Index (Cytoscape Swing App API (swing-app-api) 3.7.0 API)

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

A

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 that is always enabled.
AbstractCyAction(String, CyApplicationManager, String, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction: Creates a new AbstractCyAction object that is enabled for the specific "enableFor" state.
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: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp: Deprecated.

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.
AbstractCyJob - Class in org.cytoscape.jobs: This can be used as a base class for custom implementations of CyJob
AbstractCyJob(String, String, CyJobExecutionService, CyJobDataService, CyJobMonitor) - Constructor for class org.cytoscape.jobs.AbstractCyJob
AbstractCyNetworkReader - Class in org.cytoscape.io.read
AbstractCyNetworkReader(InputStream, CyApplicationManager, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
AbstractCyNetworkReader(InputStream, CyNetworkViewFactory, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
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: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp: Deprecated.

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 control.
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.
AbstractGUITunableHandler.TunableFieldPanel - Class in org.cytoscape.work.swing: The main goal of this panel is to store the handler's label and control, in order to make it possible to consistently align labels and controls created by different AbstractGUITunableHandler subclasses when creating the Tunable form.
AbstractInputStreamTaskFactory - Class in org.cytoscape.io.read: TODO: Missing documentation
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
AbstractNetworkSearchTaskFactory - Class in org.cytoscape.application.swing.search: This abstract implementation of NetworkSearchTaskFactory makes the method AbstractNetworkSearchTaskFactory.getQueryComponent() optional.
AbstractNetworkSearchTaskFactory(String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
AbstractNetworkSearchTaskFactory(String, String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
AbstractNetworkSearchTaskFactory(String, String, String, Icon, URL) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
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
AbstractParallelPartitionLayoutTask - Class in org.cytoscape.view.layout: This is an even more helpful implementation of a LayoutAlgorithm Task that extends AbstractPartitionLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractParallelPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractParallelPartitionLayoutTask: Creates a new AbstractPartitionLayoutTask object.
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.
AbstractRootNetworkCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyRootNetworks.
AbstractRootNetworkCollectionTask(Collection<CyRootNetwork>) - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTask
AbstractRootNetworkCollectionTaskFactory - Class in org.cytoscape.task: A RootNetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractRootNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTaskFactory
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.
AbstractStringTunableHandler - Class in org.cytoscape.command
AbstractStringTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
AbstractStringTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
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
AbstractTransformer<C,E> - Class in org.cytoscape.filter.model: A convenience base class for Transformers.
AbstractTransformer() - Constructor for class org.cytoscape.filter.model.AbstractTransformer: Creates a new AbstractTransformer.
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>, VisualProperty<V>, CyEventHelper) - 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, ContinuousMappingCellRendererFactory) - 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(C, E) - Method in interface org.cytoscape.filter.model.Filter: Returns true if this filter accepts the given element from context.
accepts(URI, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
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: Deprecated.

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: Overridden to add any new components to the content panel, as might be expected.
add(Component, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Overridden to add any new components to the content panel, as might be expected.
add(Component, Object) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Overridden to add any new components to the content panel, as might be expected.
add(Component, Object, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Overridden to add any new components to the content panel, as might be expected.
add(String, Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Overridden to add any new components to the content panel, as might be expected.
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.
addAnnotation(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Add an annotation to the specified network view.
addAnnotations(Collection<? extends Annotation>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Adds annotations to the specified network view.
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.
addArrow(ArrowAnnotation) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Add an arrow annotation to this annotation.
addBasicVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Deprecated.
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.
addCollapseListener(BasicCollapsiblePanel.CollapseListener) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
addData(CyJobData, String, Map<Object, Object>) - Method in interface org.cytoscape.jobs.CyJobDataService: Add generic key, value pairs to a CyJobData item.
addData(CyJobData, String, Object) - Method in interface org.cytoscape.jobs.CyJobDataService: Add a single data item to a CyJobData object.
addData(CyJobData, String, CyNetwork, List<? extends CyIdentifiable>, List<String>, List<String>) - Method in interface org.cytoscape.jobs.CyJobDataService: An optional method to add network data to a CyJobData item.
addData(CyJobData, String, CyTable, List<CyRow>, List<String>) - Method in interface org.cytoscape.jobs.CyJobDataService: An optional method to add table data to a CyJobData item.
addData(CyJobData, String, CyNetworkView, List<? extends CyIdentifiable>, List<VisualProperty<?>>) - Method in interface org.cytoscape.jobs.CyJobDataService: An optional method to add network view data to a CyJobData item.
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.
addIcon(String, Icon) - Method in interface org.cytoscape.util.swing.IconManager
addIconFont(Font) - Method in interface org.cytoscape.util.swing.IconManager
addIdentifierMapping(Class<?>, String, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
addJob(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager: Add a job to be managed by the job manager.
addListener(TransformerListener) - Method in class org.cytoscape.filter.model.AbstractTransformer
addListener(TransformerListener) - Method in interface org.cytoscape.filter.model.Transformer: Subscribes the given listener to changes in this Transformer's parameters.
addListener(BoundedChangeListener<N>) - Method in class org.cytoscape.work.util.AbstractBounded: Adds a listener that will listen for changes to this object
addListener(ListChangeListener<T>) - Method in class org.cytoscape.work.util.ListSelection: Adds a listener that will listen for changes to this object
addMember(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: Add a new annotation to the group.
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
addNamedTransformer(NamedTransformer<C, E>) - Method in interface org.cytoscape.filter.TransformerContainer: Add a NamedTransformer to this container.
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 and sets the network as current.
addNetwork(CyNetwork, boolean) - 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 and sets the new view as current.
addNetworkView(CyNetworkView, boolean) - 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.
addPaletteProvider(PaletteProvider) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Add a palette provider to the manager.
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(SavePolicy) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Create an empty CySubNetwork which can have a different save policy from that of this root network, as long as the root network's policy is not SavePolicy.DO_NOT_SAVE.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Create a CySubNetwork containing the specified CyNodes and CyEdges.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>, SavePolicy) - 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.
addVisualPropertyValueEditor(VisualPropertyValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Add value editor--invoked by OSGi when a new bundle exports an instance.
addVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Add a new VisualStyle to this manager.
ADJACENCY_TRANSFORMER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Adjacency Transformer, which finds adjacent nodes and edges based on how they are connected to the input nodes.
adjustColumnPreferredWidth(JTable, int) - Static method in class org.cytoscape.util.swing.ColumnResizer: Adjust one table column to its preferred width.
adjustColumnPreferredWidth(JTable, int, boolean) - Static method in class org.cytoscape.util.swing.ColumnResizer: Adjust one table column to its preferred width.
adjustColumnPreferredWidths(JTable) - Static method in class org.cytoscape.util.swing.ColumnResizer: Adjust the columns in the table to their preferred widths.
adjustColumnPreferredWidths(JTable, boolean) - 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.
allFinished(FinishStatus) - Method in interface org.cytoscape.work.TaskObserver: Called by a TaskManager to tell us that the task iterator has completed.
AnalyzeNetworkCollectionTaskFactory - Interface in org.cytoscape.task.analyze: Provides a TaskIterator to analyze a collection of networks.
Annotation - Interface in org.cytoscape.view.presentation.annotations: This is the base interface for all Annotations.
AnnotationFactory<T extends Annotation> - Interface in org.cytoscape.view.presentation.annotations: An interface describing a factory used to create Annotations.
AnnotationManager - Interface in org.cytoscape.view.presentation.annotations: The annotation manager is responsible for managing all of the annotations currently assigned to a particular org.cytoscape.view.model.NetworkView.
append(Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter: Appends filter to the list of children.
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(C, E, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.ElementTransformer: Transforms the given element.
apply(C, TransformerSource<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.HolisticTransformer: Transforms the elements in source from context.
apply(CyRow, View<? extends CyIdentifiable>) - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
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.
applyTunables(Object, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter: Applies each value from the key-value pairs in tunableValues to the tunable in the given object whose name matches the corresponding key.
ApplyVisualStyleTaskFactory - Interface in org.cytoscape.task.visualize: Marker interface which provides a task iterator for applying a visual style to views.
APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties: Define standard context menus.
AppsFinishedStartingEvent - Class in org.cytoscape.app.event: An event that occurs when the Cytoscape core has started, and any installed apps have either finished starting or failed to start.
AppsFinishedStartingEvent(Object) - Constructor for class org.cytoscape.app.event.AppsFinishedStartingEvent: Create a new event with the given source.
AppsFinishedStartingListener - Interface in org.cytoscape.app.event: Listener for the AppsFinishedStartingEvent.
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.
arrangeWindows(CyNetworkViewDesktopMgr.ArrangeType) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr: Request the desktop view manager to tile (or untile) the current network windows.
ARROW - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Pointy triangle shaped arrow
ARROW_SHORT - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Shorter pointy triangle shaped arrow
ArrowAnnotation - Interface in org.cytoscape.view.presentation.annotations: This is the interface for an arrow annotation.
ArrowAnnotation.AnchorType - Enum in org.cytoscape.view.presentation.annotations: This enum is used to indicate how the arrow is anchored to the source or target.
ArrowAnnotation.ArrowEnd - Enum in org.cytoscape.view.presentation.annotations: This enum is used to indicate which end of the arrow the operation is referring to.
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.
associateMonitor(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager: Associate a monitor with a job.
associateMonitor(CyJob, String, int) - Method in interface org.cytoscape.jobs.CyJobManager: Associate a handler with a job.
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.
AvailableCommands - Interface in org.cytoscape.command: TODO: Missing documentation

B

BACKGROUND - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: The background canvas
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.
BasicCollapsiblePanel.CollapseListener - Interface in org.cytoscape.util.swing
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.
BIRDS_EYE_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
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.
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.
BOTH_CONTEXT - Static variable in annotation type org.cytoscape.work.Tunable
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.
BoundedChangeListener<N> - Interface in org.cytoscape.work.util: Classes which wish to listen for changes in AbstractBounded objects (BoundedDouble, BoundedFloat, etc.) should implement this interface and add themselves as observers (listeners) to the 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.
BoundedTextAnnotation - Interface in org.cytoscape.view.presentation.annotations: The BoundedText annotation is a ShapeAnnotation that also implements Text.
boundsChanged(AbstractBounded) - Method in interface org.cytoscape.work.util.BoundedChangeListener
BrewerType - Enum in org.cytoscape.util.color
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.
Builder() - Constructor for class org.cytoscape.session.CySession.Builder

