A B C D E F G H I J K L M N O P 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

The primary app interface for Cytoscape that all apps must extend.

AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp

The constructor that all apps must call using "super(adapter);" where the "adapter" is a CyAppAdapter reference provided as an argument to the constructor.

AbstractCyEdit - Class in org.cytoscape.work.undo

A small class used to create new undoable edits.

AbstractCyEdit(String) - Constructor for class org.cytoscape.work.undo.AbstractCyEdit

Constructor.

AbstractCyEvent<T> - Class in org.cytoscape.event

A base implementation of CyEvent that can be used by events.

AbstractCyEvent(T, Class<?>) - Constructor for class org.cytoscape.event.AbstractCyEvent

Constructor.

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

The primary Swing-based app interface for Cytoscape that all Swing-based apps must extend.

AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp

The constructor that all apps must call using "super(adapter);" where the "adapter" is a CySwingAppAdapter reference provided as an argument to the constructor.

AbstractEdgeViewTask - Class in org.cytoscape.task

The base class for all tasks that need to operate on an edge view and possibly its associated network view.

AbstractEdgeViewTask(View<CyEdge>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractEdgeViewTask

Base constructor for all tasks that need an edge view to operate on.

AbstractEdgeViewTaskFactory - Class in org.cytoscape.task

An EdgeViewTaskFactory that is always ready to produce a TaskIterator.

AbstractEdgeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractEdgeViewTaskFactory

AbstractFunction - Class in org.cytoscape.equations

Base class for all Function implementations.

AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction

Base class constructor for easy creation of Functions from function argument descriptors.

AbstractGUITunableHandler - Class in org.cytoscape.work.swing

Base class for the various Swing implementations of TunableHandler.

AbstractGUITunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler

Standard base class constructor for TunableHandlers that deal with Tunables that annotate a 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

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.

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

A method that attempts to determine whether the specified URI can be read by the Reader using this filter.

accepts(InputStream, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter

This method always returns false in this particular implementation.

accepts(URI, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter

A method that attempts to determine whether the specified URI can be read by the Reader using this filter.

accepts(InputStream, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter

A method that attempts to determine whether the specified InputStream can be read by the Reader using this filter.

acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor

Returns true if this ArgDescriptor accepts multiple arguments, otherwise false.

acceptsMultipleArgs() - Method in enum org.cytoscape.equations.ArgType

Returns true if this type accepts multiple args.

ActionEnableSupport - Class in org.cytoscape.application.swing

A class that allows the enabled state of an Action of JMenuItem to managed in a consistent way.

ActionEnableSupport(DynamicSubmenuListener, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport

Constructor.

ActionEnableSupport(Action, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport

Constructor.

ActionEnableSupport(JMenuItem, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport

Constructor.

actuallyShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent

Returns true if no reason is provided to abort the shutdown and false if anyone processing this event wants to prevent shutdown.

adapter - Variable in class org.cytoscape.app.AbstractCyApp

Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.

add(URL) - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker

Adds "newURL" to the list of recently opened file names and trims the list if it has exceeded its maximum length.

add(Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel

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.

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.

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

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.

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

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

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_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.

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_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties

Name space for a command

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

Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.

controlsMutuallyExclusiveNestedChildren() - Method in interface org.cytoscape.work.TunableHandler

Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.

CORE_PROPRERTY_NAME - Static variable in class org.cytoscape.property.SimpleCyProperty

Core Cytoscape Property (Cytoscape System Property)

countMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable

Returns the number of rows with the in the specified column with the specified value.

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, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable

Create a column of the specified name and the specified type.

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.

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, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable

Create a column of Lists with the specified name and the specified element type.

createMenuItem(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.application.swing.CyEdgeViewContextMenuFactory

This method should return a CyMenuItem to be added to the context menu of the specified edge view.

createMenuItem(CyNetworkView) - 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.

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, 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.

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(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory

Provisions this factory with the collection of networks that will be passed into any task created by it.

createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory

Provisions this factory with the CyNetwork that will be passed into any task created by it.

createTaskIterator(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory

Provisions this factory with the collection of network views that will be passed into any task created by it.

createTaskIterator(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory

Creates a task iterator using the specified network view and points.

createTaskIterator(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory

Creates a new TaskIterator using the given CyNetworkView

createTaskIterator(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory

Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.

createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory

Create a task iterator for loading a network from a file.

createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory

Create 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(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(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.

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.

CyAction - Interface in org.cytoscape.application.swing

An interface that describes how an action should be placed within the menus and/or toolbars of the Swing application.

CyAppAdapter - Interface in org.cytoscape.app

A Java-only api providing access to Cytoscape functionality.

CyApplicationConfiguration - Interface in org.cytoscape.application

Application-wide setting will be accessible through this interface.

CyApplicationManager - Interface in org.cytoscape.application

Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.

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.

CyColumn - Interface in org.cytoscape.model

This class describes a column in a CyTable.

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.

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.

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.

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

A Swing-specific extension of CyAppAdapter that serves as a Java-only api providing access to core Cytoscape functionality.

CySwingApplication - Interface in org.cytoscape.application.swing

This interface provides basic access to the Swing objects that constitute this application.

