is an interface for managing Cytoscape's meta-network implementation.
CyRootNetworkManager - Interface in org.cytoscape.model.subnetwork: A manager that provides access to the CyRootNetwork objects associated with CyNetwork objects.
CyRow - Interface in org.cytoscape.model: This interface represents one row in a CyTable.
CyServiceRegistrar - Interface in org.cytoscape.service.util: An interface to hide the OSGi dependencies needed to register services dynamically at runtime.
CySession - Class in org.cytoscape.session: A session is an immutable snapshot of the data contents of Cytoscape.
CySession.Builder - Class in org.cytoscape.session: A implementation of the builder pattern used to construct immutable instances of CySession objects.
CySession.Builder() - Constructor for class org.cytoscape.session.CySession.Builder
CySessionManager - Interface in org.cytoscape.session: This class primarily acts as a listener and tracks the state of the Cytoscape application.
CySessionReader - Interface in org.cytoscape.io.read: An extension of the Task interface that returns a org.cytoscape.property.session.Cysession object.
CySessionReaderManager - Interface in org.cytoscape.io.read: An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CySessionReader for the input.
CySessionWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a CySession to be specified and written.
CySessionWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing CySession objects.
CyShutdown - Interface in org.cytoscape.application: A service that will shutdown Cytoscape cleanly.
CyShutdownEvent - Class in org.cytoscape.application.events: An event fired immediately before Cytoscape will be shutdown.
CyShutdownEvent(Object) - Constructor for class org.cytoscape.application.events.CyShutdownEvent: Constructor.
CyShutdownListener - Interface in org.cytoscape.application.events: The listener for the CyShutdownEvent.
CyStartEvent - Class in org.cytoscape.application.events: An event fired after Cytoscape startup mostly complete (but not necessarily 100 percent).
CyStartEvent(Object) - Constructor for class org.cytoscape.application.events.CyStartEvent: Constructor.
CyStartListener - Interface in org.cytoscape.application.events: The listener for the CyStartEvent.
CySubNetwork - Interface in org.cytoscape.model.subnetwork: A CySubNetwork is a CyNetwork that is contained within a parent CyNetwork.
CySwingAppAdapter - Interface in org.cytoscape.app.swing: A Swing-specific extension of CyAppAdapter that serves as a Java-only api providing access to core Cytoscape functionality.
CySwingApplication - Interface in org.cytoscape.application.swing: This interface provides basic access to the Swing objects that constitute this application.
CyTable - Interface in org.cytoscape.model: A simple representation of a table object consisting of rows and columns.
CyTable.Mutability - Enum in org.cytoscape.model: Mutability of the table specifies whether or not it is able to be deleted..
CyTable.SavePolicy - Enum in org.cytoscape.model: The SavePolicy of a table specifies whether or not it will be saved.
CyTableFactory - Interface in org.cytoscape.model: An interface describing a factory used for creating CyTable objects.
CyTableFactory.InitialTableSize - Enum in org.cytoscape.model: A description of the initial size of the table.
CyTableManager - Interface in org.cytoscape.model: A singleton object that provides access to the available tables in the system.
CyTableMetadata - Interface in org.cytoscape.model: A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.
CyTableReader - Interface in org.cytoscape.io.read: An extension of the Task interface that returns an array of CyTable objects.
CyTableReaderManager - Interface in org.cytoscape.io.read: An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyTableReader for the input.
CyTableUtil - Class in org.cytoscape.model: A collection of state-less, static utility methods provided to simplify querying of table objects.
CyTableWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a CyTable to be specified and written.
CyTableWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing CyTable objects.
CytoPanel - Interface in org.cytoscape.application.swing: Interface to a CytoPanel.
CytoPanelComponent - Interface in org.cytoscape.application.swing: An interface that allows a component to be registered as a service that will then be added to the appropriate CytoPanel.
CytoPanelComponentSelectedEvent - Class in org.cytoscape.application.swing.events: The event fired to indicate that a CytoPanelComponent has been selected.
CytoPanelComponentSelectedEvent(Object, CytoPanel, int) - Constructor for class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent: Constructor.
CytoPanelComponentSelectedListener - Interface in org.cytoscape.application.swing.events: The listener for handling CytoPanelComponentSelectedEvent.
CytoPanelName - Enum in org.cytoscape.application.swing: An enum that describes CytoPanels uses compass directions to describe their location within the application.
CytoPanelState - Enum in org.cytoscape.application.swing: The different display states available for a CytoPanel.
CytoPanelStateChangedEvent - Class in org.cytoscape.application.swing.events: An event to indicate that a CytoPanel has changed state.
CytoPanelStateChangedEvent(Object, CytoPanel, CytoPanelState) - Constructor for class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent: Constructor.
CytoPanelStateChangedListener - Interface in org.cytoscape.application.swing.events: A listener for handling CytoPanelStateChangedEvents.
CyVersion - Interface in org.cytoscape.application: An interface providing access to version information about this version of the Cytoscape application.
CyWriter - Interface in org.cytoscape.io.write: A marker interface used to identify tasks involved in writing data.
CyWriterFactory - Interface in org.cytoscape.io.write: A marker interface used to identify factories that create CyWriter instances.
CyWriterManager<W extends CyWriterFactory> - Interface in org.cytoscape.io.write: A CyWriterManager aggregates CyWriterFactory services for specific DataCategories and provides a mechanism for choosing the CyWriterFactory given a particular file type.

D

DASH_DOT - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Dash space dot space dash, etc.
DataCategory - Enum in org.cytoscape.io: An enum that captures the types of data the IO package can read and write.
DataImportFinishedEvent<T> - Class in org.cytoscape.io.webservice.events: An event indicating that data has been successfully imported.
DataImportFinishedEvent(WebServiceClient, T) - Constructor for class org.cytoscape.io.webservice.events.DataImportFinishedEvent: Constructs the event.
DataImportFinishedListener - Interface in org.cytoscape.io.webservice.events: Listener for DataImportFinishedEvent.
DataSource - Interface in org.cytoscape.io.datasource: Immutable data source object, which represents one data file associated with an URL.
DataSource - Class in org.cytoscape.property.bookmark: Java class for anonymous complex type.
DataSource() - Constructor for class org.cytoscape.property.bookmark.DataSource
DataSourceManager - Interface in org.cytoscape.io.datasource: Entry point to access all data sources implemented as OSGi services.
decrement(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Decrement the location of this node by (x,y).
decrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Decrement the displacement recorded for this node by (x,y).
DEF_WEB_BROWSER_PROP_NAME - Static variable in interface org.cytoscape.util.swing.OpenBrowser: The name of a property for a Properties object used to define an alternative web browser command.
DEFAULT_ATTRS - Static variable in interface org.cytoscape.model.CyNetwork: The name of the default public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
DEFAULT_EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: The default edge bend.
DEFAULT_LAYOUT_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: The name of the default layout.
DEFAULT_LAYOUT_PROPERTY_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: The name of the default layout property.
DEFAULT_PAYLOAD_INTERVAL_MILLIS - Static variable in interface org.cytoscape.event.CyEventHelper: The default number of milliseconds to wait before the next time that we will check for payload events to fire.
DEFAULT_PROPS_CONFIG_DIR - Static variable in interface org.cytoscape.property.CyProperty: The name of the default directory where we will look for properties files.
DefaultDataSource - Class in org.cytoscape.io.datasource: Basic implementation of DataSource.
DefaultDataSource(String, String, String, DataCategory, URL) - Constructor for class org.cytoscape.io.datasource.DefaultDataSource: Constructor for the default data source.
defaultEdgeWeight - Variable in class org.cytoscape.view.layout.EdgeWeighter
DefaultViewEditor - Interface in org.cytoscape.view.vizmap.gui: Default View Editor is the component to display available visual properties and its default view for given Visual Style.
DefaultViewPanel - Interface in org.cytoscape.view.vizmap.gui: GUI component to display default appearance of current Visual Style.
DefaultVisualizableVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property to represent abstract concept such as Node or Edge.
DefaultVisualizableVisualProperty(String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty
defineHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.Handle: Define this handle.
delayedFireTableDataChanged() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Invokes fireTableDataChanged after all the pending events have been processed.
deleteBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Delete a bookmark (pDataSource) from the category (pCategoryName) in the bookmarks object (pBookmarks)
deleteColumn(String) - Method in interface org.cytoscape.model.CyTable: Will delete the column of the specified name.
DeleteColumnTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting a column.
DeleteSelectedNodesAndEdgesTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting selected nodes and edges.
deleteTable(long) - Method in interface org.cytoscape.model.CyTableManager: Deletes a mutable table.
DeleteTableTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting a table.
DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Triangle shaped arrow
dependsOn() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the dependsOn property of the associated Tunable.
dependsOn() - Method in interface org.cytoscape.work.TunableHandler: Returns the dependsOn property of the associated Tunable.
description - Variable in class org.cytoscape.io.BasicCyFileFilter
description - Variable in class org.cytoscape.property.bookmark.Bookmarks
DeselectAllEdgesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for deselecting all of the edges.
DeselectAllNodesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for deselecting all of the nodes.
DeselectAllTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for deselecting all of the items.
destroyGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager: Destroy a group.
destroyNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager: Destroys a network.
DestroyNetworkTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for destruction of networks.
destroyNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Destroys a network view.
DestroyNetworkViewTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator that destroys a network view.
DialogTaskManager - Interface in org.cytoscape.work.swing: A specialization of TaskManager that creates a JDialog configuration object and expects the dialog parent to be a Window.
DIAMOND - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Diamond shaped arrow
DIAMOND - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Diamond shape.
DISCRETE - Static variable in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: A label string describing the mapping.
DiscreteMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings: An interface describing a discrete mapping from attribute value to visual property.
DiscreteMappingGenerator<V> - Interface in org.cytoscape.view.vizmap.gui.util: Generates Discrete mapping for a set of attribute values and a Visual Property.
DiscreteRange<T> - Class in org.cytoscape.view.model: Defines a discrete range of values for VisualPropertys.
DiscreteRange(Class<T>, Set<T>) - Constructor for class org.cytoscape.view.model.DiscreteRange: Constructor for this DiscreteRange.
discreteTableCellRenderer - Variable in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor: The cell renderer for discrete mappings.
distance(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance between this node and another node
distance(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance between this node and a location
doLayout(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractLayoutTask: This method is designed to actually encapsulate the layout algorithm.
doLayout(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.
DOT - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Dot space dot, etc.
DoubleList - Class in org.cytoscape.equations: An convenience implementation of ArrayList<Double> that allows for strong type checking.
DoubleList(double...) - Constructor for class org.cytoscape.equations.DoubleList: Constructor.
doubleToLong(double) - Static method in class org.cytoscape.equations.EquationUtil: Checked conversion of a double to a long following the Excel™ rules.
DoubleVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Double values.
DoubleVisualProperty(Double, Range<Double>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DoubleVisualProperty: Constructor.
DoubleVisualProperty(Double, Range<Double>, String, String, boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DoubleVisualProperty: Constructor.
drawIcon(int, int, boolean) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingEditor: Returns an icon representing this editor for use in a user interface.
DropDownMenuButton - Class in org.cytoscape.util.swing: Button with drop down menu.
DropDownMenuButton(AbstractAction) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton: Creates a new DropDownMenuButton object.
DynamicSubmenuListener - Interface in org.cytoscape.work.swing: An extension of MenuListener that is used to describe dynamic submenus.

E

EDGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_SOURCE_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_STROKE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_STROKE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_TARGET_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EdgeBendVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Edge Bend values.
EdgeBendVisualProperty(Bend, String, String) - Constructor for class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: Constructor.
edgeCount() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the number of edges in this partition
edgeIterator() - Method in class org.cytoscape.view.layout.LayoutPartition: Return an iterator over all of the LayoutEdges in this partition
edgeView - Variable in class org.cytoscape.task.AbstractEdgeViewTask: The edge view that descendant tasks will operate on.
EdgeViewTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified View<CyEdge> within the specified CyNetworkView.
edgeWeighter - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: The EdgeWeighter used for edge weight calculations.
EdgeWeighter - Class in org.cytoscape.view.layout: The EdgeWeighter class.
EdgeWeighter() - Constructor for class org.cytoscape.view.layout.EdgeWeighter
EditNetworkTitleTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for editing a network's title.
EDITOR_WINDOW_CLOSED - Static variable in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Tell vizMapper main which editor is disabled/enabled.
EDITOR_WINDOW_OPENED - Static variable in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Editor window state
EditorManager - Interface in org.cytoscape.view.vizmap.gui.editor: Manages all editor objects for the VizMap GUI.
ELLIPSE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Ellipse shape.
ENABLE_FOR - Static variable in interface org.cytoscape.work.ServiceProperties: Action should be enabled or disabled by states if this property is set
ENABLE_FOR_NETWORK - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when at least one network exists.
ENABLE_FOR_NETWORK_AND_VIEW - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when at least one network WITH view exists.
ENABLE_FOR_NETWORK_WITHOUT_VIEW - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when at least one network with NO view exists.
ENABLE_FOR_SELECTED_EDGES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when edges have been selected in a network.
ENABLE_FOR_SELECTED_NODES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when nodes have been selected in a network.
ENABLE_FOR_SELECTED_NODES_OR_EDGES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when either nodes or edges have been selected in a network.
ENABLE_FOR_TABLE - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when at least one network exists.
EQUAL_DASH - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Equal dash and space
equals(Object) - Method in class org.cytoscape.equations.Equation: Compares one Equation to another.
equals(Object) - Method in class org.cytoscape.util.swing.FileChooserFilter
equalValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Will be used when the domain value is exactly equal to the associated boundary domain value
Equation - Class in org.cytoscape.equations: The class representing an equation.
Equation(String, Set<String>, Map<String, Object>, Object[], int[], Class<?>) - Constructor for class org.cytoscape.equations.Equation: Constructs an Equation.
EquationCompiler - Interface in org.cytoscape.equations: Compiler that compiles equations to byte (non-Java) code.
EquationParser - Interface in org.cytoscape.equations: Parser for a string representing an equation.
EquationUtil - Class in org.cytoscape.equations: Various static utility methods relating to equations.
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.AbstractFunction: Used to invoke this function.
evaluateFunction(Object[]) - Method in interface org.cytoscape.equations.Function: Used to invoke this function.
execute(Equation, Map<String, IdentDescriptor>) - Method in interface org.cytoscape.equations.Interpreter: Executes the code represented by "equation".
execute(TaskIterator) - Method in interface org.cytoscape.work.TaskManager: This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
executionContext - Variable in class org.cytoscape.work.AbstractTaskManager: The execution context of the task manager.
exit(int) - Method in interface org.cytoscape.application.CyShutdown: Calling this method indicates that the application should shutdown.
expand(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Expand this group in the designated network.
ExpandGroupTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator expanding a group from a node view.
ExportNetworkImageTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting networks as image.
ExportNetworkViewTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting network views.
ExportSelectedTableTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting the current table.
ExportTableTaskFactory - Interface in org.cytoscape.task.write: This task factory provides a task iterator for writing a specified table to a specified file.
ExportVizmapTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting the vizmap visual style.
extensions - Variable in class org.cytoscape.io.BasicCyFileFilter

F

FileChooserFilter - Class in org.cytoscape.util.swing: Used to hold extension(s) of acceptable file types and a short description of them.
FileChooserFilter(String, String) - Constructor for class org.cytoscape.util.swing.FileChooserFilter: Construct this FileChooserFilter using one acceptable file type extension.
FileChooserFilter(String, String[]) - Constructor for class org.cytoscape.util.swing.FileChooserFilter: Construct this FileChooserFilter using multiple acceptable file type extensions.
FileUtil - Interface in org.cytoscape.util.swing: Provides a platform-dependent way to open files.
fireEditingCanceled() - Method in class org.cytoscape.util.swing.AbstractCellEditor: Notify all listeners that have registered interest for notification on this event type.
fireEditingStopped() - Method in class org.cytoscape.util.swing.AbstractCellEditor: Notify all listeners that have registered interest for notification on this event type.
fireEvent(E) - Method in interface org.cytoscape.event.CyEventHelper: Calls each listener found in the Service Registry identified by the listenerClass interface by the supplied CyEvent.
fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Notify all listeners that have registered interest for notification on this event type.
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Notify all listeners that have registered interest for notification on this event type.
fitContent() - Method in interface org.cytoscape.view.model.CyNetworkView: Utility method to fit content to the presentation container (usually a Swing Window).
FitContentEvent - Class in org.cytoscape.view.model.events: Fit network visualization to the given container.
FitContentEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitContentEvent: Fit the size of network view to the current container.
FitContentListener - Interface in org.cytoscape.view.model.events: Listener for FitContentEvent.
fitSelected() - Method in interface org.cytoscape.view.model.CyNetworkView: Utility method to fit selected graph objects to the presentation container.
FitSelectedEvent - Class in org.cytoscape.view.model.events: Fit only selected graph object views to the container.
FitSelectedEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitSelectedEvent: Fit the selected part of network view to the container.
FitSelectedListener - Interface in org.cytoscape.view.model.events: Listener for FitSelectedEvent.
fixEdges() - Method in class org.cytoscape.view.layout.LayoutPartition: Convenience routine to update the source and target for all of the edges in a partition.
flushPayloadEvents() - Method in interface org.cytoscape.event.CyEventHelper: Forces accumulated payload events to be fired.
FontVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Font values.
FontVisualProperty(Font, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.FontVisualProperty: Constructor.
format - Variable in class org.cytoscape.property.bookmark.DataSource
Function - Interface in org.cytoscape.equations: The basic description of a Function.
FunctionError - Exception in org.cytoscape.equations: A class describing an error in a function.
FunctionError(String, int) - Constructor for exception org.cytoscape.equations.FunctionError: Constructor.
FunctionUtil - Class in org.cytoscape.equations: A collection of static methods that may be useful for the implementation of built-in functions.