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
cancelJob(CyJob) - Method in interface org.cytoscape.jobs.CyJobExecutionService: Cancel a running job.
cancelJob(CyJob) - Method in interface org.cytoscape.jobs.CyJobManager: Cancel the specified job
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.
CANVAS - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: Arg map key to initialize the canvas to draw this annotation on
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
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
checkDependency(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler: To check the dependencies of this GUITunableHandler with the others.
checkJobStatus(CyJob) - Method in interface org.cytoscape.jobs.CyJobExecutionService: Check on the status of a running job.
CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Circle shaped arrow
clamp(N) - Method in class org.cytoscape.work.util.AbstractBounded: Clamps the value of the Bounded object.
clamp(Double) - Method in class org.cytoscape.work.util.BoundedDouble: Clamp the value to be within the range.
clamp(Float) - Method in class org.cytoscape.work.util.BoundedFloat: Clamp the value to be within the range.
clamp(Integer) - Method in class org.cytoscape.work.util.BoundedInteger: Clamp the value to be within the range.
clamp(Long) - Method in class org.cytoscape.work.util.BoundedLong: Clamp the value to be within the range.
clear() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker: Clears the list of recently opened file names.
clear() - Method in interface org.cytoscape.jobs.CyJobData: Clear all of the data
clearValueLock(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View: Clear value lock for given VisualProperty.
clearVisualProperties() - Method in interface org.cytoscape.view.model.View: Clear all VisualProperty values previously set to this view.
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?
collapsed() - Method in interface org.cytoscape.util.swing.BasicCollapsiblePanel.CollapseListener
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?
collect(T) - Method in interface org.cytoscape.filter.model.TransformerSink: Called for each element that is produced from a transformation.
COLOR - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the text color
ColorButton - Class in org.cytoscape.util.swing: JButton that opens a Color Chooser when clicked and shows the previously set color as an icon.
ColorButton(Color) - Constructor for class org.cytoscape.util.swing.ColorButton
ColorUtils - Class in org.cytoscape.util.color
ColorUtils() - Constructor for class org.cytoscape.util.color.ColorUtils
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.
COLUMN_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
COLUMN_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Column Filter, which finds nodes and edges based on their column values.
COLUMN_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
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.
columnName - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: Mapping attribute name.
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.
columnType - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction: Type of attribute.
COMMAND - Static variable in interface org.cytoscape.work.ServiceProperties: Name of command used by Command Executor
COMMAND_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties: Description for a command
COMMAND_EXAMPLE_JSON - Static variable in interface org.cytoscape.work.ServiceProperties: A valid JSON string representative of the expected JSON output of a command.
COMMAND_LONG_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties: Prose description for a command
COMMAND_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties: Name space for a command
COMMAND_SUPPORTS_JSON - Static variable in interface org.cytoscape.work.ServiceProperties: Indicates if the command supports JSON output.
CommandExecutorTaskFactory - Interface in org.cytoscape.command: TODO: Missing documentation
compare(TunableHandler, TunableHandler) - Method in class org.cytoscape.work.TunableGravityOrderer
compareTo(LayoutEdge) - Method in class org.cytoscape.view.layout.LayoutEdge
compareTo(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
compareTo(VisualLexiconNode) - Method in class org.cytoscape.view.model.VisualLexiconNode: Compare by display name of this Visual Property.
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
CompositeFilter<C,E> - Interface in org.cytoscape.filter.model: A Filter that computes the set-union or set-intersection of the Filters it contains.
CompositeFilter.Type - Enum in org.cytoscape.filter.model: Determines how a CompositeFilter combines the results of its contained Filters.
configurationProperties - Variable in class org.cytoscape.application.swing.AbstractCyAction: The configuration properties.
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.
containsColumn(String) - Method in class org.cytoscape.model.events.RowsSetEvent: Returns true if any of the changed records' column name is colName
containsDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Check if a DataSource already existed in the DataSourceManager
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.
containsKey(String) - Method in interface org.cytoscape.jobs.CyJobData: Test to see if a key exists in the current CyJobData.
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
CONTEXT - Static variable in class org.cytoscape.work.AbstractTunableHandler
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.
ContinuousMappingCellRendererFactory - Interface in org.cytoscape.view.vizmap.gui.editor: A factory for creating TableCellRenderers for a particular ContinuousMappingEditor.
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>, ContinuousMapping<K, V>, CyEventHelper) - 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.
CONTRAST - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: This value allows the image contrast to be adjusted
controlsMutuallyExclusiveNestedChildren() - Method in class org.cytoscape.work.AbstractTunableHandler
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 in the user namespace.
countMatchingRows(String, String, Object) - Method in interface org.cytoscape.model.CyTable: Returns the number of rows with the in the specified column with the specified value.
createAnnotation(Class<? extends T>, CyNetworkView, Map<String, String>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: Create an annotation.
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, String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type in the specified namespace.
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.
createColumn(String, String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type in the specified namespace.
createColumnIdentifier(String) - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifierFactory: Returns a CyColumnIdentifier that represents a CyColumn from a default network CyTable (a table associated with a CyNetwork, CyNode or CyEdge).
createCompositeFilter(Class<C>, Class<E>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a new empty CompositeFilter that selects elements of type elementType from an object of type contextType.
createCyJob(String) - Method in interface org.cytoscape.jobs.CyJobExecutionService: Create an empty (unsubmitted) CyJob
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>}
createEditor(CyCustomGraphics2<T>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Creates a UI component that configures the given CyCustomGraphics2.
createElementTransformer() - Method in interface org.cytoscape.filter.model.ElementTransformerFactory: Returns a new ElementTransformer with the same id as this factory.
createFilter() - Method in interface org.cytoscape.filter.model.FilterFactory: Returns a new Filter with the same id as this factory.
createFor(NetworkTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkViewTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkViewCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(TableTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
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(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.HandleFactory: Creates a new instance of the Handle.
createHelpButton(String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
createHolisticTransformer() - Method in interface org.cytoscape.filter.model.HolisticTransformerFactory
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, 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 in the specified namespace.
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.
createListColumn(String, 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 in the specified namespace.
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) - Method in interface org.cytoscape.application.swing.CyNetworkViewContextMenuFactory: This method should return a CyMenuItem to be added to the context menu of the specified network 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.
createNamedTransformer(String, List<Transformer<C, E>>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a new NamedTransformer with the given name and list of transformers.
createNetwork() - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object.
createNetwork(SavePolicy) - 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.
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.
createNetworkWithPrivateTables(SavePolicy) - 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.
createOkCancelPanel(JButton, JButton) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create a standard Cytoscape panel (usually added to the bottom of a dialog) that contains an "OK" and/or a "Cancel" button.
createOkCancelPanel(JButton, JButton, String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create OK, Cancel and Help
createOkCancelPanel(JButton, JButton, JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create a standard Cytoscape panel (usually added to the bottom of a dialog) that contains an "OK" and/or a "Cancel" button, as well as other extra components.
createOkCancelPanel(JButton, JButton, String, JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to include a help button in the bottom left corner.
createPanelBorder() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create a simple panel Border which looks native on the current Look and Feel.
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.
createSerializer() - Method in interface org.cytoscape.work.properties.TunablePropertySerializerFactory
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.
createTableCellRenderer(ContinuousMappingEditor<? extends Number, ?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingCellRendererFactory
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
createTaskIterator(TaskObserver, String...) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
createTaskIterator(List<String>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
createTaskIterator(String, String, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified command.
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(CyNetwork) - Method in interface org.cytoscape.task.create.CloneNetworkTaskFactory: Returns a TaskIterator that clones the given network.
createTaskIterator(Collection<CyNetwork>, CyNetworkViewFactory) - Method in interface org.cytoscape.task.create.CreateNetworkViewTaskFactory: Use this method to create a network view for each of the passed networks.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFactory: Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesOnlyTaskFactory: Returns a TaskIterator that creates a new network from the selected nodes in the given network.
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, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory: Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyTableReader) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory: Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyTable, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.JoinTablesTaskTaskFactory
createTaskIterator(CyTable, Collection<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, boolean, List<CyNetwork>, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory
createTaskIterator(CyTable, CyTable, List<String>, String, boolean, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MergeTablesTaskFactory: Creates a task iterator for merging two data tables.
createTaskIterator(CyColumn, String) - Method in interface org.cytoscape.task.edit.RenameColumnTaskFactory: Create a task iterator for renaming a selected column.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.HideTaskFactory: Creates a task iterator that will hide the given nodes and edges.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.UnHideTaskFactory: Creates a task iterator that will show the given nodes and edges.
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(List<File>, CyRootNetwork) - Method in interface org.cytoscape.task.read.LoadMultipleNetworkFilesTaskFactory: Creates a task iterator for loading one or more networks from supported files (e.g.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory: Creates a task iterator for loading a network from a file.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory: Creates a task iterator for loading a network from a file.
createTaskIterator(URL, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkURLTaskFactory: Creates a task iterator for loading a URL into a network.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadTableFileTaskFactory: Creates the task iterator for importing an attribute file to a table.
createTaskIterator(URL) - Method in interface org.cytoscape.task.read.LoadTableURLTaskFactory: Creates the task iterator for importing an attribute file to a table.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory: Creates a task iterator for loading files into visual styles.
createTaskIterator(File, TaskObserver) - 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(File, boolean) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory: Creates a task iterator for loading a session from a file, with an option to let the user confirm it before disposing the current session if it is not empty.
createTaskIterator(Collection<CyRootNetwork>) - Method in interface org.cytoscape.task.RootNetworkCollectionTaskFactory: Provisions this factory with the collection of root-networks that will be passed into any task created by it.
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(CyNetwork, File) - Method in interface org.cytoscape.task.write.ExportNetworkTaskFactory: Creates the task iterator for exporting networks.
createTaskIterator(CyNetworkView, File) - Method in interface org.cytoscape.task.write.ExportNetworkViewTaskFactory: Creates the task iterator for exporting network views.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportSelectedNetworkTaskFactory: Creates the task iterator for exporting the selected network.
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.ExportVizmapTaskFactory: Creates a task iterator for exporting the vizmap 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 containing 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.
createTaskIterator(TaskIterator, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.work.TunableSetter: This version of createTaskIterator adds a TaskObserver argument.
createTaskStatusPanel() - Method in interface org.cytoscape.work.swing.StatusBarPanelFactory
createTaskStatusPanel() - Method in interface org.cytoscape.work.swing.TaskStatusPanelFactory: Deprecated.
createTitledBorder(String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create a Titled Border which looks native on the current Look and Feel.
createTransformer(String) - Method in interface org.cytoscape.filter.TransformerManager: Returns a new Transformer with the given id.
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 method.
createView(Transformer<?, ?>) - Method in interface org.cytoscape.filter.view.TransformerViewFactory: Creates a UI panel that configures the given transformer.
createVisualMappingFunction(String, Class<K>, 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.
CROSS_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Triangle shaped arrow with a cross hatch
CROSS_OPEN_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled triangle shaped arrow with a cross hatch
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.
CustomGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics: This interface defines the minimum interface to add a custom graphics to a CyNode.
CUSTOMSHAPE - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: A flag that this is a "custom" shape
Cy2DGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics: Custom graphic layer interface that allows a custom graphics implementation to draw directly onto the CyNetworkView's Graphics2D object.
CY_EDGE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_EDGE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_VIEW_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_VIEW_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NODE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NODE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_ROW_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
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: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
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.
cyApplicationManager - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
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.
CyColorPaletteChooser - Interface in org.cytoscape.util.swing: This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColorPaletteChooserFactory - Interface in org.cytoscape.util.swing: This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColumn - Interface in org.cytoscape.model: This class describes a column in a CyTable.
CyColumnComboBox - Class in org.cytoscape.application.swing: An implementation of JComboBox that displays a list of CyColumns with their namespace icons.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>, Predicate<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox: Creates a CyColumnComboBox.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox: Creates a CyColumnComboBox with all entries enabled.
CyColumnIdentifier - Interface in org.cytoscape.view.presentation.property.values: Interface used to carry and save information that represents a CyColumn (usually from a network CyTable).
CyColumnIdentifierFactory - Interface in org.cytoscape.view.presentation.property.values: A factory for creating CyColumnIdentifier objects.
CyColumnPresentation - Interface in org.cytoscape.application.swing: Service that allows UI presentation to be given for a column namespace.
CyColumnPresentationManager - Interface in org.cytoscape.application.swing: This class provides access to registered CyColumnPresentation service objects.
CyColumnSelector - Class in org.cytoscape.application.swing: An Swing control that allows the user to select a set of CyColumn objects.
CyColumnSelector(IconManager, CyColumnPresentationManager) - Constructor for class org.cytoscape.application.swing.CyColumnSelector: Creates a CyColumnSelector.
cyColumnsToJson(Collection<CyColumn>) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a list of references (via column name) for a collection of CyColumn.
CyCustomGraphics<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics: Base interface for all Custom Graphics.
CyCustomGraphics2<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics: Just an extension of CyCustomGraphics which provides a way for the custom graphics instance to define itself as a set of properties.
CyCustomGraphics2Factory<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics: Factory to create CyCustomGraphics2 objects.
CyCustomGraphicsFactory<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics: This interface provides the factory to create CyCustomGraphics objects.
CyDisposable - Interface in org.cytoscape.model: An interface for objects that require an explicit clean up at the end of their lifecycle.
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.
CyGroupSettingsManager - Interface in org.cytoscape.group: The CyGroupSettingsManager is responsible for providing an interface to all of the possible settings controlling CyGroups, including the default settings and group specific settings.
CyGroupSettingsManager.DoubleClickAction - Enum in org.cytoscape.group: The DoubleClickAciton enum provides the options for what to do when the user double-clicks on either a group node or a node that's a member of a group.
CyGroupSettingsManager.GroupViewType - Enum in org.cytoscape.group: The CyGroupSettingsManager.GroupViewType enum provides the options for how to visualize a group.
CyHelpBroker - Interface in org.cytoscape.application.swing: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. 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.
cyIdentifiablesToJson(Collection<? extends CyIdentifiable>) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a list of references (via SUID) for a collection of CyIdentifiable.
CyJob - Interface in org.cytoscape.jobs: A CyJob represents all of the state information necessary to marshal and unmarshal data, submit jobs, query job status, and fetch results.
CyJobData - Interface in org.cytoscape.jobs: CyJobData presents a general interface to sending data to and receiving data from a job.
CyJobDataService - Interface in org.cytoscape.jobs: The main interface for the marshalling and unmarshalling of data to be exchanged with remote services.
CyJobExecutionService - Interface in org.cytoscape.jobs: The CyJobExecutionService is a stateless service that can be used to provide remote job services, including the execution, cancellation, status checking, and retrieval of results.
CyJobManager - Interface in org.cytoscape.jobs: CyJobManager is responsible for managing all currently running CyJobs, including polling for changes in the Status of the job and notifying the CyJobMonitor provided by the App of the change in status.
CyJobMonitor - Interface in org.cytoscape.jobs: Apps are expected to implement this interface to receive notifications about job completions.
CyJobStatus - Class in org.cytoscape.jobs: This object stores information about the status of a CyJob, including the actual job status (CyJobStatus.Status) and any message returned from the remote execution.
CyJobStatus(CyJobStatus.Status, String) - Constructor for class org.cytoscape.jobs.CyJobStatus
CyJobStatus.Status - Enum in org.cytoscape.jobs: This enum contains the primary status returned from the remote execution.
CyJSONUtil - Interface in org.cytoscape.util.json: This interface provides some very basic JSON representations of Cytoscape objects.
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 - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader: Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.
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.
CyNetworkViewContextMenuFactory - 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 network view.
CyNetworkViewDesktopMgr - Interface in org.cytoscape.application.swing: Interface for managing CyNetworkViews within the desktop where they reside.
CyNetworkViewDesktopMgr.ArrangeType - Enum in org.cytoscape.application.swing
cyNetworkViewFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader: Will be used for creating network views.
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.
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, boolean) - Constructor for class org.cytoscape.application.events.CyShutdownEvent: Constructor.
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: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
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..
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 for managing registered CyTables.
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.
CyToolTip - Class in org.cytoscape.util.swing
CyToolTip(JComponent, String, String, Icon) - Constructor for class org.cytoscape.util.swing.CyToolTip
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.
CytoPanelComponent2 - Interface in org.cytoscape.application.swing: Implement this interface rather than CytoPanelComponent, if you want to allow your component to be retrieved from the CytoPanel by its identifier.
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.
CyTransformerReader - Interface in org.cytoscape.io.read
CyTransformerWriter - Interface in org.cytoscape.io.write
CyUserLog - Interface in org.cytoscape.application: This contains the name of the user log.
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.
dataService - Variable in class org.cytoscape.jobs.AbstractCyJob
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).
decrement(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Decrement the location of this node by (x,y,z).
decrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Decrement the displacement recorded for this node by (x,y).
decrementDisp(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Decrement the displacement recorded for this node by (x,y,z).
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_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
DEFAULT_EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: The default edge bend.
DEFAULT_FONT_NAME - Static variable in interface org.cytoscape.util.swing.IconManager
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_POSITION - Static variable in class org.cytoscape.view.presentation.property.values.ObjectPosition
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: Deprecated.
DefaultViewPanel - Interface in org.cytoscape.view.vizmap.gui: Deprecated.
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.
DEGREE_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Degree Filter, which finds nodes based on their degree.
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 with the specified fully-qualified name.
deleteColumn(String, String) - Method in interface org.cytoscape.model.CyTable: Will delete the column of the specified name in the specified namespace.
DeleteColumnTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting a column.
deleteDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Remove a DataSource from the DataSourceManager
deleteRows(Collection<?>) - Method in interface org.cytoscape.model.CyTable: Deletes the rows corresponding to the given primary keys and returns true if at least one row was deleted.
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
DELTA_SHORT_1 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Shorter triangle shaped arrow
DELTA_SHORT_2 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Even shorter triangle shaped arrow
dependsOn() - Method in class org.cytoscape.work.AbstractTunableHandler
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.
deserialize(Object) - Method in interface org.cytoscape.jobs.CyJobDataService: This method is used to create a new CyJobData object from a serialized data object retrieved from a remote execution.
deserialize(Reader) - Method in interface org.cytoscape.jobs.CyJobDataService: This method is used to create a new CyJobData object from a serialized data stream retrieved from a remote execution.
deserialize(InputStream) - Method in interface org.cytoscape.jobs.CyJobDataService: This method is used to create a new CyJobData object from a serialized data stream retrieved from a remote execution.
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.
DIAMOND_SHORT_1 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Sorter diamond shaped arrow
DIAMOND_SHORT_2 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Even shorter diamond shaped arrow
DirectlyPresentableTunableHandler - Interface in org.cytoscape.work.swing: TODO: Missing documentation
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.
dispose() - Method in interface org.cytoscape.model.CyDisposable: Free up any memory or resources used by this object.
disposeCurrentSession() - Method in interface org.cytoscape.session.CySessionManager: Disposes the current session.
distance(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 2D) between this node and another node.
distance(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 2D) between this node and a location.
distance3D(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 3D) between this node and another node.
distance3D(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 3D) 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.AbstractParallelPartitionLayoutTask: AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.
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.
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.
draw(Graphics2D, Shape, CyNetworkView, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.presentation.customgraphics.Cy2DGraphicLayer: This method is called by Cytoscape when a CyNetworkView is being updated in order to let the custom graphics draw onto its Graphics2D object.
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.
DropDownMenuButton(JPopupMenu) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
DropDownMenuButton() - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
DynamicSubmenuListener - Interface in org.cytoscape.work.swing: An extension of MenuListener that is used to describe dynamic submenus.
DynamicTaskFactoryProvisioner - Interface in org.cytoscape.task: TODO: Missing documentation

E

EDGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: If Edge Bend is defined, edges will be rendered as straight or curved lines.
EDGE_DYNAMIC_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_EDIT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text used for the edge label.
EDGE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The font used for the edge label.
EDGE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The size of the font used for the edge label.
EDGE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The opacity of the color of the edge label.
EDGE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The type of stoke used to render the line (solid, dashed, etc.)
EDGE_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (including the stroke and arrows) when it is selected or unselected.
EDGE_PREFERENCES_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (stroke and arrows) when selected.
EDGE_SOURCE_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The shape of the arrow on the source node end of the edge.
EDGE_SOURCE_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_STROKE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge line when selected.
EDGE_STROKE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge line.
EDGE_TARGET_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The shape of the arrow on the target node end of the edge.
EDGE_TARGET_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text of the tooltip that appears when a mouse hovers over the edge.
EDGE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The opacity of the of the edge.
EDGE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (stroke and arrows) when it is not selected.
EDGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Hides the edge if set to false.
EDGE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The width of the edge line.
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.
EDGECOLOR - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The color of the border
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
EdgeList - Class in org.cytoscape.command.util: This class implements a wrapper for a List of CyEdges that can be used by the Tunables mechanism.
EdgeList() - Constructor for class org.cytoscape.command.util.EdgeList: Empty constructor for an EdgeList.
EdgeList(CyNetwork) - Constructor for class org.cytoscape.command.util.EdgeList: Constructor for EdgeList when the network is known at time of creation.
EDGEOPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The opacity of the border
edgesChanged() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns true if the selection stated of edges has changed.
EDGETHICKNESS - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The thickness of the border
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.
ElementTransformer<C,E> - Interface in org.cytoscape.filter.model: A transformer that transforms its input one element at a time and pushes the results into the given sink.
ElementTransformerFactory<C,E> - Interface in org.cytoscape.filter.model: A factory for creating ElementTransformers.
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_ALWAYS - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable always.
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_SINGLE_NETWORK - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when only one network is selected.
ENABLE_FOR_TABLE - Static variable in class org.cytoscape.application.swing.ActionEnableSupport: Enable when at least one network exists.
eqnTypeIsCompatible(Class<?>, Class<?>, Class<?>) - Static method in class org.cytoscape.equations.EquationUtil: Returns whether the given column type is compatible with an equation type
EQUAL_DASH - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Equal dash and space
equalizeSize(JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Resizes the given components making them equal in size.
equals(Object) - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
equals(Object) - Method in class org.cytoscape.equations.Equation: Compares one Equation to another.
equals(Object) - Method in class org.cytoscape.util.swing.FileChooserFilter
equals(Object) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Compare two ObjectPositions
equals(Object) - Method in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
equals(Object) - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
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.
EquationFunctionAddedEvent - Class in org.cytoscape.equations.event
EquationFunctionAddedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionAddedEvent
EquationFunctionAddedListener - Interface in org.cytoscape.equations.event
EquationFunctionRemovedEvent - Class in org.cytoscape.equations.event
EquationFunctionRemovedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionRemovedEvent
EquationFunctionRemovedListener - Interface in org.cytoscape.equations.event
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.
eventHelper - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
execService - Variable in class org.cytoscape.jobs.AbstractCyJob
execute(Equation, Map<String, IdentDescriptor>) - Method in interface org.cytoscape.equations.Interpreter: Executes the code represented by "equation".
execute(C, Transformer<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager: Applies transformer to the context.
execute(C, List<Transformer<C, E>>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager: Applies the given chain of transformers to the context.
execute(C, TransformerSource<C, E>, List<Transformer<C, E>>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager: Applies the given chain of transformers to the context, via source.
execute(TaskIterator) - Method in interface org.cytoscape.work.TaskManager: This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
execute(TaskIterator, TaskObserver) - Method in interface org.cytoscape.work.TaskManager: This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
executeJob(CyJob, String, Map<String, Object>, CyJobData) - Method in interface org.cytoscape.jobs.CyJobExecutionService: Submit a CyJob for remote execution.
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.
exit(int, boolean) - 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.
expanded() - Method in interface org.cytoscape.util.swing.BasicCollapsiblePanel.CollapseListener
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.
ExportNetworkTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting network views.
ExportNetworkViewTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting network views.
ExportSelectedNetworkTaskFactory - Interface in org.cytoscape.task.write
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

fetchResults(CyJob, CyJobData) - Method in interface org.cytoscape.jobs.CyJobExecutionService: After a CyJob status returns CyJobStatus.Status.FINISHED, this method is used to fetch the results from the job execution.
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.
FILLCOLOR - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The fill color of the shape
FILLOPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The opacity of the shape fill
Filter<C,E> - Interface in org.cytoscape.filter.model: A transformer that decides whether to accept or reject elements.
FilterFactory<C,E> - Interface in org.cytoscape.filter.model: A factory for creating Filters.
FinishStatus - Class in org.cytoscape.work: Indicates the status of a task iterator when it has finished for TaskObservers.
FinishStatus(FinishStatus.Type, Task, Exception) - Constructor for class org.cytoscape.work.FinishStatus
FinishStatus.Type - Enum in org.cytoscape.work
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.
fitShapeToText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: This method causes the shape to be resized to fit the provided text.
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.
flushPayloadEvents(Object) - Method in interface org.cytoscape.event.CyEventHelper: Forces accumulated payload events to be fired.
FONTFAMILY - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font family
FONTSIZE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font size
FONTSTYLE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font style
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.
forceShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent: Returns true if we want to force the shutdown without any user prompt
FOREGROUND - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: The foreground canvas
format - Variable in class org.cytoscape.property.bookmark.DataSource
FORMAT - Static variable in class org.cytoscape.work.AbstractTunableHandler
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(int) - Method in interface org.cytoscape.filter.model.CompositeFilter: Returns the Filter at the given index.
get(String) - Method in interface org.cytoscape.jobs.CyJobData: Returns the Object that contains the value for the specified key, or null if that key doesn't exist.
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, 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(String, 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: Deprecated.