CyTable - Interface in org.cytoscape.model

A simple representation of a table object consisting of rows and columns.

CyTable.Mutability - Enum in org.cytoscape.model

Mutability of the table specifies whether or not it is able to be deleted..

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.

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_LAYOUT_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager

The name of the default layout.

DEFAULT_LAYOUT_PROPERTY_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager

The name of the default layout property.

DEFAULT_PAYLOAD_INTERVAL_MILLIS - Static variable in interface org.cytoscape.event.CyEventHelper

The default number of milliseconds to wait before the next time that we will check for payload events to fire.

DEFAULT_PROPS_CONFIG_DIR - Static variable in interface org.cytoscape.property.CyProperty

The name of the default directory where we will look for properties files.

DefaultDataSource - Class in org.cytoscape.io.datasource

Basic implementation of DataSource.

DefaultDataSource(String, String, String, DataCategory, URL) - Constructor for class org.cytoscape.io.datasource.DefaultDataSource

Constructor for the default data source.

defaultEdgeWeight - Variable in class org.cytoscape.view.layout.EdgeWeighter

DefaultViewEditor - Interface in org.cytoscape.view.vizmap.gui

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 of the specified name.

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

Returns the dependsOn property of the associated Tunable.

dependsOn() - Method in interface org.cytoscape.work.TunableHandler

Returns the dependsOn property of the associated Tunable.

description - Variable in class org.cytoscape.io.BasicCyFileFilter

description - Variable in class org.cytoscape.property.bookmark.Bookmarks

DeselectAllEdgesTaskFactory - Interface in org.cytoscape.task.select

This interface provides a task iterator for deselecting all of the edges.

DeselectAllNodesTaskFactory - Interface in org.cytoscape.task.select

This interface provides a task iterator for deselecting all of the nodes.

DeselectAllTaskFactory - Interface in org.cytoscape.task.select

This interface provides a task iterator for deselecting all of the items.

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.

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.

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

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

EDGE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

EDGE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

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

EDGE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_SOURCE_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_STROKE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_STROKE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_TARGET_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EDGE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

EdgeBendVisualProperty - Class in org.cytoscape.view.presentation.property

Visual Property for Edge Bend values.

EdgeBendVisualProperty(Bend, String, String) - Constructor for class org.cytoscape.view.presentation.property.EdgeBendVisualProperty

Constructor.

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

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.

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.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.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.

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.

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.

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, Class<? extends T>, T) - Method in interface org.cytoscape.model.CyRow

Returns the value found for this row in the specified column with the specified type.

get_ApplyPreferredLayoutTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ApplyPreferredLayoutTaskFactory.

get_ApplyVisualStyleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ApplyVisualStyleTaskFactory.

get_CloneNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CloneNetworkTaskFactory.

get_CollapseGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CollapseGroupTaskFactory.

get_ConnectSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ConnectSelectedNodesTaskFactory.

get_CreateNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CreateNetworkViewTaskFactory.

get_DeleteColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeleteColumnTaskFactory.

get_DeleteSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeleteSelectedNodesAndEdgesTaskFactory.

get_DeleteTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeleteTableTaskFactory.

get_DeselectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeselectAllEdgesTaskFactory.

get_DeselectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeselectAllNodesTaskFactory.

get_DeselectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DeselectAllTaskFactory.

get_DestroyNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DestroyNetworkTaskFactory.

get_DestroyNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of DestroyNetworkViewTaskFactory.

get_EditNetworkTitleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of EditNetworkTitleTaskFactory.

get_ExpandGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExpandGroupTaskFactory.

get_ExportNetworkImageTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExportNetworkImageTaskFactory.

get_ExportNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExportNetworkViewTaskFactory.

get_ExportSelectedTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExportSelectedTableTaskFactory.

get_ExportTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExportTableTaskFactory.

get_ExportVizmapTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of ExportVizmapTaskFactory.

get_GroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of GroupNodesTaskFactory.

get_HideSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of HideSelectedEdgesTaskFactory.

get_HideSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of HideSelectedNodesTaskFactory.

get_HideSelectedTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of HideSelectedTaskFactory.

get_InvertSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of InvertSelectedEdgesTaskFactory.

get_InvertSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of InvertSelectedNodesTaskFactory.

get_LoadNetworkFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of LoadNetworkFileTaskFactory.

get_LoadNetworkURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of LoadNetworkURLTaskFactory.

get_LoadTableFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of LoadTableFileTaskFactory.

get_LoadTableURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of LoadTableURLTaskFactory.

get_LoadVizmapFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of LoadVizmapFileTaskFactory.

get_MapGlobalToLocalTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of MapGlobalToLocalTableTaskFactory.

get_MapTableToNetworkTablesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of MapTableToNetworkTablesTaskFactory.

get_NewEmptyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of NewEmptyNetworkViewFactory.

get_NewNetworkSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of NewNetworkSelectedNodesAndEdgesTaskFactory.

get_NewNetworkSelectedNodesOnlyTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of NewNetworkSelectedNodesOnlyTaskFactory.

get_NewSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of NewSessionTaskFactory.

get_OpenSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of OpenSessionTaskFactory.

get_RenameColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of RenameColumnTaskFactory.