G

genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.AbstractNode
genCode(Stack<CodeAndSourceLocation>) - Method in interface org.cytoscape.equations.TreeNode: Generated code for this node and pushes it onto the execution stack.
generateMap(Set<T>) - Method in interface org.cytoscape.view.vizmap.gui.util.DiscreteMappingGenerator: For a given set of attribute values, create discrete mapping.
get(String, Class<? extends T>) - Method in interface org.cytoscape.model.CyRow: Returns the value found for this row in the specified column with the specified type.
get(String, Class<? extends T>, T) - Method in interface org.cytoscape.model.CyRow: Returns the value found for this row in the specified column with the specified type.
get_ApplyPreferredLayoutTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ApplyPreferredLayoutTaskFactory.
get_ApplyVisualStyleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ApplyVisualStyleTaskFactory.
get_CloneNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CloneNetworkTaskFactory.
get_CollapseGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CollapseGroupTaskFactory.
get_ConnectSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ConnectSelectedNodesTaskFactory.
get_CreateNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CreateNetworkViewTaskFactory.
get_DeleteColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeleteColumnTaskFactory.
get_DeleteSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeleteSelectedNodesAndEdgesTaskFactory.
get_DeleteTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeleteTableTaskFactory.
get_DeselectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeselectAllEdgesTaskFactory.
get_DeselectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeselectAllNodesTaskFactory.
get_DeselectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DeselectAllTaskFactory.
get_DestroyNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DestroyNetworkTaskFactory.
get_DestroyNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DestroyNetworkViewTaskFactory.
get_EditNetworkTitleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of EditNetworkTitleTaskFactory.
get_ExpandGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExpandGroupTaskFactory.
get_ExportNetworkImageTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExportNetworkImageTaskFactory.
get_ExportNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExportNetworkViewTaskFactory.
get_ExportSelectedTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExportSelectedTableTaskFactory.
get_ExportTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExportTableTaskFactory.
get_ExportVizmapTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of ExportVizmapTaskFactory.
get_GroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of GroupNodesTaskFactory.
get_HideSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of HideSelectedEdgesTaskFactory.
get_HideSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of HideSelectedNodesTaskFactory.
get_HideSelectedTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of HideSelectedTaskFactory.
get_InvertSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of InvertSelectedEdgesTaskFactory.
get_InvertSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of InvertSelectedNodesTaskFactory.
get_LoadNetworkFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of LoadNetworkFileTaskFactory.
get_LoadNetworkURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of LoadNetworkURLTaskFactory.
get_LoadTableFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of LoadTableFileTaskFactory.
get_LoadTableURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of LoadTableURLTaskFactory.
get_LoadVizmapFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of LoadVizmapFileTaskFactory.
get_MapGlobalToLocalTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of MapGlobalToLocalTableTaskFactory.
get_MapTableToNetworkTablesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of MapTableToNetworkTablesTaskFactory.
get_NewEmptyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of NewEmptyNetworkViewFactory.
get_NewNetworkSelectedNodesAndEdgesTaskFatory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of NewNetworkSelectedNodesAndEdgesTaskFatory.
get_NewNetworkSelectedNodesOnlyTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of NewNetworkSelectedNodesOnlyTaskFactory.
get_NewSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of NewSessionTaskFactory.
get_OpenSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of OpenSessionTaskFactory.
get_RenameColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of RenameColumnTaskFactory.
get_SaveSessionAsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SaveSessionAsTaskFactory.
get_SelectAdjacentEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectAdjacentEdgesTaskFactory.
get_SelectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectAllEdgesTaskFactory.
get_SelectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectAllNodesTaskFactory.
get_SelectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectAllTaskFactory.
get_SelectConnectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectConnectedNodesTaskFactory.
get_SelectFirstNeighborsNodeViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectFirstNeighborsNodeViewTaskFactory.
get_SelectFirstNeighborsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryInEdge() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryOutEdge() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFromFileListTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of SelectFromFileListTaskFactory.
get_UnGroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UnGroupNodesTaskFactory.
get_UnGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UnGroupTaskFactory.
get_UnHideAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UnHideAllEdgesTaskFactory.
get_UnHideAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UnHideAllNodesTaskFactory.
get_UnHideAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UnHideAllTaskFactory.
getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction: Returns the accelerator KeyStroke defined for this action.
getAcceleratorKeyStroke() - Method in interface org.cytoscape.application.swing.CyAction: Returns the accelerator KeyStroke defined for this action.
getAdjacentEdgeIterable(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Gets an Iteable of edges that connect to this node.
getAdjacentEdgeList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Get the list of edges that connect to this node.
getAggregators(Class) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators for a particular Class.
getAggregators() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators.
getAll() - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: Gets all map values.
getAllDataSources() - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data sources registered as OSGi services
getAllDescendants(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon: Get collection of visual properties for a given object type (node/edge/network).
getAllDescendants(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getAllHandles() - Method in interface org.cytoscape.view.presentation.property.values.Bend: Get List of all handles on this edge
getAllLayouts() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Returns a collection of all available layouts.
getAllPoints() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets all Data Points.
getAllRenderingEngines() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Get all RenderingEngines registered in this manager.
getAllRows() - Method in interface org.cytoscape.model.CyTable: Return a list of all the rows stored in this data table.
getAllTables(boolean) - Method in interface org.cytoscape.model.CyTableManager: Returns a Set of all tables with the specified visibility.
getAllValues() - Method in interface org.cytoscape.model.CyRow: Returns a map of column names to Objects that contain the values contained in this Row.
getAllViews() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a list of all View including those for Nodes, Edges, and Network.
getAllVisualLexicon() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Returns a Set of all VisualLexicons.
getAllVisualMappingFunctions() - Method in interface org.cytoscape.view.vizmap.VisualStyle: Returns all VisualMappingFunctions in this style.
getAllVisualProperties() - Method in interface org.cytoscape.view.model.VisualLexicon: Returns the Set of VisualPropertys supported by this Renderer.
getAllVisualProperties() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getAllVisualPropertyDependencies() - Method in interface org.cytoscape.view.vizmap.VisualStyle: Get all dependencies for this style.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Returns all available VisualStyles managed by this object.
getAppConfigurationDirectoryLocation(Class<?>) - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns the absolute path to the configuration directory of a particular app.
getAppFileListMap() - Method in class org.cytoscape.session.CySession: Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.
getAppFileListMap() - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent: This method is not meant to be used by listeners for this event, although you can and no harm should come to you.
getArgAsBoolean(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
getArgAsDouble(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgAsLong(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
getArgAsString(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
getArgName() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the name of the argument.
getArgNumber() - Method in exception org.cytoscape.equations.FunctionError: Returns the argument number the error is associated with.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
getAttribute(DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Given the attribute name, return the value in a bookmark
getAttribute() - Method in class org.cytoscape.property.bookmark.DataSource: Gets the value of the attribute property.
getAttributeSelectors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns set of selector for available attributes (table columns).
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyPropertyWriterManager: Returns the CyFileFilters known to this CyWriter manager.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyWriterManager: Returns a list of the available CyFileFilters that define the available output types.
getAverageLocation() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the average location of the nodes in this partition
getBaseNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: The initial network of CyNodes and CyEdges.
getBooleans(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of booleans.
getBugFixVersion() - Method in interface org.cytoscape.application.CyVersion: The third of the three numbers defining the version of the software, meaning "5" if the version is "3.2.5".
getCategory() - Method in class org.cytoscape.property.bookmark.Bookmarks: Gets the value of the category property.
getCategory(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Select specific category from a list of categories.
getCategoryOrDataSource() - Method in class org.cytoscape.property.bookmark.Category: Gets the value of the categoryOrDataSource property.
getCellEditors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns editors for individual cells in discrete mapping editor.
getCellEditorValue() - Method in class org.cytoscape.util.swing.AbstractCellEditor
getChangeSources() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChangeSources() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChildKey() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildKey() - Method in interface org.cytoscape.work.TunableHandler: Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildren() - Method in class org.cytoscape.view.model.VisualLexiconNode: Returns collection of all children of this node.
getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation
getCode() - Method in class org.cytoscape.equations.Equation: Returns the compiled code (not Java byte code!) for the VM representing this Equation.
getColumn(String) - Method in interface org.cytoscape.model.CyTable: Returns the type of a column for this table.
getColumn() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the name of the column of the data that was set.
getColumnClass(int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Returns the class of the column specified in the argument.
getColumnClass(int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the type for column number column.
getColumnClass(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the class of the column at the given column number.
getColumnCount() - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the number of available columns.
getColumnCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the number of columns in the TreeTabelModel.
getColumnName(int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the name for column number column.
getColumnName(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the column name at the given column number.
getColumnNames(CyTable) - Static method in class org.cytoscape.model.CyTableUtil: Returns all the column names of a given table.
getColumns() - Method in interface org.cytoscape.model.CyTable: Returns the column types for all columns in this table.
getCompatibleTypes() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the types that are compatible with this argument.
getCompatibleTypes() - Method in enum org.cytoscape.equations.ArgType: Returns an array of compatible Class types.
getComponent() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the Component to be added to the CytoPanel.
getComponent() - Method in interface org.cytoscape.application.swing.ToolBarComponent: Returns the Component to be added to the ToolBar.
getComponentAt(int) - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the component at index.
getConfiguration(TaskFactory, Object) - Method in interface org.cytoscape.work.TaskManager: Returns a configuration object generated from the Tunables read from the TaskFactory.
getConfigurationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns absolute path to .cytoscape location.
getConnectingEdgeList(CyNode, CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Get the list of edges that connect two nodes.
getContent() - Method in class org.cytoscape.property.bookmark.Attribute: Gets the value of the content property.
getContentPane() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: This class requires that all content be placed within a designated panel, this method returns that panel.
getContentTypes() - Method in class org.cytoscape.io.BasicCyFileFilter: The MIME content types supported by this filter.
getContentTypes() - Method in interface org.cytoscape.io.CyFileFilter: The MIME content types supported by this filter.
getContinuousEditor(VisualProperty<?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns the continuous editor for the specified visual property.
getContinuousEditorType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getContinuousEditorType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns type of Continuous Editor.
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: A custom cell renderer for Continuous table cells.
getCoreProperties() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyProperty of type Properties.
getCurrentNetwork() - Method in interface org.cytoscape.application.CyApplicationManager: Provides access to the current network.
getCurrentNetworkView() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the current network view.
getCurrentRenderingEngine() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the rendering engine associated with the current network view.
getCurrentSession() - Method in interface org.cytoscape.session.CySessionManager: This method returns a CySession object describing the current state of Cytoscape.
getCurrentSessionFileName() - Method in interface org.cytoscape.session.CySessionManager: Returns the name of the current session file.
getCurrentTable() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the currently active table.
getCurrentVisualStyle() - Method in interface org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager: Returns currently selected Visual Style.
getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyApplicationManager.
getCyEventHelper() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyEventHelper.
getCyGroupAggregationManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyGroupAggregationManager.
getCyGroupFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyGroupFactory.
getCyGroupManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyGroupManager.
getCyLayoutAlgorithmManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyLayoutAlgorithmManager.
getCyNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkFactory.
getCyNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkManager.
getCyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkViewFactory.
getCyNetworkViewManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkViewManager.
getCyNetworkViewReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkReaderManager.
getCyNetworkViewWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyNetworkViewWriterManager.
getCyPropertyReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyPropertyReaderManager.
getCyPropertyWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyPropertyWriterManager.
getCyRootNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyRootNetworkManager.
getCyServiceRegistrar() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyServiceRegistrar.
getCySessionManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CySessionManager.
getCySessionReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CySessionReaderManager.
getCySessionWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CySessionWriterManager.
getCySwingApplication() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Returns an instance of CySwingApplication.
getCyTableFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyTableFactory.
getCyTableManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyTableManager.
getCyTableReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyTableReaderManager.
getCyTableWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyTableWriterManager.
getCytoPanel(CytoPanelName) - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the appropriate CytoPanel for the specified compass direction.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent: Returns the CytoPanel on which a component was selected.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent: Returns the CytoPanel whose state has changed.
getCytoPanelComponentCount() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the number of components in the CytoPanel.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the position in the layout.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the name of the CytoPanel that this component should be added to.
getCyVersion() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of CyVersion.
getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter: The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.CyFileFilter: The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.datasource.DataSource: DataCategory of this data.
getDataCategory() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getDataSourceList(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Traverse bookmark tree and get a list of data sources from the specified category.
getDataSourceManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of DataSourceManager.
getDataSources(DataCategory) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data sources under the given category.
getDataSources(String) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data sources from a data provider
getDataTableComboBoxEditor(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Attribute selector for the given table entry type.
getDataType() - Method in interface org.cytoscape.view.vizmap.gui.util.DiscreteMappingGenerator: Returns the type of the visual property.
getDefault() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getDefault() - Method in interface org.cytoscape.view.model.VisualProperty: The default value of this property.
getDefaultComboBoxEditor(String) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Get JComboBox type editor
getDefaultEdgeTable() - Method in interface org.cytoscape.model.CyNetwork: A convenience method returns the default attribute table for the edges of this network.
getDefaultIcon(int, int) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getDefaultIcon(int, int) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: This is for default view editor.
getDefaultLayout() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Returns the default layout.
getDefaultLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getDefaultLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the default instance of the layout context.
getDefaultNetworkTable() - Method in interface org.cytoscape.model.CyNetwork: A convenience method returns the default attribute table for this network.
getDefaultNodeTable() - Method in interface org.cytoscape.model.CyNetwork: A convenience method returns the default attribute table for the nodes of this network.
getDefaultStyle() - Method in interface org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager: Returns Default Visual Style.
getDefaultValue() - Method in interface org.cytoscape.model.CyColumn: Returns the default value for the column, possibly null.
getDefaultValue(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Returns default value for the VisualProperty.
getDefaultVariableValues() - Method in class org.cytoscape.equations.Equation: Returns default values for variable references, if any.
getDefaultVariableValues() - Method in interface org.cytoscape.equations.EquationParser: Returns a map of variable names to their default values, if any.
getDefaultView(VisualStyle) - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewEditor: For a given visual style name, return a component containing a graphical view of the specified visual style.
getDefaultViewEditor() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI: Returns Default View Editor.
getDefaultViewPanel() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI: Returns Default View Panel.
getDefaultVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Provide default VisualLexicon from a default engine factory.
getDefaultVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Return default VisualStyle.
getDegree() - Method in class org.cytoscape.view.layout.LayoutNode: Return the node's degree (i.e.
getDependency() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDependency() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the description of the argument.
getDescription() - Method in class org.cytoscape.io.BasicCyFileFilter: A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.CyFileFilter: A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.datasource.DataSource: Description for this data.
getDescription() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getDescription() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getDescription() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Get human-readable description of this client.
getDescription() - Method in class org.cytoscape.property.bookmark.Bookmarks: Gets the value of the description property.
getDescription() - Method in class org.cytoscape.util.swing.FileChooserFilter: Returns the short description of the acceptable file type.
getDescription() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the associated Tunable's description.
getDescription() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's description.
getDialogTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Returns an instance of DialogTaskManager.
getDisabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Get set of Visual Properties to be disabled in the lexicon.
getDiscreteTableCellRenderer() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getDiscreteTableCellRenderer() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: A custom cell renderer for Discrete table cells.
getDisplayName() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getDisplayName() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Returns display name of this client.
getDisplayName() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getDisplayName() - Method in interface org.cytoscape.view.model.VisualProperty: Returns a short string suitable for presentation to humans.
getDisplayName() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
getDisplayName() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue: Name of this value type.
getDisplayName() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Provides human-readable name of this dependency.
getDoubles(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of doubles.
getEdge(long) - Method in interface org.cytoscape.model.CyNetwork: Return the CyEdge that has the index.
getEdge() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the Edge this LayoutEdge represents
getEdgeCount() - Method in interface org.cytoscape.model.CyNetwork: Return the number of edges in this network.
getEdgeList() - Method in interface org.cytoscape.model.CyNetwork: Return a list of the edges in this network.
getEdgeList() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the list of LayoutEdges within this partition.
getEdges() - Method in class org.cytoscape.model.events.AboutToRemoveEdgesEvent: Returns the collection of edges about to be removed.
getEdgesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil: A utility method that returns a list of edges that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getEdgeView(CyEdge) - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a View for a specified Edge.
getEdgeViews() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a list of Views for all CyEdges in the network.
getEdgeViews() - Method in class org.cytoscape.view.model.events.AboutToRemoveEdgeViewsEvent: Returns the Collection of Views of type CyEdge that are about to be removed.
getEdgeViews() - Method in class org.cytoscape.view.model.events.AddedEdgeViewsEvent: Returns new edge view added to the source network view object.
getEditingRow() - Method in class org.cytoscape.util.swing.JTreeTable: Returns the row being edited.
getEnabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Get set of Visual Properties to be enabled in the lexicon.
getEquation() - Method in interface org.cytoscape.equations.EquationCompiler: If compile() returns true, this returns the result of the compilation.
getErrorEquation(String, Class<?>, String) - Method in interface org.cytoscape.equations.EquationCompiler: A factory method that returns an Equation that always fails at runtime.
getErrorMsg() - Method in interface org.cytoscape.equations.EquationParser: If parse() failed, this will return the last error messages.
getExtension(String) - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a string of the characters following the last '.' in the input string, which is to say the file extension assuming that the input string represents a file name.
getExtensions() - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in interface org.cytoscape.io.CyFileFilter: Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in class org.cytoscape.util.swing.FileChooserFilter: Returns an array of the extensions associated with this FileChooserFilter.
getExternalEdgeList() - Method in interface org.cytoscape.group.CyGroup: Returns the list of exterior edges connected to the nodes within this group.
getFactories() - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager: Returns all available factories.
getFactory(Class<?>) - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager: Factory for the specific mapping type.
getFile(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileFilter() - Method in interface org.cytoscape.io.CyFileFilterProvider: Return the file filter associated with the IOFactory.
getFileFilter() - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory: Return the file filter associated with the IOFactory.
getFiles(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFormat() - Method in class org.cytoscape.property.bookmark.DataSource: Gets the value of the format property.
getFunction(String) - Method in interface org.cytoscape.equations.EquationParser: Returns the function associated with the name "functionName" or null if no such function exists.
getFunctionSummary() - Method in class org.cytoscape.equations.AbstractFunction: Used to provide help for users.
getFunctionSummary() - Method in interface org.cytoscape.equations.Function: Used to provide help for users.
getGlobalTables() - Method in interface org.cytoscape.model.CyTableManager: Returns a set of all global tables.
getGravityTracker(String) - Method in class org.cytoscape.util.swing.JMenuTracker: This method will fetch an existing menu or create a new one if a menu with the specified name does not exist.
getGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Return the group the corresponds to a particular node in a CyNetwork.
getGroupNetwork() - Method in interface org.cytoscape.group.CyGroup: Returns the network referenced by this group.
getGroupNode() - Method in interface org.cytoscape.group.CyGroup: Return the CyNode that represents this group in the network.
getGroups() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the associated Tunable's groups or nesting hierarchy.
getGroups() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's groups or nesting hierarchy.
getGroupSet(CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Provides the set of all the groups known to the groups manager in a particular network.
getGroupsForNode(CyNode) - Method in interface org.cytoscape.group.CyGroupManager: Return the list of CyGroups this node is in.
getGroupsForNode(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Return the list of CyGroups this node is in for a particular network.
getHandler(String) - Method in interface org.cytoscape.view.vizmap.gui.event.VizMapEventHandlerManager: Returns handler for the event.
getHandlers(Object) - Method in class org.cytoscape.work.AbstractTunableInterceptor: Returns a map of TunableHandler objects that have been found to process the fields and methods annotated with Tunable.
getHeader(InputStream, int) - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a string containing the specified number of lines from the beginning of the file.
getHeight() - Method in class org.cytoscape.view.layout.LayoutNode: Return the height of this node
getHeight() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total height of all of the LayoutNodes
getHelpBroker() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Returns the HelpBroker.
getHelpSet() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Returns the HelpSet.
getHref() - Method in class org.cytoscape.property.bookmark.DataSource: Gets the value of the href property.
getIcon() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the Icon to be used along with the title in the tab for this this component.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutNode: Return the node's identifier.
getIdString() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getIdString() - Method in interface org.cytoscape.view.model.VisualProperty: Returns a short string used to identify this visual property and suitable for serializing to XML and other text formats.
getImportedObject() - Method in class org.cytoscape.io.webservice.events.DataImportFinishedEvent: Returns the object that was imported.
getIndex() - Method in class org.cytoscape.view.layout.LayoutNode: Returns the index of this LayoutNode.
getIndex(Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend: Get index of a Handle
getIndexOfChild(Object, Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Returns the index of a child given a parent.
getInputStream(String) - Method in interface org.cytoscape.io.util.StreamUtil: Gets the input stream from given a string.
getInputStream(URL) - Method in interface org.cytoscape.io.util.StreamUtil: Gets the input stream from given URL.
getInternalEdgeList() - Method in interface org.cytoscape.group.CyGroup: Returns the list of edges contained within this group.
getJFrame() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JFrame that contains the application.
getJMenu(String) - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JMenu for the specified name and null if no menu exists for the name.
getJMenuBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JMenuBar object for the application.
getJPanel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns the panel associated with this GUITunableHandler.
getJPanel() - Method in interface org.cytoscape.work.swing.GUITunableHandler: To get the panel that contains the GUI representation (JTextField, JFileChooser, JLabel, JList ...)
getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JToolBar object for the application.
getLastErrorMsg() - Method in interface org.cytoscape.equations.EquationCompiler: Returns an error message for an error encountered during a call to compile, if any.
getLastInternalError() - Method in interface org.cytoscape.model.CyTable: Returns a descriptive message for certain internal errors.
getLastVisualStyle() - Method in class org.cytoscape.view.vizmap.gui.event.SelectedVisualStyleSwitchedEvent: Returns current Visual Style
getLayout(String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Returns a layout algorithm of the specified name and null if no algorithm exists with that name.
getLeftChild() - Method in class org.cytoscape.equations.AbstractNode
getLeftChild() - Method in interface org.cytoscape.equations.TreeNode: Returns the left child if it exists or null if it doesn't.
getList(String, Class<T>) - Method in interface org.cytoscape.model.CyRow: Returns the value found for this row in the specified column with the specified type.
getList(String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow: Returns the value found for this row in the specified column with the specified type.
getListElementType() - Method in interface org.cytoscape.model.CyColumn: Returns the data type of the list elements if the column type is List.class otherwise null.
getListenerClass() - Method in class org.cytoscape.event.AbstractCyEvent: The Class of the listener that is expected to handle this event.
getListenerClass() - Method in interface org.cytoscape.event.CyEvent: The Class of the listener that is expected to handle this event.
getLoadedFileName() - Method in class org.cytoscape.session.events.SessionLoadedEvent: Returns the file name of the session just loaded.
getLoadedSession() - Method in class org.cytoscape.session.events.SessionLoadedEvent: Returns the session that was just loaded.
getLocalTables(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyTableManager: Returns set of all local tabses for the given data type.
getLocation() - Method in interface org.cytoscape.io.datasource.DataSource: Location of this data file.
getLocation() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getLogWeight() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the current value for this edge's logWeight (-log(weight)).
getLongs(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of longs.
getLowerBound() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the lower limit of the object.
getMajorVersion() - Method in interface org.cytoscape.application.CyVersion: The first of the three numbers defining the version of the software, meaning "3" if the version is "3.2.5".
getMappingColumnName() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getMappingColumnName() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns attribute name used in this mapping.
getMappingColumnType() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getMappingColumnType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns data type of mapping attribute.
getMappingFunctionSelector() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns selector for Mapping Type.
getMappingFunctionType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory: Returns the type of this VisualMappingFunctionFactory.
getMappingTable() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getMappingTable() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns table used for this mapping.
getMapValue(K) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: Gets Value for Specified Key.
getMatchingFactory(CyFileFilter) - Method in interface org.cytoscape.io.write.CyWriterManager: Returns a CyWriterFactory for the appropriate filter.
getMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable: Returns all the rows of a specified column that contain a certain value for that column.
getMax() - Method in class org.cytoscape.view.model.ContinuousRange: Returns the maximum value of this range.
getMaxX() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum X location of all of the LayoutNodes
getMaxY() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum Y location of all of the LayoutNodes
getMenu() - Method in interface org.cytoscape.util.swing.GravityTracker: Returns the JPopupMenu or JMenu that this gravity tracker tracks.
getMenu() - Method in class org.cytoscape.util.swing.MenuGravityTracker
getMenu() - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
getMenuGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction: Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in interface org.cytoscape.application.swing.CyAction: Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in class org.cytoscape.application.swing.CyMenuItem: Returns the gravity used to place the menu item in a menu.
getMenuItem() - Method in class org.cytoscape.application.swing.CyMenuItem: Returns the menu item to be placed in a menu according to the specified menu gravity.
getMin() - Method in class org.cytoscape.view.model.ContinuousRange: Returns the minimum value of this range.
getMinorVersion() - Method in interface org.cytoscape.application.CyVersion: The second of the three numbers defining the version of the software, meaning "2" if the version is "3.2.5".
getMinX() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum X location of all of the LayoutNodes
getMinY() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum Y location of all of the LayoutNodes
getModel() - Method in interface org.cytoscape.view.model.View: Get source data structure, such as CyNode, CyEdge, etc.
getMostRecentlyOpenedURL() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker: Returns the last addition or null if there are no URLs.
getMutability() - Method in interface org.cytoscape.model.CyTable: The table can be deleted if this returns Mutability.MUTABLE, otherwise it cannot be deleted!
getName() - Method in class org.cytoscape.application.swing.AbstractCyAction: Returns the name of the action.
getName() - Method in interface org.cytoscape.application.swing.CyAction: Returns the name of the action.
getName() - Method in class org.cytoscape.equations.AbstractFunction: Used to parse the function string.
getName() - Method in interface org.cytoscape.equations.Function: Used to parse the function string.
getName() - Method in interface org.cytoscape.io.datasource.DataSource: Name of this data source
getName() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getName() - Method in interface org.cytoscape.model.CyColumn: Returns the name of the column.
getName() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.bookmark.Attribute: Gets the value of the name property.
getName() - Method in class org.cytoscape.property.bookmark.Category: Gets the value of the name property.
getName() - Method in class org.cytoscape.property.bookmark.DataSource: Gets the value of the name property.
getName() - Method in interface org.cytoscape.property.CyProperty: Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.SimpleCyProperty: Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getName() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the computer-readable name of the layout.
getName() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns a name representing a tunable property.
getName() - Method in interface org.cytoscape.work.TunableHandler: Returns a name representing a tunable property.