Returns an instance of ApplyPreferredLayoutTaskFactory.
get_ApplyVisualStyleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ApplyVisualStyleTaskFactory.
get_CloneNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CloneNetworkTaskFactory.
get_CollapseGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CollapseGroupTaskFactory.
get_ConnectSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ConnectSelectedNodesTaskFactory.
get_CreateNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CreateNetworkViewTaskFactory.
get_DeleteColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeleteColumnTaskFactory.
get_DeleteSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeleteSelectedNodesAndEdgesTaskFactory.
get_DeleteTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeleteTableTaskFactory.
get_DeselectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeselectAllEdgesTaskFactory.
get_DeselectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeselectAllNodesTaskFactory.
get_DeselectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DeselectAllTaskFactory.
get_DestroyNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DestroyNetworkTaskFactory.
get_DestroyNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DestroyNetworkViewTaskFactory.
get_EditNetworkTitleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of EditNetworkTitleTaskFactory.
get_ExpandGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExpandGroupTaskFactory.
get_ExportNetworkImageTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExportNetworkImageTaskFactory.
get_ExportNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExportNetworkViewTaskFactory.
get_ExportSelectedTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExportSelectedTableTaskFactory.
get_ExportTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExportTableTaskFactory.
get_ExportVizmapTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of ExportVizmapTaskFactory.
get_GroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of GroupNodesTaskFactory.
get_HideSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of HideSelectedEdgesTaskFactory.
get_HideSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of HideSelectedNodesTaskFactory.
get_HideSelectedTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of HideSelectedTaskFactory.
get_InvertSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of InvertSelectedEdgesTaskFactory.
get_InvertSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of InvertSelectedNodesTaskFactory.
get_LoadNetworkFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of LoadNetworkFileTaskFactory.
get_LoadNetworkURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of LoadNetworkURLTaskFactory.
get_LoadTableFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of LoadTableFileTaskFactory.
get_LoadTableURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of LoadTableURLTaskFactory.
get_LoadVizmapFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of LoadVizmapFileTaskFactory.
get_MapGlobalToLocalTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of MapGlobalToLocalTableTaskFactory.
get_MapTableToNetworkTablesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of MapTableToNetworkTablesTaskFactory.
get_NewEmptyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of NewEmptyNetworkViewFactory.
get_NewNetworkSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of NewNetworkSelectedNodesAndEdgesTaskFactory.
get_NewNetworkSelectedNodesOnlyTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of NewNetworkSelectedNodesOnlyTaskFactory.
get_NewSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of NewSessionTaskFactory.
get_OpenSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of OpenSessionTaskFactory.
get_RenameColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of RenameColumnTaskFactory.
get_SaveSessionAsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SaveSessionAsTaskFactory.
get_SelectAdjacentEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectAdjacentEdgesTaskFactory.
get_SelectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectAllEdgesTaskFactory.
get_SelectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectAllNodesTaskFactory.
get_SelectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectAllTaskFactory.
get_SelectConnectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectConnectedNodesTaskFactory.
get_SelectFirstNeighborsNodeViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectFirstNeighborsNodeViewTaskFactory.
get_SelectFirstNeighborsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryInEdge() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryOutEdge() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFromFileListTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of SelectFromFileListTaskFactory.
get_UnGroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UnGroupNodesTaskFactory.
get_UnGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UnGroupTaskFactory.
get_UnHideAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UnHideAllEdgesTaskFactory.
get_UnHideAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UnHideAllNodesTaskFactory.
get_UnHideAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UnHideAllTaskFactory.
getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction
getAcceleratorKeyStroke() - Method in interface org.cytoscape.application.swing.CyAction: Returns the accelerator KeyStroke defined for this action.
getActionListener() - Method in class org.cytoscape.work.swing.util.UserAction
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.
getAggregator(CyGroup, CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the Aggregator that will be used to aggregate the values in a specific CyColumn for all of the nodes in a group onto the corresponding column in the group 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.
getAllCategories() - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data categories
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.jobs.CyJobData: Return all of the values in this CyJobData
getAllValues() - Method in interface org.cytoscape.model.CyRow: Returns a map of fully-qualified 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.
getAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the anchor of the label (or other object).
getAnchorType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the anchor type for one end of the arrow
getAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Retrieve the list of annotations for a specific network view.
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".
getArgDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the description field for this argument.
getArgExampleStringValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the defaultStringValue field for this argument.
getArgLongDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the longDescription field for this argument.
getArgMap() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the argument map that is used to serialize this annotation.
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.
getArgRequired(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the required field for this argument.
getArgTooltip(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the tooltip field for this argument.
getArgType(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the type of the argument.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
getArgTypeString(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a human-readable string for this argument of the form: argument=<type>
getArguments(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of arguments for the specified namespace and command in alphabetical order.
getArgValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Deprecated.
getArrowColor(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the color of one end of the arrow
getArrows() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get all arrows that are currently linked to this annotation.
getArrowSize(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the size of one end of the arrow
getArrowType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the type of one end of the arrow
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).
getAvailableCommands() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of AvailableCommands.
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.
getBorderColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) color.
getBorderOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) opacity.
getBorderWidth() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) width.
getBounds(CyNetworkView) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr: Deprecated.
This method has been deprecated in version 3.4.
getBounds2D() - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer: Return the bounds of the area covered by this CustomGraphicLayer as a Rectangle2D
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".
getCanvasName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Return the canvas that this Annotation is on
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
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
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.
getColor() - Method in class org.cytoscape.util.swing.ColorButton
getColorPaletteChooser(PaletteType, boolean) - Method in interface org.cytoscape.util.swing.CyColorPaletteChooserFactory
getColors() - Method in interface org.cytoscape.util.color.Palette: Return the palette as an array of colors
getColors(int) - Method in interface org.cytoscape.util.color.Palette: Return the palette as an array of colors of the requested length.
getColumn(String) - Method in interface org.cytoscape.model.CyTable: Returns the column with the specified fully-qualified name.
getColumn(String, String) - Method in interface org.cytoscape.model.CyTable: Returns the column for the specified name in the specified namespace.
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.
getColumnName() - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifier
getColumnNames(CyTable) - Static method in class org.cytoscape.model.CyTableUtil: Returns all the column names of a given table.
getColumnPresentation(String) - Method in interface org.cytoscape.application.swing.CyColumnPresentationManager: Returns a CyColumnPresentation for the given namespace.
getColumnRecords(String) - Method in class org.cytoscape.model.events.RowsSetEvent: Returns all of the RowSetRecords whose specified column value is set.
getColumns() - Method in interface org.cytoscape.model.CyTable: Returns the column types for all columns in this table.
getColumns(String) - Method in interface org.cytoscape.model.CyTable: Returns the column types for all columns in this table in the given namespace.
getColumns() - Method in class org.cytoscape.model.events.RowsSetEvent: Returns a unmodifiable Set of the names of the columns that are contained in this event.
getCommandExecutorTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CommandExecutorTaskFactory which can be used to execute commands.
getCommands(String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of available commands in alphabetical order for the specified namespace.
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 the passed index.
getCompositeFilter() - Method in interface org.cytoscape.filter.model.SubFilterTransformer
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 CytoscapeConfiguration 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
getContentTypes() - Method in interface org.cytoscape.io.CyFileFilter: The MIME content types supported by this filter.
getContext() - Method in class org.cytoscape.work.AbstractTunableHandler: This returns the context of the Tunable.
getContextType() - Method in interface org.cytoscape.filter.model.Transformer: Returns the type of the context object this Transformer is compatible with.
getContextType() - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the type of the context object this TransformerSource is compatible with.
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.
getControl() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
getCoreProperties() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyProperty of type Properties.
getCurrentDirectory() - Method in interface org.cytoscape.application.CyApplicationManager: Get the current working directory.
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.
getCurrentNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the NetworkViewRenderer associated with the current RenderingEngine.
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.VisualMappingManager: Returns currently selected Visual Style.
getCyApplicationConfiguration() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.
getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyApplicationManager.
getCyEventHelper() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyEventHelper.
getCyGroupAggregationManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyGroupAggregationManager.
getCyGroupFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyGroupFactory.
getCyGroupManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyGroupManager.
getCyLayoutAlgorithmManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyLayoutAlgorithmManager.
getCyNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkFactory.
getCyNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkManager.
getCyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkViewFactory.
getCyNetworkViewManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkViewManager.
getCyNetworkViewReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkReaderManager.
getCyNetworkViewWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyNetworkViewWriterManager.
getCyPropertyReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyPropertyReaderManager.
getCyPropertyWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyPropertyWriterManager.
getCyRootNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyRootNetworkManager.
getCyServiceRegistrar() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyServiceRegistrar.
getCySessionManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CySessionManager.
getCySessionReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CySessionReaderManager.
getCySessionWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CySessionWriterManager.
getCySwingApplication() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Deprecated.

Returns an instance of CySwingApplication.
getCyTableFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyTableFactory.
getCyTableManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyTableManager.
getCyTableReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyTableReaderManager.
getCyTableWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

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: Deprecated.

Returns an instance of CyVersion.
getData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Extract data from a CyJobData object.
getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter
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
getDataInstance() - Method in interface org.cytoscape.jobs.CyJobDataService: Returns an empty instance of CyJobData that may be used with this service.
getDataService() - Method in interface org.cytoscape.jobs.CyJobExecutionService: Return the CyJobDataService that is used by service to marshall and unmarshall data for the remote service.
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: Deprecated.

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.
getDefaultAggregation(Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the default Aggregator for a specific column type as expressed as a java Class.
getDefaultAggregation(CyGroup, Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the Aggregator for a specific column type as expressed as a java Class that will be used in the specified CyGroup.
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 Cytoscape's 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.
getDefaultListAggregation(Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the default Aggregator for a specific List column type as expressed as a java Class.
getDefaultListAggregation(CyGroup, Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the Aggregator for a specific List column type as expressed as a java Class that will be used in the specified CyGroup.
getDefaultNetworkTable() - Method in interface org.cytoscape.model.CyNetwork: A convenience method returns the default attribute table for this network.
getDefaultNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the NetworkViewRenderer that should be used to create CyNetworkViews.
getDefaultNodeTable() - Method in interface org.cytoscape.model.CyNetwork: A convenience method returns the default attribute table for the nodes of this network.
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: Deprecated.
getDefaultViewEditor() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI: Deprecated.
getDefaultViewPanel() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI: Deprecated.
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
getDependency() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDepth() - Method in class org.cytoscape.view.layout.LayoutNode: Return the height of this node
getDepth() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total depth of all of the LayoutNodes
getDescription() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getDescription() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An optional short text describing what this search provider does.
getDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the description of the specified command in the specified namespace.
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the description of the argument.
getDescription() - Method in class org.cytoscape.io.BasicCyFileFilter
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
getDescription() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's description.
getDesktopViewAreaSize() - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr: Deprecated.
This method has been deprecated in version 3.4.
getDialogTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Deprecated.

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 enum org.cytoscape.io.DataCategory
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 interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Display name is a simple description of this image object.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Return the CyCustomGraphics2 name which is will be displayed to the user.
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.
getDisplayNames() - Static method in enum org.cytoscape.view.presentation.property.values.Position: Return a sorted list containing all of the display names for all of the Position anchors.
getDoubleClickAction() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current default CyGroupSettingsManager.DoubleClickAction.
getDoubleClickAction(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current CyGroupSettingsManager.DoubleClickAction for the specified group.
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 SUID.
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(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a edgelist into a list of CyEdges.
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.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.
getElementCount(C) - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the number of elements that could be produced from the given context.
getElementList(C) - Method in interface org.cytoscape.filter.model.TransformerSource: Returns a List of elements from the given context.
getElementType() - Method in interface org.cytoscape.filter.model.Transformer: Returns the type of the elements this Transformer is compatible with.
getElementType() - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the type of the elements this TransformerSource is compatible with.
getEnableAttributeAggregation() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not we're enabling aggregation.
getEnableAttributeAggregation(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not we're enabling aggregation for a specific group.
getEnabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Get set of Visual Properties to be enabled in the lexicon.
getEnabled() - Method in class org.cytoscape.work.swing.util.UserAction
getEquation() - Method in interface org.cytoscape.equations.EquationCompiler: If compile() returns true, this returns the result of the compilation.
getErrorColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
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.
getExampleJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a valid JSON string representative of the expected JSON output of the command.
getExampleStringValue() - Method in class org.cytoscape.work.AbstractTunableHandler
getExampleStringValue() - Method in interface org.cytoscape.work.TunableHandler: Returns the exampleStringValue property of the associated Tunable.
getException() - Method in class org.cytoscape.session.events.SessionLoadCancelledEvent: Deprecated.
getException() - Method in class org.cytoscape.session.events.SessionSaveCancelledEvent
getException() - Method in class org.cytoscape.work.FinishStatus: Returns the exception thrown by the task that failed, or null if the task iterator succeeded or was cancelled.
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
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.
getFile(Component, String, int, String, 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.
getFiles(Component, String, int, String, 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.
getFillColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the fill color.
getFillOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Return the fill opacity, a value between 0.0 (fully transparent) and 100.0 (fully opaque).
getFitRatio() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Get the fit ratio for this custom graphic.
getFolder(Component, String, String) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object representing a folder, this method should be used instead of rolling your own JFileChooser.
getFont() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font being used
getFont() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font being used
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font family to be used for the text display
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font family to be used for the text display
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the size of the font used to display the text
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the size of the font used to display the text
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font style
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font style
getFormat() - Method in class org.cytoscape.property.bookmark.DataSource: Gets the value of the format property.
getFormat() - Method in class org.cytoscape.work.AbstractTunableHandler: Provides a format string suitable for passing to String.format.
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.
getGravity() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the gravity value for the annotation.
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
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.
getGroupViewType() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current default CyGroupSettingsManager.GroupViewType.
getGroupViewType(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current CyGroupSettingsManager.GroupViewType for the specified group.
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 list 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
getHeight() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Returns height of current object.
getHelpBroker() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpBroker.
getHelpSet() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. 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.
getIcon() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getIcon() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An icon that represents this search provider.
getIcon(String) - Method in interface org.cytoscape.util.swing.IconManager
getIcon() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: An icon that represents this AnnotationFactory.
getIcon(int, int) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
getIconFont(float) - Method in interface org.cytoscape.util.swing.IconManager: Returns the font that renders the text as an icon.
getIconFont(String, float) - Method in interface org.cytoscape.util.swing.IconManager
getIconHeight() - Method in class org.cytoscape.util.swing.TextIcon
getIconWidth() - Method in class org.cytoscape.util.swing.TextIcon
getId() - Method in interface org.cytoscape.application.NetworkViewRenderer
getId() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getId() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Returns the unique id of this network search provider.
getId() - Method in interface org.cytoscape.filter.model.Transformer: Returns the unique id of this type of Transformer.
getId() - Method in interface org.cytoscape.filter.model.TransformerFactory: Returns the unique id of the Transformer produced by this factory.
getId() - Method in interface org.cytoscape.filter.view.TransformerViewFactory: Returns the unique id of the Transformer this factory produces views for.
getId() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: Returns the unique id of the AnnotationFactory implementation.
getId() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Return the prefix to identify this Custom Graphics factory.
getIdentifier() - Method in interface org.cytoscape.application.swing.CytoPanelComponent2: Returns this component's identifier, which should be unique.
getIdentifier() - Method in interface org.cytoscape.util.color.Palette: Return the internal identifier of this palette.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the edge's identifier.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutNode: Return the node's identifier.
getIdentifier() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Immutable session-unique identifier of this custom graphic generated by the custom graphics manager.
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.
getIdString() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Provides serializable string of this dependency.
getImage() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the image currently assigned to this annotation
getImageBrightness() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the brightness adjustment for this image.
getImageContrast() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the contrast adjustment for this image
getImageOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the current opacity of the image.
getImageURL() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Get the URL for the image to be displayed
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.
getInfoColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
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.
getInstallationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns absolute path to Cytoscape installation directory location.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Get a new instance of a CyCustomGraphics2.
getInstance(CyCustomGraphics2<T>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Get a new instance of a CyCustomGraphics2 that is a clone of the passed argument.
getInstance(Map<String, Object>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Get a new instance of a CyCustomGraphics2 with the passed properties.
getInstance(URL) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Get a new instance of the CyCustomGraphics based on pulling the data from a URL.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Get a new instance of the CyCustomGraphics.
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.
getJobDataService() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobDataService() - Method in interface org.cytoscape.jobs.CyJob: Return the CyJobDataService that was used to create this job.
getJobExecutionService() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobExecutionService() - Method in interface org.cytoscape.jobs.CyJob: Return the CyJobExecutionService that created this job.
getJobId() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobId() - Method in interface org.cytoscape.jobs.CyJob: Return the ID for this job.
getJobMonitor() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobMonitor() - Method in interface org.cytoscape.jobs.CyJob: Return the service that handles status changes for this job.
getJobName() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobName() - Method in interface org.cytoscape.jobs.CyJob: Return the name for this job
getJobs() - Method in interface org.cytoscape.jobs.CyJobManager: Return the list of CyJobs currently managed by the CyJobManager.
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 ...)
getJSON() - Method in interface org.cytoscape.work.json.JSONResult
getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JToolBar object for the application.
getJustify() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the justification of the label (or other object).
getKeys() - Method in class org.cytoscape.model.events.RowsDeletedEvent: Returns the primary keys of the rows for this event.
getLabel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
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.
getLayers(CyNetworkView, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Get layers that belong to this object.
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.
getLength() - Method in interface org.cytoscape.filter.model.CompositeFilter: Returns the number of direct children Filters contained by this CompositeFilter.
getLineColor() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the line color for this arrow
getLineWidth() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the line width for this arrow
getList(String, Class<T>) - Method in interface org.cytoscape.model.CyRow: Returns a list which is a view on the underlying column value for this row.
getList(String, String, Class<T>) - Method in interface org.cytoscape.model.CyRow: Returns a list which is a view on the underlying column value for this row.
getList(String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow: Returns a list which is a view on the underlying column value for this row.
getList(String, String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow: Returns a list which is a view on the underlying column value for this row.
getListAggregators(Class<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of List aggregators for a particular Class.
getListAggregators() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators for List columns.
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.
getListeners() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the list of listeners that will listen for changes to this object
getListeners() - Method in class org.cytoscape.work.util.ListSelection: Returns the list of listeners that will listen for changes to this object
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 tables 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)).
getLongDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the longDescription of the specified command in the specified namespace.
getLongDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
getLongDescription() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's longDescription
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".
getMapData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Extract a map from a CyJobData object.
getMappedColumns() - Method in interface org.cytoscape.view.presentation.property.values.MappableVisualPropertyValue
getMappedValue(CyRow) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns the mapped value for a CyRow.
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.
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.
getMatchingKeys(String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable: Returns all the keys of a specified column that match the given value.
getMatchingKeys(String, String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable: Returns all the keys of a specified column that match the given value.
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.
getMatchingRows(String, 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
getMaxZ() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum Z location of all of the LayoutNodes
getMembers() - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: Return the list of members for this group
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
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.
getMessage() - Method in class org.cytoscape.jobs.CyJobStatus: Return any message associated with the job status.
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
getMinZ() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum Z 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.
getMultiLineLabel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
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
getName() - Method in interface org.cytoscape.application.swing.CyAction: Returns the name of the action.
getName() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getName() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: A short name to be displayed to the user.
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.filter.model.NamedTransformer: Returns the name of this NamedTransformer.
getName() - Method in interface org.cytoscape.filter.model.Transformer: Returns the user-friendly display name of this type of Transformer.
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 enum org.cytoscape.jobs.CyJobStatus.Status
getName() - Method in interface org.cytoscape.model.CyColumn: Returns the fully-qualified 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 interface org.cytoscape.util.color.Palette: Return the name of this palette.
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 interface org.cytoscape.view.presentation.annotations.Annotation: Get the name for this annotation.
getName() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: A short name to be displayed to the user.
getName() - Method in enum org.cytoscape.view.presentation.property.values.Justification: Return the display name of this justification type.
getName() - Method in enum org.cytoscape.view.presentation.property.values.Position: Return the display name of this anchor position.
getName() - Method in class org.cytoscape.work.AbstractTunableHandler
getName() - Method in interface org.cytoscape.work.TunableHandler: Returns a name representing a tunable property.
getNamedTransformer(String) - Method in interface org.cytoscape.filter.TransformerContainer: Returns the transformer with the given name, or null if a transformer with the given name does not exist in this container.
getNamedTransformers() - Method in interface org.cytoscape.filter.TransformerContainer: Returns the list of transformers contained in this container.
getNameOnly() - Method in interface org.cytoscape.model.CyColumn: Returns the name portion without the namespace.
getNameOnly() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the name portion without the namespace.
getNames() - Static method in enum org.cytoscape.view.presentation.property.values.Justification: Return the display names for all of the Justifcation values
getNamespace() - Method in interface org.cytoscape.model.CyColumn: Returns the namespace of the column, or null if the column does not have a namespace.
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<? extends org.cytoscape.model.CyIdentifiable>).
getNamespace() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the namespace of the column, or null if the column does not have a namespace.
getNamespaceDescription() - Method in interface org.cytoscape.application.swing.CyColumnPresentation: Returns a String description of the namespace.
getNamespaceIcon() - Method in interface org.cytoscape.application.swing.CyColumnPresentation: Returns an icon associated with the namespace.
getNamespaces() - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of available command namespaces in alphabetical order.
getNamespaces() - Method in interface org.cytoscape.model.CyTable: Returns all the namespaces used in the table.
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(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a network into a CyNetwork.
getNetwork() - Method in class org.cytoscape.command.util.EdgeList: Return the network used by this EdgeList
getNetwork() - Method in class org.cytoscape.command.util.NodeList: Get the network for this nodelist
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.
getNetwork() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns the CyNetwork event source.
getNetworkData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Optional method to extract network data from a CyJobData object.
getNetworkForTable(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns the network this table is registered with.
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 class org.cytoscape.io.read.AbstractCyNetworkReader
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(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a network view into a CyNetworkView.
getNetworkView() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Return the view that this Annotation is for
getNetworkView() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent: Get the The target network view model.
getNetworkViewFactory() - Method in interface org.cytoscape.application.NetworkViewRenderer
getNetworkViewFactory() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
getNetworkViewRenderer(String) - Method in interface org.cytoscape.application.CyApplicationManager: Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.
getNetworkViewRendererList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
getNetworkViewRendererSet() - Method in interface org.cytoscape.application.CyApplicationManager: Returns a set with all the NetworkViewRenderer objects that have been registered.
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.
getNewNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the name name portion without the namespace.
getNewNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the new namespace of the column, or null if the column does not have a namespace.
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.
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 SUID.
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(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a nodelist into a list of CyNodes.
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.
getNodeMap() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader: Returns map from key value to existing CyNode.
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.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.
getOffsetX() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the X offset of the object
getOffsetY() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the Y offset of the object
getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old name of the column.
getOldNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old name portion without the namespace.
getOldNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old namespace of the column, or null if the column did not have a namespace.
getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: The old properties before they were modified.
getOldTitle() - Method in class org.cytoscape.model.events.TableTitleChangedEvent
getOptionsComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: This implementation simply returns null, which means that no options component will be displayed, unless the subclass overwrites this method to return a custom component.
getOptionsComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: You can use this method to return a component that contains extra search parameters.
getOrdinal(int) - Static method in class org.cytoscape.equations.FunctionUtil: Converts an integer to an ordinal string.
getOverrideAggregation(CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the override aggregation setting for a column (if any).
getOverrideAggregation(CyGroup, CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the override aggregation setting for a column (if any) in a specific group.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer: Return the Paint to be used to fill the Shape.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.ImageCustomGraphicLayer: Return the TexturePaint to be used as an image to fill a node
getPaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Paint to fill the shape with.
getPalette(String) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its name
getPalette(String, int) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette of the specified size by its name
getPalette(Object) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its internal identifier
getPalette(Object, int) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its internal identifier
getPaletteProvider(String) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the palette provider that matches the name in the argument.
getPaletteProviders() - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the list of currently registered palette providers
getPaletteProviders(PaletteType, boolean) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the list of currently registered palette providers that provide palettes of the requested type.
getPaletteTypes() - Method in interface org.cytoscape.util.color.PaletteProvider: Return the list of org.cytoscape.util.color.Palette.PaletteTypes supported by this provider
getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Deprecated.