get_SaveSessionAsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SaveSessionAsTaskFactory.

get_SelectAdjacentEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectAdjacentEdgesTaskFactory.

get_SelectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectAllEdgesTaskFactory.

get_SelectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectAllNodesTaskFactory.

get_SelectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectAllTaskFactory.

get_SelectConnectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectConnectedNodesTaskFactory.

get_SelectFirstNeighborsNodeViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectFirstNeighborsNodeViewTaskFactory.

get_SelectFirstNeighborsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectFirstNeighborsTaskFactory.

get_SelectFirstNeighborsTaskFactoryInEdge() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectFirstNeighborsTaskFactory.

get_SelectFirstNeighborsTaskFactoryOutEdge() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectFirstNeighborsTaskFactory.

get_SelectFromFileListTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of SelectFromFileListTaskFactory.

get_UnGroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of UnGroupNodesTaskFactory.

get_UnGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of UnGroupTaskFactory.

get_UnHideAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of UnHideAllEdgesTaskFactory.

get_UnHideAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of UnHideAllNodesTaskFactory.

get_UnHideAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of UnHideAllTaskFactory.

getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction

Returns the accelerator KeyStroke defined for this action.

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

Returns the accelerator KeyStroke defined for this action.

getAdjacentEdgeIterable(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork

Gets an Iteable of edges that connect to this node.

getAdjacentEdgeList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork

Get the list of edges that connect to this node.

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 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.

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.

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

Returns the value of the argument.

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

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

Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.

getChildKey() - Method in interface org.cytoscape.work.TunableHandler

Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.

getChildren() - Method in class org.cytoscape.view.model.VisualLexiconNode

Returns collection of all children of this node.

getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation

getCode() - Method in class org.cytoscape.equations.Equation

Returns the compiled code (not Java byte code!) for the VM representing this Equation.

getColor() - Method in class org.cytoscape.util.swing.ColorButton

getColumn(String) - Method in interface org.cytoscape.model.CyTable

Returns the column for the specified name.

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.

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.

getCommandExecutorTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter

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 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

The MIME content types supported by this filter.

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

Returns an instance of CyProperty of type Properties.

getCurrentNetwork() - Method in interface org.cytoscape.application.CyApplicationManager

Provides access to the current network.

getCurrentNetworkView() - Method in interface org.cytoscape.application.CyApplicationManager

Returns the current network view.

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

getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyApplicationManager.

getCyEventHelper() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyEventHelper.

getCyGroupAggregationManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyGroupAggregationManager.

getCyGroupFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyGroupFactory.

getCyGroupManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyGroupManager.

getCyLayoutAlgorithmManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyLayoutAlgorithmManager.

getCyNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkFactory.

getCyNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkManager.

getCyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkViewFactory.

getCyNetworkViewManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkViewManager.

getCyNetworkViewReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkReaderManager.

getCyNetworkViewWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyNetworkViewWriterManager.

getCyPropertyReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyPropertyReaderManager.

getCyPropertyWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyPropertyWriterManager.

getCyRootNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyRootNetworkManager.

getCyServiceRegistrar() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyServiceRegistrar.

getCySessionManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CySessionManager.

getCySessionReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CySessionReaderManager.

getCySessionWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CySessionWriterManager.

getCySwingApplication() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter

Returns an instance of CySwingApplication.

getCyTableFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyTableFactory.

getCyTableManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyTableManager.

getCyTableReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyTableReaderManager.

getCyTableWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyTableWriterManager.

getCytoPanel(CytoPanelName) - Method in interface org.cytoscape.application.swing.CySwingApplication

Returns the appropriate CytoPanel for the specified compass direction.

getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent

Returns the CytoPanel on which a component was selected.

getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent

Returns the CytoPanel whose state has changed.

getCytoPanelComponentCount() - Method in interface org.cytoscape.application.swing.CytoPanel

Returns the number of components in the CytoPanel.

getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanel

Returns the position in the layout.

getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanelComponent

Returns the name of the CytoPanel that this component should be added to.

getCyVersion() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of CyVersion.

getData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService

Extract data from a CyJobData object.

getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter

The DataCategory supported by this filter.

getDataCategory() - Method in interface org.cytoscape.io.CyFileFilter

The DataCategory supported by this filter.

getDataCategory() - Method in interface org.cytoscape.io.datasource.DataSource

DataCategory of this data.

getDataCategory() - Method in class org.cytoscape.io.datasource.DefaultDataSource

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

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(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

A short, human readable description of the file extensions suitable for display in FileChoosers.

getDescription() - Method in interface org.cytoscape.io.CyFileFilter

A short, human readable description of the file extensions suitable for display in FileChoosers.

getDescription() - Method in interface org.cytoscape.io.datasource.DataSource

Description for this data.

getDescription() - Method in class org.cytoscape.io.datasource.DefaultDataSource

getDescription() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient

getDescription() - Method in interface org.cytoscape.io.webservice.WebServiceClient

Get human-readable description of this client.

getDescription() - Method in class org.cytoscape.property.bookmark.Bookmarks

Gets the value of the description property.

getDescription() - Method in class org.cytoscape.util.swing.FileChooserFilter

Returns the short description of the acceptable file type.

getDescription() - Method in class org.cytoscape.work.AbstractTunableHandler

Returns the associated Tunable's description.

getDescription() - Method in interface org.cytoscape.work.TunableHandler

Returns the associated Tunable's description.