getNamespace() - Method in interface org.cytoscape.model.CyTableMetadata: Returns the namespace used as the key to this object's table in CyNetworkTableManager.getTables(org.cytoscape.model.CyNetwork, java.lang.Class).
getNeighborList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.
getNeighbors() - Method in class org.cytoscape.view.layout.LayoutNode: Convenience function to return the list of neighbors (connected nodes) of this node.
getNetwork() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent: Returns the network associated with this event.
getNetwork(long) - Method in interface org.cytoscape.model.CyNetworkManager: Returns the network corresponding to the provided ID
getNetwork() - Method in interface org.cytoscape.model.CyTableMetadata: Returns all the networks associated with this object's table.
getNetworkPointer() - Method in interface org.cytoscape.model.CyNode: Returns the network referenced by this node.
getNetworks() - Method in class org.cytoscape.application.events.SetSelectedNetworksEvent: Returns the list of networks selected.
getNetworks() - Method in interface org.cytoscape.io.read.CyNetworkReader: Returns an array of networks read after executing the run() method of Task.
getNetworks() - Method in class org.cytoscape.session.CySession: Returns a set of all CyNetwork objects contained in this Session.
getNetworkSet() - Method in interface org.cytoscape.group.CyGroup: Return the list of CyNetworks this group is in.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkManager: Provides the set of all the networks known to the network manager.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns a read-only set of all networks managed by this instance.
getNetworkView() - Method in class org.cytoscape.application.events.SetCurrentNetworkViewEvent: Returns the network view associated with this event.
getNetworkView() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent: Get the The target network view model.
getNetworkViews() - Method in class org.cytoscape.application.events.SetSelectedNetworkViewsEvent: Returns the list of network views that have been selected.
getNetworkViews() - Method in class org.cytoscape.session.CySession: Returns a set of all CyNetworkView objects contained in this Session.
getNetworkViews(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Returns a collection of network views corresponding to the specified network, if found.
getNetworkViewSet() - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Provides the set of network views that are currently known to the network manager.
getNewColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the new name of the column.
getNewProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: The new properties after being modified.
getNewState() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent: Returns the new state of the CytoPanel.
getNewVisualStyle() - Method in class org.cytoscape.view.vizmap.gui.event.SelectedVisualStyleSwitchedEvent: Returns Visual Style to be switched to
getNextSUID() - Static method in class org.cytoscape.model.SUIDFactory: Returns the next available SUID.
getNode(long) - Method in interface org.cytoscape.model.CyNetwork: Return the CyNode that has the index.
getNode() - Method in class org.cytoscape.view.layout.LayoutNode: Accessor function to return the Node associated with this LayoutNode.
getNodeCount() - Method in interface org.cytoscape.model.CyNetwork: Return the number of nodes in this network.
getNodeList() - Method in interface org.cytoscape.group.CyGroup: Returns the list of nodes contained within this group.
getNodeList() - Method in interface org.cytoscape.model.CyNetwork: Return a list of the nodes in this network.
getNodeList() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the list of LayoutNodes within this partition.
getNodes() - Method in class org.cytoscape.model.events.AboutToRemoveNodesEvent: Returns the collection of nodes about to be removed.
getNodesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil: A utility method that returns a list of nodes that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getNodeView() - Method in class org.cytoscape.view.layout.LayoutNode: Accessor function to return the View associated with this LayoutNode.
getNodeView(CyNode) - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a View for a specified Node.
getNodeViews() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a list of Views for all CyNodes in the network.
getNodeViews() - Method in class org.cytoscape.view.model.events.AboutToRemoveNodeViewsEvent: Returns a Collection of Views of type CyNode that are about to be removed.
getNodeViews() - Method in class org.cytoscape.view.model.events.AddedNodeViewsEvent: Returns new node view object.
getNumTasks() - Method in class org.cytoscape.work.TaskIterator: Returns the current total number of tasks in the iterator.
getObject(Long, Class<T>) - Method in class org.cytoscape.session.CySession: When a session is restored, Cytoscape automatically generates new SUIDs.
getObject(String, Class<T>) - Method in class org.cytoscape.session.CySession: When a session is restored, Cytoscape automatically generates new SUIDs.
getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old name of the column.
getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: The old properties before they were modified.
getOrdinal(int) - Static method in class org.cytoscape.equations.FunctionUtil: Converts an integer to an ordinal string.
getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Returns an instance of PanelTaskManager.
getParams() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the parsed result from Tunable.getParams().
getParams() - Method in interface org.cytoscape.work.TunableHandler: Returns the parsed result from Tunable.getParams().
getParent() - Method in class org.cytoscape.view.model.VisualLexiconNode: Get the parent of this VP node.
getParentVisualProperty() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Returns the parent visual property for this dependency.
getParser() - Method in interface org.cytoscape.equations.EquationCompiler: Returns the parser which can be used for checking the syntax of equations.
getParseTree() - Method in interface org.cytoscape.equations.EquationParser: Returns the parse tree.
getPartitionNumber() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the partition number of this partition
getPayloadCollection() - Method in class org.cytoscape.event.AbstractCyPayloadEvent: Returns an unmodifiable collection of payload objects.
getPayloadCollection() - Method in interface org.cytoscape.event.CyPayloadEvent: Returns a collection of payload objects.
getPoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets Specified Point.
getPointCount() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets Total Point Count.
getPossibleArgTypes(Class[]) - Method in class org.cytoscape.equations.AbstractFunction: Used with the equation builder.
getPossibleArgTypes(Class<?>[]) - Method in interface org.cytoscape.equations.Function: Used with the equation builder.
getPreferredMenu() - Method in class org.cytoscape.application.swing.AbstractCyAction: This method returns a Menu specification string.
getPreferredMenu() - Method in interface org.cytoscape.application.swing.CyAction: This method returns a Menu specification string.
getPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit: Returns a human-readable description of this edit that will be used in logs and other descriptions of the edit.
getPresentationWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of PresentationWriterManager.
getPrimaryKey() - Method in interface org.cytoscape.model.CyTable: Returns the column type of the primary key for this table.
getProperties() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Return a property object.
getProperties() - Method in interface org.cytoscape.property.CyProperty: Return a property object.
getProperties() - Method in class org.cytoscape.property.SimpleCyProperty: Return a property object.
getProperties() - Method in class org.cytoscape.session.CySession: Returns a set of CyProperty objects defined for this session.
getProperties() - Method in interface org.cytoscape.view.presentation.RenderingEngine: Get property values for the rendering engine, like LOD.
getProperty() - Method in interface org.cytoscape.io.read.CyPropertyReader: Return a property object.
getPropertyEditor() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getPropertyEditor() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns PropertyEditor object for this data type.
getPropertyType() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Returns the type of the property object.
getPropertyType() - Method in interface org.cytoscape.property.CyProperty: Returns the type of the property object.
getPropertyType() - Method in class org.cytoscape.property.SimpleCyProperty: Returns the type of the property object.
getProvider() - Method in interface org.cytoscape.io.datasource.DataSource: Name of this data provider for this source.
getProvider() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifiedName() - Method in interface org.cytoscape.work.TunableHandler: Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifier() - Method in interface org.cytoscape.application.CyVersion: Any text following the last digit of the bug fix version.
getQueryBuilderGUI() - Method in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient: Returns query builder UI.
getQueryBuilderGUI() - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUIClient: Returns query builder UI.
getRange() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getRange() - Method in interface org.cytoscape.view.model.VisualProperty: Returns the Range of this VisualProperty.
getRange() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Gets BoundaryRangeValues.
getRaw(String) - Method in interface org.cytoscape.model.CyRow: Returns the Object that contains the value for the specified column.
getRawValue() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the raw value that the data was set as.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager: Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader task.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager: Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader task.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager: Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager: Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager: Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager: Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager: Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager: Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager: Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager: Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getRecentlyOpenedURLs() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker: Returns the current list of recently opened file names.
getRedoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit: Returns a human-readable description of this edit that will be used in redo menu items.
getRegisteredFunctions() - Method in interface org.cytoscape.equations.EquationParser: Returns the set of currently registered functions.
getRenderingEngine() - Method in class org.cytoscape.application.events.SetCurrentRenderingEngineEvent: Return the rendering engine (presentation) that has been set as current.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAboutToBeRemovedEvent: Returns the RenderingEngine associated with the deleted presentation.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAddedEvent: Get new rendering engine.
getRenderingEngine() - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewPanel: Get dummy network view.
getRenderingEngineManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of RenderingEngineManager.
getRenderingEngines(View<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Get rendering engines for the given view model.
getReturnType() - Method in class org.cytoscape.equations.AbstractFunction: Returns the static return type of this function.
getReturnType() - Method in interface org.cytoscape.equations.Function
getRightChild() - Method in class org.cytoscape.equations.AbstractNode
getRightChild() - Method in interface org.cytoscape.equations.TreeNode: Returns the right child if it exists or null if it doesn't.
getRoot() - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Returns the root of this AbstractTreeTableModel.
getRootNetwork() - Method in interface org.cytoscape.group.CyGroup: Return the root network for this group.
getRootNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetworkManager: Converts a CyNetwork to a CyRootNetwork
getRootNetwork() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Return the CyRootNetwork that contains this CySubNetwork.
getRootVisualProperty() - Method in interface org.cytoscape.view.model.VisualLexicon: Get root of this tree.
getRootVisualProperty() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getRow(CyIdentifiable, String) - Method in interface org.cytoscape.model.CyNetwork: Returns the row for the specified table name for this object.
getRow(CyIdentifiable) - Method in interface org.cytoscape.model.CyNetwork: A convenience method that returns the row in the default table for this object.
getRow(Object) - Method in interface org.cytoscape.model.CyTable: Returns the row specified by the primary key object and if a row for the specified key does not yet exist in the table, a new row will be created and the new row will be returned.
getRow() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the CyRow of the data that was set.
getRow() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the CyRow for this LayoutEdge
getRow() - Method in class org.cytoscape.view.layout.LayoutNode: Accessor function to return the CyRow associated with this LayoutNode.
getRowCount() - Method in interface org.cytoscape.model.CyTable: Returns the number of rows in this table.
getRowCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the number of rows in the JTree.
getSavedFileName() - Method in class org.cytoscape.session.events.SessionSavedEvent: Returns the file name of the session just loaded.
getSavedSession() - Method in class org.cytoscape.session.events.SessionSavedEvent: Returns the session that was just loaded.
getSavePolicy() - Method in interface org.cytoscape.model.CyTable: Returns how (or if) this CyTable should be saved.
getSavePolicy() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in interface org.cytoscape.property.CyProperty: Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in class org.cytoscape.property.SimpleCyProperty: Returns the CyProperty.SavePolicy of the CyProperty.
getSearchResult() - Method in class org.cytoscape.io.webservice.events.SearchFinishedEvent: Returns The search result.
getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the currently selected component.
getSelectedIndex() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the currently selected index.
getSelectedIndex() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent: Returns the index of the CytoPanelComponent selected.
getSelectedNetworks() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the list of selected networks.
getSelectedNetworkViews() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the list of selected network views.
getSelectedValue() - Method in class org.cytoscape.work.util.ListSingleSelection: Get the item that is currently selected.
getSelectedValues() - Method in class org.cytoscape.work.util.ListMultipleSelection: Get the items that are currently selected.
getSerializableString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Bend: Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Handle: Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue: Returns serializable representation of this value.
getService(BundleContext, Class<S>) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that attempts to get a service of the specified type.
getService(BundleContext, Class<S>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that attempts to get a service of the specified type and that passes the specified filter.
getService(Class<S>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that attempts to get a service of the specified type.
getService(Class<S>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that attempts to get a service of the specified type and that passes the specified filter.
getServiceLocation() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getServiceLocation() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Returns resource location of this service, i.e., service URL.
getSession() - Method in interface org.cytoscape.io.read.CySessionReader: Returns a CySession object
getSharedEdgeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the edge table shared by all subnetworks.
getSharedNetworkTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the network table shared by all subnetworks.
getSharedNodeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the node table shared by all subnetworks.
getSize() - Method in enum org.cytoscape.model.CyTableFactory.InitialTableSize: Returns the actual size value for the given enum.
getSource() - Method in class org.cytoscape.event.AbstractCyEvent: The object that fired the event.
getSource() - Method in interface org.cytoscape.event.CyEvent: The object that fired the event.
getSource() - Method in interface org.cytoscape.model.CyEdge: Returns the source node determining this edge.
getSource() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the source of this edge
getSourceColumn() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the name of the column from the source table which contains the values this column provides.
getSourceJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the name of the column from the source table used for the join.
getSourceLocation() - Method in class org.cytoscape.equations.AbstractNode
getSourceLocation() - Method in class org.cytoscape.equations.CodeAndSourceLocation
getSourceLocation() - Method in interface org.cytoscape.equations.TreeNode: Returns the start of the location in the equation where the code was found that was turned into a node in the parse tree.
getSourceLocations() - Method in class org.cytoscape.equations.Equation: Returns the starting points in the original equation for each node in the parse tree that resulted from the original equation.
getSourceTable() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the originating table for this column if this column is virtual.
getState() - Method in interface org.cytoscape.application.swing.CytoPanel: Gets the state of the CytoPanel.
getState() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns a string representation of the value of the Tunable associated with this GUITunableHandler.
getState() - Method in interface org.cytoscape.work.swing.GUITunableHandler: To get the current value of a Handler (or path for a FileHandler, or selected item(s) for ListMultipleSelection ListSingleSelection, ...)
getStatusToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the status JToolBar of the application.
getStrings(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Converts all arguments, including Lists to a uniform array of strings.
getSubNetworkList() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Will return A list of all CySubNetworks contained in this root network.
getSuggestedNetworkTitle(String) - Method in interface org.cytoscape.session.CyNetworkNaming: Generates a unique network title based on a provided suggestion.
getSuggestedSubnetworkTitle(CyNetwork) - Method in interface org.cytoscape.session.CyNetworkNaming: Generates a unique title for a subnetwork based on a parent network.
getSUID() - Method in interface org.cytoscape.model.CyIdentifiable: Returns the SUID of the implementing object.
getSupportedClasses() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of classes for which have aggregators.
getSupportedEdgeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getSupportedEdgeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedNodeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getSupportedNodeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedType() - Method in interface org.cytoscape.group.data.Aggregator: Return the Class this aggregator supports
getSupportsSelectedOnly() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getSupportsSelectedOnly() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns true if this algorithm supports being applied to only the currently selected nodes.
getTable() - Method in interface org.cytoscape.model.CyColumn: Returns the table for this column.
getTable(CyNetwork, Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns the table with the specified namespace and type from the network.
getTable() - Method in interface org.cytoscape.model.CyRow: Returns the CyTable that this row belongs to.
getTable(long) - Method in interface org.cytoscape.model.CyTableManager: Returns the table with the specified SUID.
getTable() - Method in interface org.cytoscape.model.CyTableMetadata: Returns the table whose metadata is described by this instance.
getTable() - Method in class org.cytoscape.model.events.TableAboutToBeDeletedEvent: Returns the table that is about to be deleted from the table manager.
getTable() - Method in class org.cytoscape.model.events.TableAddedEvent: Returns the table added to the table manager.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
getTables() - Method in interface org.cytoscape.io.read.CyTableReader: Return an array of CyTable objects.
getTables(CyNetwork, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns a read-only map of all of the tables for the specified type from the network.
getTables() - Method in class org.cytoscape.session.CySession: Returns a set of all CyTable objects contained in this Session.
getTarget() - Method in interface org.cytoscape.model.CyEdge: Returns the target node determining this edge.
getTarget() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the target of this edge
getTargetDataType() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getTargetDataType() - Method in interface org.cytoscape.view.model.VisualProperty: VisualProperty is always associated with a data type.
getTargetJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the name of the column from the target table used for the join.
getTargetObjectType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ListEditor: Type of object managed by this editor.
getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of TaskManager.
getThisComponent() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the Component that is this CytoPanel.
getTitle() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the title of the tab within the CytoPanel for this component.
getTitle() - Method in enum org.cytoscape.application.swing.CytoPanelName: Returns the human readable title used for labeling this CytoPanel.
getTitle() - Method in interface org.cytoscape.model.CyTable: Returns a human readable name for the CyTable.
getTitle() - Method in interface org.cytoscape.view.vizmap.VisualStyle: Returns name of this visual style.
getToolbarGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction: Returns the gravity used to place this action in the toolbar.
getToolBarGravity() - Method in class org.cytoscape.application.swing.AbstractToolBarComponent: Returns the gravity value for this toolbar component.
getToolbarGravity() - Method in interface org.cytoscape.application.swing.CyAction: Returns the gravity used to place this action in the toolbar.
getToolBarGravity() - Method in interface org.cytoscape.application.swing.ToolBarComponent: Returns the gravity used to place this component in the toolbar.
getToolTipText(MouseEvent) - Method in class org.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 org.cytoscape.util.swing.JTreeTable: Returns the tree that is being shared between the model.
getType() - Method in class org.cytoscape.equations.AbstractNode
getType() - Method in class org.cytoscape.equations.Equation: The overall type of the Equation, e.g.
getType() - Method in interface org.cytoscape.equations.EquationParser: Returns the result type of the parsed equation if the parse succeeded, otherwise null.
getType() - Method in class org.cytoscape.equations.IdentDescriptor: Returns the, possibly adjusted, type of the descriptor as one of the types internally supported by equations.
getType() - Method in interface org.cytoscape.equations.TreeNode: Returns the type of this node.
getType() - Method in interface org.cytoscape.model.CyColumn: Returns the data type of the column.
getType() - Method in interface org.cytoscape.model.CyTableMetadata: Returns the type of the data associated with this object's table.
getType() - Method in class org.cytoscape.view.model.ContinuousRange
getType() - Method in class org.cytoscape.view.model.DiscreteRange
getType() - Method in interface org.cytoscape.view.model.Range: Type of object used in this range.
getType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor: Get type of the value to be edited.
getType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns the type of object managed in the Visual property.
getType() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the class type of the field or method annotated by Tunable.
getType() - Method in interface org.cytoscape.work.TunableHandler: Returns the class type of the field or method annotated by Tunable.
getUndoableEditSupport() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport: Returns the UndoableEditSupport associated with this UndoSupport instance.
getUndoManager() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport: Returns the UndoManager associated with this UndoSupport instance.
getUndoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit: Returns a human-readable description of this edit that will be used in undo menu items.
getUndoSupport() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of UndoSupport.
getUpperBound() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the upper limit of the object.
getURLConnection(URL) - Method in interface org.cytoscape.io.util.StreamUtil: Obtain a URLConnection for a given URL.
getUsageDescription() - Method in class org.cytoscape.equations.AbstractFunction: Used to provide help for users.
getUsageDescription() - Method in interface org.cytoscape.equations.Function: Used to provide help for users.
getValidationState(Appendable) - Method in interface org.cytoscape.work.TunableValidator: Executes the validation test on the annotated Tunables.
getValue() - Method in class org.cytoscape.equations.IdentDescriptor: Returns the value of the descriptor.
getValue() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the value that the data was set as.
getValue() - Method in class org.cytoscape.view.model.events.ViewChangeRecord: Returns the value that the visual property has been changed to.
getValue() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Gets Point Value.
getValue() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns an object describing a field annotated with Tunable or null if no field has been associated with this handler.
getValue() - Method in interface org.cytoscape.work.TunableHandler: Returns an object describing a field annotated with Tunable or null if no field has been associated with this handler.
getValue() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the value.
getValueAt(Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the value to be displayed for node node, at column number column.
getValueAt(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the value at the given row and column.
getValueEditor(Class<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns value editor for the given data type.
getValues(Class<? extends T>) - Method in interface org.cytoscape.model.CyColumn: Returns all the values, some of which may be null, for this given column.
getVariableReferences() - Method in class org.cytoscape.equations.Equation: Returns all the variable references that occur as part if this Equation.
getVariableReferences() - Method in interface org.cytoscape.equations.EquationParser: Returns all the variable names that have been detected in the most recently parsed equation.
getVersion() - Method in interface org.cytoscape.application.CyVersion: The full version as a string, for example "3.2.5-alpha".
getVersion() - Method in class org.cytoscape.property.bookmark.Bookmarks: Gets the value of the version property.
getView() - Method in class org.cytoscape.view.model.events.ViewChangeRecord: Returns the view that has been changed.
getViewModel() - Method in interface org.cytoscape.view.presentation.RenderingEngine: Returns View being rendered.
getViewVisualStyleMap() - Method in class org.cytoscape.session.CySession: Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.
getVirtualColumnInfo() - Method in interface org.cytoscape.model.CyColumn: Returns information about the virtual column definition of this column.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngine: Provide all compatible Visual Properties as a VisualLexicon.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory: Returns supported VisualLexicon supported by this rendering engine implementation.
getVisualLexiconNode(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon: Get a tree node in for the given VisualProperty.
getVisualLexiconNode(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getVisualMappingFunction(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Get current VisualMappingFunction for the VisualProperty.
getVisualMappingFunctionContinuousFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionDiscreteFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionPassthroughFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of VisualMappingFunctionFactory.
getVisualMappingManager() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of VisualMappingManager.
getVisualProperties() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: A set of Visual Properties to be set by the parent if locked.
getVisualProperty() - Method in class org.cytoscape.view.model.events.ViewChangeRecord: Returns the visual property that has been changed.
getVisualProperty(VisualProperty<T>) - Method in interface org.cytoscape.view.model.View: Get the actual value for the given visual property.
getVisualProperty() - Method in class org.cytoscape.view.model.VisualLexiconNode: Returns wrapped VisualProperty object.
getVisualProperty() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getVisualProperty() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Visual Property associated with this function.
getVisualPropertyEditor(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns the VisualPropertyEditor for the given VisualProperty.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent: Get the VisualStyle that was set to the network view.
getVisualStyle(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Returns the VisualStyle associated with the target network view model.
getVisualStyleAdded() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent: Get the newly created VisualStyle.
getVisualStyleFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Returns an instance of VisualStyleFactory.
getVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader: Returns a list of VisualStyle objects.
getVisualStyles() - Method in class org.cytoscape.session.CySession: Returns a set containing all VisualStyles defined for this session.
getVisualStyleToBeRemoved() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent: Returns target VisualStyle to be removed from manager.
getWeight() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the current value for this edge's weight.
getWidth() - Method in class org.cytoscape.view.layout.LayoutNode: Return the width of this node
getWidth() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total width of all of the LayoutNodes
getWriter(CyNetwork, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager: Returns the CyWriter Task that will attempt to write the specified network to the specified file of the specified file type.
getWriter(CyNetwork, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager: Returns the CyWriter Task that will attempt to write the specified network to the specified output steam of the specified file type.
getWriter(CyNetworkView, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager: Returns the CyWriter Task that will attempt to write the specified view to the specified file of the specified file type.
getWriter(CyNetworkView, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager: Returns the CyWriter Task that will attempt to write the specified view to the specified output steam of the specified file type.
getWriter(Object, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager: Returns the CyWriter Task that will attempt to write the specified property object to the specified file of the specified file type.
getWriter(Object, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager: Returns the CyWriter Task that will attempt to write the specified property object to the specified output stream of the specified file type.
getWriter(CySession, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CySessionWriterManager: Returns the CyWriter Task that will attempt to write the specified session to the specified file of the specified file type.
getWriter(CySession, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CySessionWriterManager: Returns the CyWriter Task that will attempt to write the specified session to the specified output stream of the specified file type.
getWriter(CyTable, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyTableWriterManager: Returns the CyWriter Task that will attempt to write the specified table to the specified file of the specified file type.
getWriter(CyTable, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyTableWriterManager: Returns the CyWriter Task that will attempt to write the specified table to the specified output stream of the specified file type.
getWriter(View<?>, RenderingEngine<?>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.PresentationWriterManager: Returns the CyWriter Task that will attempt to write the specified view to the specified file of the specified file type.
getWriter(View<?>, RenderingEngine<?>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.PresentationWriterManager: Returns the CyWriter Task that will attempt to write the specified view to the specified output stream of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.VizmapWriterManager: Returns the CyWriter Task that will attempt to write the specified vizmap to the specified file of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.VizmapWriterManager: Returns the CyWriter Task that will attempt to write the specified vizmap to the specified output stream of the specified file type.
getX() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current X value for this LayoutNode.
getX() - Method in class org.cytoscape.view.layout.LayoutPoint: Returns the X location of the point.
getXDisp() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current X displacement value for this LayoutNode.
getY() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current Y value for this LayoutNode.
getY() - Method in class org.cytoscape.view.layout.LayoutPoint: Returns the Y location of the point.
getYDisp() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current Y displacement value for this LayoutNode.
GravityTracker - Interface in org.cytoscape.util.swing: This interface sepecifies a tracker that will be used to insert items (submenus, menu items and separators) into a menu based on their "gravity" or "weight".
greaterValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Will be used for interpolation upon larger domain values
GroupAboutToBeDestroyedEvent - Class in org.cytoscape.group.events: This event signals that a group is about to be destroyed -- i.e.
GroupAboutToBeDestroyedEvent(CyGroupManager, CyGroup) - Constructor for class org.cytoscape.group.events.GroupAboutToBeDestroyedEvent: Constructs event.
GroupAboutToBeDestroyedListener - Interface in org.cytoscape.group.events: Listener for GroupAboutToBeDestroyedEvent
GroupAboutToBeRemovedEvent - Class in org.cytoscape.group.events: This event signals that a group is about to be removed from a network, but not completely deleted.
GroupAboutToBeRemovedEvent(CyGroup, CyNetwork) - Constructor for class org.cytoscape.group.events.GroupAboutToBeRemovedEvent: Constructs event.
GroupAboutToBeRemovedListener - Interface in org.cytoscape.group.events: Listener for GroupAboutToBeRemovedEvent
GroupAboutToCollapseEvent - Class in org.cytoscape.group.events: This event signals that a group is either about to be expanded or collapsed in a particular network.
GroupAboutToCollapseEvent(CyGroup, CyNetwork, boolean) - Constructor for class org.cytoscape.group.events.GroupAboutToCollapseEvent: Constructs event.
GroupAboutToCollapseListener - Interface in org.cytoscape.group.events: Listener for GroupAboutToCollapseEvent
GroupAddedEvent - Class in org.cytoscape.group.events: This event signals that a new group has been added.
GroupAddedEvent(CyGroupManager, CyGroup) - Constructor for class org.cytoscape.group.events.GroupAddedEvent: Constructs event.
GroupAddedListener - Interface in org.cytoscape.group.events: Listener for GroupAddedEvent
GroupAddedToNetworkEvent - Class in org.cytoscape.group.events: This event signals that an existing group has been added to a new network.
GroupAddedToNetworkEvent(CyGroup, CyNetwork) - Constructor for class org.cytoscape.group.events.GroupAddedToNetworkEvent: Constructs event.
GroupAddedToNetworkListener - Interface in org.cytoscape.group.events: Listener for GroupAddedToNetworkEvent
GroupCollapsedEvent - Class in org.cytoscape.group.events: This event signals that a group has either been expanded or collapsed in a particular network.
GroupCollapsedEvent(CyGroup, CyNetwork, boolean) - Constructor for class org.cytoscape.group.events.GroupCollapsedEvent: Constructs event.
GroupCollapsedListener - Interface in org.cytoscape.group.events: Listener for GroupCollapsedEvent
GroupEdgesAddedEvent - Class in org.cytoscape.group.events: This event signals that edges have been added to the network.
GroupEdgesAddedEvent(CyGroup, CyEdge) - Constructor for class org.cytoscape.group.events.GroupEdgesAddedEvent: Constructs event.
GroupEdgesAddedEvent(CyGroup, List<CyEdge>) - Constructor for class org.cytoscape.group.events.GroupEdgesAddedEvent: Constructs event.
GroupEdgesAddedListener - Interface in org.cytoscape.group.events: Listener for GroupEdgesAddedEvent
GroupEdgesRemovedEvent - Class in org.cytoscape.group.events: This event signals that edges have been removed from the network.
GroupEdgesRemovedEvent(CyGroup, CyEdge) - Constructor for class org.cytoscape.group.events.GroupEdgesRemovedEvent: Constructs event.
GroupEdgesRemovedEvent(CyGroup, List<CyEdge>) - Constructor for class org.cytoscape.group.events.GroupEdgesRemovedEvent: Constructs event.
GroupEdgesRemovedListener - Interface in org.cytoscape.group.events: Listener for GroupEdgesRemovedEvent
GroupNodesAddedEvent - Class in org.cytoscape.group.events: This event signals that edges have been added to the network.
GroupNodesAddedEvent(CyGroup, CyNode) - Constructor for class org.cytoscape.group.events.GroupNodesAddedEvent: Constructs event.
GroupNodesAddedEvent(CyGroup, List<CyNode>) - Constructor for class org.cytoscape.group.events.GroupNodesAddedEvent: Constructs event.
GroupNodesAddedListener - Interface in org.cytoscape.group.events: Listener for GroupNodesAddedEvent
GroupNodesRemovedEvent - Class in org.cytoscape.group.events: This event signals that edges have been removed from the network.
GroupNodesRemovedEvent(CyGroup, CyNode) - Constructor for class org.cytoscape.group.events.GroupNodesRemovedEvent: Constructs event.
GroupNodesRemovedEvent(CyGroup, List<CyNode>) - Constructor for class org.cytoscape.group.events.GroupNodesRemovedEvent: Constructs event.
GroupNodesRemovedListener - Interface in org.cytoscape.group.events: Listener for GroupNodesRemovedEvent
GroupNodesTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for grouping nodes.
gui - Variable in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
GUITunableHandler - Interface in org.cytoscape.work.swing: An extension of TunableHandler with added functionality to support the construction of a Swing-based UI.
GUITunableHandlerFactory<T extends GUITunableHandler> - Interface in org.cytoscape.work.swing: A specialization fo TunableHandlerFactory for GUITunableHandler.