Returns an instance of PanelTaskManager.
getParams() - Method in class org.cytoscape.work.AbstractTunableHandler
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.
getParent() - Method in interface org.cytoscape.work.swing.TunableUIHelper: Get the parent of the current Tunable dialog.
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
getPath() - Method in class org.cytoscape.jobs.AbstractCyJob
getPath() - Method in interface org.cytoscape.jobs.CyJob: Return the base path for communicating with the remote service for this job
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.
getPollInterval() - Method in class org.cytoscape.jobs.AbstractCyJob
getPollInterval() - Method in interface org.cytoscape.jobs.CyJob: Return the time in seconds between calls to checkJobStatus.
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.
getPossibleValues() - Method in class org.cytoscape.work.util.ListSelection: To get all the items of the List values.
getPreferredMenu() - Method in class org.cytoscape.application.swing.AbstractCyAction
getPreferredMenu() - Method in interface org.cytoscape.application.swing.CyAction: This method returns a Menu specification string.
getPrefix() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Return the prefix to identify this custom graphics factory.
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: Deprecated.

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.application.swing.AbstractCyAction: Return the config props.
getProperties() - Method in interface org.cytoscape.application.swing.CyAction: Returns the configuration properties that were passed to the CyAction when it was created.
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.customgraphics.CyCustomGraphics2: Provides an optional map of key/value properties which define the custom graphics instance.
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.
getPropertyEditor(VisualProperty<T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor2: 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
getProvider(DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Get the provider name from DataSource object
getProviderName() - Method in interface org.cytoscape.util.color.PaletteProvider: Return the human-readable string identifier for this PaletteProvider.
getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler
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.
getQuery() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
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.
getQueryComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: This implementation simply returns null, which means Cytoscape will provide a default query component, unless the subclass overwrites this method to return a custom component.
getQueryComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Use this method to return a component that contains the main or mandatory search fields.
If this task factory provides its own query component, make sure the returned JComponent fires a PropertyChangeEvent for the property NetworkSearchTaskFactory.QUERY_PROPERTY whenever its fields change in a way that affects the return of the TaskFactory.isReady() method.
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.
getRaw(String, 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.
getRenderedImage() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: From layers of graphics objects, render a composite scaled Image object.
getRendererId() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns the ID of the renderer that must be used to render this view.
getRendererId() - Method in interface org.cytoscape.view.presentation.RenderingEngine: This method must return the same ID which is returned by the associated implementation of NetworkViewRenderer.
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: Deprecated.
getRenderingEngineFactory(String) - Method in interface org.cytoscape.application.NetworkViewRenderer
getRenderingEngineManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of RenderingEngineManager.
getRenderingEngines(View<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Get rendering engines for the given view model.
getRequired() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns true if this Tunable must be set (i.e.
getResultClasses() - Method in interface org.cytoscape.work.ObservableTask: Return the classes that can be used to query {@link org.cytoscape.work.ObservableTask#getResults(Class)
getResults(Class<? extends R>) - Method in interface org.cytoscape.work.ObservableTask: Return the results from this task (if any)
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() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader: Get target network collection, i.e., parent root network for all networks to be loaded.
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.
getRootNetworkList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
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.
getRowList(CyTable, String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a rowlist into a list of CyRows.
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.CyNetwork: Returns how (or if) this CyNetwork should be saved.
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.
getSelectedColor() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
getSelectedColumnNames() - Method in class org.cytoscape.application.swing.CyColumnSelector: Returns the names of the CyColumns that have been selected.
getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the currently selected component.
getSelectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getSelectedEdges(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil: Equivalent to
getSelectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the edges in the network that are currently selected.
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.
getSelectedItem() - Method in class org.cytoscape.application.swing.CyColumnComboBox: Override getSelectedItem() and use covariant return type to change return type to CyColumn.
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.
getSelectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getSelectedNodes(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil: Equivalent to
getSelectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the nodes in the network that are currently selected.
getSelectedPalette() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
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.
getSerializedData(CyJobData) - Method in interface org.cytoscape.jobs.CyJobDataService: This method is used to extract the data from the CyJobData object in a form that is appropriate for use by the job execution service.
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.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobDataService: The name of the service.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobExecutionService: The name of the service.
getSession() - Method in interface org.cytoscape.io.read.CySessionReader: Returns a CySession object
getShape() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the current shape as a Shape object
getShape() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Shape
getShapeType() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the current shape type as a String
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.
getShortName() - Method in enum org.cytoscape.view.presentation.property.values.Justification: Return the short name of this justification type
getShortName() - Method in enum org.cytoscape.view.presentation.property.values.Position: Return the short name of this anchor position.
getSize() - Method in enum org.cytoscape.model.CyTableFactory.InitialTableSize: Returns the actual size value for the given enum.
getSmallFontSize() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
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
getSource() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Return the source Annotation for this arrow.
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.
getSpecificZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the specific zoom for this annotation
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, ...)
getStatus() - Method in class org.cytoscape.jobs.CyJobStatus: Return the CyJobStatus.Status of the remote job
getStatusToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the status JToolBar of the application.
getStreamUtil() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of StreamUtil.
getStrings(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Converts all arguments, including Lists to a uniform array of strings.
getStroke() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Stroke to use to outline the Shape provided by the PaintedShape.getShape() method above.
getStrokePaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Paint to use to color the Stroke returned by PaintedShape.getStroke().
getSubNetworkList() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Will return A list of all CySubNetworks contained in this root network.
getSucceeded() - Static method in class org.cytoscape.work.FinishStatus: Get a FinishStatus instance that indicates success.
getSuccessColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
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.
getSupportedArrows() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the list of supported arrow shapes
getSupportedClass() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
getSupportedClass() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Return the class that this factory creates.
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.
getSupportedListClasses() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of classes of List for which have aggregators.
getSupportedListType() - Method in interface org.cytoscape.group.data.Aggregator: Return the base Class of the List, if this is a list type.
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.
getSupportedShapes() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the list of supported shapes.
getSupportedType() - Method in interface org.cytoscape.group.data.Aggregator: Return the Class this aggregator supports
getSupportedValueRange(VisualProperty<T>) - Method in interface org.cytoscape.view.model.VisualLexicon: Returns a filtered value range for a VisualProperty that uses a DiscreteRange.
getSupportedValueRange(VisualProperty<T>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getSupportsJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns true if the command is expected to provide JSON output.
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(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a table into a CyTable.
getTable() - Method in class org.cytoscape.command.util.RowList: Get the table for this rowlist
getTable() - Method in interface org.cytoscape.model.CyColumn: Returns the table for this column.
getTable(Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetwork: Returns the table with the specified namespace and type from this network.
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
getTableData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Optional method to extract table data (usually not model associated tables) from a CyJobData object.
getTableNamespace(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns the namespace of this table.
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.
getTableType(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.
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
getTarget() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Return the target object for this arrow.
getTargetAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the anchor of the target (e.g.
getTargetColumnList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
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.
getTask() - Method in class org.cytoscape.work.FinishStatus: Returns the task that was cancelled or that had failed, or returns null if the task iterator succeeded.
getTaskIterator() - Method in class org.cytoscape.work.AbstractTask
getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of TaskManager.
getTaskObserver() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getTaskObserver() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: If you want to be notified when the search task is finished, you should return a TaskObserver here.
getText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the text to be displayed as part of the annotation
getText() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the text to be displayed as part of the annotation
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the color of the text to be displayed
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the color of the text to be displayed
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 class org.cytoscape.io.read.AbstractCyNetworkReader
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
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.
getTooltip() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the tooltip annotation for this Tunable if there is one.
getToolTipImage() - Method in class org.cytoscape.application.swing.AbstractCyAction
getToolTipImage() - Method in interface org.cytoscape.application.swing.CyAction: Optional image to be displayed in the target component's tool tip.
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.
getTransformers() - Method in interface org.cytoscape.filter.model.NamedTransformer: Returns the List of Transformers contained within this NamedTransformer.
getTransformerSource(Class<C>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a TransformerSource for the given contextType.
getTranslatedValueType() - Method in interface org.cytoscape.view.vizmap.mappings.ValueTranslator: Returns compatible input data type.
getTree() - Method in class org.cytoscape.util.swing.JTreeTable: Returns the tree that is being shared between the model.
getTunableHandler() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
getTunablePropertySerializerFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of TunablePropertySerializerFactory.
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.filter.model.CompositeFilter: Returns the type of combining semantics used by this filter.
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 interface org.cytoscape.util.color.Palette: This is the type of the palette, using the Cynthia Brewer's classification.
getType() - Method in class org.cytoscape.view.layout.EdgeWeighter
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 interface org.cytoscape.view.presentation.annotations.AnnotationFactory
getType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
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
getType() - Method in class org.cytoscape.work.FinishStatus: Specifies how the task iterator completed.
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: Deprecated.

Returns an instance of UndoSupport.
getUnqualifiedName(Class<?>) - Static method in class org.cytoscape.equations.EquationUtil: Returns the unqualified name of the given class
getUnselectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getUnselectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the edges in the network that are currently unselected.
getUnselectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getUnselectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the nodes in the network that are currently unselected.
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.
getUseNestedNetworks() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the default setting for whether or not to create a nested network view on collapsed nodes.
getUseNestedNetworks(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not to create a nested network view on collapsed nodes for the specified CyGroup.
getUUID() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the UUID of this annotation
getValidationState(Appendable) - Method in interface org.cytoscape.work.TunableValidator: Executes the validation test on the annotated Tunables.
getValue() - Method in class org.cytoscape.command.util.EdgeList: Return the edgeList for this tunable
getValue() - Method in class org.cytoscape.command.util.NodeList: Get the list of nodes
getValue() - Method in class org.cytoscape.command.util.RowList: Get the list of rows
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
getValue() - Method in interface org.cytoscape.work.TunableHandler: Returns an object describing a field / get method annotated with Tunable or null if no field / get method 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.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor: Get type of the value to be edited.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyValueEditor: Get type of the value to be edited.
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.
getViewData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Optional method to extract data for a CyNetworkView from a CyJobData object.
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: Deprecated.

Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionDiscreteFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionPassthroughFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of VisualMappingFunctionFactory.
getVisualMappingManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

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.SetCurrentVisualStyleEvent: Get the newly selected current Visual Style.
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: Deprecated.

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.
getWarnColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
getWarning() - Method in class org.cytoscape.filter.model.ValidationWarning
getWebsite() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getWebsite() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An optional URL the user can use to find more information about this search provider.
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
getWidth() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Returns width of current object.
getWindow(Class<?>) - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUI: Returns the Window that contains the unified web service UI.
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.
getZ() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current Z value for this LayoutNode.
getZ() - Method in class org.cytoscape.view.layout.LayoutPoint: Returns the Z location of the point.
getZDisp() - Method in class org.cytoscape.view.layout.LayoutNode: Return the current Z displacement value for this LayoutNode.
getZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the current zoom for this annotation
GRAVITY - Static variable in class org.cytoscape.work.AbstractTunableHandler
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
GROUP - Static variable in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Optional property key that tells Cytoscape under which group it should add the editor created by this factory (see CyCustomGraphics2Factory.createEditor(CyCustomGraphics2)).
GROUP_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
GROUP_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
GROUP_NAME_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
GROUP_NAME_EXAMPLE_STRING2 - Static variable in interface org.cytoscape.command.StringToModel
GROUP_NAME_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel: Group terms
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
GroupAnnotation - Interface in org.cytoscape.view.presentation.annotations: The GroupAnnotation is a container for a collection of annotations that should be grouped together.
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
GUI_CONTEXT - Static variable in annotation type org.cytoscape.work.Tunable
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_CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Half-Circle shaped arrow
HALF_TOP - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Top Half of a triangle shaped arrow
handle() - Method in class org.cytoscape.command.AbstractStringTunableHandler
Handle - Interface in org.cytoscape.view.presentation.property.values: Defines a handle, an anchor point in the edge.
handle() - Method in interface org.cytoscape.work.properties.TunablePropertyHandler: Typically don't need to implement this method, default implementation is empty.
handle() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
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(AppsFinishedStartingEvent) - Method in interface org.cytoscape.app.event.AppsFinishedStartingListener: Handles the given event.
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(EquationFunctionAddedEvent) - Method in interface org.cytoscape.equations.event.EquationFunctionAddedListener
handleEvent(EquationFunctionRemovedEvent) - Method in interface org.cytoscape.equations.event.EquationFunctionRemovedListener
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(RowsDeletedEvent) - Method in interface org.cytoscape.model.events.RowsDeletedListener: 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(SelectedNodesAndEdgesEvent) - Method in interface org.cytoscape.model.events.SelectedNodesAndEdgesListener
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(TablePrivacyChangedEvent) - Method in interface org.cytoscape.model.events.TablePrivacyChangedListener: Handler method for TablePrivacyChangedListener.
handleEvent(TableTitleChangedEvent) - Method in interface org.cytoscape.model.events.TableTitleChangedListener
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(SessionAboutToBeLoadedEvent) - Method in interface org.cytoscape.session.events.SessionAboutToBeLoadedListener: Processes the SessionAboutToBeLoadedEvent when it is fired.
handleEvent(SessionAboutToBeSavedEvent) - Method in interface org.cytoscape.session.events.SessionAboutToBeSavedListener: Processes the specified event when fired.
handleEvent(SessionLoadCancelledEvent) - Method in interface org.cytoscape.session.events.SessionLoadCancelledListener: Deprecated.

Processes the specified event when fired.
handleEvent(SessionLoadedEvent) - Method in interface org.cytoscape.session.events.SessionLoadedListener: Processes the specified event when fired.
handleEvent(SessionSaveCancelledEvent) - Method in interface org.cytoscape.session.events.SessionSaveCancelledListener: 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(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(ViewChangedEvent<?>) - Method in interface org.cytoscape.view.model.events.ViewChangedListener
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(SetCurrentVisualStyleEvent) - Method in interface org.cytoscape.view.vizmap.events.SetCurrentVisualStyleListener: Update states/GUI using newly selected current VisualStyle information.
handleEvent(VisualMappingFunctionChangedEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualMappingFunctionChangedListener
handleEvent(VisualPropertyDependencyChangedEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualPropertyDependencyChangedListener
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(VisualStyleChangedEvent) - Method in interface org.cytoscape.view.vizmap.events.VisualStyleChangedListener
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.
HandleFactory - Interface in org.cytoscape.view.presentation.property.values: Factory of the handle object.
handleInteractivityChanged(boolean) - Method in interface org.cytoscape.filter.view.InteractivityChangedListener: Called by the transformation subsystem to indicate the state of interactivity has changed.
handlerMap - Variable in class org.cytoscape.work.AbstractTunableInterceptor: Store the Handlers.
handleSettingsChanged() - Method in interface org.cytoscape.filter.model.TransformerListener: Called by a Transformer to indicate that its settings have changed in some way.
hashCode() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
hashCode() - Method in class org.cytoscape.equations.Equation
hashCode() - Method in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
hashCode() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
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.
HEIGHT - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The height of the shape
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.
HideTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding the given nodes and edges.
HideUnselectedEdgesTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding unselected edges.
HideUnselectedNodesTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding unselected nodes.
HideUnselectedTaskFactory - Interface in org.cytoscape.task.hide: This interface provides a task iterator for hiding unselected nodes and edges.
HolisticTransformer<C,E> - Interface in org.cytoscape.filter.model: A transformer that takes its input altogether, transforms it, and pushes the results into the given sink.
HolisticTransformerFactory<C,E> - Interface in org.cytoscape.filter.model: A factory for creating HolisticTransformers.
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