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

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.

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.

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.

getException() - Method in class org.cytoscape.session.events.SessionLoadCancelledEvent

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

Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.

getExtensions() - Method in interface org.cytoscape.io.CyFileFilter

Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.

getExtensions() - Method in class org.cytoscape.util.swing.FileChooserFilter

Returns an array of the extensions associated with this FileChooserFilter.

getExternalEdgeList() - Method in interface org.cytoscape.group.CyGroup

Returns the list of exterior edges connected to the nodes within this group.

getFactories() - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager

Returns all available factories.

getFactory(Class<?>) - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager

Factory for the specific mapping type.

getFile(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil

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

getFile(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil

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

getFileFilter() - Method in interface org.cytoscape.io.CyFileFilterProvider

Return the file filter associated with the IOFactory.

getFileFilter() - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory

Return the file filter associated with the IOFactory.

getFiles(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil

Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.

getFiles(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil

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

getFiles(Component, String, int, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil

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

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.

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

Returns the associated Tunable's groups or nesting hierarchy.

getGroups() - Method in interface org.cytoscape.work.TunableHandler

Returns the associated Tunable's groups or nesting hierarchy.

getGroupSet(CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager

Provides the set of all the groups known to the groups manager in a particular network.

getGroupsForNode(CyNode) - Method in interface org.cytoscape.group.CyGroupManager

Return the list of CyGroups this node is in.

getGroupsForNode(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager

Return the list of CyGroups this node is in for a particular network.

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(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.

getId() - Method in interface org.cytoscape.application.NetworkViewRenderer

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.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 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 ...)

getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication

Returns the JToolBar object for the application.

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, 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.

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)).

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.

getMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable

Returns all the rows of a specified column that contain a certain value for that column.

getMax() - Method in class org.cytoscape.view.model.ContinuousRange

Returns the maximum value of this range.

getMaxX() - Method in class org.cytoscape.view.layout.LayoutPartition

Return the maximum X location of all of the LayoutNodes

getMaxY() - Method in class org.cytoscape.view.layout.LayoutPartition

Return the maximum Y location of all of the LayoutNodes

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

Returns the gravity used to place the menu item for this action.

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

Returns the gravity used to place the menu item for this action.

getMenuGravity() - Method in class org.cytoscape.application.swing.CyMenuItem

Returns the gravity used to place the menu item in a menu.

getMenuItem() - Method in class org.cytoscape.application.swing.CyMenuItem

Returns the menu item to be placed in a menu according to the specified menu gravity.

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

Returns the name of the action.

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

Returns the name of the action.

getName() - Method in class org.cytoscape.equations.AbstractFunction

Used to parse the function string.

getName() - Method in interface org.cytoscape.equations.Function

Used to parse the function string.

getName() - Method in interface org.cytoscape.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 name of the column.

getName() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader

Returns the name of the CyProperty.

getName() - Method in class org.cytoscape.property.bookmark.Attribute

Gets the value of the name property.

getName() - Method in class org.cytoscape.property.bookmark.Category

Gets the value of the name property.

getName() - Method in class org.cytoscape.property.bookmark.DataSource

Gets the value of the name property.

getName() - Method in interface org.cytoscape.property.CyProperty

Returns the name of the CyProperty.

getName() - Method in class org.cytoscape.property.SimpleCyProperty

Returns the name of the CyProperty.

getName() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm

getName() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm

Returns the computer-readable name of the layout.

getName() - Method in class org.cytoscape.work.AbstractTunableHandler

Returns a name representing a tunable property.

getName() - Method in interface org.cytoscape.work.TunableHandler

Returns a name representing a tunable property.

getNamespace() - Method in interface org.cytoscape.model.CyTableMetadata

Returns the namespace used as the key to this object's table in CyNetworkTableManager.getTables(org.cytoscape.model.CyNetwork, java.lang.Class<? extends org.cytoscape.model.CyIdentifiable>).

getNamespaces() - Method in interface org.cytoscape.command.AvailableCommands

Returns a list of available command namespaces in alphabetical order.

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.

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() - 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.

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.

getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent

Returns the old name of the column.

getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent

The old properties before they were modified.

getOldTitle() - Method in class org.cytoscape.model.events.TableTitleChangedEvent

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.

getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter

Returns an instance of PanelTaskManager.

getParams() - Method in class org.cytoscape.work.AbstractTunableHandler

Returns the parsed result from Tunable.getParams().

getParams() - Method in interface org.cytoscape.work.TunableHandler

Returns the parsed result from Tunable.getParams().

getParent() - Method in class org.cytoscape.view.model.VisualLexiconNode

Get the parent of this VP node.

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

This method returns a Menu specification string.