H

HALF_BOTTOM - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Bottom Half of a triangle shaped arrow
HALF_TOP - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Top Half of a triangle shaped arrow
Handle - Interface in org.cytoscape.view.presentation.property.values: Defines a handle, an anchor point in the edge.
handle() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Updates an annotated object with the current value as retrieved from the the user interface generated by this handler.
handle() - Method in interface org.cytoscape.work.TunableHandler: Updates an annotated object with the current value as retrieved from the the user interface generated by this handler.
handleEvent(CyShutdownEvent) - Method in interface org.cytoscape.application.events.CyShutdownListener: Process the specified event.
handleEvent(CyStartEvent) - Method in interface org.cytoscape.application.events.CyStartListener: Process the specified event.
handleEvent(SetCurrentNetworkEvent) - Method in interface org.cytoscape.application.events.SetCurrentNetworkListener: Processes the specified event when fired.
handleEvent(SetCurrentNetworkViewEvent) - Method in interface org.cytoscape.application.events.SetCurrentNetworkViewListener: Processes the specified event when fired.
handleEvent(SetCurrentRenderingEngineEvent) - Method in interface org.cytoscape.application.events.SetCurrentRenderingEngineListener: Processes the specified event when fired.
handleEvent(SetSelectedNetworksEvent) - Method in interface org.cytoscape.application.events.SetSelectedNetworksListener: Processes the specified event when fired.
handleEvent(SetSelectedNetworkViewsEvent) - Method in interface org.cytoscape.application.events.SetSelectedNetworkViewsListener: Processes the specified event when fired.
handleEvent(RowsSetEvent) - Method in class org.cytoscape.application.swing.AbstractViewUpdater: Called whenever CyRows are changed.
handleEvent(CytoPanelComponentSelectedEvent) - Method in interface org.cytoscape.application.swing.events.CytoPanelComponentSelectedListener: Handles specified event.
handleEvent(CytoPanelStateChangedEvent) - Method in interface org.cytoscape.application.swing.events.CytoPanelStateChangedListener: Handles specified event.
handleEvent(PreferencesUpdatedEvent) - Method in interface org.cytoscape.application.swing.events.PreferencesUpdatedListener: Process the specified event.
handleEvent(GroupAboutToBeDestroyedEvent) - Method in interface org.cytoscape.group.events.GroupAboutToBeDestroyedListener: The method that should handle the specified event.
handleEvent(GroupAboutToBeRemovedEvent) - Method in interface org.cytoscape.group.events.GroupAboutToBeRemovedListener: The method that should handle the specified event.
handleEvent(GroupAboutToCollapseEvent) - Method in interface org.cytoscape.group.events.GroupAboutToCollapseListener: The method that should handle the specified event.
handleEvent(GroupAddedEvent) - Method in interface org.cytoscape.group.events.GroupAddedListener: The method that should handle the specified event.
handleEvent(GroupAddedToNetworkEvent) - Method in interface org.cytoscape.group.events.GroupAddedToNetworkListener: The method that should handle the specified event.
handleEvent(GroupCollapsedEvent) - Method in interface org.cytoscape.group.events.GroupCollapsedListener: The method that should handle the specified event.
handleEvent(GroupEdgesAddedEvent) - Method in interface org.cytoscape.group.events.GroupEdgesAddedListener: The method that should handle the specified event.
handleEvent(GroupEdgesRemovedEvent) - Method in interface org.cytoscape.group.events.GroupEdgesRemovedListener: The method that should handle the specified event.
handleEvent(GroupNodesAddedEvent) - Method in interface org.cytoscape.group.events.GroupNodesAddedListener: The method that should handle the specified event.
handleEvent(GroupNodesRemovedEvent) - Method in interface org.cytoscape.group.events.GroupNodesRemovedListener: The method that should handle the specified event.
handleEvent(DataImportFinishedEvent<?>) - Method in interface org.cytoscape.io.webservice.events.DataImportFinishedListener: The method that should handle the specified event.
handleEvent(SearchFinishedEvent<?>) - Method in interface org.cytoscape.io.webservice.events.SearchFinishedListener: The method that should handle the specified event.
handleEvent(AboutToRemoveEdgesEvent) - Method in interface org.cytoscape.model.events.AboutToRemoveEdgesListener: The method that should handle the specified event.
handleEvent(AboutToRemoveNodesEvent) - Method in interface org.cytoscape.model.events.AboutToRemoveNodesListener: The method that should handle the specified event.
handleEvent(AddedEdgesEvent) - Method in interface org.cytoscape.model.events.AddedEdgesListener: The method that should handle the specified event.
handleEvent(AddedNodesEvent) - Method in interface org.cytoscape.model.events.AddedNodesListener: The method that should handle the specified event.
handleEvent(ColumnCreatedEvent) - Method in interface org.cytoscape.model.events.ColumnCreatedListener: The method that should handle the specified event.
handleEvent(ColumnDeletedEvent) - Method in interface org.cytoscape.model.events.ColumnDeletedListener: The method that should handle the specified event.
handleEvent(ColumnNameChangedEvent) - Method in interface org.cytoscape.model.events.ColumnNameChangedListener: The method that should handle the specified event.
handleEvent(NetworkAboutToBeDestroyedEvent) - Method in interface org.cytoscape.model.events.NetworkAboutToBeDestroyedListener: The method that should handle the specified event.
handleEvent(NetworkAddedEvent) - Method in interface org.cytoscape.model.events.NetworkAddedListener: The method that should handle the specified event.
handleEvent(NetworkDestroyedEvent) - Method in interface org.cytoscape.model.events.NetworkDestroyedListener: The method that should handle the specified event.
handleEvent(RemovedEdgesEvent) - Method in interface org.cytoscape.model.events.RemovedEdgesListener: The method that should handle the specified event.
handleEvent(RemovedNodesEvent) - Method in interface org.cytoscape.model.events.RemovedNodesListener: The method that should handle the specified event.
handleEvent(RowsCreatedEvent) - Method in interface org.cytoscape.model.events.RowsCreatedListener: The method that should handle the specified event.
handleEvent(RowsSetEvent) - Method in interface org.cytoscape.model.events.RowsSetListener: The method that should handle the specified event.
handleEvent(SetNetworkPointerEvent) - Method in interface org.cytoscape.model.events.SetNetworkPointerListener: The method that should handle the specified event.
handleEvent(TableAboutToBeDeletedEvent) - Method in interface org.cytoscape.model.events.TableAboutToBeDeletedListener: The method that should handle the specified event.
handleEvent(TableAddedEvent) - Method in interface org.cytoscape.model.events.TableAddedListener: The method that should handle the specified event.
handleEvent(TableDeletedEvent) - Method in interface org.cytoscape.model.events.TableDeletedListener: The method that should handle the specified event.
handleEvent(UnsetNetworkPointerEvent) - Method in interface org.cytoscape.model.events.UnsetNetworkPointerListener: The method that should handle the specified event.
handleEvent(PropertyUpdatedEvent) - Method in interface org.cytoscape.property.PropertyUpdatedListener: Method for handling the event.
handleEvent(SessionAboutToBeSavedEvent) - Method in interface org.cytoscape.session.events.SessionAboutToBeSavedListener: Processes the specified event when fired.
handleEvent(SessionLoadedEvent) - Method in interface org.cytoscape.session.events.SessionLoadedListener: Processes the specified event when fired.
handleEvent(SessionSavedEvent) - Method in interface org.cytoscape.session.events.SessionSavedListener: Processes the specified event when fired.
handleEvent(AboutToRemoveEdgeViewsEvent) - Method in interface org.cytoscape.view.model.events.AboutToRemoveEdgeViewsListener: Process event.
handleEvent(AboutToRemoveNodeViewsEvent) - Method in interface org.cytoscape.view.model.events.AboutToRemoveNodeViewsListener: Process event.
handleEvent(AddedEdgeViewsEvent) - Method in interface org.cytoscape.view.model.events.AddedEdgeViewsListener: Process event.
handleEvent(AddedNodeViewsEvent) - Method in interface org.cytoscape.view.model.events.AddedNodeViewsListener: Process event.
handleEvent(FitContentEvent) - Method in interface org.cytoscape.view.model.events.FitContentListener: Process the event.
handleEvent(FitSelectedEvent) - Method in interface org.cytoscape.view.model.events.FitSelectedListener: Fit the selected nodes/edges to the current container.
handleEvent(NetworkViewAboutToBeDestroyedEvent) - Method in interface org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener: Process event.
handleEvent(NetworkViewAddedEvent) - Method in interface org.cytoscape.view.model.events.NetworkViewAddedListener: Process event.
handleEvent(NetworkViewChangedEvent) - Method in interface org.cytoscape.view.model.events.NetworkViewChangedListener: Process event.
handleEvent(NetworkViewDestroyedEvent) - Method in interface org.cytoscape.view.model.events.NetworkViewDestroyedListener: Process event.
handleEvent(UpdateNetworkPresentationEvent) - Method in interface org.cytoscape.view.model.events.UpdateNetworkPresentationListener: Listener implementing this method will redraw the presentation if necessary.
handleEvent(RenderingEngineAboutToBeRemovedEvent) - Method in interface org.cytoscape.view.presentation.events.RenderingEngineAboutToBeRemovedListener: Perform pre-deletion tasks in this method.
handleEvent(RenderingEngineAddedEvent) - Method in interface org.cytoscape.view.presentation.events.RenderingEngineAddedListener: Listener can extract source RenderingEngine object in this method.
handleEvent(VisualStyleAboutToBeRemovedEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedListener: Update states/GUI using deleted VisualStyle information.
handleEvent(VisualStyleAddedEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualStyleAddedListener: Do something with a new VisualStyle.
handleEvent(VisualStyleSetEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualStyleSetListener: Do something after a VisualStyle is set to a CyNetworkView.
handleEvent(LexiconStateChangedEvent) - Method in interface org.cytoscape.view.vizmap.gui.event.LexiconStateChangedListener: Handles the specified event.
handleEvent(SelectedVisualStyleSwitchedEvent) - Method in interface org.cytoscape.view.vizmap.gui.event.SelectedVisualStyleSwitchedListener: Handles the specified event.
HandleFactory - Interface in org.cytoscape.view.presentation.property.values: Factory of the handle object.
handlerMap - Variable in class org.cytoscape.work.AbstractTunableInterceptor: Store the Handlers.
hashCode() - Method in class org.cytoscape.equations.Equation
hasNext() - Method in class org.cytoscape.work.TaskIterator: Returns true if a call to next() would return another Task, otherwise false.
hasTunables(Object) - Method in class org.cytoscape.work.AbstractTunableInterceptor: Tests an object to see if any of its fields or method have Tunable annotations.
HEXAGON - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Hexagonal shape.
HIDDEN_ATTRS - Static variable in interface org.cytoscape.model.CyNetwork: The name of the default hidden CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
HideSelectedEdgesTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding selected edges.
HideSelectedNodesTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding selected nodes.
HideSelectedTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding all of the selected items.
horizontal - Variable in class org.cytoscape.work.swing.AbstractGUITunableHandler: If true, the associated GUI element should be laid out next to others in the same group, if false, it should be vertically stacked relative to the others.
href - Variable in class org.cytoscape.property.bookmark.DataSource