ICON_500PX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADDRESS_BOOK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADDRESS_BOOK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADDRESS_CARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADDRESS_CARD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADJUST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ADN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ALIGN_CENTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ALIGN_JUSTIFY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ALIGN_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ALIGN_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AMAZON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AMBULANCE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AMERICAN_SIGN_LANGUAGE_INTERPRETING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANCHOR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANDROID - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGELLIST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_DOUBLE_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_DOUBLE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_DOUBLE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_DOUBLE_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ANGLE_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_APPLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARCHIVE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AREA_CHART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_O_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_O_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_O_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_O_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_CIRCLE_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROW_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROWS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROWS_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROWS_H - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ARROWS_V - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ASSISTIVE_LISTENING_SYSTEMS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ASTERISK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AUDIO_DESCRIPTION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_AUTOMOBILE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BACKWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BALANCE_SCALE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BAN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BANDCAMP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BANK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BAR_CHART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BAR_CHART_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BARCODE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BARS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATTERY_EMPTY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATTERY_FULL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATTERY_HALF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATTERY_QUARTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BATTERY_THREE_QUARTERS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BED - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BEER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BEHANCE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BEHANCE_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BELL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BELL_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BELL_SLASH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BELL_SLASH_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BICYCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BINOCULARS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BIRTHDAY_CAKE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BITBUCKET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BITBUCKET_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BITCOIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BLACK_TIE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BLIND - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BLUETOOTH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BLUETOOTH_B - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOLD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOLT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOMB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOOK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOOKMARK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BOOKMARK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BRAILLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BRIEFCASE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BTC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BUG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BUILDING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BUILDING_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BULLHORN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BULLSEYE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_BUYSELLADS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CAB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALCULATOR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR_CHECK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR_MINUS_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR_PLUS_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CALENDAR_TIMES_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CAMERA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CAMERA_RETRO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CAR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_SQUARE_O_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_SQUARE_O_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_SQUARE_O_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_SQUARE_O_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CARET_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CART_ARROW_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CART_PLUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_AMEX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_DINERS_CLUB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_DISCOVER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_JCB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_MASTERCARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_PAYPAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_STRIPE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CC_VISA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CERTIFICATE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHAIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHAIN_BROKEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHECK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHECK_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHECK_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHECK_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHECK_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_CIRCLE_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_CIRCLE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_CIRCLE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_CIRCLE_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHEVRON_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHILD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CHROME - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CIRCLE_O_NOTCH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CIRCLE_THIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLIPBOARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLOCK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLONE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLOSE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLOUD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLOUD_DOWNLOAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CLOUD_UPLOAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CNY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CODE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CODE_FORK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CODEPEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CODIEPIE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COFFEE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COGS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COLUMNS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENT_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENTING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENTING_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENTS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMMENTS_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMPASS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COMPRESS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CONNECTDEVELOP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CONTAO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COPY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_COPYRIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CREATIVE_COMMONS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CREDIT_CARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CREDIT_CARD_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CROP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CROSSHAIRS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CSS3 - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CUBE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CUBES - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CUT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_CUTLERY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DASHBOARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DASHCUBE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DATABASE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DEAF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DEDENT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DELICIOUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DESKTOP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DEVIANTART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DIAMOND - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DIGG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DOLLAR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DOT_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DOWNLOAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DRIBBBLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DROPBOX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_DRUPAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EDGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EDIT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EERCAST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EJECT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ELLIPSIS_H - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ELLIPSIS_V - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EMPIRE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVELOPE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVELOPE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVELOPE_OPEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVELOPE_OPEN_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVELOPE_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ENVIRA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ERASER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ETSY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EUR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EURO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXCHANGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXCLAMATION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXCLAMATION_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXCLAMATION_TRIANGLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXPAND - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXPEDITEDSSL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXTERNAL_LINK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EXTERNAL_LINK_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EYE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EYE_SLASH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_EYEDROPPER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FACEBOOK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FACEBOOK_F - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FACEBOOK_OFFICIAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FACEBOOK_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FAST_BACKWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FAST_FORWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FAX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FEMALE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FIGHTER_JET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_ARCHIVE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_AUDIO_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_CODE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_EXCEL_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_IMAGE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_MOVIE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_PDF_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_PHOTO_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_PICTURE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_POWERPOINT_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_SOUND_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_TEXT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_TEXT_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_VIDEO_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_WORD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILE_ZIP_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILES_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FILTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FIRE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FIRE_EXTINGUISHER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FIREFOX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FIRST_ORDER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLAG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLAG_CHECKERED - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLAG_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLASH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLASK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLICKR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FLOPPY_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FOLDER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FOLDER_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FOLDER_OPEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FOLDER_OPEN_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FONT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FONT_AWESOME - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FONTICONS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FORT_AWESOME - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FORUMBEE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FORWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FOURSQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FREE_CODE_CAMP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FROWN_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_FUTBOL_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GAMEPAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GAVEL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GBP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GEAR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GEARS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GENDERLESS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GET_POCKET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GG_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GIFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GIT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GIT_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GITHUB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GITHUB_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GITHUB_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GITLAB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GITTIP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GLASS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GLIDE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GLIDE_G - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GLOBE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GOOGLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GOOGLE_PLUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GOOGLE_PLUS_OFFICIAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GOOGLE_PLUS_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GOOGLE_WALLET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GRADUATION_CAP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GRATIPAY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GRAV - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_GROUP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_H_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HACKER_NEWS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_LIZARD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_O_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_O_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_O_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_O_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_PAPER_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_PEACE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_POINTER_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_ROCK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_SCISSORS_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HAND_SPOCK_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HANDSHAKE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HASHTAG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HDD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HEADER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HEADPHONES - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HEART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HEART_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HEARTBEAT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HISTORY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOME - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOSPITAL_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOTEL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_1 - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_2 - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_3 - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_END - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_HALF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOURGLASS_START - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HOUZZ - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_HTML5 - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_I_CURSOR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ID_BADGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ID_CARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ID_CARD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ILS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_IMAGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_IMDB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INBOX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INDENT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INDUSTRY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INFO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INFO_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INSTAGRAM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INSTITUTION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_INTERNET_EXPLORER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_IOXHOST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ITALIC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_JOOMLA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_JPY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_JSFIDDLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_KEY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_KEYBOARD_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_KRW - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LANGUAGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LAPTOP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LASTFM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LASTFM_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEAF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEANPUB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEGAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEMON_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEVEL_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LEVEL_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIFE_BOUY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIFE_BUOY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIFE_RING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIFE_SAVER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIGHTBULB_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINE_CHART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINKEDIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINKEDIN_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINODE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LINUX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIST_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIST_OL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LIST_UL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LOCATION_ARROW - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LOCK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LONG_ARROW_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LONG_ARROW_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LONG_ARROW_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LONG_ARROW_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_LOW_VISION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAGIC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAGNET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAIL_FORWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAIL_REPLY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAIL_REPLY_ALL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MALE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAP_MARKER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAP_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAP_PIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAP_SIGNS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MARS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MARS_DOUBLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MARS_STROKE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MARS_STROKE_H - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MARS_STROKE_V - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MAXCDN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MEANPATH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MEDIUM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MEDKIT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MEETUP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MEH_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MERCURY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MICROCHIP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MICROPHONE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MICROPHONE_SLASH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MINUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MINUS_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MINUS_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MINUS_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MIXCLOUD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MOBILE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MOBILE_PHONE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MODX - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MONEY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MOON_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MORTAR_BOARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MOTORCYCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MOUSE_POINTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_MUSIC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_NAVICON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_NEUTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_NEWSPAPER_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OBJECT_GROUP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OBJECT_UNGROUP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ODNOKLASSNIKI - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ODNOKLASSNIKI_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OPENCART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OPENID - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OPERA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OPTIN_MONSTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_OUTDENT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAGELINES - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAINT_BRUSH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAPER_PLANE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAPER_PLANE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAPERCLIP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PARAGRAPH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PASTE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAUSE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAUSE_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAUSE_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAW - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PAYPAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PENCIL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PENCIL_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PENCIL_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PERCENT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PHONE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PHONE_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PHOTO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PICTURE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PIE_CHART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PIED_PIPER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PIED_PIPER_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PIED_PIPER_PP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PINTEREST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PINTEREST_P - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PINTEREST_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLANE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLAY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLAY_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLAY_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLUG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLUS_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLUS_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PLUS_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PODCAST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_POWER_OFF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PRINT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PRODUCT_HUNT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_PUZZLE_PIECE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QQ - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QRCODE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUESTION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUESTION_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUESTION_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUORA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUOTE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_QUOTE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RANDOM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RAVELRY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REBEL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RECYCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REDDIT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REDDIT_ALIEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REDDIT_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REFRESH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REGISTERED - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REMOVE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RENREN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REORDER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REPEAT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REPLY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_REPLY_ALL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RETWEET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RMB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ROAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ROCKET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ROTATE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ROTATE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_ROUBLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RSS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RSS_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RUB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RUBLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_RUPEE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SAFARI - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SAVE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SCISSORS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SCRIBD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SEARCH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SEARCH_MINUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SEARCH_PLUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SELLSY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SEND - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SEND_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SERVER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHARE_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHARE_ALT_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHARE_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHARE_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHEKEL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHEQEL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHIELD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHIP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHIRTSINBULK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHOPPING_BAG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHOPPING_BASKET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHOPPING_CART - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SHOWER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SIGN_IN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SIGN_LANGUAGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SIGN_OUT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SIGNAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SIMPLYBUILT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SITEMAP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SKYATLAS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SKYPE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SLACK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SLIDERS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SLIDESHARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SMILE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SNAPCHAT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SNAPCHAT_GHOST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SNAPCHAT_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SNOWFLAKE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SOCCER_BALL_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_ALPHA_ASC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_ALPHA_DESC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_AMOUNT_ASC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_AMOUNT_DESC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_ASC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_DESC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_NUMERIC_ASC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_NUMERIC_DESC - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SORT_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SOUNDCLOUD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SPACE_SHUTTLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SPINNER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SPOON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SPOTIFY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SQUARE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STACK_EXCHANGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STACK_OVERFLOW - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR_HALF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR_HALF_EMPTY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR_HALF_FULL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR_HALF_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STAR_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STEAM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STEAM_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STEP_BACKWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STEP_FORWARD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STETHOSCOPE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STICKY_NOTE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STICKY_NOTE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STOP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STOP_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STOP_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STREET_VIEW - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STRIKETHROUGH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STUMBLEUPON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_STUMBLEUPON_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUBSCRIPT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUBWAY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUITCASE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUN_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUPERPOWERS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUPERSCRIPT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_SUPPORT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TABLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TABLET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TACHOMETER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TAG - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TAGS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TASKS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TAXI - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TELEGRAM - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TELEVISION - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TENCENT_WEIBO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TERMINAL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TEXT_HEIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TEXT_WIDTH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TH_LARGE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TH_LIST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THEMEISLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THERMOMETER_EMPTY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THERMOMETER_FULL - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THERMOMETER_HALF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THERMOMETER_QUARTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THERMOMETER_THREE_QUARTERS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THUMB_TACK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THUMBS_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THUMBS_O_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THUMBS_O_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_THUMBS_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TICKET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TIMES - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TIMES_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TIMES_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TINT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_LEFT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_OFF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_ON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_RIGHT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TOGGLE_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRADEMARK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRAIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRANSGENDER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRANSGENDER_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRASH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRASH_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TREE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRELLO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRIPADVISOR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TROPHY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRUCK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TRY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TTY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TUMBLR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TUMBLR_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TURKISH_LIRA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TWITCH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TWITTER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_TWITTER_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UMBRELLA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNDERLINE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNDO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNIVERSAL_ACCESS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNIVERSITY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNLINK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNLOCK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNLOCK_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UNSORTED - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_UPLOAD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USB - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_CIRCLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_CIRCLE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_MD - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_PLUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_SECRET - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USER_TIMES - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_USERS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VENUS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VENUS_DOUBLE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VENUS_MARS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIACOIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIADEO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIADEO_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIDEO_CAMERA - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIMEO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VIMEO_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VINE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VK - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VOLUME_CONTROL_PHONE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VOLUME_DOWN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VOLUME_OFF - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_VOLUME_UP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WARNING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WECHAT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WEIBO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WEIXIN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WHATSAPP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WHEELCHAIR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WHEELCHAIR_ALT - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WIFI - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WIKIPEDIA_W - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOW_CLOSE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOW_CLOSE_O - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOW_MAXIMIZE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOW_MINIMIZE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOW_RESTORE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WINDOWS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WON - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WORDPRESS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WPBEGINNER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WPEXPLORER - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WPFORMS - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_WRENCH - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_XING - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_XING_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_Y_COMBINATOR - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YAHOO - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YELP - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YEN - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YOAST - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YOUTUBE - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YOUTUBE_PLAY - Static variable in interface org.cytoscape.util.swing.IconManager
ICON_YOUTUBE_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager
IconManager - Interface in org.cytoscape.util.swing: Interface that provides constants for simple icons that can be used by Cytoscape and third party apps in order to create a more consistent GUI.
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).
ImageAnnotation - Interface in org.cytoscape.view.presentation.annotations: This annotation positions an image on on the screen.
ImageCustomGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics: This interface defines a CustomGraphicLayer that paints an image on a node.
ImportDataTableTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for importing a table data in a network data table.
IN_CONTEXT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties: Action will be added to context menu if this flag is set to true.
IN_MENU_BAR - Static variable in interface org.cytoscape.work.ServiceProperties: Action (or TaskFactory) 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 (or TaskFactory) 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).
increment(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Increment the location of this node by (x,y,z).
incrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Increment the displacement recorded for this node by (x,y).
incrementDisp(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Increment the displacement recorded for this node by (x,y,z).
indexOf(Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter: Returns the index of filter within the list of children, or -1 if filter is not in that list.
indexOfComponent(Component) - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the index for the specified component.
indexOfComponent(String) - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the index for the component that has the specified identifier.
inMenuBar - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether the action is in a menu.
inputStream - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader: Data stream for the networks to be created.
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.
insert(int, Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter: Inserts filter at the given index within the list of children.
INSERT_SEPARATOR_AFTER - Static variable in interface org.cytoscape.work.ServiceProperties: Insert separator after this menu item
INSERT_SEPARATOR_BEFORE - Static variable in interface org.cytoscape.work.ServiceProperties: Insert separator before this menu item
INSERT_TOOLBAR_SEPARATOR_AFTER - Static variable in interface org.cytoscape.work.ServiceProperties: Insert separator after this toolbar item
INSERT_TOOLBAR_SEPARATOR_BEFORE - Static variable in interface org.cytoscape.work.ServiceProperties: Insert separator before this toolbar item
insertHandleAt(int, Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend: Insert a Handle to the specified position in the Bend
insertSeparatorAfter - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether a menu separator should be inserted after this item
insertSeparatorAfter() - Method in class org.cytoscape.application.swing.AbstractCyAction: Insert a separator after this menu item.
insertSeparatorAfter() - Method in interface org.cytoscape.application.swing.CyAction: Insert a separator after this menu item.
insertSeparatorBefore - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether a menu separator should be inserted before this item
insertSeparatorBefore() - Method in class org.cytoscape.application.swing.AbstractCyAction: Insert a separator before this menu item.
insertSeparatorBefore() - Method in interface org.cytoscape.application.swing.CyAction: Insert a separator before this menu item.
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.
insertToolbarSeparatorAfter - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether a toolbar separator should be inserted after this item
insertToolbarSeparatorAfter() - Method in class org.cytoscape.application.swing.AbstractCyAction: Insert a separator after this menu item.
insertToolbarSeparatorBefore - Variable in class org.cytoscape.application.swing.AbstractCyAction: Indicates whether a toolbar separator should be inserted before this item
insertToolbarSeparatorBefore() - Method in class org.cytoscape.application.swing.AbstractCyAction: Insert a separator before this toolbar item.
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.
INTERACTION_TRANSFORMER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Interaction Transformer, which finds nodes based on how they are connected to the input edges.
InteractivityChangedListener - Interface in org.cytoscape.filter.view: Listens for changes in the system-level state of interactivity.
interpolateColors(Color[], int) - Method in class org.cytoscape.util.color.ColorUtils: Return an array of colors of the requested length that is created by interpolating the colors provided in the input array.
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: Deprecated.
isAlwaysFalse() - Method in interface org.cytoscape.filter.model.Filter: Returns true if the accepts() method will always return false for all inputs.
isAquaLAF() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
isBasic(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Deprecated.
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).
isColorBlindSafe() - Method in interface org.cytoscape.util.color.Palette: Return true if the palette is color blind safe.
isCompatible(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Returns true if given VisualProperty is compatible with current rendering engine.
isCompatibleList(Class) - Method in class org.cytoscape.equations.ArgDescriptor: Returns true if "listType", which must be some type of List is a type compatible with this argument descriptor.
isCompatibleWith(Class) - Method in class org.cytoscape.equations.ArgDescriptor: Tests to see if the specified class is compatible with this ArgType.
isCurrentNetwork() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns true if the network event source is the current network.
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.
isDirectlyLocked(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View: Returns true if the given VisualProperty's value has been locked.
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.
isDone() - Method in class org.cytoscape.jobs.CyJobStatus: Static method to determine if a job is "done", where done means that it is no longer processing for any reason.
isEnabled - Variable in class org.cytoscape.application.swing.AbstractToolBarComponent: Whether the toolbar component is enabled or not.
isFilled() - Method in interface org.cytoscape.view.presentation.property.values.ArrowShape
isForcedToSetDirectly() - Method in interface org.cytoscape.work.swing.DirectlyPresentableTunableHandler: If this method returns true, the boolean will be presented to set directly from GUI without being a part of a parent panel.
isGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Test to see if this node represents a CyGroup in a particular CyNetwork.
isHorizontal() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
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.
isLockedValue() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
isLowerBoundStrict() - Method in class org.cytoscape.work.util.AbstractBounded: Does the value have to be strictly greater than the lower bound?
isMac() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Returns true if the current operating system is Mac OS X.
isNimbusLAF() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
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() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: A default implementation that simply checks whether or not the String returned by AbstractNetworkSearchTaskFactory.getQuery() is empty.
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(Collection<CyRootNetwork>) - Method in class org.cytoscape.task.AbstractRootNetworkCollectionTaskFactory: Returns true if the supplied collection of root-networks is not null or empty.
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(Collection<CyRootNetwork>) - Method in interface org.cytoscape.task.RootNetworkCollectionTaskFactory: Returns true if this task factory is ready to produce a task iterator.
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: Returns true if the TaskFactory has all necessary preconditions needed to generate a task that will execute properly, false otherwise.
isScalarArgType(Class) - Static method in class org.cytoscape.equations.FunctionUtil: Tests whether the argument is one of the scalar types used by equations.
isSelected() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Return true if this annotation is currently selected
isSet(String) - Method in interface org.cytoscape.model.CyRow: Indicates whether the column of the specified type contains a non-null value.
isSet(String, String) - Method in interface org.cytoscape.model.CyRow: Indicates whether the column of the specified type contains a non-null value.
isSet(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View: Indicates whether or not the passed visual property is set with 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 the value of the given VisualProperty or one of its ancestors is locked.
isVirtual() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns true if the column is virtual, otherwise false.
isWindows() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Returns true if the current operating system is any modern Windows distribution.
isWinLAF() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil

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.
jobId - Variable in class org.cytoscape.jobs.AbstractCyJob
jobMonitor - Variable in class org.cytoscape.jobs.AbstractCyJob
jobName - Variable in class org.cytoscape.jobs.AbstractCyJob
jobStatusChanged(CyJob, CyJobStatus) - Method in interface org.cytoscape.jobs.CyJobMonitor: This method is called whenever the status of a job changes.
joinColumnName(String, String) - Static method in interface org.cytoscape.model.CyColumn: Joins a namespace and a name string into a fully-qualified column name.
JoinTablesTaskTaskFactory - Interface in org.cytoscape.task.edit: TODO: Missing documentation
JSONResult - Interface in org.cytoscape.work.json: This interface is intended to facilitate retrieving valid JSON strings from ObservableTask.getResults(Class).
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.
Justification - Enum in org.cytoscape.view.presentation.property.values: An ENUM that provides information about text justification.

K

KEY_TYPE_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
KEY_TYPE_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
keySet() - Method in interface org.cytoscape.jobs.CyJobData: Return the enumerated set of keys in this CyJobData.