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

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

getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler

Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.

getQualifiedName() - Method in interface org.cytoscape.work.TunableHandler

Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.

getQualifier() - Method in interface org.cytoscape.application.CyVersion

Any text following the last digit of the bug fix version.

getQueryBuilderGUI() - Method in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient

Returns query builder UI.

getQueryBuilderGUI() - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUIClient

Returns query builder UI.

getRange() - Method in class org.cytoscape.view.model.AbstractVisualProperty

getRange() - Method in interface org.cytoscape.view.model.VisualProperty

Returns the Range of this VisualProperty.

getRange() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint

Gets BoundaryRangeValues.

getRaw(String) - Method in interface org.cytoscape.model.CyRow

Returns the Object that contains the value for the specified column.

getRawValue() - Method in class org.cytoscape.model.events.RowSetRecord

Returns the raw value that the data was set as.

getReader(URI, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager

Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader task.

getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager

Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader task.

getReader(URI, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager

Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.

getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager

Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.

getReader(URI, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager

Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.

getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager

Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.

getReader(URI, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager

Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.

getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager

Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.

getReader(URI, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager

Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.

getReader(InputStream, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager

Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.

getRecentlyOpenedURLs() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker

Returns the current list of recently opened file names.

getRedoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit

Returns a human-readable description of this edit that will be used in redo menu items.

getRegisteredFunctions() - Method in interface org.cytoscape.equations.EquationParser

Returns the set of currently registered functions.

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

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.

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.

getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel

Returns the currently selected component.

getSelectedIndex() - Method in interface org.cytoscape.application.swing.CytoPanel

Returns the currently selected index.

getSelectedIndex() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent

Returns the index of the CytoPanelComponent selected.

getSelectedNetworks() - Method in interface org.cytoscape.application.CyApplicationManager

Returns the list of selected networks.

getSelectedNetworkViews() - Method in interface org.cytoscape.application.CyApplicationManager

Returns the list of selected network views.

getSelectedValue() - Method in class org.cytoscape.work.util.ListSingleSelection

Get the item that is currently selected.

getSelectedValues() - Method in class org.cytoscape.work.util.ListMultipleSelection

Get the items that are currently selected.

getSerializableString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue

getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Bend

Create string representation of this object for parsing.

getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Handle

Create string representation of this object for parsing.

getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue

Returns serializable representation of this value.

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.

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

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

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.

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.

getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of TaskManager.

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

Returns the gravity used to place this action in the toolbar.

getToolBarGravity() - Method in class org.cytoscape.application.swing.AbstractToolBarComponent

Returns the gravity value for this toolbar component.

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

Returns the gravity used to place this action in the toolbar.

getToolBarGravity() - Method in interface org.cytoscape.application.swing.ToolBarComponent

Returns the gravity used to place this component in the toolbar.

getTooltip() - Method in class org.cytoscape.work.AbstractTunableHandler

Returns the tooltip annotation for this Tunable if there is one.

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.

getTunablePropertySerializerFactory() - Method in interface org.cytoscape.app.CyAppAdapter

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 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 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

Returns the class type of the field or method annotated by Tunable.

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

Returns an instance of UndoSupport.

getUpperBound() - Method in class org.cytoscape.work.util.AbstractBounded

Returns the upper limit of the object.

getURLConnection(URL) - Method in interface org.cytoscape.io.util.StreamUtil

Obtain a URLConnection for a given URL.

getUsageDescription() - Method in class org.cytoscape.equations.AbstractFunction

Used to provide help for users.

getUsageDescription() - Method in interface org.cytoscape.equations.Function

Used to provide help for users.

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

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 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

Returns an instance of VisualMappingFunctionFactory.

getVisualMappingFunctionDiscreteFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of VisualMappingFunctionFactory.

getVisualMappingFunctionPassthroughFactory() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of VisualMappingFunctionFactory.

getVisualMappingManager() - Method in interface org.cytoscape.app.CyAppAdapter

Returns an instance of VisualMappingManager.

getVisualProperties() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency

A set of Visual Properties to be set by the parent if locked.

getVisualProperty() - Method in class org.cytoscape.view.model.events.ViewChangeRecord

Returns the visual property that has been changed.

getVisualProperty(VisualProperty<T>) - Method in interface org.cytoscape.view.model.View

Get the actual value for the given visual property.

getVisualProperty() - Method in class org.cytoscape.view.model.VisualLexiconNode

Returns wrapped VisualProperty object.

getVisualProperty() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction

getVisualProperty() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction

Visual Property associated with this function.

getVisualPropertyEditor(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager

Returns the VisualPropertyEditor for the given VisualProperty.

getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.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

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

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)).

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 Group annotation is a container for a collextion 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_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(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(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

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(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.equations.Equation

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.