I

ID - Static variable in interface org.cytoscape.work.ServiceProperties: Unique ID of an OSGi service.
IdentDescriptor - Class in org.cytoscape.equations: Used to hold a current value for an equation's variable reference.
IdentDescriptor(Object) - Constructor for class org.cytoscape.equations.IdentDescriptor: Initializes a new IdentDescriptor and provides minimal type translation (from Integer to Long).
IN_MENU_BAR - Static variable in interface org.cytoscape.work.ServiceProperties: Action will be added to menu bar if this flag is set to true
IN_NETWORK_PANEL_CONTEXT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties: Action will be added to network panel's context menu if this flag is set to true
IN_TOOL_BAR - Static variable in interface org.cytoscape.work.ServiceProperties: Action will be added to tool bar if this flag is set to true
includeMax() - Method in class org.cytoscape.view.model.ContinuousRange: Returns true if the maximum value is included in this range.
includeMin() - Method in class org.cytoscape.view.model.ContinuousRange: Returns true if the minimum value is included in this range.
incr - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: The value used for spacing nodes.
increment(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Increment the location of this node by (x,y).
incrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Increment the displacement recorded for this node by (x,y).
indexOfComponent(Component) - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the index for the specified component.
inMenuBar - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether the action is in a menu.
InputStreamTaskFactory - Interface in org.cytoscape.io.read: A super interface that allows the input stream to be set for reader task factories.
inRange(T) - Method in class org.cytoscape.view.model.ContinuousRange
inRange(T) - Method in class org.cytoscape.view.model.DiscreteRange
inRange(T) - Method in interface org.cytoscape.view.model.Range: Return true if the given value is in the range defined in this class.
insertHandleAt(int, Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend: Insert a Handle to the specified position in the Bend
insertTasksAfter(Task, Task...) - Method in class org.cytoscape.work.TaskIterator: Inserts "newTasks" immediately after "referenceTask".
insertTasksAfter(Task, TaskIterator) - Method in class org.cytoscape.work.TaskIterator: Inserts "newTasks" immediately after "referenceTask".
insertTasksAfterCurrentTask(Task...) - Method in class org.cytoscape.work.AbstractTask: Inserts "newTasks" after the current Task, in the TaskIterator that is being managed by this class.
insertTasksAfterCurrentTask(TaskIterator) - Method in class org.cytoscape.work.AbstractTask: Inserts "newTasks" after the current Task, in the TaskIterator that is being managed by this class.
IntegerVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Integer values.
IntegerVisualProperty(Integer, Range<Integer>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.IntegerVisualProperty: Constructor.
INTERACTION - Static variable in interface org.cytoscape.model.CyEdge: A String column created by default for every CyEdge that holds the interaction description of the edge.
Interpreter - Interface in org.cytoscape.equations: Executes the code represented by an equation.
inToolBar - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether the action is in the toolbar.
InvertSelectedEdgesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for inverting the selected edges.
InvertSelectedNodesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for inverting the selected nodes.
isAdvancedMode() - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Check the status of display mode
isBasic(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Check whether given Visual Property is categorized as Basic or not.
isCellEditable(EventObject) - Method in class org.cytoscape.util.swing.AbstractCellEditor
isCellEditable(Object, int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: By default, make the column with the Tree in it the only editable one.
isCellEditable(EventObject) - Method in class org.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 org.cytoscape.util.swing.TreeTableModel: Indicates whether the the value for node node, at column number column is editable.
isCellEditable(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns whether the cell at the given location is editable.
isChildOf(VisualProperty<?>, VisualProperty<?>, VisualLexicon) - Static method in class org.cytoscape.view.presentation.property.VisualPropertyUtil: Check whether the given VisualProperty is a child of parent vp or not.
isCollapsed(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Return whether this group is expanded or collapsed in the designated network.
isCollapsed() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Returns the current state of the panel, collapsed (true) or expanded (false).
isCompatible(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Returns true if given VisualProperty is compatible with current rendering engine.
isCompatibleWith(Class) - Method in class org.cytoscape.equations.ArgDescriptor: Tests to see if the specified class is compatible with this ArgType.
isDefaultShape(ArrowShape) - Static method in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
isDefaultShape(NodeShape) - Static method in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Returns true if the specified shape is one of the possible default shape values.
isDependencyEnabled() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Returns whether or not this dependency is enabled.
isDirected() - Method in interface org.cytoscape.model.CyEdge: This will return true if the edge is directed and false if the node is undirected.
isDiscrete() - Method in class org.cytoscape.view.model.ContinuousRange
isDiscrete() - Method in class org.cytoscape.view.model.DiscreteRange
isDiscrete() - Method in interface org.cytoscape.view.model.Range: If this range is a set of discrete values, return true.
isEnabled - Variable in class org.cytoscape.application.swing.AbstractToolBarComponent: Whether the toolbar component is enabled or not.
isGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Test to see if this node represents a CyGroup in a particular CyNetwork.
isImmutable() - Method in interface org.cytoscape.model.CyColumn: Returns true if the column is immutable i.e.
isImmutable() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns true if this virtual column was originally created immutable.
isInMenuBar() - Method in class org.cytoscape.application.swing.AbstractCyAction: By default all CytoscapeActions wish to be included in the menu bar at the 'preferredMenuName' location is specified and the 'Tools' menu not.
isInMenuBar() - Method in interface org.cytoscape.application.swing.CyAction: Returns whether the action should be in the menu bar.
isInNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Check to see if this group is defined in a particular network.
isInToolBar() - Method in class org.cytoscape.application.swing.AbstractCyAction: By default no CytoscapeActions will be included in the toolbar.
isInToolBar() - Method in interface org.cytoscape.application.swing.CyAction: Returns whether the action should be in the tool bar.
isLeaf(Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Returns true if the specified node is a leaf, false otherwise.
isLocked() - Method in class org.cytoscape.view.layout.LayoutNode: Returns "true" if this node is locked, false otherwise.
isLowerBoundStrict() - Method in class org.cytoscape.work.util.AbstractBounded: Does the value have to be strictly greater than the lower bound?
isOptional() - Method in class org.cytoscape.equations.ArgDescriptor: Returns whether the ArgType is optional.
isOptional() - Method in enum org.cytoscape.equations.ArgType: Returns true if this type is optional.
isPrimaryKey() - Method in interface org.cytoscape.model.CyColumn: Returns true if the column is the primary key, otherwise false.
isPublic() - Method in interface org.cytoscape.model.CyTable: A public CyTable is a table that is accessible to the user through the user interface.
isReady(InputStream, String) - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory: Returns true if the factory is ready to be produce a TaskIterator and false otherwise.
isReady(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory: Returns true if the factory is ready to be produce a TaskIterator and false otherwise.
isReady(View<CyEdge>, CyNetworkView) - Method in class org.cytoscape.task.AbstractEdgeViewTaskFactory: Returns true if the supplied edge and network views are not null.
isReady(Collection<CyNetwork>) - Method in class org.cytoscape.task.AbstractNetworkCollectionTaskFactory: Returns true if the supplied collection is not null.
isReady(CyNetwork) - Method in class org.cytoscape.task.AbstractNetworkTaskFactory: Returns true if the supplied network is not null.
isReady(Collection<CyNetworkView>) - Method in class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory: Returns true if the supplied collection is not null.
isReady(CyNetworkView, Point2D, Point2D) - Method in class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory: Returns true if the supplied view and coordinates are not null.
isReady(CyNetworkView) - Method in class org.cytoscape.task.AbstractNetworkViewTaskFactory: Returns true if the supplied network view is not null.
isReady(View<CyNode>, CyNetworkView) - Method in class org.cytoscape.task.AbstractNodeViewTaskFactory: Returns true of the supplied network and node views are not null.
isReady(CyColumn, Object) - Method in class org.cytoscape.task.AbstractTableCellTaskFactory: Returns true if the supplied column and value are not null.
isReady(CyColumn) - Method in class org.cytoscape.task.AbstractTableColumnTaskFactory: Returns true if the supplied column is not null.
isReady(CyTable) - Method in class org.cytoscape.task.AbstractTableTaskFactory: Returns true if the supplied table is not null.
isReady(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory: Returns true if this task factory is ready to produce a task iterator.
isReady(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory: Returns true if the node view and network view are in a state that is ready to be processed by the generated tasks and false otherwise.
isReady(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory: Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns true if the task factory is ready to produce a task iterator.
isReady() - Method in class org.cytoscape.work.AbstractTaskFactory
isReady() - Method in interface org.cytoscape.work.TaskFactory
isScalarArgType(Class) - Static method in class org.cytoscape.equations.FunctionUtil: Tests whether the argument is one of the scalar types used by equations.
isSet(String) - Method in interface org.cytoscape.model.CyRow: Indicates whether the column of the specified type contains a non-null value.
isSupported(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon: Test the given Visual Property is supported in this Lexicon.
isSupported(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
isTypeOfList(Class) - Static method in class org.cytoscape.equations.FunctionUtil: Tests whether the argument is some kind of List.
isUpperBoundStrict() - Method in class org.cytoscape.work.util.AbstractBounded: Does the value have to be strictly lower than the upper bound?
isValueLocked(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View: Returns true if current VisualProperty value is locked.
isVirtual() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns true if the column is virtual, otherwise false.

J

JMenuTracker - Class in org.cytoscape.util.swing: A class that creates and manages hierarchies of JMenu objects.
JMenuTracker(JPopupMenu) - Constructor for class org.cytoscape.util.swing.JMenuTracker: This constructor allows you to specify a root JPopupMenu that all parent-less menus will be added to.
JMenuTracker(JMenuBar) - Constructor for class org.cytoscape.util.swing.JMenuTracker: This constructor allows you to specify a root menubar that all parent-less menus will be added to.
JStatusBar - Class in org.cytoscape.util.swing: Simple status bar with 3 fields.
JStatusBar() - Constructor for class org.cytoscape.util.swing.JStatusBar: Creates a new JStatusBar object.
JTreeTable - Class in org.cytoscape.util.swing: This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the JTable.
JTreeTable(TreeTableModel) - Constructor for class org.cytoscape.util.swing.JTreeTable: Creates a new JTreeTable object.
JTreeTable.TreeTableCellEditor - Class in org.cytoscape.util.swing: TreeTableCellEditor implementation.
JTreeTable.TreeTableCellEditor() - Constructor for class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor

L

LARGE_ICON_URL - Static variable in interface org.cytoscape.work.ServiceProperties: Location of large icon data for desktop application
LAST_DIRECTORY - Static variable in interface org.cytoscape.util.swing.FileUtil: The Cytoscape property that stores the last save/load directory.
LAYOUT_ALGORITHM - Static variable in class org.cytoscape.view.layout.AbstractLayoutTask: The table column name that provides the layout algorithm name.
layoutAttribute - Variable in class org.cytoscape.view.layout.AbstractLayoutTask: The attribute to be used for this layout.
LayoutEdge - Class in org.cytoscape.view.layout: The LayoutEdge class.
LayoutEdge(CyEdge, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutEdge: Create a LayoutEdge that will contain information about this edge.
LayoutEdge(CyEdge, LayoutNode, LayoutNode, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutEdge: Create a LayoutEdge that will contains information about this edge, and that record that it connects LayoutNodes v1 and v2.
LayoutEdit - Class in org.cytoscape.view.layout: An undoable edit that will undo and redo of a layout algorithm applied to a network view.
LayoutEdit(String, CyNetworkView) - Constructor for class org.cytoscape.view.layout.LayoutEdit: Constructor.
LayoutNode - Class in org.cytoscape.view.layout: The LayoutNode class.
LayoutNode(View<CyNode>, int, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutNode: The main constructor for a LayoutNode.
layoutPartion(LayoutPartition) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Override this method and layout the LayoutPartion just like you would a NetworkView.
LayoutPartition - Class in org.cytoscape.view.layout: The LayoutPartition class contains all of the information about a single graph partition, where a partition is defined as all nodes in a graph that connect only to each other.
LayoutPartition(int, int) - Constructor for class org.cytoscape.view.layout.LayoutPartition: LayoutPartition: use this constructor to create an empty LayoutPartition.
LayoutPartition(CyNetworkView, Collection<View<CyNode>>, EdgeWeighter) - Constructor for class org.cytoscape.view.layout.LayoutPartition: LayoutPartition: use this constructor to create a LayoutPartition that includes the entire network.
LayoutPoint - Class in org.cytoscape.view.layout: Simple immutable object which represents a point (x, y).
LayoutPoint(double, double) - Constructor for class org.cytoscape.view.layout.LayoutPoint: Constructor.
lesserValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Will be used for interpolation upon smaller domain values
LexiconStateChangedEvent - Class in org.cytoscape.view.vizmap.gui.event: Tell listeners a enabled/disabled visual properties.
LexiconStateChangedEvent(Object, Set<VisualProperty<?>>, Set<VisualProperty<?>>) - Constructor for class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Constructor of the event.
LexiconStateChangedListener - Interface in org.cytoscape.view.vizmap.gui.event: Listener for LexiconStateChangedEvent.
LineType - Interface in org.cytoscape.view.presentation.property.values: Marker interface for line types.
LineTypeVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for LineType values.
LineTypeVisualProperty(LineType, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Constructor.
LIST_UPDATED - Static variable in class org.cytoscape.util.swing.CheckBoxJList: The name of the property change that indicates that the list has been updated.
ListEditor - Interface in org.cytoscape.view.vizmap.gui.editor: Generic editor for discrete values, such as Shape, Line Type, etc.
listenerList - Variable in class org.cytoscape.util.swing.AbstractCellEditor
listenerList - Variable in class org.cytoscape.util.swing.AbstractTreeTableModel: The EventListenerList associated with this AbstractTreeTableModel.
listenForChange() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the listenForChange property of the associated Tunable.
listenForChange() - Method in interface org.cytoscape.work.TunableHandler: Returns the listenForChange property of the associated Tunable.
ListMultipleSelection<T> - Class in org.cytoscape.work.util: List with items of type T : one or more items can be selected.
ListMultipleSelection(T...) - Constructor for class org.cytoscape.work.util.ListMultipleSelection: Creates a new ListMultipleSelection object.
ListMultipleSelection(List<T>) - Constructor for class org.cytoscape.work.util.ListMultipleSelection: Creates a new ListMultipleSelection object.
ListSingleSelection<T> - Class in org.cytoscape.work.util: List with items of type T : only 1 item can be selected.
ListSingleSelection(T...) - Constructor for class org.cytoscape.work.util.ListSingleSelection: Creates a new ListSingleSelection object.
ListSingleSelection(List<T>) - Constructor for class org.cytoscape.work.util.ListSingleSelection: Creates a new ListSingleSelection object.
listToArray(List<Double>) - Static method in class org.cytoscape.equations.FunctionUtil: Converts a List to a regular double[]
LOAD - Static variable in interface org.cytoscape.util.swing.FileUtil: Equal to FileDialog.LOAD.
loadCyNetworks(URL) - Method in interface org.cytoscape.task.read.LoadNetworkURLTaskFactory: Creates a task iterator for loading a URL into a network.
LoadNetworkFileTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading networks from files.
LoadNetworkURLTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading a URL into a network.
loadStyles(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory: Return a set of VisualStyle objects read from the specified file.
LoadTableFileTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading the attribute file to a table.
LoadTableURLTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading an attribute URL to a table.
LoadVizmapFileTaskFactory - Interface in org.cytoscape.task.read: An interface for loading styles from files.
lock() - Method in class org.cytoscape.view.layout.LayoutNode: Register this node as being "locked".
lockedNodeCount() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the number of locked nodes within this partition
LONG_DASH - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Long dash followed by short space
LongList - Class in org.cytoscape.equations: An convenience implementation of ArrayList<Long> that allows for strong type checking.
LongList(long...) - Constructor for class org.cytoscape.equations.LongList: Constructor.
lookup(Class<?>, String) - Method in interface org.cytoscape.view.model.VisualLexicon: Returns the appropriate visual property for the descriptive string.
lookup(Class<?>, String) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon

M

MapGlobalToLocalTableTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for mapping a global to a local table.
MappingFunctionFactoryManager - Interface in org.cytoscape.view.vizmap.gui: Manages factories to create actual mappings (discrete/passthrough/continuous).
MapTableToNetworkTablesTaskFactory - Interface in org.cytoscape.task.edit
MAX_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
maxWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
MENU_GRAVITY - Static variable in interface org.cytoscape.work.ServiceProperties: Specify relative location of the action in the menu
menuCanceled(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be used at your discretion, but otherwise does nothing.
menuDeselected(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be used at your discretion, but otherwise does nothing.
menuGravity - Variable in class org.cytoscape.application.swing.AbstractCyAction: The float value placing the action within the menu.
MenuGravityTracker - Class in org.cytoscape.util.swing: This class inserts menu items and separators in a menu based on their "gravity".
MenuGravityTracker(JMenu) - Constructor for class org.cytoscape.util.swing.MenuGravityTracker: Constructor.
menuSelected(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be overridden by individual actions to set the state of menu items based on whatever unique circumstances that menu option cares about.
MIN_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
minWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
moveNodeToLocation(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutPartition: Move the node to its current X and Y values.
moveToLocation() - Method in class org.cytoscape.view.layout.LayoutNode: Move the node to its current x,y coordinate.

N

name - Variable in class org.cytoscape.application.swing.AbstractCyAction: The name of the action.
NAME - Static variable in interface org.cytoscape.model.CyNetwork: A String column created by default for every CyNetwork that holds the name of the entry.
name - Variable in class org.cytoscape.property.AbstractConfigDirPropsReader: The name of this CyProperty.
name - Variable in class org.cytoscape.property.bookmark.Attribute
name - Variable in class org.cytoscape.property.bookmark.Category
name - Variable in class org.cytoscape.property.bookmark.DataSource
netView - Variable in class org.cytoscape.task.AbstractEdgeViewTask: The network view associated with AbstractEdgeViewTask.edgeView.
netView - Variable in class org.cytoscape.task.AbstractNodeViewTask: The network view that descendants of this class will operate on.
network - Variable in class org.cytoscape.task.AbstractNetworkTask: The network that descendants of this class will operate on.
NETWORK - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_BACKGROUND_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_CENTER_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_CENTER_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_CENTER_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_HEIGHT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_SCALE_FACTOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_TITLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NETWORK_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NetworkAboutToBeDestroyedEvent - Class in org.cytoscape.model.events: This event signals that a network is about to be destroyed.
NetworkAboutToBeDestroyedEvent(CyNetworkManager, CyNetwork) - Constructor for class org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent: Constructs event.
NetworkAboutToBeDestroyedListener - Interface in org.cytoscape.model.events: Listener for NetworkAboutToBeDestroyedEvent
NetworkAddedEvent - Class in org.cytoscape.model.events: This event signals that a network has been added.
NetworkAddedEvent(CyNetworkManager, CyNetwork) - Constructor for class org.cytoscape.model.events.NetworkAddedEvent: Constructs event.
NetworkAddedListener - Interface in org.cytoscape.model.events: Listener for NetworkAddedEvent
NetworkCollectionTaskFactory - Interface in org.cytoscape.task: Produces a task iterator for the specified collection of networks.
NetworkDestroyedEvent - Class in org.cytoscape.model.events: This event signals that a Network has been destroyed.
NetworkDestroyedEvent(CyNetworkManager) - Constructor for class org.cytoscape.model.events.NetworkDestroyedEvent: Constructs event.
NetworkDestroyedListener - Interface in org.cytoscape.model.events: Listener for NetworkDestroyedEvent
networkExists(long) - Method in interface org.cytoscape.model.CyNetworkManager: Tests whether a network has been registered with the network manager or not.
NetworkImportWebServiceClient - Interface in org.cytoscape.io.webservice: Marker interface for web service clients that have ability to import network data.
networks(Set<CyNetwork>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified networks.
networks - Variable in class org.cytoscape.task.AbstractNetworkCollectionTask: The collection of networks that descendants will operate on.
NetworkTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyNetwork.
networkView - Variable in class org.cytoscape.view.layout.AbstractLayoutTask: The network view that the layout will be applied to.
NetworkViewAboutToBeDestroyedEvent - Class in org.cytoscape.view.model.events: When a CyNetworkView is about to be destroyed, this event will be fired.
NetworkViewAboutToBeDestroyedEvent(CyNetworkViewManager, CyNetworkView) - Constructor for class org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedEvent: Creates the event for network views that are about to be destroyed.
NetworkViewAboutToBeDestroyedListener - Interface in org.cytoscape.view.model.events: Listener for NetworkViewAboutToBeDestroyedEvent.
NetworkViewAddedEvent - Class in org.cytoscape.view.model.events: When a CyNetworkView is added to a CyNetworkViewManager, this event will be fired.
NetworkViewAddedEvent(CyNetworkViewManager, CyNetworkView) - Constructor for class org.cytoscape.view.model.events.NetworkViewAddedEvent: Creates the event for network views that are added.
NetworkViewAddedListener - Interface in org.cytoscape.view.model.events: Listener for NetworkViewAddedEvent.
NetworkViewChangedEvent - Class in org.cytoscape.view.model.events: Fired to indicated that a CyNetworkView has been modified in some way.
NetworkViewChangedEvent(CyNetworkView, Collection<ViewChangeRecord<CyNetwork>>) - Constructor for class org.cytoscape.view.model.events.NetworkViewChangedEvent: Constructor.
NetworkViewChangedListener - Interface in org.cytoscape.view.model.events: Listener for NetworkViewChangedEvent.
NetworkViewCollectionTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified collection of network views.
NetworkViewDestroyedEvent - Class in org.cytoscape.view.model.events: When a CyNetworkView is destroyed, this event will be fired.
NetworkViewDestroyedEvent(CyNetworkViewManager) - Constructor for class org.cytoscape.view.model.events.NetworkViewDestroyedEvent: Creates the event for network views that are destroyed.
NetworkViewDestroyedListener - Interface in org.cytoscape.view.model.events: Listener for NetworkViewDestroyedEvent.
NetworkViewLocationTaskFactory - Interface in org.cytoscape.task: An extension of TaskFactory that provides support for tasks that need to know the a location within a CyNetworkView to perform their task.
networkViews(Set<CyNetworkView>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified network views.
networkViews - Variable in class org.cytoscape.task.AbstractNetworkViewCollectionTask: A collection of network views to operate on for any descendants of this class.
NetworkViewTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyNetworkView.
NewEmptyNetworkViewFactory - Interface in org.cytoscape.task.create: An interface for creating new, empty network views.
NewNetworkSelectedNodesAndEdgesTaskFatory - Interface in org.cytoscape.task.create: This interface provides a task iterator for creating networks from selected nodes and edges.
NewNetworkSelectedNodesOnlyTaskFactory - Interface in org.cytoscape.task.create: This interface provides a task iterator for creating networks from selected nodes only.
NewSessionTaskFactory - Interface in org.cytoscape.task.create: This interface provides a task iterator for creating a new session.
next() - Method in class org.cytoscape.work.TaskIterator: Returns the next Task in order if the TaskIterator can still yield more Tasks, otherwise throws an exception.
NODE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_BORDER_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_BORDER_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_BORDER_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_BORDER_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_FILL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_HEIGHT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_NESTED_NETWORK_IMAGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
NODE_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
nodeCount() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the number of nodes in this partition
nodeIterator() - Method in class org.cytoscape.view.layout.LayoutPartition: Return an iterator over all of the LayoutNodes in this partition
NodeShape - Interface in org.cytoscape.view.presentation.property.values: Marker interface for node shapes.
NodeShapeVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for NodeShape values.
NodeShapeVisualProperty(NodeShape, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Constructor.
nodesToLayOut - Variable in class org.cytoscape.view.layout.AbstractLayoutTask: The node views that will be laid out by the algorithm.
nodeView - Variable in class org.cytoscape.task.AbstractNodeViewTask: The node view that descendants of this class will operate on.
NodeViewTaskFactory - Interface in org.cytoscape.task: A task factory that creates a task that operates on the specified View<CyNode> within the specified CyNetworkView.
NONE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: No arrow
NONE_ZERO_POSITIVE_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
normalizeWeight(LayoutEdge) - Method in class org.cytoscape.view.layout.EdgeWeighter
notifyChangeListeners() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Notifies all dependents that this object has changed.
notifyChangeListeners() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Notify listeners that this object has changed, i.e.
notifyDependents() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Notifies all dependents that this object has changed.
notifyDependents() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Notify dependents that this object has changed, i.e.
NullDataType - Interface in org.cytoscape.view.model: An empty/null data type marker interface for Visual Properties holding no actual data.
NullVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for root.
NullVisualProperty(String, String) - Constructor for class org.cytoscape.view.presentation.property.NullVisualProperty: Constructor.
numericallySafeSum(double[]) - Static method in class org.cytoscape.equations.FunctionUtil: Carefully adds the numbers in "a" minimising loss of precision.