L

LABEL_FONT - Static variable in class org.cytoscape.work.swing.AbstractGUITunableHandler: The default label font.
LARGE_ICON_ID - Static variable in interface org.cytoscape.work.ServiceProperties: The String ID of the Icon to be used in a swing component, usually a tool bar button (see ServiceProperties.IN_TOOL_BAR).
LARGE_ICON_URL - Static variable in interface org.cytoscape.work.ServiceProperties: Location of large icon data for desktop application (see ServiceProperties.IN_TOOL_BAR).
LAST_DIRECTORY - Static variable in interface org.cytoscape.util.swing.FileUtil: Deprecated.
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.
layoutPartition(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, z).
LayoutPoint(double, double) - Constructor for class org.cytoscape.view.layout.LayoutPoint: 2D Constructor, the Z coordinate is set to 0.
LayoutPoint(double, double, double) - Constructor for class org.cytoscape.view.layout.LayoutPoint: 3D 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.
LIGHTNESS - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: This value allows the image brighteness to be adjusted
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.
listChanged(ListSelection<T>) - Method in interface org.cytoscape.work.util.ListChangeListener
listChanged() - Method in class org.cytoscape.work.util.ListSelection: Alert all listeners that the list has changed
ListChangeListener<T> - Interface in org.cytoscape.work.util: Classes which wish to listen for changes in ListSelection objects (ListSingleSelection, ListMultipleSelection) should implement this interface and add themselves as observers (listeners) to the object.
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
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.
listPaletteIdentifiers(PaletteType, boolean) - Method in interface org.cytoscape.util.color.PaletteProvider: List all of the palettes available from this provider, optionally restricted by the palette type and whether or not the palette is color blind safe.
listPaletteNames(PaletteType, boolean) - Method in interface org.cytoscape.util.color.PaletteProvider: List all of the palettes available from this provider, optionally restricted by the palette type and whether or not the palette is color blind safe.
ListSelection<T> - Class in org.cytoscape.work.util: A ListSelection object.
ListSelection(List<T>) - Constructor for class org.cytoscape.work.util.ListSelection: Creates a new ListSelection 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.
loadData(CyJob, TaskMonitor) - Method in interface org.cytoscape.jobs.CyJobMonitor: This method is called when when the job status transitions to FINISHED and the user has indicated that they are ready to load the data from the task.
LoadMultipleNetworkFilesTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading networks from multiple files at once.
LoadNetworkFileTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for loading networks from a file.
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.
loadStyles(InputStream) - 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 importing the attribute file to one of network tables(Node,Edge or Network Table).
LoadTableURLTaskFactory - Interface in org.cytoscape.task.read: This interface provides a task iterator for importing an attribute URL to one of network tables(Node,Edge or Network Table).
LoadVizmapFileTaskFactory - Interface in org.cytoscape.task.read: An interface for loading styles from files.
LOCAL_ATTRS - Static variable in interface org.cytoscape.model.CyNetwork: The name of the local public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
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
LookAndFeelUtil - Class in org.cytoscape.util.swing: Class that provides useful methods to help create standard and consistent UI on the current Look and Feel and OS.
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

makeSmall(JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: If one of the components is a JSlider, make sure this method is called after the slider has been added to its parent container and had its UI assigned, otherwise it will have no effect on the slider's labels.
MapGlobalToLocalTableTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for mapping a global to a local table.
MappableVisualPropertyValue - Interface in org.cytoscape.view.presentation.property.values: This is a special VisualPropertyValue that allows a VisualProperty value to be specified as depending on one or more CyColumns.
MappingFunctionFactoryManager - Interface in org.cytoscape.view.vizmap.gui: Manages factories to create actual mappings (discrete/passthrough/continuous).
MapTableToNetworkTablesTaskFactory - Interface in org.cytoscape.task.edit: TODO: Missing documentation
MAX_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
maxWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
MEMBERS - Static variable in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: A comma-separate list of the UUIDs of the annotations that are part of this group
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.
MergeTablesTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator for merging two data tables.
message - Variable in class org.cytoscape.jobs.CyJobStatus
MIN_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
minWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
moveAnnotation(Point2D) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Move an annotation to the specified location
moveNodeToLocation(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutPartition: Move the node to its current X and Y values.
moveNodeToLocation3D(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutPartition: Move the node to its current X, Y and Z values.
moveToLocation() - Method in class org.cytoscape.view.layout.LayoutNode: Move the node to its current x,y coordinate (ignores the value of the z coordinate).
moveToLocation3D() - Method in class org.cytoscape.view.layout.LayoutNode: Move the node to its current x,y,z coordinate.

N

NAME - Static variable in interface org.cytoscape.application.CyUserLog: Use this name to obtain the user log.
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
NAME - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: Arg map key to initialize the name of this annotation
NamedTransformer<C,E> - Interface in org.cytoscape.filter.model: A chain of Transformers with a user-defined name.
NAMESPACE - Static variable in interface org.cytoscape.application.swing.CyColumnPresentation: OSGi property, use to provide the namespace to associate this presentation with.
NAMESPACE_SEPARATOR - Static variable in interface org.cytoscape.model.CyColumn
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_ADD_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_BACKGROUND_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The background color of the network view.
NETWORK_CENTER_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The X location of network view center.
NETWORK_CENTER_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The Y location of network view center.
NETWORK_CENTER_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NETWORK_DELETE_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NETWORK_EDIT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_GROUP_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_HEIGHT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The height of the network view.
NETWORK_LAYOUT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_PREFERENCES_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_SCALE_FACTOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The zoom level of the network view.
NETWORK_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NETWORK_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The size (width and height) of the network view.
NETWORK_TITLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The title of the network view.
NETWORK_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The width of the network view.
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 - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader: Array of networks to be returned.
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.
networks - Variable in class org.cytoscape.task.AbstractRootNetworkCollectionTask: The collection of root-networks that subclasses will operate on.
NetworkSearchTaskFactory - Interface in org.cytoscape.application.swing.search: Task Factory that has to be implemented in order to create and register a Network Search provider.
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.
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.
NetworkViewRenderer - Interface in org.cytoscape.application
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.
newCancelled(Task) - Static method in class org.cytoscape.work.FinishStatus: Construct a new FinishStatus object that indicates cancellation.
NewEmptyNetworkViewFactory - Interface in org.cytoscape.task.create: An interface for creating new, empty network views.
newFailed(Task, Exception) - Static method in class org.cytoscape.work.FinishStatus: Construct a new FinishStatus object that indicates failure.
NewNetworkSelectedNodesAndEdgesTaskFactory - 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_ADD_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_BORDER_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The type of line used for the border of the node.
NODE_BORDER_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the border of the node.
NODE_BORDER_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_BORDER_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_DYNAMIC_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_EDIT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_FILL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the node.
NODE_GROUP_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_HEIGHT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The height of the node.
NODE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text used for the node label.
NODE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the node label.
NODE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The font used for the node label.
NODE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The size of the font used for the node label.
NODE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The maximum width of the node label.
NODE_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_NESTED_NETWORK_IMAGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: A boolean value that indicates whether a nested network should be visualized (assuming a nested network is present for the specified node).
NODE_NESTED_NETWORKS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_OPACITY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: See BasicVisualLexicon.NODE_TRANSPARENCY
NODE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole node, including its border, label and selected paint.
NODE_PREFERENCES_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
NODE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
NODE_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The shape of the node.
NODE_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The size of the node.
NODE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text of the tooltip that appears when a mouse hovers over the node.
NODE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The opacity of the color of the node.
NODE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Hides the node if set to false.
NODE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The width of the node.
NODE_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: X location of the node.
NODE_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Y location of the node.
NODE_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Z location of the node.
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
NodeList - Class in org.cytoscape.command.util: This class implements a wrapper for a List of CyNodes that can be used by the Tunables mechanism.
NodeList() - Constructor for class org.cytoscape.command.util.NodeList: Create a new NodeList object with no initial network
NodeList(CyNetwork) - Constructor for class org.cytoscape.command.util.NodeList: Create a new NodeList object with an initial network
nodesChanged() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns true if the selection state of nodes has changed.
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.
NOGUI_CONTEXT - Static variable in annotation type org.cytoscape.work.Tunable
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.
notifyListeners() - Method in class org.cytoscape.filter.model.AbstractTransformer: Notifies any registered listeners that this transformer's settings have changed.
NullCyNetworkView - Interface in org.cytoscape.view.model: A CyNetwork with no corresponding view.
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.
ObjectPosition - Class in org.cytoscape.view.presentation.property.values: ObjectPosition is the value that is used by Position VisualProperties.
ObjectPosition() - Constructor for class org.cytoscape.view.presentation.property.values.ObjectPosition: Creates a new ObjectPosition object.
ObjectPosition(ObjectPosition) - Constructor for class org.cytoscape.view.presentation.property.values.ObjectPosition: Copy constructor
ObjectPosition(Position, Position, Justification, double, double) - Constructor for class org.cytoscape.view.presentation.property.values.ObjectPosition: Creates a new ObjectPosition object.
ObservableTask - Interface in org.cytoscape.work: A Task that notifies its observers when it is finished executing.
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.
offset(double, double, double) - Method in class org.cytoscape.view.layout.LayoutPartition: Offset all of the nodes in the partition by a fixed amount.
OPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: The opacity of the image.
OPEN_CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled Circle shaped arrow
OPEN_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled triangle shaped arrow
OPEN_DIAMOND - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled Diamond shaped arrow
OPEN_HALF_CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled Half-Circle shaped arrow
OPEN_SQUARE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled square shaped arrow
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.event - package org.cytoscape.app.event
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.application.swing.search - package org.cytoscape.application.swing.search
org.cytoscape.command - package org.cytoscape.command: Interface to support execution of tasks as commands, including the ability to get a list of namespaces, commands, and arguments, and then execute those commands with a set of arguments.
org.cytoscape.command.util - package org.cytoscape.command.util: Tunable classes useful for command applications
org.cytoscape.equations - package org.cytoscape.equations: Various types and utility methods relating to attribute equations.
org.cytoscape.equations.event - package org.cytoscape.equations.event
org.cytoscape.event - package org.cytoscape.event: This package contains the basic interfaces necessary for defining, firing, and listening for Cytoscape events.
org.cytoscape.filter - package org.cytoscape.filter: Provides interfaces for constructing and executing Transformers and Filters.
org.cytoscape.filter.model - package org.cytoscape.filter.model: Provides interfaces and classes for defining Transformers and Filters.
org.cytoscape.filter.predicates - package org.cytoscape.filter.predicates: General purpose predicates used to perform comparisons against numbers and strings.
org.cytoscape.filter.transformers - package org.cytoscape.filter.transformers: Provides interfaces for working with the Transformers provided by the core.
org.cytoscape.filter.view - package org.cytoscape.filter.view: Provides interfaces for contributing user interfaces for Transformers to Cytoscape.
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.jobs - package org.cytoscape.jobs: This package provides a mechanism for executing remote jobs from within Cytoscape.
org.cytoscape.model - package org.cytoscape.model: This package has the core interfaces of network and table data structures that are foundational to 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.analyze - package org.cytoscape.task.analyze
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.color - package org.cytoscape.util.color
org.cytoscape.util.json - package org.cytoscape.util.json
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.annotations - package org.cytoscape.view.presentation.annotations: This package provides support for graphical annotations associated with a Cytoscape CyNetworkView.
org.cytoscape.view.presentation.customgraphics - package org.cytoscape.view.presentation.customgraphics: This package provides an API for augmenting a RenderingEngines node rendering with custom graphics.
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 package defines the task framework, where tasks are units of work.
org.cytoscape.work.json - package org.cytoscape.work.json
org.cytoscape.work.properties - package org.cytoscape.work.properties
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.swing.util - package org.cytoscape.work.swing.util
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
PaintedShape - Interface in org.cytoscape.view.presentation.customgraphics: This interface defines a the information required to construct a Shape that has an arbitrary fill Paint and Stroke.
paintIcon(Component, Graphics, int, int) - Method in class org.cytoscape.util.swing.TextIcon
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.
Palette - Interface in org.cytoscape.util.color: This interface provides a consistent way for various providers (ColorBrewer, ColourLovers, etc.) to provide color palettes to Cytoscape routines.
PaletteProvider - Interface in org.cytoscape.util.color: This interface provides a consistent way for various providers (ColorBrewer, ColourLovers, etc.) to provide color palettes to Cytoscape routines.
PaletteProviderManager - Interface in org.cytoscape.util.color: The PaletteProviderManager provides a way for palette providers to register themselves.
PaletteType - Interface in org.cytoscape.util.color: This is an interface for defining types of palettes.
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
parse(String) - Static method in enum org.cytoscape.view.presentation.property.values.Justification: Parse a string that contains either the short name or the display name for a justifcation and return the corresponding enum value
parse(String) - Static method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Parse a String that has been written by toSerializableString and create a new ObjectPosition that matches the text description
parse(String) - Static method in enum org.cytoscape.view.presentation.property.values.Position: Parse a string that contains either the short name or the display name for an anchor and return the corresponding enum value
parseAndSetValue(String) - Method in interface org.cytoscape.work.properties.TunablePropertyHandler: Converts the String representation to an object or primitive value and sets the tunable.
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 interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Create a new CyCustomGraphics object by parsing the string resulting from the toSerializableString() 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.
path - Variable in class org.cytoscape.jobs.AbstractCyJob
pollInterval - Variable in class org.cytoscape.jobs.AbstractCyJob
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.
Position - Enum in org.cytoscape.view.presentation.property.values: An ENUM that provides values for the various anchors that may be used for text, customgraphics, etc.
postEdit(AbstractCyEdit) - Method in interface org.cytoscape.work.undo.UndoSupport: Posts the specified edit to the Cytoscape undo stack.
Predicate - Enum in org.cytoscape.filter.predicates: Various predicates that can be used to test conditions in Transformers.
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
processArg(String) - Method in class org.cytoscape.command.AbstractStringTunableHandler: Each specific handler really only needs to implement this method and all it does is convert the String input into a value of the appropriate type.
processArg(String) - Method in interface org.cytoscape.command.StringTunableHandler
processArgString(String) - Method in class org.cytoscape.command.AbstractStringTunableHandler
processArgString(String) - Method in interface org.cytoscape.command.StringTunableHandler
processClick() - Method in class org.cytoscape.util.swing.CheckBoxJList
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.
put(String, Object) - Method in interface org.cytoscape.jobs.CyJobData: Set the value for a particular key.
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.

Q

QUERY_PROPERTY - Static variable in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Name of the property that indicates that the provided query or options component changed the query parameters.

R

randomizeLocations(boolean) - Method in class org.cytoscape.view.layout.LayoutPartition: Randomize the graph locations.
randomizeLocations() - Method in class org.cytoscape.view.layout.LayoutPartition: Randomize the graph locations (ignoring Z values).
Range<T> - Interface in org.cytoscape.view.model: Defines a range of values for VisualPropertys.
read(InputStream) - Method in interface org.cytoscape.io.read.CyTransformerReader
recenter - Variable in class org.cytoscape.view.layout.AbstractLayoutTask: Determines whether the resulting set of nodes should be moved back to their original centroid after being laid out.
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.
refresh(Object) - Method in interface org.cytoscape.work.swing.TunableUIHelper: Recreate the Tunable UI.
refreshEquations(CyTable, EquationCompiler) - Static method in class org.cytoscape.equations.EquationUtil: Refreshes all the equations in the given CyTable
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(BundleContext, Object) - Method in class org.cytoscape.service.util.AbstractCyActivator
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: Deprecated.
Functions registered using this method will work, but will not update properly if the containing bundle is updated. To register a Function, please use CyActivator or CyServiceRegistrar's registerService method to register as a service so updates can be handled properly.
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(BundleContext, Object, Class<?>) - Method in class org.cytoscape.service.util.AbstractCyActivator
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, BiConsumer<S, Map<String, String>>, BiConsumer<S, Map<String, String>>, Class<S>) - 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, BiConsumer<S, Map<String, String>>, BiConsumer<S, Map<String, String>>, Class<S>, 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(int) - Method in interface org.cytoscape.filter.model.CompositeFilter: Removes the Filter at the given index from the list of children and returns in.
remove(URL) - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker: Removes the passed URL from the list of recently opened file names.
remove(String) - Method in interface org.cytoscape.jobs.CyJobData: Remove the data for a key
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
removeAllTables(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkTableManager: Removes all tables associated with the given network.
removeAnnotation() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Deprecated.
Use AnnotationManager#removeAnnotation() instead.
removeAnnotation(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Remove an annotation from its network view.
removeAnnotations(Collection<? extends Annotation>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Removes annotations from its network view .
removeArrow(ArrowAnnotation) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Remove an arrow from this annotation.
removeCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
removeCollapeListener(BasicCollapsiblePanel.CollapseListener) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
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.
removeIcon(String) - Method in interface org.cytoscape.util.swing.IconManager
removeIconFont(String) - Method in interface org.cytoscape.util.swing.IconManager
removeIncompatibleVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Remove incompatible VisualProperty from list if new RenderingEngine can handle it.
removeJob(CyJob) - Method in interface org.cytoscape.jobs.CyJobManager: Remove a job from being managed by the job manager.
removeListener(TransformerListener) - Method in class org.cytoscape.filter.model.AbstractTransformer
removeListener(TransformerListener) - Method in interface org.cytoscape.filter.model.Transformer: Unsubscribes the given listener from changes in this Transformer's parameters.
removeListener(BoundedChangeListener<N>) - Method in class org.cytoscape.work.util.AbstractBounded: Removes a listener from the list that will listen for changes to this object
removeListener(ListChangeListener<T>) - Method in class org.cytoscape.work.util.ListSelection: Removes a listener from the list that will listen for changes to this object
removeMember(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: Remove an annotation from the group
removeNamedTransformer(String) - Method in interface org.cytoscape.filter.TransformerContainer: Remove a transformer from this container.
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.
removePaletteProvider(PaletteProvider) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Remove a palette provider from the manager.
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.
removeVisualPropertyValueEditor(VisualPropertyValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Remove an editor from manager--invoked by OSGi when a bundle that exports an instance is being unloaded.
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.
RequestsUIHelper - Interface in org.cytoscape.work.swing: Interface to indicate that an app wants to have a UI helper provided.
reset() - Method in interface org.cytoscape.application.CyApplicationManager: Releases all currently held references and resources.
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.
resizeIcon(Icon, int) - Static method in interface org.cytoscape.util.swing.IconManager: Resizes an icon so that its maximum dimension (width or height) is no larger than the given 'max' parameter.
restoreEdge(CyEdge) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Causes the given edge to (temporarily) remain in the root network even if it has already been removed from all subnetworks.
restoreJobFromSession(CySession, File) - Method in interface org.cytoscape.jobs.CyJobExecutionService: This is method is called by the CyJobManager to restore the job and reestablish the job with the remote service.
restoreNetwork(CyJob, CyNetworkManager, Long, boolean) - Static method in class org.cytoscape.jobs.SUIDUtil: This method is used to restore a saved network based on the network SUID.
restoreNode(CyNode) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Causes the given node to (temporarily) remain in the root network even if it has already been removed from all subnetworks.
restoreSUIDs(CyJob, CyNetwork, List<Long>, boolean) - Static method in class org.cytoscape.jobs.SUIDUtil: Method to restore Cytoscape objects based on a list of SUIDs that were sent to the remote service as saved in the hidden table.
retrievePalette(Object) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Retrieve a palette previously saved
RootNetworkCollectionTaskFactory - Interface in org.cytoscape.task: Produces a task iterator for the specified collection of root-networks.
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.
ROW_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
ROW_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
rowExists(Object) - Method in interface org.cytoscape.model.CyTable: Returns true if a row exists for the specified primary key and false otherwise.
RowList - Class in org.cytoscape.command.util: This class implements a wrapper for a List of table rows that can be used by the Tunables mechanism.
RowList() - Constructor for class org.cytoscape.command.util.RowList: Create a new RowList object with no initial table
RowList(CyTable) - Constructor for class org.cytoscape.command.util.RowList: Create a new RowList object with an initial table
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
RowsDeletedEvent - Class in org.cytoscape.model.events: This event signals that rows have been Deleted.
RowsDeletedEvent(CyTable, Collection<Object>) - Constructor for class org.cytoscape.model.events.RowsDeletedEvent: Constructs event.
RowsDeletedListener - Interface in org.cytoscape.model.events: Listener for RowsDeletedEvent
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
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
saveBookmark(Bookmarks, String, DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Store a bookmark object in bookmarks object
saveDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Save a DataSource to the DataSourceManager
saveJobInSession(CyJob, File) - Method in interface org.cytoscape.jobs.CyJobExecutionService: This is method is called by the CyJobManager to save sufficient information as part of the session to be able to restore and reestablish the job with the remote service.
savePalette(Object, Palette) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Save a palette.
SavePolicy - Enum in org.cytoscape.model: The SavePolicy of an object specifies whether or not it will be saved.
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.
SaveSessionTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for saving a session.
saveSUIDs(CyJob, CyNetwork, List<? extends CyIdentifiable>) - Static method in class org.cytoscape.jobs.SUIDUtil: This method may be used to save a list of SUIDs that have been sent to a remote service so that they may be restored later
SEARCH_REQUESTED_PROPERTY - Static variable in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Name of the property that indicates that a search action has been requested by the custom query component.
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.
SelectedNodesAndEdgesEvent - Class in org.cytoscape.model.events: Event that signals when the selection state of nodes and/or edges has changed within a network.
SelectedNodesAndEdgesEvent(CyNetwork, boolean, boolean, boolean) - Constructor for class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
SelectedNodesAndEdgesListener - Interface in org.cytoscape.model.events: Listener for SelectedNodesAndEdgesEvent
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.
selectionChanged(ListSelection<T>) - Method in interface org.cytoscape.work.util.ListChangeListener
selectionChanged() - Method in class org.cytoscape.work.util.ListSelection: Alert all listeners that the selection has changed
ServiceProperties - Interface in org.cytoscape.work: Reserved keywords for OSGi service properties (meta data).
SessionAboutToBeLoadedEvent - Class in org.cytoscape.session.events: This event is fired right before Cytoscape begins to load a session.
SessionAboutToBeLoadedEvent(Object) - Constructor for class org.cytoscape.session.events.SessionAboutToBeLoadedEvent: Constructor.
SessionAboutToBeLoadedListener - Interface in org.cytoscape.session.events: Any object that needs to know that a CySession is about to be loaded or created should implement this listener.
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 should listen to this event.
SessionLoadCancelledEvent - Class in org.cytoscape.session.events: Deprecated.
Just listen to SessionLoadedEvent instead now.
SessionLoadCancelledEvent(Object) - Constructor for class org.cytoscape.session.events.SessionLoadCancelledEvent: Deprecated.
SessionLoadCancelledEvent(Object, Exception) - Constructor for class org.cytoscape.session.events.SessionLoadCancelledEvent: Deprecated.