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_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_AMBULANCE - 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_ASTERISK - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_AT - 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_BAN - 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_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_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_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_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_DISCOVER - 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_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_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_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_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_COPY - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_COPYRIGHT - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_CREDIT_CARD - 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_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_EDIT - 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_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_ERASER - 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_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_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_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_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_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_GITTIP - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_GLASS - 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_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_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_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_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_HTML5 - 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_INBOX - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_INDENT - 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_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_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_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_MARKER - 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_MEH_O - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_MERCURY - 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_MOBILE - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_MOBILE_PHONE - 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_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_OPENID - 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_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_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_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_POWER_OFF - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_PRINT - 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_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_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_SQUARE - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_REFRESH - 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_SAVE - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_SCISSORS - 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_CART - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_SIGN_IN - 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_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_STOP - 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_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_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_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_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_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_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_USD - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_USER - Static variable in interface org.cytoscape.util.swing.IconManager

ICON_USER_MD - 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_VIDEO_CAMERA - 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_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_WIFI - 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_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_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_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 will be added to menu bar if this flag is set to true

IN_NETWORK_PANEL_CONTEXT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

Action will be added to network panel's context menu if this flag is set to true

IN_TOOL_BAR - Static variable in interface org.cytoscape.work.ServiceProperties

Action will be added to tool bar if this flag is set to true

includeMax() - Method in class org.cytoscape.view.model.ContinuousRange

Returns true if the maximum value is included in this range.

includeMin() - Method in class org.cytoscape.view.model.ContinuousRange

Returns true if the minimum value is included in this range.

incr - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask

The value used for spacing nodes.

increment(double, double) - Method in class org.cytoscape.view.layout.LayoutNode

Increment the location of this node by (x,y).

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

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 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 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.

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.

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.

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).

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.

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.

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(InputStream, String) - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory

Returns true if the factory is ready to be produce a TaskIterator and false otherwise.

isReady(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory

Returns true if the factory is ready to be produce a TaskIterator and false otherwise.

isReady(View<CyEdge>, CyNetworkView) - Method in class org.cytoscape.task.AbstractEdgeViewTaskFactory

Returns true if the supplied edge and network views are not null.

isReady(Collection<CyNetwork>) - Method in class org.cytoscape.task.AbstractNetworkCollectionTaskFactory

Returns true if the supplied collection is not null.

isReady(CyNetwork) - Method in class org.cytoscape.task.AbstractNetworkTaskFactory

Returns true if the supplied network is not null.

isReady(Collection<CyNetworkView>) - Method in class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory

Returns true if the supplied collection is not null.

isReady(CyNetworkView, Point2D, Point2D) - Method in class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory

Returns true if the supplied view and coordinates are not null.

isReady(CyNetworkView) - Method in class org.cytoscape.task.AbstractNetworkViewTaskFactory

Returns true if the supplied network view is not null.

isReady(View<CyNode>, CyNetworkView) - Method in class org.cytoscape.task.AbstractNodeViewTaskFactory

Returns true of the supplied network and node views are not null.

isReady(CyColumn, Object) - Method in class org.cytoscape.task.AbstractTableCellTaskFactory

Returns true if the supplied column and value are not null.

isReady(CyColumn) - Method in class org.cytoscape.task.AbstractTableColumnTaskFactory

Returns true if the supplied column is not null.

isReady(CyTable) - Method in class org.cytoscape.task.AbstractTableTaskFactory

Returns true if the supplied table is not null.

isReady(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory

Returns true if this task factory is ready to produce a task iterator.

isReady(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory

Returns true if the node view and network view are in a state that is ready to be processed by the generated tasks and false otherwise.

isReady(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory

Returns true if this task factory is ready to produce a TaskIterator.

isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm

isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm

Returns true if the task factory is ready to produce a task iterator.

isReady() - Method in class org.cytoscape.work.AbstractTaskFactory

isReady() - Method in interface org.cytoscape.work.TaskFactory

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(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.

JoinTablesTaskTaskFactory - Interface in org.cytoscape.task.edit

TODO: Missing documentation

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.

K

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_URL - Static variable in interface org.cytoscape.work.ServiceProperties

Location of large icon data for desktop application

LAST_DIRECTORY - Static variable in interface org.cytoscape.util.swing.FileUtil

The Cytoscape property that stores the last save/load directory.

LAYOUT_ALGORITHM - Static variable in class org.cytoscape.view.layout.AbstractLayoutTask

The table column name that provides the layout algorithm name.

layoutAttribute - Variable in class org.cytoscape.view.layout.AbstractLayoutTask

The attribute to be used for this layout.

LayoutEdge - Class in org.cytoscape.view.layout

The LayoutEdge class.

LayoutEdge(CyEdge, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutEdge

Create a LayoutEdge that will contain information about this edge.

LayoutEdge(CyEdge, LayoutNode, LayoutNode, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutEdge

Create a LayoutEdge that will contains information about this edge, and that record that it connects LayoutNodes v1 and v2.

LayoutEdit - Class in org.cytoscape.view.layout

An undoable edit that will undo and redo of a layout algorithm applied to a network view.

LayoutEdit(String, CyNetworkView) - Constructor for class org.cytoscape.view.layout.LayoutEdit

Constructor.

LayoutNode - Class in org.cytoscape.view.layout

The LayoutNode class.

LayoutNode(View<CyNode>, int, CyRow) - Constructor for class org.cytoscape.view.layout.LayoutNode

The main constructor for a LayoutNode.

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

Returns the listenForChange property of the associated Tunable.

listenForChange() - Method in interface org.cytoscape.work.TunableHandler

Returns the listenForChange property of the associated Tunable.

ListMultipleSelection<T> - Class in org.cytoscape.work.util

List with items of type T : one or more items can be selected.

ListMultipleSelection(T...) - Constructor for class org.cytoscape.work.util.ListMultipleSelection

Creates a new ListMultipleSelection object.