O

ObjectFactory - Class in org.cytoscape.property.bookmark: This object contains factory methods for each Java content interface and Java element interface generated in the org.cytoscape.property.bookmark package.
ObjectFactory() - Constructor for class org.cytoscape.property.bookmark.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.cytoscape.property.bookmark
objectMap(Map<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified old ID maps.
OCTAGON - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Octagonal shape.
offset(double, double) - Method in class org.cytoscape.view.layout.LayoutPartition: Offset all of the nodes in the partition by a fixed amount.
OpenBrowser - Interface in org.cytoscape.util.swing: A utility provided as an OSGi service for opening a web browser.
OpenSessionTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading a session.
openURL(String) - Method in interface org.cytoscape.util.swing.OpenBrowser: Opens a web browser pointing to the specified URL.
org.cytoscape.app - package org.cytoscape.app: This is the Cytoscape App API, which supports development of Cytoscape 3.X apps in a manner similar to apps developed in Cytoscape 2.X.
org.cytoscape.app.swing - package org.cytoscape.app.swing: This is the Cytoscape Swing App API, which supports development of Cytoscape 3.X apps in a manner similar to apps developed in Cytoscape 2.X and provides full access to the Swing specific services of the Cytoscape API in addition to all other services provided in Cytoscape App API.
org.cytoscape.application - package org.cytoscape.application: This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.application.events - package org.cytoscape.application.events: This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
org.cytoscape.application.swing - package org.cytoscape.application.swing: This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
org.cytoscape.application.swing.events - package org.cytoscape.application.swing.events: This package defines the various events fired by the Cytoscape Swing Application API.
org.cytoscape.equations - package org.cytoscape.equations: Various types and utility methods relating to attribute equations.
org.cytoscape.event - package org.cytoscape.event: This package contains the basic interfaces necessary for defining, firing, and listening for Cytoscape events.
org.cytoscape.group - package org.cytoscape.group: This package provides an API for creating and managing groups in Cytoscape.
org.cytoscape.group.data - package org.cytoscape.group.data: An api for configuring CyGroups.
org.cytoscape.group.events - package org.cytoscape.group.events: This package contains the various events and listeners related to group management, creation, and destruction.
org.cytoscape.io - package org.cytoscape.io: Handle import/export of Cytoscape data structures to/from local files/remote URLs.
org.cytoscape.io.datasource - package org.cytoscape.io.datasource: API to provide data files as a bundle.
org.cytoscape.io.read - package org.cytoscape.io.read: Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.util - package org.cytoscape.io.util: A small number of utilities related to IO.
org.cytoscape.io.webservice - package org.cytoscape.io.webservice: Interfaces for SOAP/REST web service clients, web services that return results as networks or tables, or query results.
org.cytoscape.io.webservice.client - package org.cytoscape.io.webservice.client: Provides an abstract class for all web service clients, i.e.
org.cytoscape.io.webservice.events - package org.cytoscape.io.webservice.events: This package defines events/listeners related to data query/import from web services.
org.cytoscape.io.webservice.swing - package org.cytoscape.io.webservice.swing: Web Service Clients with Swing GUI.
org.cytoscape.io.write - package org.cytoscape.io.write: This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
org.cytoscape.model - package org.cytoscape.model: This package contains the core interfaces that define the basic network and table data types that constitute the foundation of Cytoscape.
org.cytoscape.model.events - package org.cytoscape.model.events: This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
org.cytoscape.model.subnetwork - package org.cytoscape.model.subnetwork: This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.property - package org.cytoscape.property: This package provides a general property service interface for providing access to different types of property objects as OSGi services.
org.cytoscape.property.bookmark - package org.cytoscape.property.bookmark: This package provides a set of utility methods to manipulate the bookmarks XML format which is used to store and categorize collections of URL bookmarks pointing to data sources.
org.cytoscape.service.util - package org.cytoscape.service.util: This package contains a simple utility for registering OSGi services without requiring use of the OSGi API.
org.cytoscape.session - package org.cytoscape.session: This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
org.cytoscape.session.events - package org.cytoscape.session.events: This package contains the interfaces and classes necessary to capturing, session change events.
org.cytoscape.task - package org.cytoscape.task: This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.create - package org.cytoscape.task.create: This package provides a variety of task factory interfaces for creating new instances of network and other objects.
org.cytoscape.task.destroy - package org.cytoscape.task.destroy: This package includes a set of task factory interfaces for deleting or or destroying objects within Cytoscape.
org.cytoscape.task.edit - package org.cytoscape.task.edit: This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
org.cytoscape.task.hide - package org.cytoscape.task.hide: This package includes a set of task factory interfaces showing and hiding nodes and edges within network views.
org.cytoscape.task.read - package org.cytoscape.task.read: This package contains a set of task factory interfaces for reading various Cytoscape objects from files and URLs.
org.cytoscape.task.select - package org.cytoscape.task.select: This package includes a set of task factory interfaces for selecting, de-selecting and inverting selections of nodes, edges, or combinations of both based on specific criteria.
org.cytoscape.task.visualize - package org.cytoscape.task.visualize: This package include a set of task factory interfaces used to manipulate the visualizations of network views.
org.cytoscape.task.write - package org.cytoscape.task.write: This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.util.swing - package org.cytoscape.util.swing: This package contains misc helper classes for Cytoscape Desktop application.
org.cytoscape.view.layout - package org.cytoscape.view.layout: This package provides access to the available layout algorithms, as well as provides abstract layout classes and layout information containers for the convenience of implementing other layout algorithms.
org.cytoscape.view.model - package org.cytoscape.view.model: Module for View Models and Visual Properties.
org.cytoscape.view.model.events - package org.cytoscape.view.model.events: Definitions for View-Model related events and their listeners.
org.cytoscape.view.presentation - package org.cytoscape.view.presentation: API set for rendering engines (visualizers).
org.cytoscape.view.presentation.events - package org.cytoscape.view.presentation.events: Event implementations and listener interfaces for the Presentation layer.
org.cytoscape.view.presentation.property - package org.cytoscape.view.presentation.property: Implementations of basic VisualProperty objects and VisualLexicons.
org.cytoscape.view.presentation.property.values - package org.cytoscape.view.presentation.property.values: Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
org.cytoscape.view.vizmap - package org.cytoscape.view.vizmap: Visual Mapping basic API module.
org.cytoscape.view.vizmap.events - package org.cytoscape.view.vizmap.events: Events for Visual Mappings.
org.cytoscape.view.vizmap.gui - package org.cytoscape.view.vizmap.gui: This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
org.cytoscape.view.vizmap.gui.editor - package org.cytoscape.view.vizmap.gui.editor: Provides editors for Visual Properties and editor managers for VizMap GUI.
org.cytoscape.view.vizmap.gui.event - package org.cytoscape.view.vizmap.gui.event: Provides events and listeners of LexiconState, visual style switch and vizMap event, as well as VizMap event handler manager.
org.cytoscape.view.vizmap.gui.util - package org.cytoscape.view.vizmap.gui.util: Create discrete mapping for a given set of attribute values
org.cytoscape.view.vizmap.mappings - package org.cytoscape.view.vizmap.mappings: APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.
org.cytoscape.work - package org.cytoscape.work: This packages everything relating to tasks in Cytoscape.
org.cytoscape.work.swing - package org.cytoscape.work.swing: This packages provides Swing-specific specialisations of concepts from work-api This includes TaskFactory, TaskManager, and TaskIterator.
org.cytoscape.work.swing.undo - package org.cytoscape.work.swing.undo: This packages provides Swing-specific extensions for undo support.
org.cytoscape.work.undo - package org.cytoscape.work.undo: Cytoscape's undo framework.
org.cytoscape.work.util - package org.cytoscape.work.util: Various supporting classes for Cytoscape the work (Task) framework.

P

PAINT_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
paintComponent(Graphics) - Method in class org.cytoscape.util.swing.DropDownMenuButton
PaintVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Paint values.
PaintVisualProperty(Paint, Range<Paint>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.PaintVisualProperty: Constructor.
panel - Variable in class org.cytoscape.work.swing.AbstractGUITunableHandler: JPanel that will contain the GUI representation of the TunableHandler.
PanelTaskManager - Interface in org.cytoscape.work.swing: A specialization of a TaskManager that creates a JPanel configuration object and expects its execution context to be another JPanel.
PARALLELOGRAM - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Parallelogram shape.
parse(String, Map<String, Class<?>>) - Method in interface org.cytoscape.equations.EquationParser: Returns true if the parse succeeded otherwise false
parseSerializableString(String) - Method in interface org.cytoscape.view.model.VisualProperty: Returns an object of type T given a string serialized from the getSerializableString(T value) method.
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.BooleanVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.DoubleVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.FontVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.IntegerVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.LineTypeVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.NullVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.PaintVisualProperty
parseSerializableString(String) - Method in class org.cytoscape.view.presentation.property.StringVisualProperty
parseSerializableString(String) - Method in interface org.cytoscape.view.presentation.property.values.BendFactory: Creates an instance of edge bend from serializable string.
partition(CyNetworkView, boolean, EdgeWeighter) - Static method in class org.cytoscape.view.layout.PartitionUtil: Partition the graph -- this builds the LayoutEdge and LayoutNode arrays as a byproduct.
partition(CyNetworkView, Collection<CyNode>, EdgeWeighter) - Static method in class org.cytoscape.view.layout.PartitionUtil: Partition the graph -- this builds the LayoutEdge and LayoutNode arrays as a byproduct.
partitionList - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: The list of LayoutPartition objects that get laid out.
PartitionUtil - Class in org.cytoscape.view.layout: This class also provides static methods that are used to partition a network.
PASSTHROUGH - Static variable in interface org.cytoscape.view.vizmap.mappings.PassthroughMapping: A label describing the mapping.
PassthroughMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings: An interface describing a passthrough or identity mapping from attribute value to visual property.
popupMenuCanceled(PopupMenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be used at your discretion, but otherwise does nothing.
PopupMenuGravityTracker - Class in org.cytoscape.util.swing: This class inserts menu items and separators in a menu based on their "gravity".
PopupMenuGravityTracker(JPopupMenu) - Constructor for class org.cytoscape.util.swing.PopupMenuGravityTracker: Constructor.
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be used at your discretion, but otherwise does nothing.
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction: This method can be overridden by individual actions to set the state of menu items based on whatever unique circumstances that menu option cares about.
postEdit(AbstractCyEdit) - Method in interface org.cytoscape.work.undo.UndoSupport: Posts the specified edit to the Cytoscape undo stack.
PreferencesUpdatedEvent - Class in org.cytoscape.application.swing.events: An event indicating that system preferences have been updated.
PreferencesUpdatedEvent(Object, Properties, Properties) - Constructor for class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: Constructor.
PreferencesUpdatedListener - Interface in org.cytoscape.application.swing.events: A listener for the PreferencesUpdatedEvent.
PREFERRED_ACTION - Static variable in interface org.cytoscape.work.ServiceProperties: Preferred action properties.
PREFERRED_MENU - Static variable in interface org.cytoscape.work.ServiceProperties: Preferred menu item for an action
preferredMenu - Variable in class org.cytoscape.application.swing.AbstractCyAction: The name describing the preferred menu for the action.
PresentationWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a View rendered by the specified RenderingEngine to be specified and written.
PresentationWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing View objects.
primaryKeyValue - Variable in class org.cytoscape.task.AbstractTableCellTask: The primary key of the CyTable cell
printCanvas(Graphics) - Method in interface org.cytoscape.view.presentation.RenderingEngine: Render presentation on the given Java 2D Canvas.
printDisp() - Method in class org.cytoscape.view.layout.LayoutNode: Return a string representation of the node's displacement
printLocation() - Method in class org.cytoscape.view.layout.LayoutNode: Return a string representation of the node's location
processEvent(PropertyChangeEvent) - Method in interface org.cytoscape.view.vizmap.gui.event.VizMapEventHandler: Process event.
properties(Set<CyProperty<?>>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified properties.
propertyEditor - Variable in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor: The property editor.
PropertySheetUtil - Class in org.cytoscape.view.vizmap.gui.util: Utility class to provide access to basic set of Visual Properties.
PropertySheetUtil() - Constructor for class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
PropertyUpdatedEvent - Class in org.cytoscape.property: This event signals that a CyProperty is updated.
PropertyUpdatedEvent(CyProperty<?>) - Constructor for class org.cytoscape.property.PropertyUpdatedEvent: Constructs the event.
PropertyUpdatedListener - Interface in org.cytoscape.property: Listener interface for PropertyUpdatedEvent.
props - Variable in class org.cytoscape.property.AbstractConfigDirPropsReader: The Properties object created for this class.
ProvidesTitle - Annotation Type in org.cytoscape.work: An annotation type that can be applied to a method which returns a String that will be used for the title of a Tunable user interface dialog window.
putAll(Map<K, T>) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: Adds All Members of Specified Map.
putMapValue(K, T) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: Puts New Key/Value in Map.

R

randomizeLocations() - Method in class org.cytoscape.view.layout.LayoutPartition: Randomize the graph locations.
Range<T> - Interface in org.cytoscape.view.model: Defines a range of values for VisualPropertys.
RecentlyOpenedTracker - Interface in org.cytoscape.io.util: Manages list of recently opened files.
recordTunableState(Object) - Method in interface org.cytoscape.work.TunableRecorder: The method called for each tunable object processed by a TaskManager.
RECTANGLE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Rectangular shape.
redo() - Method in class org.cytoscape.view.layout.LayoutEdit
redo() - Method in class org.cytoscape.work.undo.AbstractCyEdit: The method that performs the redo.
registerAllServices(BundleContext, Object, Properties) - Method in class org.cytoscape.service.util.AbstractCyActivator: A utility method that registers the specified service object as an OSGi service for all interfaces that the object implements.
registerAllServices(Object, Properties) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: This method registers an object as an OSGi service for all interfaces that the object implements and with the specified properties.
registerFunction(Function) - Method in interface org.cytoscape.equations.EquationParser: After registering an attribute function "func" it can be used in attribute equations.
registerService(BundleContext, Object, Class<?>, Properties) - Method in class org.cytoscape.service.util.AbstractCyActivator: A utility method that registers the specified service object as an OSGi service of the specified type.
registerService(Object, Class<?>, Properties) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: This method registers an object as an OSGi service with the specified service interface and properties.
registerServiceListener(BundleContext, Object, String, String, Class<?>, Class<?>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(BundleContext, Object, String, String, Class<?>) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(BundleContext, Object, String, String, Class<?>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(BundleContext, Object, String, String, Class<?>, Class<?>) - Method in class org.cytoscape.service.util.AbstractCyActivator: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(Object, String, String, Class<?>, Class<?>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(Object, String, String, Class<?>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(Object, String, String, Class<?>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
registerServiceListener(Object, String, String, Class<?>, Class<?>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar: A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.
remove() - Method in class org.cytoscape.work.TaskIterator: Unsupported -> always throws an exception!
removeAction(CyAction) - Method in interface org.cytoscape.application.swing.CySwingApplication: Remove the specified CyAction from the application.
removeAggregator(Aggregator) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Remove an aggregator from the available aggregators.
removeAllHandles() - Method in interface org.cytoscape.view.presentation.property.values.Bend: Remove all Handles on this Bend
removeCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
removeComponent(Component) - Method in interface org.cytoscape.util.swing.GravityTracker: Removes an item from this tracker and the corresponding menu.
removeComponent(Component) - Method in class org.cytoscape.util.swing.MenuGravityTracker
removeComponent(Component) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
RemovedEdgesEvent - Class in org.cytoscape.model.events: Just a signal in case anyone wants to resync after an edge has been removed.
RemovedEdgesEvent(CyNetwork) - Constructor for class org.cytoscape.model.events.RemovedEdgesEvent: Constructs event.
RemovedEdgesListener - Interface in org.cytoscape.model.events: Listener for RemovedEdgesEvents.
RemovedNodesEvent - Class in org.cytoscape.model.events: Just a signal in case anyone wants to resync after a node has been removed.
RemovedNodesEvent(CyNetwork) - Constructor for class org.cytoscape.model.events.RemovedNodesEvent: Constructs event.
RemovedNodesListener - Interface in org.cytoscape.model.events: Listener for RemovedNodesEvents.
removeEdges(List<CyEdge>) - Method in interface org.cytoscape.group.CyGroup: Remove a set of edges from a group.
removeEdges(Collection<CyEdge>) - Method in interface org.cytoscape.model.CyNetwork: Remove an edge from the network and delete the edge (if it only exists in this network).
removeEdges(Collection<CyEdge>) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Removes a edge from this CySubNetwork but not from the CyRootNetwork.
removeGroupFromNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Remove a group from a network.
removeHandleAt(int) - Method in interface org.cytoscape.view.presentation.property.values.Bend: Remove a Handle at the given index.
removeIncompatibleVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Remove incompatible VisualProperty from list if new RenderingEngine can handle it.
removeNodes(List<CyNode>) - Method in interface org.cytoscape.group.CyGroup: Remove a set of nodes and their edges from a group
removeNodes(Collection<CyNode>) - Method in interface org.cytoscape.model.CyNetwork: Remove a node from the network and delete the node (if it only exists in this network).
removeNodes(Collection<CyNode>) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Removes a node from this CySubNetwork but not from the CyRootNetwork.
removePoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Removes a Point from the List.
removeRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Remove a rendering engine.
removeSubNetwork(CySubNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Removes the subnetwork from the root network, but not the nodes and edges contained in the subnetwork.
removeTable(CyNetwork, Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetworkTableManager: Removes the table with the specified namespace and type from the network.
removeTreeModelListener(TreeModelListener) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
removeTunableHandlerFactory(TunableHandlerFactory<T>, Map) - Method in class org.cytoscape.work.AbstractTunableInterceptor: Allows TunableHandlerFactory services to be removed from the list of factories used to process Tunables.
removeTunableRecorder(TunableRecorder, Map) - Method in class org.cytoscape.work.AbstractTaskManager: Removes the specified TunableRecorder service from the task manager.
removeValueEditor(ValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Remove an editor from manager (through OSGi).
removeVisualMappingFunction(VisualProperty<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Remove a VisualMappingFunction for the VisualProperty.
removeVisualPropertyDependency(VisualPropertyDependency<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Remove a VisualPropertyDependency.
removeVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Remove a VisualStyle from this manager.
RenameColumnTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for renaming a column.
RenderingEngine<T> - Interface in org.cytoscape.view.presentation: RenderingEngine is an interface for all visualizers which renders.
RenderingEngineAboutToBeRemovedEvent - Class in org.cytoscape.view.presentation.events: When presentation (rendered graphics) is destroyed, this event should be fired.
RenderingEngineAboutToBeRemovedEvent(RenderingEngineManager, RenderingEngine<?>) - Constructor for class org.cytoscape.view.presentation.events.RenderingEngineAboutToBeRemovedEvent: Construct an event for destroyed RenderingEngine.
RenderingEngineAboutToBeRemovedListener - Interface in org.cytoscape.view.presentation.events: Listener for RenderingEngineAboutToBeRemovedEvent.
RenderingEngineAddedEvent - Class in org.cytoscape.view.presentation.events: When new presentation is created, its factory always creates a RenderingEngine).
RenderingEngineAddedEvent(RenderingEngineManager, RenderingEngine<?>) - Constructor for class org.cytoscape.view.presentation.events.RenderingEngineAddedEvent: Create an event for newly created presentation.
RenderingEngineAddedListener - Interface in org.cytoscape.view.presentation.events: Listener for RenderingEngineAddedEvent.
RenderingEngineFactory<T> - Interface in org.cytoscape.view.presentation: A factory class to create visualization for a given view model.
RenderingEngineManager - Interface in org.cytoscape.view.presentation: Manager for RenderingEngine objects.
reset() - Method in interface org.cytoscape.group.CyGroupManager: Releases all currently held references and resources.
reset() - Method in interface org.cytoscape.model.CyNetworkManager: Releases all currently held references and resources.
reset() - Method in interface org.cytoscape.model.CyNetworkTableManager: Clears all the network-table relationships.
reset() - Method in interface org.cytoscape.model.CyTableManager: Releases all currently held references and resources.
reset() - Method in class org.cytoscape.view.layout.EdgeWeighter
reset() - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Releases all currently held references and resources.
reset() - Method in interface org.cytoscape.work.undo.UndoSupport: Clears the undo stack.
resetNodes() - Method in class org.cytoscape.view.layout.LayoutPartition: Reset all of the data maintained for the LayoutNodes contained within this partition, including the min, max and average x and y values.
rootVisualProperty - Variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The Root of this tree.
ROUND_RECTANGLE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Rectangular shape with rounded corners.
row - Variable in class org.cytoscape.task.AbstractRowTask: The row that descendants will operate on.
rowExists(Object) - Method in interface org.cytoscape.model.CyTable: Returns true if a row exists for the specified primary key and false otherwise.
RowsCreatedEvent - Class in org.cytoscape.model.events: This event signals that rows have been created.
RowsCreatedEvent(CyTable, Collection<Object>) - Constructor for class org.cytoscape.model.events.RowsCreatedEvent: Constructs event.
RowsCreatedListener - Interface in org.cytoscape.model.events: Listener for RowsCreatedEvent
RowSetRecord - Class in org.cytoscape.model.events: Holds a record of a CyRow that was set and what it was set to.
RowSetRecord(CyRow, String, Object, Object) - Constructor for class org.cytoscape.model.events.RowSetRecord: Constructs a RowSetRecord.
RowsSetEvent - Class in org.cytoscape.model.events: This event signals that rows have been set.
RowsSetEvent(CyTable, Collection<RowSetRecord>) - Constructor for class org.cytoscape.model.events.RowsSetEvent: Constructs Event.
RowsSetListener - Interface in org.cytoscape.model.events: Listener for RowsSetEvent
RowTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyRow.
run(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractLayoutTask: This method is called when the Task begins execution.
run(TaskMonitor) - Method in class org.cytoscape.work.AbstractTask: This method is called when the Task begins execution.
run(TaskMonitor) - Method in interface org.cytoscape.work.Task: This method is called when the Task begins execution.