Use this constructor if the session load was cancelled because of an exception.
SessionLoadCancelledListener - Interface in org.cytoscape.session.events: Deprecated.
Use SessionLoadedListener instead.
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
SessionLoadedListener - Interface in org.cytoscape.session.events: A listener for SessionLoadedEvents.
SessionSaveCancelledEvent - Class in org.cytoscape.session.events: This event is fired when a session save task is cancelled, which can also happen because of exceptions.
SessionSaveCancelledEvent(Object) - Constructor for class org.cytoscape.session.events.SessionSaveCancelledEvent: Constructor.
SessionSaveCancelledEvent(Object, Exception) - Constructor for class org.cytoscape.session.events.SessionSaveCancelledEvent: Use this constructor if the session save was cancelled because of an exception.
SessionSaveCancelledListener - Interface in org.cytoscape.session.events: A listener for SessionSaveCancelledEvents.
SessionSavedEvent - Class in org.cytoscape.session.events: TODO: Missing documentation
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: Sets the specified column for this row to the specified value.
set(String, String, T) - Method in interface org.cytoscape.model.CyRow: Sets 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.
setAcceleratorKeyStroke(KeyStroke) - Method in interface org.cytoscape.application.swing.CyAction: was defined in AbstractCyAction, but not in this interface
setActionListener(ActionListener) - Method in class org.cytoscape.work.swing.util.UserAction
setAnchor(Position) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Set the anchor of the label (or other object).
setAnchorType(ArrowAnnotation.ArrowEnd, ArrowAnnotation.AnchorType) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the anchor type for one end of the arrow
setArrowColor(ArrowAnnotation.ArrowEnd, Paint) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the color of one end of the arrow
setArrowSize(ArrowAnnotation.ArrowEnd, double) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the size of one end of the arrow
setArrowType(ArrowAnnotation.ArrowEnd, String) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the type of one end of the arrow
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.
setBorderColor(Paint) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the border (stroke) color.
setBorderOpacity(double) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the border (stroke) opacity.
setBorderWidth(double) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the border (stroke) width.
setBounds(CyNetworkView, Rectangle) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr: Deprecated.
This method has been deprecated in version 3.4 and does not do anything anymore.
setBounds(N, N) - Method in class org.cytoscape.work.util.AbstractBounded: Set the upper bound (upper) and lower bound (lower) of the Bounded Object.
setCanvas(String) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Set the canvas for this annotation.
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.
setColor(Color) - Method in class org.cytoscape.util.swing.ColorButton: Sets a new color and fires a PropertyChangeEvent for the property "color".
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.
setControl(Component) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
setCurrentDirectory(File) - Method in interface org.cytoscape.application.CyApplicationManager: Set the current working directory.
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.
setCurrentVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Set the specified VisualStyle as the current one.
SetCurrentVisualStyleEvent - Class in org.cytoscape.view.vizmap.events: TODO: Missing documentation
SetCurrentVisualStyleEvent(Object, VisualStyle) - Constructor for class org.cytoscape.view.vizmap.events.SetCurrentVisualStyleEvent
SetCurrentVisualStyleListener - Interface in org.cytoscape.view.vizmap.events: TODO: Missing documentation
setCustomShape(Shape) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set a custom shape to be drawn.
setDefaultAggregation(Class<?>, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the default Aggregator for a specific column type as expressed as a java Class.
setDefaultAggregation(CyGroup, Class<?>, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the Aggregator for a specific column type as expressed as a java Class that will be used in the specified CyGroup.
setDefaultAggregation(CyGroup, Class<?>, String) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the Aggregator for a specific column type as expressed as a java Class that will be used in the specified CyGroup.
setDefaultLayout(CyLayoutAlgorithm) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Changes Cytoscape's default layout.
setDefaultListAggregation(Class<?>, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the default Aggregator for a specific List column type as expressed as a java Class.
setDefaultListAggregation(CyGroup, Class<?>, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the Aggregator for a specific List column type as expressed as a java Class that will be used in the specified CyGroup.
setDefaultListAggregation(CyGroup, Class<?>, String) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the Aggregator for a specific List column type as expressed as a java Class that will be used in the specified CyGroup.
setDefaultNetworkViewRenderer(NetworkViewRenderer) - Method in interface org.cytoscape.application.CyApplicationManager: Sets the NetworkViewRenderer that should be used to create CyNetworkViews.
setDefaultOkCancelKeyStrokes(JRootPane, Action, Action) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Maps the standard key strokes (usually ENTER and ESCAPE) to the passed OK and/or Cancel actions.
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 2D displacement of this LayoutNode.
setDisp(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the 3D displacement of this LayoutNode.
setDisplayName(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Set human readable display name.
setDoubleClickAction(CyGroupSettingsManager.DoubleClickAction) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the current default CyGroupSettingsManager.DoubleClickAction.
setDoubleClickAction(CyGroup, CyGroupSettingsManager.DoubleClickAction) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the CyGroupSettingsManager.DoubleClickAction for a specific group.
setEdgeWeighter(EdgeWeighter) - Method in class org.cytoscape.view.layout.LayoutPartition: Set the EdgeWeighter to use for this partition.
setEnableAttributeAggregation(boolean) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the setting for whether or not we're aggregating values from member nodes onto the group node.
setEnableAttributeAggregation(CyGroup, boolean) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the setting for whether or not we're aggregating values for member nodes onto the group node for a specific group.
setEnabled(boolean) - Method in interface org.cytoscape.work.swing.DynamicSubmenuListener: Enables or disables the dynamically created menus.
setEnabled(boolean) - Method in class org.cytoscape.work.swing.util.UserAction
setEventHelper(CyEventHelper) - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: The VisualStyle implementation should use this method to pass a valid CyEventHelper after this dependency is added to the visual style object.
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.
setFillColor(Paint) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the fill color.
setFillOpacity(double) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the fill opacity, a value between 0.0 (fully transparent) and 100.0 (fully opaque).
setFitRatio(float) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Set the fit ratio for this custom graphic.
setFont(Font) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the font to be used.
setFont(Font) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the font to be used.
setFontFamily(String) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the font family to be used for the text display
setFontFamily(String) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the font family to be used for the text display
setFontSize(double) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the size of the font used to display the text
setFontSize(double) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the size of the font used to display the text
setFontStyle(int) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the font style
setFontStyle(int) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the font style
setFormat(String) - Method in class org.cytoscape.property.bookmark.DataSource: Sets the value of the format property.
setGroupViewType(CyGroupSettingsManager.GroupViewType) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the current default CyGroupSettingsManager.GroupViewType.
setGroupViewType(CyGroup, CyGroupSettingsManager.GroupViewType) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the CyGroupSettingsManager.GroupViewType for a specific group.
setHeight(int) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Set height of Custom Graphics.
setHref(String) - Method in class org.cytoscape.property.bookmark.DataSource: Sets the value of the href property.
setIdentifier(Long) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Set the session-unique identifier of this custom graphics.
setImage(Image) - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Set the image to be displayed as part of this annotation
setImage(URL) - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Set a URL to fetch the image from.
setImageBrightness(int) - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Set the brightness adjustment for the image.
setImageContrast(int) - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Set the contrast adjustment for the image.
setImageOpacity(float) - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Set the opacity of the image.
setIsInMenuBar(boolean) - Method in class org.cytoscape.application.swing.AbstractCyAction
setIsInMenuBar(boolean) - Method in interface org.cytoscape.application.swing.CyAction: To support configurable menus and tools, setIsInMenuBar added for 3.6
setIsInToolBar(boolean) - Method in class org.cytoscape.application.swing.AbstractCyAction
setIsInToolBar(boolean) - Method in interface org.cytoscape.application.swing.CyAction: To support configurable menus and tools, setIsInToolBar added for 3.6
setJobMonitor(CyJobMonitor) - Method in class org.cytoscape.jobs.AbstractCyJob
setJobMonitor(CyJobMonitor) - Method in interface org.cytoscape.jobs.CyJob: Set the service that handles status changes for this job.
setJustify(Justification) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Set the justification of the label (or other object).
setLabel(String, JLabel) - Method in interface org.cytoscape.application.swing.CyColumnPresentationManager: Sets the text and icon of the given JLabel so that it represents the given column in an esthetically pleasing way.
setLabel(String, Consumer<Icon>, Consumer<String>) - Method in interface org.cytoscape.application.swing.CyColumnPresentationManager: Calls the given Consumer callbacks with an icon and text string that represents the given column in an esthetically pleasing way.
setLabel(JLabel) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
setLeftLabel(String) - Method in class org.cytoscape.util.swing.JStatusBar: Set the left label of this JStatusBar.
setLineColor(Paint) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the line color for this arrow
setLineWidth(double) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the line width for this arrow
setLocation(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the 2D location of this LayoutNode.
setLocation(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the 3D 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.
setLowerBoundStrict(boolean) - Method in class org.cytoscape.work.util.AbstractBounded: Set the lower bound strict policy to lowerStrict.
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.
setMenuGravity(float) - Method in interface org.cytoscape.application.swing.CyAction: To support configurable menus and tools, setMenuGravity added for 3.6
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
setModality(Dialog.ModalityType) - Method in interface org.cytoscape.work.swing.TunableUIHelper: Set the modality of the parent dialog.
setMode(boolean) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Deprecated.
setMultiLineLabel(JTextArea) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
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, 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.
setName(String) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Set the name for this annotation.
setNetwork(CyNetwork) - Method in class org.cytoscape.command.util.EdgeList: Set the network to be used by this EdgeList
setNetwork(CyNetwork) - Method in class org.cytoscape.command.util.NodeList: Set the network for this nodelist
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.
setNetworkViewRendererList(ListSingleSelection<NetworkViewRenderer>) - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
setNormalizedBounds(double, double) - Method in class org.cytoscape.view.layout.EdgeWeighter
setOffset(double) - Method in class org.cytoscape.work.AbstractTunableHandler
setOffsetX(double) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Set the X offset of the object
setOffsetY(double) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Set the Y offset of the object
setOverrideAggregation(CyColumn, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: set the override aggregation setting for a column (if any).
setOverrideAggregation(CyGroup, CyColumn, Aggregator<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager: set the override aggregation setting for a column in a group (if any).
setPartitionNumber(int) - Method in class org.cytoscape.view.layout.LayoutPartition: Set the partition number of this partition
setPollInterval(int) - Method in class org.cytoscape.jobs.AbstractCyJob
setPollInterval(int) - Method in interface org.cytoscape.jobs.CyJob: Set the time in seconds between calls to checkJobStatus.
setPopupMenu(JPopupMenu) - Method in class org.cytoscape.util.swing.DropDownMenuButton
setPossibleValues(List<T>) - Method in class org.cytoscape.work.util.ListSelection: Changes the set of possible values in the list
setPreferredMenu(String) - Method in class org.cytoscape.application.swing.AbstractCyAction: Sets the preferredMenuString.
setPreferredMenu(String) - Method in interface org.cytoscape.application.swing.CyAction: To support configurable menus and tools, setPreferredMenu added for 3.6
setProgress(double) - Method in interface org.cytoscape.work.TaskMonitor: Sets the progress completed by the Task.
setPublic(boolean) - Method in interface org.cytoscape.model.CyTable: Sets the privacy flag for the CyTable.
setQuery(String) - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: This method is called by Cytoscape whenever the user changes the query text.
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.
setRootNetworkList(ListSingleSelection<String>) - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
setRowHeight(int) - Method in class org.cytoscape.util.swing.JTreeTable: Overridden to pass the new rowHeight to the tree.
setSavePolicy(SavePolicy) - Method in interface org.cytoscape.model.CyTable: Sets how (or if) this CyTable should be saved.
setSelected(boolean) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Set the selected state for this annotation
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.
setShapeType(String) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the current shape type
setSize(double, double) - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Set the size of the shape.
setSource(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the source Annotation for this arrow.
setSpecificZoom(double) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Set the specific zoom for this annotation
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 the task is currently doing.
setTable(CyTable) - Method in class org.cytoscape.command.util.RowList: Set the table for this rowlist
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.
setTarget(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the target for this arrow assuming the target is an Annotation
setTarget(CyNode) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the target for this arrow assuming the target is a CyNode
setTarget(Point2D) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Set the target for this arrow assuming the target is a point on the canvas
setTargetAnchor(Position) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Set the anchor of the target object (e.g.
setTargetColumnList(ListSingleSelection<String>) - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
setTaskIterator(TaskIterator) - Method in class org.cytoscape.work.AbstractTask: This method is used by a TaskIterator to set itself on the newly added Task.
setTaskStatus(int) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Used for
setText(String) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the text to be displayed as part of the annotation
setText(String) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the text to be displayed as part of the annotation
setTextColor(Color) - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Set the color of the text to be displayed
setTextColor(Color) - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Set the color of the text to be displayed
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.
setToolbarGravity(float) - Method in interface org.cytoscape.application.swing.CyAction: To support configurable menus and tools, setToolbarGravity added for 3.6
setToolTipText(String) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: Sets the tooltip text of this BasicCollapsiblePanel.
setTunableDirectly(Window) - Method in interface org.cytoscape.work.swing.DirectlyPresentableTunableHandler: This method allows us to bypass the normal tunable support when there is only one tunable in a Task.
setTunables(Object, Properties) - Method in interface org.cytoscape.work.properties.TunablePropertySerializer: Takes the properties and applies them to the tunables in the object.
setType(CompositeFilter.Type) - Method in interface org.cytoscape.filter.model.CompositeFilter: Sets the type of combining semantics used by this filter.
setType(ListSingleSelection<WeightTypes>) - Method in class org.cytoscape.view.layout.EdgeWeighter
setUIHelper(TunableUIHelper) - Method in interface org.cytoscape.work.swing.RequestsUIHelper: This method will be called by the Tunable UI handler to provide a helper object that might be used for some interaction with the Tunable UI.
setUpperBoundStrict(boolean) - Method in class org.cytoscape.work.util.AbstractBounded: Set the upper bound strict policy to upperStrict.
setUseNestedNetworks(boolean) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the default setting for whether or not to create a nested network view on collapsed nodes.
setUseNestedNetworks(CyGroup, boolean) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Set the setting for whether or not to create a nested network view on collapsed nodes for a specific CyGroup.
setValue(List<CyEdge>) - Method in class org.cytoscape.command.util.EdgeList: Set the edgeList for this tunable
setValue(List<CyNode>) - Method in class org.cytoscape.command.util.NodeList: Set the list of nodes
setValue(List<CyRow>) - Method in class org.cytoscape.command.util.RowList: Set the list of rows
setValue(K) - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Sets Point Value.
setValue(Object) - Method in class org.cytoscape.work.AbstractTunableHandler
setValue(Object) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
setValue(Object) - Method in interface org.cytoscape.work.TunableHandler: Attempts to set the value of the associated field or set method that has been annotated with 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
setWidth(int) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Set width of Custom Graphics.
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.
setZ(double) - Method in class org.cytoscape.view.layout.LayoutNode: Set the Z location of this LayoutNode.
setZoom(double) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Set the current zoom for this annotation
ShapeAnnotation - Interface in org.cytoscape.view.presentation.annotations: A Shape annotation supports annotations that can be drawn and filled on the graphics canvas.
ShapeAnnotation.ShapeType - Enum in org.cytoscape.view.presentation.annotations
shapeName() - Method in enum org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
SHAPETYPE - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The shape type
SHARED_ATTRS - Static variable in interface org.cytoscape.model.subnetwork.CyRootNetwork: The name of the table containing the attributes shared by all subnetworks of this root network.
SHARED_DEFAULT_ATTRS - Static variable in interface org.cytoscape.model.subnetwork.CyRootNetwork: The name of the table that enables sharing default attributes with 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.
showDialog(Component, String, Palette, Color, int) - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
showDialog(Component, String, Palette, int) - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
showEditor(Component) - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewEditor: Deprecated.
showEditor(Component, S) - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor: Display the editor and get a new value.
showEditor(Component, S, VisualProperty<S>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyValueEditor: Display the editor and get a new value.
showMessage(TaskMonitor.Level, String) - Method in interface org.cytoscape.work.TaskMonitor: Sets the status message that describes what the task is currently doing.
showVisualPropertyValueEditor(Component, VisualProperty<V>, V) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Display value editor to get a new value.
shutDown() - Method in class org.cytoscape.service.util.AbstractCyActivator: Cleans up resources used by the app.
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 interface org.cytoscape.util.color.Palette: Return the number of colors natively in the palette.
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_ID - Static variable in interface org.cytoscape.work.ServiceProperties: The String ID of the Icon to be used in a swing component, usually a menu item (see ServiceProperties.IN_MENU_BAR).
SMALL_ICON_URL - Static variable in interface org.cytoscape.work.ServiceProperties: Location of small icon data for desktop application (see ServiceProperties.IN_MENU_BAR).
SOLID - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Solid line
splitColumnName(String) - Static method in interface org.cytoscape.model.CyColumn: Splits a column name into a namespace part and a name part at the first occurrence of a "::".
SQUARE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Square shaped arrow
status - Variable in class org.cytoscape.jobs.CyJobStatus
StatusBarPanelFactory - Interface in org.cytoscape.work.swing: Creates a JPanel that is shown at the bottom of the Cytoscape Desktop.
NOTE: this is not meant to be implemented by App developers.
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
StringToModel - Interface in org.cytoscape.command: The service implementing StringToModel provides a common mechanism for converting command arguments into Cytoscape model elements.
StringTunableHandler - Interface in org.cytoscape.command
StringTunableHandlerFactory<T extends StringTunableHandler> - Interface in org.cytoscape.command
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.
SubFilterTransformer<C,E> - Interface in org.cytoscape.filter.model: A Transformer that contains a CompositeFilter that it uses to filter its output.
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.
SUIDUtil - Class in org.cytoscape.jobs: This utility class provides methods to save and restore SUIDs that are sent to remote execution environments across sessions.
SUIDUtil() - Constructor for class org.cytoscape.jobs.SUIDUtil
supportsMime(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Given a mime type, return true if this CyCustomGraphicsFactory can utilize this type of data.
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: Deprecated.