ListMultipleSelection(List<T>) - Constructor for class org.cytoscape.work.util.ListMultipleSelection

Creates a new ListMultipleSelection object.

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.

LoadNetworkFileTaskFactory - Interface in org.cytoscape.task.read

This interface provides a task iterator for loading networks from files.

LoadNetworkURLTaskFactory - Interface in org.cytoscape.task.read

This interface provides a task iterator for loading a URL into a network.

loadStyles(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory

Return a set of VisualStyle objects read from the specified file.

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

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

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

A chain of Transformers with a user-defined name.

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

NETWORK_CENTER_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NETWORK_CENTER_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NETWORK_CENTER_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NETWORK_DELETE_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

NETWORK_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

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

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

NETWORK_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

NETWORK_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NETWORK_TITLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NETWORK_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NetworkAboutToBeDestroyedEvent - Class in org.cytoscape.model.events

This event signals that a network is about to be destroyed.

NetworkAboutToBeDestroyedEvent(CyNetworkManager, CyNetwork) - Constructor for class org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent

Constructs event.

NetworkAboutToBeDestroyedListener - Interface in org.cytoscape.model.events

Listener for NetworkAboutToBeDestroyedEvent

NetworkAddedEvent - Class in org.cytoscape.model.events

This event signals that a network has been added.

NetworkAddedEvent(CyNetworkManager, CyNetwork) - Constructor for class org.cytoscape.model.events.NetworkAddedEvent

Constructs event.

NetworkAddedListener - Interface in org.cytoscape.model.events

Listener for NetworkAddedEvent

NetworkCollectionTaskFactory - Interface in org.cytoscape.task

Produces a task iterator for the specified collection of networks.

NetworkDestroyedEvent - Class in org.cytoscape.model.events

This event signals that a Network has been destroyed.

NetworkDestroyedEvent(CyNetworkManager) - Constructor for class org.cytoscape.model.events.NetworkDestroyedEvent

Constructs event.

NetworkDestroyedListener - Interface in org.cytoscape.model.events

Listener for NetworkDestroyedEvent

networkExists(long) - Method in interface org.cytoscape.model.CyNetworkManager

Tests whether a network has been registered with the network manager or not.

NetworkImportWebServiceClient - Interface in org.cytoscape.io.webservice

Marker interface for web service clients that have ability to import network data.

networks - 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.

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

NODE_BORDER_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_BORDER_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_BORDER_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_DEPTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_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

NODE_GROUP_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

NODE_HEIGHT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_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

NODE_NESTED_NETWORKS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties

NODE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

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

NODE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_X_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_Y_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

NODE_Z_LOCATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

nodeCount() - Method in class org.cytoscape.view.layout.LayoutPartition

Return the number of nodes in this partition

nodeIterator() - Method in class org.cytoscape.view.layout.LayoutPartition

Return an iterator over all of the LayoutNodes in this partition

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

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.

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.

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.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.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.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.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.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.

PaintVisualProperty - Class in org.cytoscape.view.presentation.property

Visual Property for Paint values.

PaintVisualProperty(Paint, Range<Paint>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.PaintVisualProperty

Constructor.

panel - Variable in class org.cytoscape.work.swing.AbstractGUITunableHandler

JPanel that will contain the GUI representation of the TunableHandler.

PanelTaskManager - Interface in org.cytoscape.work.swing

A specialization of a TaskManager that creates a JPanel configuration object and expects its execution context to be another JPanel.

PARALLELOGRAM - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty

Parallelogram shape.

parse(String, Map<String, Class<?>>) - Method in interface org.cytoscape.equations.EquationParser

Returns true if the parse succeeded otherwise false

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.

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.

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.

registerAllServices(BundleContext, Object, Properties) - Method in class org.cytoscape.service.util.AbstractCyActivator

A utility method that registers the specified service object as an OSGi service for all interfaces that the object implements.

registerAllServices(Object, Properties) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

This method registers an object as an OSGi service for all interfaces that the object implements and with the specified properties.

registerFunction(Function) - Method in interface org.cytoscape.equations.EquationParser

After registering an attribute function "func" it can be used in attribute equations.

registerService(BundleContext, Object, Class<?>, Properties) - Method in class org.cytoscape.service.util.AbstractCyActivator

A utility method that registers the specified service object as an OSGi service of the specified type.

registerService(Object, Class<?>, Properties) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

This method registers an object as an OSGi service with the specified service interface and properties.

registerServiceListener(BundleContext, Object, String, String, Class<?>, Class<?>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(BundleContext, Object, String, String, Class<?>) - Method in class org.cytoscape.service.util.AbstractCyActivator

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(BundleContext, Object, String, String, Class<?>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(BundleContext, Object, String, String, Class<?>, Class<?>) - Method in class org.cytoscape.service.util.AbstractCyActivator

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(Object, String, String, Class<?>, Class<?>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(Object, String, String, Class<?>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(Object, String, String, Class<?>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

registerServiceListener(Object, String, String, Class<?>, Class<?>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

A method that will cause the specified register/unregister methods on the listener object to be called any time that a service of the specified type is registered or unregistered.

remove(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

Remove the annotation.

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

Remove an annotation 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.