S

SAVE - Static variable in interface org.cytoscape.util.swing.FileUtil: Equal to FileDialog.SAVE.
saveBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Store a bookmark object in bookmarks object
savePolicy - Variable in class org.cytoscape.property.AbstractConfigDirPropsReader: The SavePolicy of this CyProperty.
SaveSessionAsTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for saving a session in a specified file.
SearchFinishedEvent<T> - Class in org.cytoscape.io.webservice.events: An event that indicates a search has completed.
SearchFinishedEvent(WebServiceClient, T) - Constructor for class org.cytoscape.io.webservice.events.SearchFinishedEvent: Constructs the event.
SearchFinishedListener - Interface in org.cytoscape.io.webservice.events: Listener for SearchFinishedEvent.
SearchWebServiceClient - Interface in org.cytoscape.io.webservice: Marker interface for web service clients sending search query and getting arbitrary search result.
SelectAdjacentEdgesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting adjacent edges.
SelectAllEdgesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting all of the edges.
SelectAllNodesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting all of the nodes.
SelectAllTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting all of the items.
SelectConnectedNodesTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting connected nodes.
SELECTED - Static variable in interface org.cytoscape.model.CyNetwork: A boolean column created by default for every CyNode or CyEdge that holds the selection state of the entry.
SelectedVisualStyleManager - Interface in org.cytoscape.view.vizmap.gui: Manages current (selected) Visual Style.
SelectedVisualStyleSwitchedEvent - Class in org.cytoscape.view.vizmap.gui.event: This event will be fired when current Visual Style is switched.
SelectedVisualStyleSwitchedEvent(Object, VisualStyle, VisualStyle) - Constructor for class org.cytoscape.view.vizmap.gui.event.SelectedVisualStyleSwitchedEvent: Constructor for this event.
SelectedVisualStyleSwitchedListener - Interface in org.cytoscape.view.vizmap.gui.event: Listener for SelectedVisualStyleSwitchedEvent.
SelectFirstNeighborsNodeViewTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting neighbor nodes.
SelectFirstNeighborsTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting the first neighbors.
SelectFromFileListTaskFactory - Interface in org.cytoscape.task.select: This interface provides a task iterator for selecting items based on a file.
serialVersionUID - Static variable in class org.cytoscape.equations.BooleanList
serialVersionUID - Static variable in class org.cytoscape.equations.DoubleList
serialVersionUID - Static variable in class org.cytoscape.equations.LongList
serialVersionUID - Static variable in class org.cytoscape.equations.StringList
ServiceProperties - Interface in org.cytoscape.work: Reserved keywords for OSGi service properties (meta data).
SessionAboutToBeSavedEvent - Class in org.cytoscape.session.events: This event is fired synchronously by the CySessionManager at beginning of the CySessionManager.getCurrentSession() method.
SessionAboutToBeSavedEvent(CySessionManager) - Constructor for class org.cytoscape.session.events.SessionAboutToBeSavedEvent: Constructor.
SessionAboutToBeSavedListener - Interface in org.cytoscape.session.events: Any object that needs to know that a CySession is about to be created listen to this event.
SessionLoadedEvent - Class in org.cytoscape.session.events: This event is fired after a new session has been set in the CySessionManager.setCurrentSession(CySession, String) method and is used to notify interested parties in the change of state.
SessionLoadedEvent(CySessionManager, CySession, String) - Constructor for class org.cytoscape.session.events.SessionLoadedEvent: Constructor.
SessionLoadedListener - Interface in org.cytoscape.session.events: A listener for SessionLoadedEvents.
SessionSavedEvent - Class in org.cytoscape.session.events
SessionSavedEvent(Object, CySession, String) - Constructor for class org.cytoscape.session.events.SessionSavedEvent
SessionSavedListener - Interface in org.cytoscape.session.events: A listener for SessionSavedEvents.
set(String, T) - Method in interface org.cytoscape.model.CyRow: Set the specified column for this row to the specified value.
setAcceleratorKeyStroke(KeyStroke) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the accelerator KeyStroke for this action.
setBendFactory(BendFactory) - Method in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: Sets the bend factory that is used behind the scenes to create bend objects.
setCenterLabel(String) - Method in class org.cytoscape.util.swing.JStatusBar: Set the center label of this JStatusBar.
setCollapsed(boolean) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Collapses or expands the panel.
setConfigurationContext(Object) - Method in interface org.cytoscape.work.TunableMutator: Used configure the TunableMutator so that it builds its configuration object in the correct location.
setContent(String) - Method in class org.cytoscape.property.bookmark.Attribute: Sets the value of the content property.
setCurrentNetwork(CyNetwork) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the current network to the specified network.
SetCurrentNetworkEvent - Class in org.cytoscape.application.events: An event signaling that the a network has been set to current.
SetCurrentNetworkEvent(CyApplicationManager, CyNetwork) - Constructor for class org.cytoscape.application.events.SetCurrentNetworkEvent: Constructor.
SetCurrentNetworkListener - Interface in org.cytoscape.application.events: A listener for SetCurrentNetworkEvents.
setCurrentNetworkView(CyNetworkView) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the current network view to the specified network view.
SetCurrentNetworkViewEvent - Class in org.cytoscape.application.events: An event indicating that a network view has been set to current.
SetCurrentNetworkViewEvent(CyApplicationManager, CyNetworkView) - Constructor for class org.cytoscape.application.events.SetCurrentNetworkViewEvent: Constructor.
SetCurrentNetworkViewListener - Interface in org.cytoscape.application.events: A listener for SetCurrentNetworkViewEvents.
setCurrentRenderingEngine(RenderingEngine<CyNetwork>) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the current rendering engine.
SetCurrentRenderingEngineEvent - Class in org.cytoscape.application.events: This event signals that a RenderingEngine has been set as current.
SetCurrentRenderingEngineEvent(CyApplicationManager, RenderingEngine<CyNetwork>) - Constructor for class org.cytoscape.application.events.SetCurrentRenderingEngineEvent: Constructor.
SetCurrentRenderingEngineListener - Interface in org.cytoscape.application.events: Listener for SetCurrentRenderingEngineEvent.
setCurrentSession(CySession, String) - Method in interface org.cytoscape.session.CySessionManager: This method allows a new session to be set and in doing so erases and overrides the current session!
setCurrentTable(CyTable) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the currently active table.
setDefaultValue(VisualProperty<V>, S) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Set default value for the VisualProperty.
setDependency(boolean) - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Enables or disables the dependency based on the boolean parameter.
setDescription(String) - Method in class org.cytoscape.property.bookmark.Bookmarks: Sets the value of the description property.
setDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the displacement of this LayoutNode.
setEdgeWeighter(EdgeWeighter) - Method in class org.cytoscape.view.layout.LayoutPartition: Set the EdgeWeighter to use for this partition.
setEnabled(boolean) - Method in interface org.cytoscape.work.swing.DynamicSubmenuListener: Enables or disables the dynamically created menus.
setExecutionContext(C) - Method in class org.cytoscape.work.AbstractTaskManager: Simple sets the executionContext to the specified input value.
setExecutionContext(C) - Method in interface org.cytoscape.work.TaskManager: Allows a user of a TaskManager to set the execution context for the task, for example the parent Window of a dialog or the top-level menu for menu generation.
setFormat(String) - Method in class org.cytoscape.property.bookmark.DataSource: Sets the value of the format property.
setHref(String) - Method in class org.cytoscape.property.bookmark.DataSource: Sets the value of the href property.
setLeftLabel(String) - Method in class org.cytoscape.util.swing.JStatusBar: Set the left label of this JStatusBar.
setLocation(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the location of this LayoutNode.
setLockedValue(VisualProperty<? extends T>, V) - Method in interface org.cytoscape.view.model.View: Set locked value.
setLogWeight(double) - Method in class org.cytoscape.view.layout.LayoutEdge: Set the log weight for this LayoutEdge.
setMaxWeightCutoff(double) - Method in class org.cytoscape.view.layout.EdgeWeighter
setMenuGravity(float) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the gravity used to order this action in the menu bar.
setMenuTitle(String) - Method in interface org.cytoscape.work.swing.DynamicSubmenuListener: Sets the name of the top level menu.
setMinWeightCutoff(double) - Method in class org.cytoscape.view.layout.EdgeWeighter
setMode(boolean) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Switch the current display mode.
setName(String) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the name of the action.
setName(String) - Method in interface org.cytoscape.model.CyColumn: Change the name of this column.
setName(String) - Method in class org.cytoscape.property.bookmark.Attribute: Sets the value of the name property.
setName(String) - Method in class org.cytoscape.property.bookmark.Category: Sets the value of the name property.
setName(String) - Method in class org.cytoscape.property.bookmark.DataSource: Sets the value of the name property.
setNetworkPointer(CyNetwork) - Method in interface org.cytoscape.model.CyNode: Allows a network reference for this node to be set.
SetNetworkPointerEvent - Class in org.cytoscape.model.events: Used to track setting of nested networks on nodes.
SetNetworkPointerEvent(CyNode, CyNetwork) - Constructor for class org.cytoscape.model.events.SetNetworkPointerEvent: Constructs event.
SetNetworkPointerListener - Interface in org.cytoscape.model.events: Listener for SetNetworkPointerEvents.
setNormalizedBounds(double, double) - Method in class org.cytoscape.view.layout.EdgeWeighter
setPartitionNumber(int) - Method in class org.cytoscape.view.layout.LayoutPartition: Set the partition number of this partition
setPreferredMenu(String) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the preferredMenuString.
setProgress(double) - Method in interface org.cytoscape.work.TaskMonitor: Sets the progress completed by the Task.
setRange(BoundaryRangeValues<V>) - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Sets BoundaryRangeValues.
setRightLabel(String) - Method in class org.cytoscape.util.swing.JStatusBar: Set the right label of this JStatusBar.
setRowHeight(int) - Method in class org.cytoscape.util.swing.JTreeTable: Overridden to pass the new rowHeight to the tree.
setSavePolicy(CyTable.SavePolicy) - Method in interface org.cytoscape.model.CyTable: Sets how (or if) this CyTable should be saved.
setSelectedIndex(int) - Method in interface org.cytoscape.application.swing.CytoPanel: Sets the selected index on the CytoPanel.
setSelectedItems(List<String>) - Method in class org.cytoscape.util.swing.CheckBoxJList: Sets the specified items as selected.
setSelectedNetworks(List<CyNetwork>) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the networks specified as selected.
SetSelectedNetworksEvent - Class in org.cytoscape.application.events: An event indicating the a collection of networks has been selected.
SetSelectedNetworksEvent(CyApplicationManager, List<CyNetwork>) - Constructor for class org.cytoscape.application.events.SetSelectedNetworksEvent: Constructor.
SetSelectedNetworksListener - Interface in org.cytoscape.application.events: A listener for SetSelectedNetworksEvents.
setSelectedNetworkViews(List<CyNetworkView>) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the specified network views as selected.
SetSelectedNetworkViewsEvent - Class in org.cytoscape.application.events: An event that indicates that a collection of network views has been selected.
SetSelectedNetworkViewsEvent(CyApplicationManager, List<CyNetworkView>) - Constructor for class org.cytoscape.application.events.SetSelectedNetworkViewsEvent: Constructor.
SetSelectedNetworkViewsListener - Interface in org.cytoscape.application.events: A listener for SetSelectedNetworkViewsEvents.
setSelectedValue(T) - Method in class org.cytoscape.work.util.ListSingleSelection: Set the val item of type T as selected in the ListSingleSelection.
setSelectedValues(List<T>) - Method in class org.cytoscape.work.util.ListMultipleSelection: Set the T items as selected in the ListMultipleSelection object.
setState(CytoPanelState) - Method in interface org.cytoscape.application.swing.CytoPanel: Sets the state of the CytoPanel.
setStatusMessage(String) - Method in interface org.cytoscape.work.TaskMonitor: Sets the status message that describes what a Task is currently doing.
setTable(CyNetwork, Class<? extends CyIdentifiable>, String, CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager: Associates the given table to the network using the specified namespace and type.
setTaskIterator(TaskIterator) - Method in class org.cytoscape.work.AbstractTask: This method is typically used by a TaskIterator to set itself on the newly added Task.
setTaskStatus(int) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Used for
setTitle(String) - Method in interface org.cytoscape.model.CyTable: Allows the title of the table to be set.
setTitle(String) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Set new title for this VisualStyle.
setTitle(String) - Method in interface org.cytoscape.work.TaskMonitor: Sets the title of the Task.
setTitleComponentText(String) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Sets the title of of the border title component.
setToolbarGravity(float) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the gravity used to order this action in the toolbar.
setToolBarGravity(float) - Method in class org.cytoscape.application.swing.AbstractToolBarComponent: Sets the gravity for this toolbar component.
setToolTipText(String) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Sets the tooltip text of this BasicCollapsiblePanel.
setValue(K) - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Sets Point Value.
setValue(Object) - Method in class org.cytoscape.work.AbstractTunableHandler: Attempts to set the value "newValue" on the associated Tunable.
setValue(Object) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
setValue(Object) - Method in interface org.cytoscape.work.TunableHandler: Attempts to set the value "newValue" on the associated Tunable.
setValue(N) - Method in class org.cytoscape.work.util.AbstractBounded: Set the value v as the value of the Bounded Object.
setValue(String) - Method in class org.cytoscape.work.util.AbstractBounded: Sets the value of the Bounded object.
setValue(String) - Method in class org.cytoscape.work.util.BoundedDouble: Set a new value to the BoundedDouble object
setValue(String) - Method in class org.cytoscape.work.util.BoundedFloat: Set a new value to the BoundedFloat object.
setValue(String) - Method in class org.cytoscape.work.util.BoundedInteger: Set a new value to the BoundedInteger object
setValue(String) - Method in class org.cytoscape.work.util.BoundedLong: Set a new value to the BoundedLong object.
setValueAt(Object, Object, int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Should be overridden - this is a no-op.
setValueAt(Object, Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Sets the value for node node, at column number column.
setValueAt(Object, int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Sets the value at the given row and column..
setVersion(BigDecimal) - Method in class org.cytoscape.property.bookmark.Bookmarks: Sets the value of the version property.
setViewDefault(VisualProperty<? extends T>, V) - Method in interface org.cytoscape.view.model.CyNetworkView: Sets the default value to be used for the specified visual property.
setVisualProperty(VisualProperty<? extends T>, V) - Method in interface org.cytoscape.view.model.View: Assign a value to the given Visual Property of this view.
setVisualStyle(VisualStyle, CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Set a VisualStyle to the target network view model.
setWeight(LayoutEdge) - Method in class org.cytoscape.view.layout.EdgeWeighter
setWeight(double) - Method in class org.cytoscape.view.layout.LayoutEdge: Set the weight for this LayoutEdge.
setWeightAttribute(String) - Method in class org.cytoscape.view.layout.EdgeWeighter
setWeightType(WeightTypes) - Method in class org.cytoscape.view.layout.EdgeWeighter
setX(double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the X location of this LayoutNode.
setY(double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the Y location of this LayoutNode.
SHARED_ATTRS - Static variable in interface org.cytoscape.model.subnetwork.CyRootNetwork: The name of the table shared by all subnetworks.
SHARED_INTERACTION - Static variable in interface org.cytoscape.model.subnetwork.CyRootNetwork: The name of the shared interaction column found in the SHARED_ATTRS table.
SHARED_NAME - Static variable in interface org.cytoscape.model.subnetwork.CyRootNetwork: The name of the shared name column found in the SHARED_ATTRS table.
shouldIgnoreDefault - Variable in class org.cytoscape.view.model.AbstractVisualProperty: If this is true, default value will be ignored by VizMapper.
shouldIgnoreDefault() - Method in class org.cytoscape.view.model.AbstractVisualProperty
shouldIgnoreDefault() - Method in interface org.cytoscape.view.model.VisualProperty: In some cases, default value from visual style is not suitable, such as x, y, z location of nodes.
shouldSelectCell(EventObject) - Method in class org.cytoscape.util.swing.AbstractCellEditor
showDialog(Component, String, Color) - Static method in class org.cytoscape.util.swing.CyColorChooser: Display custom color chooser dialog.
showEditor(Component) - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewEditor: Show the default view editor in the specified parent component.
showEditor(Component, S) - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor: Display the editor and get a new value.
showVisualPropertyValueEditor(Component, VisualProperty<V>, V) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Display value editor to get a new value.
silenceEventSource(Object) - Method in interface org.cytoscape.event.CyEventHelper: This method will prevent any events fired from the specified source object from being propagated to listeners.
SimpleCyProperty<P> - Class in org.cytoscape.property: A simple implementation of CyProperty suitable for general purpose use.
SimpleCyProperty(String, P, Class<? extends P>, CyProperty.SavePolicy) - Constructor for class org.cytoscape.property.SimpleCyProperty: Properties is a non-null Properties object that this CyProperty object should encapsulate.
SimpleGUITunableHandlerFactory<T extends GUITunableHandler> - Class in org.cytoscape.work.swing: A specialization for GUITunableHandlers.
SimpleGUITunableHandlerFactory(Class<T>, Class<?>...) - Constructor for class org.cytoscape.work.swing.SimpleGUITunableHandlerFactory: Constructs this BasicGUITunableHandlerFactory.
size() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the size of this partition, which is defined as the number of nodes that it contains.
SMALL_ICON_URL - Static variable in interface org.cytoscape.work.ServiceProperties: Location of small icon data for desktop application
SOLID - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Solid line
stop(BundleContext) - Method in class org.cytoscape.service.util.AbstractCyActivator: A default implementation of the BundleActivator.stop() method that cleans up any services registered, services gotten, or services being listened for as determined by calls to the utility methods provided by this class.
stopCellEditing() - Method in class org.cytoscape.util.swing.AbstractCellEditor
streamUtil - Variable in class org.cytoscape.io.BasicCyFileFilter
StreamUtil - Interface in org.cytoscape.io.util: A stateless utility class that provides special handling to support InputStreams and URLConnections over the network.
STRING_SET - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
StringList - Class in org.cytoscape.equations: An convenience implementation of ArrayList<String> that allows for strong type checking.
StringList(String...) - Constructor for class org.cytoscape.equations.StringList: Constructor.
StringVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for String values.
StringVisualProperty(String, Range<String>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.StringVisualProperty: Constructor.
StringVisualProperty(String, Range<String>, String, String, boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.StringVisualProperty: Constructor.
SUID - Static variable in interface org.cytoscape.model.CyIdentifiable: This will be used as column name of SUID.
SUIDFactory - Class in org.cytoscape.model: This singleton class returns unique, positive SUID (session unique ID) values.
swap(CyTable) - Method in interface org.cytoscape.model.CyTable: Swaps the contents and properties (such as mutability) of "otherTable" with this table.
swingAdapter - Variable in class org.cytoscape.app.swing.AbstractCySwingApp: Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.
SwingUndoSupport - Interface in org.cytoscape.work.swing.undo: In general, developers should NOT use this interface or the classes it provides access to to post edits and should use UndoSupport instead.
SynchronousTaskManager<T> - Interface in org.cytoscape.work: A marker interface that indicates that the TaskManager in question will execute the tasks found in the TaskFactory synchronously, rather than asynchronously.