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 with the current thread, blocking code execution until all tasks finish.

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_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
TABLE_TITLE_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
TABLE_TITLE_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
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.
TablePrivacyChangedEvent - Class in org.cytoscape.model.events: This event is fired when a table privacy is changed from public to private or vice versa.
TablePrivacyChangedEvent(CyTable) - Constructor for class org.cytoscape.model.events.TablePrivacyChangedEvent: Constructor method for TablePrivacyChangedEvent.
TablePrivacyChangedListener - Interface in org.cytoscape.model.events: Listener interface for handling TablePrivacyChangedEvent.
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.
TableTitleChangedEvent - Class in org.cytoscape.model.events: TODO: Missing documentation
TableTitleChangedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.TableTitleChangedEvent
TableTitleChangedListener - Interface in org.cytoscape.model.events: TODO: Missing documentation
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.
taskFinished(ObservableTask) - Method in interface org.cytoscape.work.TaskObserver: Called by an ObservableTask when it is finished executing.
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 a Task's implementation run method to inform users of the status of its execution.
TaskMonitor.Level - Enum in org.cytoscape.work: Used by the showMessage method to indicate the severity of the message.
TaskObserver - Interface in org.cytoscape.work: An observer that gets notified when an ObservableTask finishes executing.
TaskStatusPanelFactory - Interface in org.cytoscape.work.swing: Deprecated.
TEXT - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the text to display
TextAnnotation - Interface in org.cytoscape.view.presentation.annotations: A text annotation is a simple text string that is displayed on the network canvas.
TextIcon - Class in org.cytoscape.util.swing: Renders any text/font as an icon.
TextIcon(String, Font, Color, int, int) - Constructor for class org.cytoscape.util.swing.TextIcon
TextIcon(String, Font, int, int) - Constructor for class org.cytoscape.util.swing.TextIcon: The icon color is the target component's foreground.
TextIcon(String[], Font, Color[], int, int) - Constructor for class org.cytoscape.util.swing.TextIcon
TextIcon(String[], Font, int, int) - Constructor for class org.cytoscape.util.swing.TextIcon: The icon color is the target component's foreground.
TextIcon(String[], Font, Color[], int, int, Integer...) - Constructor for class org.cytoscape.util.swing.TextIcon
TextIcon(String[], Font[], Color[], int, int) - Constructor for class org.cytoscape.util.swing.TextIcon
TextIcon(String[], Font[], int, int) - Constructor for class org.cytoscape.util.swing.TextIcon: The icon color is the target component's foreground.
TextIcon(String[], Font[], Color[], int, int, Integer...) - Constructor for class org.cytoscape.util.swing.TextIcon
THUMBNAIL_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
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.
toJson(CyIdentifiable) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a reference (via SUID) for a CyIdentifiable.
toJson(CyNetwork, CyNode, CyColumn...) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of a single CyNode and its relevant data.
toJson(CyNetwork, CyEdge, CyColumn...) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of a single CyEdge and its relevant data.
toJson(CyNetwork) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of a network and its relevant data.
toJson(CyTable, boolean, boolean) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of a CyTable.
toJson(CyColumn, boolean, boolean) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of CyColumn.
toJson(CyRow, CyColumn...) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a JSON representation of a table row.
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 class org.cytoscape.work.AbstractTunableHandler
TOOLTIP - Static variable in interface org.cytoscape.work.ServiceProperties: Short tool tip text for an action.
TOOLTIP_IMAGE - Static variable in interface org.cytoscape.work.ServiceProperties: Optional tool tip image for an action (usually used in tool bars).
TOOLTIP_LONG_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties: Optional longer tool tip description for an action (usually used in tool bars).
toolTipImage - Variable in class org.cytoscape.application.swing.AbstractCyAction: Path to an optional tool tip image
TOPOLOGY_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Topology Filter, which finds nodes based on the size of their neighborhood.
toProperties(Object) - Method in interface org.cytoscape.work.properties.TunablePropertySerializer: Returns a Properties object where each property key is a qualified field name and the property value is the result of applying a TunablePropertyHandler to the tunable value.
toPropertyValue() - Method in interface org.cytoscape.work.properties.TunablePropertyHandler: Converts the value of the tunable to a String.
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() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Generate a string suitable for serializing the state of this custom graphic.
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
toSerializableString() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return a String that represents this ObjectPosition, suitable for recreating the ObjectPosition with parse
toString() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
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 enum org.cytoscape.group.CyGroupSettingsManager.DoubleClickAction
toString() - Method in enum org.cytoscape.group.CyGroupSettingsManager.GroupViewType
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 class org.cytoscape.jobs.CyJobStatus: Return a string including the status and the message, if any.
toString() - Method in enum org.cytoscape.model.CyTable.Mutability
toString() - Method in class org.cytoscape.property.SimpleCyProperty
toString() - Method in enum org.cytoscape.util.color.BrewerType
toString() - Method in interface org.cytoscape.util.color.Palette: Return the string representation of this palette (usually the name)
toString() - Method in interface org.cytoscape.util.color.PaletteType
toString() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
toString() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the human-readable name of the layout.
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 class org.cytoscape.view.layout.LayoutPoint
toString() - Method in enum org.cytoscape.view.layout.WeightTypes: Returns the name of the weighting type.
toString() - Method in class org.cytoscape.view.model.AbstractVisualProperty
toString() - Method in enum org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
toString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
toString() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return a string representation of this ObjectPosition
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.
transform(AffineTransform) - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer: Return a new CustomGraphicLayer that has been transformed by the provided AffineTransform.
Transformer<C,E> - Interface in org.cytoscape.filter.model: Transforms a stream of elements from a particular context.
TransformerContainer<C,E> - Interface in org.cytoscape.filter: A class that contains and manages a list of Transformers.
TransformerFactory<C,E> - Interface in org.cytoscape.filter.model: The base interface for all Transformer factories.
TransformerListener - Interface in org.cytoscape.filter.model: Listens for changes to Transformer parameters.
TransformerManager - Interface in org.cytoscape.filter: A class for creating and executing Transformers.
Transformers - Interface in org.cytoscape.filter.transformers: Identifiers of the Transformers supplied by the core.
TransformerSink<T> - Interface in org.cytoscape.filter.model: Collects the results of a transformation.
TransformerSource<C,E> - Interface in org.cytoscape.filter.model: Provides a sequence of elements from a context.
TransformerViewFactory - Interface in org.cytoscape.filter.view: A factory for making UI panels to configure a specific Transformer.
translate(V) - Method in interface org.cytoscape.view.vizmap.mappings.ValueTranslator: Convert input value to Visual Property value.
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.
TreeTableCellEditor() - Constructor for class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
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 public fields or a methods in a Task object that allows the Task to be configured with user supplied information.
TunableFieldPanel() - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
TunableFieldPanel(JLabel, Component) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
TunableFieldPanel(JTextArea, Component) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
TunableGravityOrderer - Class in org.cytoscape.work: This class provides a comparator to order the Tunables based on their gravity value.
TunableGravityOrderer() - Constructor for class org.cytoscape.work.TunableGravityOrderer
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.
TunablePropertyHandler - Interface in org.cytoscape.work.properties: An extension of TunableHandler with added functionality to support converting to/from a String.
TunablePropertyHandlerFactory<T extends TunablePropertyHandler> - Interface in org.cytoscape.work.properties: A specialization of TunableHandlerFactory for TunablePropertyHandler.
TunablePropertySerializer - Interface in org.cytoscape.work.properties: This is a type of tunable interceptor that converts the values annotated with Tunable annotations to and from a Properties object.
TunablePropertySerializerFactory - Interface in org.cytoscape.work.properties: Factory to create TunablePropertySerializer instances.
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.
TunableUIHelper - Interface in org.cytoscape.work.swing
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: The states the the validator 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).

UnHideTaskFactory - Interface in org.cytoscape.task.hide

This interface provides a task iterator for unhiding the given 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(Collection<CyColumn>, Collection<String>) - Method in class org.cytoscape.application.swing.CyColumnSelector

Updates the control to display the given CyColumn objects.

update() - Method in interface org.cytoscape.view.presentation.annotations.Annotation

Update the annotation.

update() - Method in interface org.cytoscape.view.presentation.property.values.MappableVisualPropertyValue

Cytoscape will call this method every time the columns corresponding to the CyColumnIdentifiers returned by
 MappableVisualPropertyValue.getMappedColumns() change.

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.

update(Object) - Method in interface org.cytoscape.work.swing.TunableUIHelper

Update all of the tunable values.

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 - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation

The URL that points to the image.

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
 
useCheckBoxMenuItem() - Method in interface org.cytoscape.application.swing.CyAction

Returns whether or not a checkbox menu item should be used.

UserAction - Class in org.cytoscape.work.swing.util

Support for a user initiated action

UserAction(ActionListener) - Constructor for class org.cytoscape.work.swing.util.UserAction

Creates a new UserAction object.





V

ValidatableTransformer<C,E> - Interface in org.cytoscape.filter.model

A marker interface that can be added to any Transformer to indicate
 that the transformer may be invalid in certain contexts.

validate(C) - Method in interface org.cytoscape.filter.model.ValidatableTransformer

Called whenever the context changes (for example when the current network changes)
 or when the TransformerListeners for this transformer are notified.

validateAndApplyTunables(Object) - Method in interface org.cytoscape.work.swing.PanelTaskManager

Validates any pending changes to the tunables in the given context
 object.

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
 
validateCreation() - Method in interface org.cytoscape.filter.model.ValidatableTransformer

Called when a filter is created through a command.

ValidationWarning - Class in org.cytoscape.filter.model

A warning message that will appear in the UI when a Transformer is invalid.

ValidationWarning(String) - Constructor for class org.cytoscape.filter.model.ValidationWarning
 
VALUE_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
 
VALUE_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
valueChanged(ListSelectionEvent) - Method in class org.cytoscape.util.swing.CheckBoxJList
 
valueChanged(AbstractBounded) - Method in interface org.cytoscape.work.util.BoundedChangeListener
 
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.CyNetworkViewDesktopMgr.ArrangeType

Returns the enum constant of this type with the specified name.

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.filter.model.CompositeFilter.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.filter.predicates.Predicate

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.group.CyGroupSettingsManager.DoubleClickAction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.group.CyGroupSettingsManager.GroupViewType

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.jobs.CyJobStatus.Status

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.CyTableFactory.InitialTableSize

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.model.SavePolicy

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.util.color.BrewerType

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.presentation.annotations.ArrowAnnotation.AnchorType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.view.presentation.annotations.ArrowAnnotation.ArrowEnd

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.view.presentation.property.values.Justification

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.view.presentation.property.values.Position

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.FinishStatus.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.cytoscape.work.TaskMonitor.Level

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.CyNetworkViewDesktopMgr.ArrangeType

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.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.filter.model.CompositeFilter.Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.filter.predicates.Predicate

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.group.CyGroupSettingsManager.DoubleClickAction

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.group.CyGroupSettingsManager.GroupViewType

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.jobs.CyJobStatus.Status

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.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.model.SavePolicy

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.util.color.BrewerType

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.presentation.annotations.ArrowAnnotation.AnchorType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.view.presentation.annotations.ArrowAnnotation.ArrowEnd

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.view.presentation.property.values.Justification

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.view.presentation.property.values.Position

Returns an array containing the constants of this enum type, in
the order they are declared.

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.FinishStatus.Type

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.cytoscape.work.TaskMonitor.Level

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.

values - Variable in class org.cytoscape.work.util.ListSelection

Declares a List of items of type T.

ValueTranslator<V,T> - Interface in org.cytoscape.view.vizmap.mappings

Translate given table value to a Visual Property value.

version - Variable in class org.cytoscape.property.bookmark.Bookmarks
 
VERSION_PROPERTY_NAME - Static variable in interface org.cytoscape.application.CyVersion

Deprecated.

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.

ViewChangedEvent<T> - Class in org.cytoscape.view.model.events

This event is fired when a VisualProperty value
 is set or removed from a View.

ViewChangedEvent(CyNetworkView, Collection<ViewChangeRecord<T>>) - Constructor for class org.cytoscape.view.model.events.ViewChangedEvent
 
ViewChangedListener - Interface in org.cytoscape.view.model.events

Listener for ViewChangedEvent.

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.

ViewChangeRecord(View<T>, VisualProperty<?>, Object, boolean) - Constructor for class org.cytoscape.view.model.events.ViewChangeRecord
 
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.

VISUAL_STYLE_PREVIEW_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
 
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.

VisualMappingFunctionChangedEvent - Class in org.cytoscape.view.vizmap.events

VisualMappingFunctions should fire this event when the contents of the mapping are modified.

VisualMappingFunctionChangedEvent(VisualMappingFunction, Collection<VisualMappingFunctionChangeRecord>) - Constructor for class org.cytoscape.view.vizmap.events.VisualMappingFunctionChangedEvent
 
VisualMappingFunctionChangedListener - Interface in org.cytoscape.view.vizmap.events

This listener is used by the VisualStyle implementation, so a style can be
 notified when its visual mappings are changed.

VisualMappingFunctionChangeRecord - Class in org.cytoscape.view.vizmap.events

This is used to create a VisualMappingFunctionChangedEvent.

VisualMappingFunctionChangeRecord() - Constructor for class org.cytoscape.view.vizmap.events.VisualMappingFunctionChangeRecord
 
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, String, Set<VisualProperty<T>>, VisualLexicon) - Constructor for class org.cytoscape.view.vizmap.VisualPropertyDependency

Constructor.

VisualPropertyDependencyChangedEvent - Class in org.cytoscape.view.vizmap.events

Visual property dependencies should fire this event when VisualPropertyDependency.setDependency(boolean)
 is called with a different value.

VisualPropertyDependencyChangedEvent(VisualPropertyDependency<?>) - Constructor for class org.cytoscape.view.vizmap.events.VisualPropertyDependencyChangedEvent
 
VisualPropertyDependencyChangedListener - Interface in org.cytoscape.view.vizmap.events

This listener is used by the VisualStyle implementation, so a style can be
 notified when VisualPropertyDependency.setDependency(boolean) is called on any of its
 visual property dependencies.

VisualPropertyDependencyFactory<T> - Interface in org.cytoscape.view.vizmap

TODO: Missing documentation

VisualPropertyEditor<T> - Interface in org.cytoscape.view.vizmap.gui.editor

Facade of all editor-related objects for a Visual Property.

VisualPropertyEditor2<T> - Interface in org.cytoscape.view.vizmap.gui.editor

If you are writing a VisualPropertyEditor but need to know
 the visual property you are editing (eg to check if the user
 inputted a value in the visual property's range), implement this interface
 in addition to VisualPropertyEditor.

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.

VisualPropertyValueEditor<V> - Interface in org.cytoscape.view.vizmap.gui.editor

Provides a GUI Editor for a data type.

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.

VisualStyleChangedEvent - Class in org.cytoscape.view.vizmap.events

When contents (default values or mappings) of an existing
 VisualStyle is modified, this event should be fired.

VisualStyleChangedEvent(VisualStyle, Collection<VisualStyleChangeRecord>) - Constructor for class org.cytoscape.view.vizmap.events.VisualStyleChangedEvent

Constructor of this event.

VisualStyleChangedListener - Interface in org.cytoscape.view.vizmap.events

TODO: Missing documentation

VisualStyleChangeRecord - Class in org.cytoscape.view.vizmap.events

This is used to create a VisualStyleChangedEvent.

VisualStyleChangeRecord() - Constructor for class org.cytoscape.view.vizmap.events.VisualStyleChangeRecord
 
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

Deprecated.

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

warn(String...) - Static method in class org.cytoscape.filter.model.ValidationWarning

Use this method with a static import to shorten the creation of Lists of ValidationWaring objects.

WebServiceClient - Interface in org.cytoscape.io.webservice

Thin wrapper for SOAP/REST web service clients.

WebServiceGUI - Interface in org.cytoscape.io.webservice.swing

Cytoscape's unified UI for accessing web services.

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.

WIDTH - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation

The width of the shape

write(OutputStream, NamedTransformer<?, ?>...) - Method in interface org.cytoscape.io.write.CyTransformerWriter
 
writeOut() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker

Writes the list of recently opened files to the file specified by the
 constructor argument.





X

X - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation

Arg map key to initialize the x location for this annotation





Y

Y - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation

Arg map key to initialize the y location for this annotation





Z

Z - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation

Arg map key to initialize the z location for this annotation.

ZOOM - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation

Arg map key to initialize the zoom value for this annotation





_

_CY_LIST_DESC - Static variable in interface org.cytoscape.command.StringToModel
 
_CY_NETWORK_DESC - Static variable in interface org.cytoscape.command.StringToModel
 
_CY_NETWORK_VIEW_DESC - Static variable in interface org.cytoscape.command.StringToModel
 
_CY_ROW_DESC - Static variable in interface org.cytoscape.command.StringToModel
 

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