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

removeNodes(List<CyNode>) - Method in interface org.cytoscape.group.CyGroup

Remove a set of nodes and their edges from a group

removeNodes(Collection<CyNode>) - Method in interface org.cytoscape.model.CyNetwork

Remove a node from the network and delete the node (if it only exists in this network).

removeNodes(Collection<CyNode>) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork

Removes a node from this CySubNetwork but not from the CyRootNetwork.

removePoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping

Removes a Point from the List.

removeRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager

Remove a rendering engine.

removeSubNetwork(CySubNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork

Removes the subnetwork from the root network, but not the nodes and edges contained in the subnetwork.

removeTable(CyNetwork, Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetworkTableManager

Removes the table with the specified namespace and type from the network.

removeTreeModelListener(TreeModelListener) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel

removeTunableHandlerFactory(TunableHandlerFactory<T>, Map) - Method in class org.cytoscape.work.AbstractTunableInterceptor

Allows TunableHandlerFactory services to be removed from the list of factories used to process Tunables.

removeTunableRecorder(TunableRecorder, Map) - Method in class org.cytoscape.work.AbstractTaskManager

Removes the specified TunableRecorder service from the task manager.

removeValueEditor(ValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager

Remove an editor from manager (through OSGi).

removeVisualMappingFunction(VisualProperty<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle

Remove a VisualMappingFunction for the VisualProperty.

removeVisualPropertyDependency(VisualPropertyDependency<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle

Remove a VisualPropertyDependency.

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.

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.

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.

rootVisualProperty - Variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon

The Root of this tree.

ROUND_RECTANGLE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty

Rectangular shape with rounded corners.

row - Variable in class org.cytoscape.task.AbstractRowTask

The row that descendants will operate on.

rowExists(Object) - Method in interface org.cytoscape.model.CyTable

Returns true if a row exists for the specified primary key and false otherwise.

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

This method is called when the Task begins execution.

run(TaskMonitor) - Method in interface org.cytoscape.work.Task

This method is called when the Task begins execution.

S

SAVE - Static variable in interface org.cytoscape.util.swing.FileUtil

Equal to FileDialog.SAVE.

saveBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil

Store a bookmark object in bookmarks object

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.

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

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.

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

This event is fired when a session load task is cancelled, which can also happen because of exceptions.

SessionLoadCancelledEvent(Object) - Constructor for class org.cytoscape.session.events.SessionLoadCancelledEvent

Constructor.

SessionLoadCancelledEvent(Object, Exception) - Constructor for class org.cytoscape.session.events.SessionLoadCancelledEvent

Use this constructor if the session load was cancelled because of an exception.

SessionLoadCancelledListener - Interface in org.cytoscape.session.events

A listener for SessionLoadCancelledEvents.

SessionLoadedEvent - Class in org.cytoscape.session.events

This event is fired after a new session has been set in the CySessionManager.setCurrentSession(CySession, String) method and is used to notify interested parties in the change of state.

SessionLoadedEvent(CySessionManager, CySession, String) - Constructor for class org.cytoscape.session.events.SessionLoadedEvent

Constructor.

SessionLoadedListener - Interface in org.cytoscape.session.events

A listener for SessionLoadedEvents.

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.

setAcceleratorKeyStroke(KeyStroke) - Method in class org.cytoscape.application.swing.AbstractCyAction

Sets the accelerator KeyStroke for this action.

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

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.

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.

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.

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.

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) - 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.

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

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.

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.

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.

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

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.

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

Attempts to set the value of the associated field or set method that has been annotated with Tunable.

setValue(Object) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler

setValue(Object) - Method in interface org.cytoscape.work.TunableHandler

Attempts to set the value 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.

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 class org.cytoscape.view.layout.LayoutPartition

Return the size of this partition, which is defined as the number of nodes that it contains.

SMALL_ICON_URL - Static variable in interface org.cytoscape.work.ServiceProperties

Location of small icon data for desktop application

SOLID - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty

Solid line

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

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.

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.

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.

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

Tool tip text for an action

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

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 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.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.

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).

unLock() - Method in class org.cytoscape.view.layout.LayoutNode

Register this node as being "unlocked".

unregisterAllServices(Object) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

This method unregisters an object as all OSGi service interfaces that the object implements.

unregisterService(Object, Class) - Method in interface org.cytoscape.service.util.CyServiceRegistrar

This method unregisters an object as an OSGi service for the specified service interface.

UnsetNetworkPointerEvent - Class in org.cytoscape.model.events

Used to track removing of nested networks from nodes.

UnsetNetworkPointerEvent(CyNode, CyNetwork) - Constructor for class org.cytoscape.model.events.UnsetNetworkPointerEvent

Constructs event.

UnsetNetworkPointerListener - Interface in org.cytoscape.model.events

Listener for UnsetNetworkPointerEvents.

unsilenceEventSource(Object) - Method in interface org.cytoscape.event.CyEventHelper

This method will allow events fired from the specified source object to be propagated to listeners.

update() - Method in 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.

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

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

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

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

V

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

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.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.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.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.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 modified.

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

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

TODO: Missing documentation

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

TODO: Missing documentation

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.

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

TODO: Missing documentation

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

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

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