T

T - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: T shaped arrow
table - Variable in class org.cytoscape.task.AbstractTableTask: The table that descendants of this class will operate on.
table - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: The table used for this mapping.
TableAboutToBeDeletedEvent - Class in org.cytoscape.model.events: This event signals that a table is about to be deleted.
TableAboutToBeDeletedEvent(CyTableManager, CyTable) - Constructor for class org.cytoscape.model.events.TableAboutToBeDeletedEvent: Constructs the event.
TableAboutToBeDeletedListener - Interface in org.cytoscape.model.events: Listener for TableAboutToBeDeletedEvent
TableAddedEvent - Class in org.cytoscape.model.events: This event will be fired when new table is added to CyTableManager.
TableAddedEvent(CyTableManager, CyTable) - Constructor for class org.cytoscape.model.events.TableAddedEvent: Constructs the table added event.
TableAddedListener - Interface in org.cytoscape.model.events: Listener for TableAddedEvent.
TableCellTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyColumn along with primary key.
TableColumnTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyColumn.
TableDeletedEvent - Class in org.cytoscape.model.events: This event signals that a table has been deleted.
TableDeletedEvent(CyTableManager) - Constructor for class org.cytoscape.model.events.TableDeletedEvent: Constructs the event.
TableDeletedListener - Interface in org.cytoscape.model.events: Listener for TableDeletedEvent
TableImportWebServiceClient - Interface in org.cytoscape.io.webservice: Maker interface for web service clients that have ability to import table data.
tables(Set<CyTableMetadata>) - Method in class org.cytoscape.session.CySession.Builder: Returns an instance of Builder that has at least been configured with the specified tables.
TableTaskFactory - Interface in org.cytoscape.task: A task factory that creates one or more tasks that operate on the specified CyTable.
Task - Interface in org.cytoscape.work: This interface specifies a unit of work to be executed asynchronously in its own Thread along with a user interface to display its progress, provide a means for the user to cancel the Task, and show information about any Exceptions thrown during its execution.
TaskFactory - Interface in org.cytoscape.work: Returns an instance of a TaskIterator.
TaskIterator - Class in org.cytoscape.work: A TaskIterator provides the functionality of sequencing tasks.
TaskIterator(int, Task...) - Constructor for class org.cytoscape.work.TaskIterator: Constructs an iterator that will yield Tasks in the order that they were passed into this constructor.
TaskIterator(Task...) - Constructor for class org.cytoscape.work.TaskIterator: Constructs an iterator that will yield Tasks in the order that they were passed into this constructor.
TaskManager<T,C> - Interface in org.cytoscape.work: Executes the Tasks found in the TaskIterator provided by a TaskFactory.
taskMonitor - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: The TaskMonitor initially set in the run method of the task.
TaskMonitor - Interface in org.cytoscape.work: Used by Tasks to modify its user interface.
TITLE - Static variable in interface org.cytoscape.work.ServiceProperties: Human-readable display name of a service
titleProviderMap - Variable in class org.cytoscape.work.AbstractTunableInterceptor: Store the title-returning methods.
TOOL_BAR_GRAVITY - Static variable in interface org.cytoscape.work.ServiceProperties: Specify relative location of the action in the tool bar
ToolBarComponent - Interface in org.cytoscape.application.swing: An interface that allows a component to be registered as a service that will then be added to the ToolBar.
toolbarGravity - Variable in class org.cytoscape.application.swing.AbstractCyAction: The float value placing the action within the toolbar.
toolbarGravity - Variable in class org.cytoscape.application.swing.AbstractToolBarComponent: The gravity for this toolbar component.
TOOLTIP - Static variable in interface org.cytoscape.work.ServiceProperties: Tool tip text for an action
toSerializableString(T) - Method in interface org.cytoscape.view.model.VisualProperty: Returns a string of the specified value suitable for serializing to XML other text output.
toSerializableString(ArrowShape) - Method in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
toSerializableString(Boolean) - Method in class org.cytoscape.view.presentation.property.BooleanVisualProperty
toSerializableString(Visualizable) - Method in class org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty
toSerializableString(Double) - Method in class org.cytoscape.view.presentation.property.DoubleVisualProperty
toSerializableString(Bend) - Method in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty
toSerializableString(Font) - Method in class org.cytoscape.view.presentation.property.FontVisualProperty
toSerializableString(Integer) - Method in class org.cytoscape.view.presentation.property.IntegerVisualProperty
toSerializableString(LineType) - Method in class org.cytoscape.view.presentation.property.LineTypeVisualProperty
toSerializableString(NodeShape) - Method in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
toSerializableString(NullDataType) - Method in class org.cytoscape.view.presentation.property.NullVisualProperty
toSerializableString(Paint) - Method in class org.cytoscape.view.presentation.property.PaintVisualProperty
toSerializableString(String) - Method in class org.cytoscape.view.presentation.property.StringVisualProperty
toString() - Method in class org.cytoscape.equations.AbstractNode: Returns s String representation of this node.
toString() - Method in class org.cytoscape.equations.Equation: Returns a textual representation of an Equation.
toString() - Method in interface org.cytoscape.group.data.Aggregator: This gets the name of the handling type supported by this aggregator, suitable for use in a menu.
toString() - Method in enum org.cytoscape.group.data.AttributeHandlingType: Returns a human readable name for this enum value.
toString() - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a human readable description of this class.
toString() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
toString() - Method in enum org.cytoscape.model.CyTable.Mutability
toString() - Method in class org.cytoscape.property.SimpleCyProperty
toString() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
toString() - Method in class org.cytoscape.view.layout.LayoutEdge: Return a string representation for this LayoutEdge.
toString() - Method in class org.cytoscape.view.layout.LayoutNode: Return a string representation of the node
toString() - Method in enum org.cytoscape.view.layout.WeightTypes: Returns the name of the weighting type.
toString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
toString() - Method in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
toString() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
total_nodes - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Total number of nodes used for taskMonitor.
translateObjectType(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Tries to map "input" to one of Double, Long, Boolean or String.
TreeNode - Interface in org.cytoscape.equations: The interface for a node within the Equation parse tree.
TreeTableModel - Interface in org.cytoscape.util.swing: TreeTableModel is the model used by a JTreeTable.
TreeTableModelAdapter - Class in org.cytoscape.util.swing: This is a wrapper class takes a TreeTableModel and implements the table model interface.
TreeTableModelAdapter(TreeTableModel, JTree) - Constructor for class org.cytoscape.util.swing.TreeTableModelAdapter: Creates a new TreeTableModelAdapter object.
TRIANGLE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty: Triangular shape.
Tunable - Annotation Type in org.cytoscape.work: An annotation type that can be applied to a field or a method in order to allow TunableInterceptor to catch it, and so to use its members to create a corresponding interface for a user.
TunableHandler - Interface in org.cytoscape.work: Interface for classes that deal with reading out and writing back Tunables and their properties.
tunableHandlerFactories - Variable in class org.cytoscape.work.AbstractTunableInterceptor: A list of TunableHandlerFactory services that have been registered.
TunableHandlerFactory<T extends TunableHandler> - Interface in org.cytoscape.work: A factory service to create a TunableHandler for a single type of object, determined by the type of the field or the return value of the getter method in the appropriate methods.
tunableMutator - Variable in class org.cytoscape.work.AbstractTaskManager: The single tunable mutator that will be used by this task manager.
TunableMutator<T extends TunableHandler,S> - Interface in org.cytoscape.work: This is a type of tunable interceptor that reads and modifies the values annotated with the Tunable annotation.
TunableRecorder<T extends TunableHandler> - Interface in org.cytoscape.work: TunableRecorder is a special type of tunable interceptor that reads the state of the tunables but does not modify the value of the tunables.
tunableRecorders - Variable in class org.cytoscape.work.AbstractTaskManager: The list of tunable recorders that will be used by this task manager.
TunableSetter - Interface in org.cytoscape.work: An API for setting tunable fields and methods with predetermined values in the Tasks found in the specified TaskIterator.
TunableValidator - Interface in org.cytoscape.work: If implemented, this interface is used to apply a test to the modified values of a Tunable.
TunableValidator.ValidationState - Enum in org.cytoscape.work: This is what the TunableValidator can return.
type - Variable in class org.cytoscape.view.layout.EdgeWeighter




U

undo - 
Variable in class org.cytoscape.view.layout.AbstractLayoutTask
Undo support for the task.
undo() - 
Method in class org.cytoscape.view.layout.LayoutEdit
 
undo() - 
Method in class org.cytoscape.work.undo.AbstractCyEdit
The method that performs the undo.
undoSupport - 
Variable in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
An undo support object available for use
UndoSupport - Interface in org.cytoscape.work.undo
A simple interface that posts edits to the Cytoscape undo stack.
UnGroupNodesTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator ungrouping a selection of nodes from a node view.
UnGroupTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator ungrouping a group from a network view.
UnHideAllEdgesTaskFactory - Interface in org.cytoscape.task.hide
This interface provides a task iterator for unhiding all edges.
UnHideAllNodesTaskFactory - Interface in org.cytoscape.task.hide
This interface provides a task iterator for unhiding all nodes.
UnHideAllTaskFactory - Interface in org.cytoscape.task.hide
This interface provides a task iterator for unhiding everything 
 (all nodes and edges).
unLock() - 
Method in class org.cytoscape.view.layout.LayoutNode
Register this node as being "unlocked".
unregisterAllServices(Object) - 
Method in interface org.cytoscape.service.util.CyServiceRegistrar
This method unregisters an object as all OSGi service
 interfaces that the object implements.
unregisterService(Object, Class) - 
Method in interface org.cytoscape.service.util.CyServiceRegistrar
This method unregisters an object as an OSGi service
 for the specified service interface.
UnsetNetworkPointerEvent - Class in org.cytoscape.model.events
Used to track removing of nested networks from nodes.
UnsetNetworkPointerEvent(CyNode, CyNetwork) - 
Constructor for class org.cytoscape.model.events.UnsetNetworkPointerEvent
Constructs event.
UnsetNetworkPointerListener - Interface in org.cytoscape.model.events
Listener for UnsetNetworkPointerEvents.
unsilenceEventSource(Object) - 
Method in interface org.cytoscape.event.CyEventHelper
This method will allow events fired from the specified source 
 object to be propagated to listeners.
update() - 
Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
The default implementation is a no-op.
update() - 
Method in interface org.cytoscape.work.swing.GUITunableHandler
This method should be implemented to update the user interface in such a way that other tunable
 handlers we listen to have changed, this tunable handler can display the appropriate inforamtion.
updateEnableState() - 
Method in class org.cytoscape.application.swing.AbstractCyAction
Triggers the enable state of the action to be updated based
 on the enableFor state of the action and the state of the
 system.
updateEnableState() - 
Method in class org.cytoscape.application.swing.ActionEnableSupport
Updates the enable state for the specified action/menuListener/menuItem
 for the specified enableFor description and the state of the system.
updateEnableState() - 
Method in interface org.cytoscape.application.swing.CyAction
Forces the action to update its enable state based on the criteria defined for
 the action.
UpdateNetworkPresentationEvent - Class in org.cytoscape.view.model.events
If something has been changed in the view model, presentation layer should
 catch the event and update its visualization.
UpdateNetworkPresentationEvent(CyNetworkView) - 
Constructor for class org.cytoscape.view.model.events.UpdateNetworkPresentationEvent
Event for updating (redrawing) presentation.
UpdateNetworkPresentationListener - Interface in org.cytoscape.view.model.events
Listener for UpdateNetworkPresentationEvent.
updateUI() - 
Method in class org.cytoscape.util.swing.JTreeTable
Overridden to message super and forward the method to the tree.
updateView() - 
Method in interface org.cytoscape.view.model.CyNetworkView
Cascading event for the presentation layer for updating presentation.
URL_PATTERN - 
Static variable in interface org.cytoscape.io.util.StreamUtil
 
urlPattern - 
Static variable in interface org.cytoscape.util.swing.FileUtil
A string that defines a simplified java regular expression for a URL.
USE_ALPHABETIC_ORDER - 
Static variable in interface org.cytoscape.util.swing.GravityTracker
 
useCheckBoxMenuItem - 
Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether to use a checkbox menu item.
useCheckBoxMenuItem() - 
Method in class org.cytoscape.application.swing.AbstractCyAction
Returns whether or not a checkbox menu item should be used.
useCheckBoxMenuItem() - 
Method in interface org.cytoscape.application.swing.CyAction
Returns whether or not a checkbox menu item should be used.



V

validateAndWriteBack(Object) - 
Method in interface org.cytoscape.work.TunableMutator
This method is called to validate and then set the values for
 fields and methods annotated with the Tunable annotation.
validateArgTypes(Class[]) - 
Method in class org.cytoscape.equations.AbstractFunction
Returns the return type of this function.
validateArgTypes(Class<?>[]) - 
Method in interface org.cytoscape.equations.Function
 
valueChanged(ListSelectionEvent) - 
Method in class org.cytoscape.util.swing.CheckBoxJList

ValueEditor<V> - Interface in org.cytoscape.view.vizmap.gui.editor
Provides a GUI Editor for a data type.
valueForPathChanged(TreePath, Object) - 
Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Should be overridden.
valueOf(String) - 
Static method in enum org.cytoscape.application.swing.CytoPanelName
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.application.swing.CytoPanelState
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.equations.ArgType
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.group.data.AttributeHandlingType
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.io.DataCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.model.CyEdge.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.model.CyTable.Mutability
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.model.CyTable.SavePolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.model.CyTableFactory.InitialTableSize
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.property.CyProperty.SavePolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.view.layout.WeightTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
Returns the enum constant of this type with the specified name.
valueOf(String) - 
Static method in enum org.cytoscape.work.TunableValidator.ValidationState
Returns the enum constant of this type with the specified name.
values() - 
Static method in enum org.cytoscape.application.swing.CytoPanelName
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.application.swing.CytoPanelState
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.equations.ArgType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.group.data.AttributeHandlingType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.io.DataCategory
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.model.CyEdge.Type
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.model.CyTable.Mutability
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.model.CyTable.SavePolicy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.model.CyTableFactory.InitialTableSize
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.property.CyProperty.SavePolicy
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.view.layout.WeightTypes
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Method in class org.cytoscape.view.model.DiscreteRange
Returns a Set of all the values for this DiscreteRange.
values() - 
Static method in enum org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
Returns an array containing the constants of this enum type, in
the order they are declared.
values() - 
Static method in enum org.cytoscape.work.TunableValidator.ValidationState
Returns an array containing the constants of this enum type, in
the order they are declared.
version - 
Variable in class org.cytoscape.property.bookmark.Bookmarks
 
VERSION_PROPERTY_NAME - 
Static variable in interface org.cytoscape.application.CyVersion
The string used to identify the Property containing the version number.
VERSION_REGEX - 
Static variable in interface org.cytoscape.application.CyVersion
The regular expression used to test the property version string.
view - 
Variable in class org.cytoscape.task.AbstractNetworkViewTask
The network view that descendants of this class will operate on.
View<S> - Interface in org.cytoscape.view.model
The base interface that defines methods used to set visual properties
 for nodes, edges, and networks.
ViewChangeRecord<T> - Class in org.cytoscape.view.model.events
A utility class used to describe one change to a View.
ViewChangeRecord(View<T>, VisualProperty<?>, Object) - 
Constructor for class org.cytoscape.view.model.events.ViewChangeRecord
Constructor.
viewExists(CyNetwork) - 
Method in interface org.cytoscape.view.model.CyNetworkViewManager
Determines whether a network view for the specified network is known to
 the network view manager.
viewVisualStyleMap(Map<CyNetworkView, String>) - 
Method in class org.cytoscape.session.CySession.Builder
Returns an instance of Builder that has at least been configured with the specified network view visual style
 name map.
VirtualColumnInfo - Interface in org.cytoscape.model
Information object for columns that stores extra Virtual Column information
 if applicable.
Visualizable - Interface in org.cytoscape.view.model
Marker interface for data types used by higher-level Visual Properties such as NODE, EDGE, or NETWORK.
VisualLexicon - Interface in org.cytoscape.view.model
A RenderingEngine should provide one, immutable lexicon implementing this interface.
VisualLexiconNode - Class in org.cytoscape.view.model
A node in the visual property tree (lexicon).
VisualLexiconNode(VisualProperty<?>, VisualLexiconNode) - 
Constructor for class org.cytoscape.view.model.VisualLexiconNode
Constructs this VisualLexiconNode.
VisualMappingFunction<K,V> - Interface in org.cytoscape.view.vizmap
This class defines how an attribute gets mapped to a visual property.

 
 It takes two values:
 
 Attribute value: node name(Strings), expression values(Numbers), ...
 Visual Property: node size(Numbers), edge color(Color), node
 shape(NodeShape), ...
 
 
 This provides the mapping function from converting the attribute to the
 visual property.
VisualMappingFunctionFactory - Interface in org.cytoscape.view.vizmap
Factory for VisualMappingFunctions.
VisualMappingManager - Interface in org.cytoscape.view.vizmap
Manager for VisualStyles.
VisualProperty<T> - Interface in org.cytoscape.view.model
An object which represents a type of visual entity, such as node color, size, etc.
VisualPropertyDependency<T> - Class in org.cytoscape.view.vizmap
Represents a set of Visual Properties to be set by their parent value if
 dependency is enabled.
VisualPropertyDependency(String, Set<VisualProperty<T>>, VisualLexicon) - 
Constructor for class org.cytoscape.view.vizmap.VisualPropertyDependency
Constructor.
VisualPropertyDependencyFactory<T> - Interface in org.cytoscape.view.vizmap
 
VisualPropertyEditor<T> - Interface in org.cytoscape.view.vizmap.gui.editor
Facade of all editor-related objects for a Visual Property.
VisualPropertyUtil - Class in org.cytoscape.view.presentation.property
Utility functions for traversing visual lexicon tree.
VisualPropertyValue - Interface in org.cytoscape.view.presentation.property.values
Object used as a Visual Property value.
VisualStyle - Interface in org.cytoscape.view.vizmap
A VisualStyle is a collection of VisualMappingFunctions and default values
 that define how a set of attributes is mapped to visual properties of View objects.
VisualStyleAboutToBeRemovedEvent - Class in org.cytoscape.view.vizmap.events
This event will be fired when VisualStyle object is removed from
 VisualMappingManager.
VisualStyleAboutToBeRemovedEvent(VisualMappingManager, VisualStyle) - 
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent
Create an event for the removed VisualStyle.
VisualStyleAboutToBeRemovedListener - Interface in org.cytoscape.view.vizmap.events
Listener for VisualStyleAboutToBeRemovedEvent.
VisualStyleAddedEvent - Class in org.cytoscape.view.vizmap.events
When new VisualStyle is added to the VisualMappingManager,
 it fires this event.
VisualStyleAddedEvent(VisualMappingManager, VisualStyle) - 
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent
Creates an event for the newly created style.
VisualStyleAddedListener - Interface in org.cytoscape.view.vizmap.events
Listener for VisualStyleAddedEvent.
VisualStyleFactory - Interface in org.cytoscape.view.vizmap
Factory for VisualStyles.
visualStyles(Set<VisualStyle>) - 
Method in class org.cytoscape.session.CySession.Builder
Returns an instance of Builder that has at least been configured with the specified properties.
VisualStyleSetEvent - Class in org.cytoscape.view.vizmap.events
Event fired when a VisualStyle is set to a network view through 
 VisualMappingManager.setVisualStyle(VisualStyle, org.cytoscape.view.model.CyNetworkView).
VisualStyleSetEvent(VisualMappingManager, VisualStyle, CyNetworkView) - 
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
Creates the event.
VisualStyleSetListener - Interface in org.cytoscape.view.vizmap.events
Listener for VisualStyleSetEvent.
VizMapEventHandler - Interface in org.cytoscape.view.vizmap.gui.event
Handler for Vizmap-GUI-local PropertyChangeEvent.
VizMapEventHandlerManager - Interface in org.cytoscape.view.vizmap.gui.event
Manages VizMapEventHandlers.
VizMapGUI - Interface in org.cytoscape.view.vizmap.gui

 The top-level GUI component of VizMap GUI.
VizmapReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns a 
 VisualStyle object.
VizmapReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons,
 processes specified input to determine the appropriate factory to
 use and then returns an instance of the correct VizmapReader 
 for the input.
VizmapWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a VisualStyle to
 be specified and written.
VizmapWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing VisualStyle objects.
vp - 
Variable in class org.cytoscape.application.swing.AbstractViewUpdater
The VisualProperty that the RowsSetListener is provided for.
vp - 
Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Visual Property used in this mapping.



W

WebServiceClient - Interface in org.cytoscape.io.webservice
Thin wrapper for SOAP/REST web service clients.
WebServiceGUIClient - Interface in org.cytoscape.io.webservice.swing
An interface that allows web service clients to provide
 their own GUI component.
WeightTypes - Enum in org.cytoscape.view.layout
An enum describing different weighting strategies.
writeOut() - 
Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Writes the list of recently opened files to the file specified by the
 constructor argument.


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