Index (Cytoscape Swing App API (swing-app-api) 3.9.0 API)

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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.
AboutToRemoveColumnViewEvent - Class in org.cytoscape.view.model.events: When column Views are about to be removed from a CyTableView, this event will be fired.
AboutToRemoveColumnViewEvent(CyTableView, View<CyColumn>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveColumnViewEvent
AboutToRemoveColumnViewListener - Interface in org.cytoscape.view.model.events: Listener for AboutToRemoveColumnViewEvent.
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.
AboutToRemoveRowViewsEvent - Class in org.cytoscape.view.model.events: When row Views are about to be removed from a CyTableView, this event will be fired.
AboutToRemoveRowViewsEvent(CyTableView, Collection<View<CyRow>>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveRowViewsEvent
AboutToRemoveRowViewsListener - Interface in org.cytoscape.view.model.events: Listener for AboutToRemoveRowViewsEvent.
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>, CyApplicationManager, CyNetworkViewManager, TaskFactory) - 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.
AbstractCyActivator - Class in org.cytoscape.service.util: A simple BundleActivator with convenience methods for registering OSGi services and either getting references to single services or registering interest in all services of a specified type.
AbstractCyActivator() - Constructor for class org.cytoscape.service.util.AbstractCyActivator: Constructor.
AbstractCyApp - Class in org.cytoscape.app: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp: Deprecated.

The constructor that all apps must call using "super(adapter);" where the "adapter" is a CyAppAdapter reference provided as an argument to the constructor.
AbstractCyEdit - Class in org.cytoscape.work.undo: A small class used to create new undoable edits.
AbstractCyEdit(String) - Constructor for class org.cytoscape.work.undo.AbstractCyEdit: Constructor.
AbstractCyEvent<T> - Class in org.cytoscape.event: A base implementation of CyEvent that can be used by events.
AbstractCyEvent(T, Class<?>) - Constructor for class org.cytoscape.event.AbstractCyEvent: Constructor.
AbstractCyJob - Class in org.cytoscape.jobs: This can be used as a base class for custom implementations of CyJob
AbstractCyJob(String, String, CyJobExecutionService, CyJobDataService, CyJobMonitor) - Constructor for class org.cytoscape.jobs.AbstractCyJob
AbstractCyNetworkReader - Class in org.cytoscape.io.read
AbstractCyNetworkReader(InputStream, CyApplicationManager, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
AbstractCyNetworkReader(InputStream, CyNetworkViewFactory, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
AbstractCyPayloadEvent<T,P> - Class in org.cytoscape.event: A base implementation of CyPayloadEvent that can be used by events.
AbstractCyPayloadEvent(T, Class<?>, Collection<P>) - Constructor for class org.cytoscape.event.AbstractCyPayloadEvent: Constructor.
AbstractCySwingApp - Class in org.cytoscape.app.swing: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp: Deprecated.

The constructor that all apps must call using "super(adapter);" where the "adapter" is a CySwingAppAdapter reference provided as an argument to the constructor.
AbstractEdgeViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on an edge view and possibly its associated network view.
AbstractEdgeViewTask(View<CyEdge>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractEdgeViewTask: Base constructor for all tasks that need an edge view to operate on.
AbstractEdgeViewTaskFactory - Class in org.cytoscape.task: An EdgeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractEdgeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractEdgeViewTaskFactory
AbstractFunction - Class in org.cytoscape.equations: Base class for all Function implementations.
AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction: Base class constructor for easy creation of Functions from function argument descriptors.
AbstractGUITunableHandler - Class in org.cytoscape.work.swing: Base class for the various Swing implementations of TunableHandler.
AbstractGUITunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that annotate a control.
AbstractGUITunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractGUITunableHandler.TunableFieldPanel - Class in org.cytoscape.work.swing: The main goal of this panel is to store the handler's label and control, in order to make it possible to consistently align labels and controls created by different AbstractGUITunableHandler subclasses when creating the Tunable form.
AbstractInputStreamTaskFactory - Class in org.cytoscape.io.read: TODO: Missing documentation
AbstractInputStreamTaskFactory(CyFileFilter) - Constructor for class org.cytoscape.io.read.AbstractInputStreamTaskFactory
AbstractLayoutAlgorithm - Class in org.cytoscape.view.layout: The AbstractLayoutAlgorithm provides a basic implementation of a layout TaskFactory.
AbstractLayoutAlgorithm(String, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutAlgorithm: The Constructor.
AbstractLayoutTask - Class in org.cytoscape.view.layout: This is a basic implementation of a LayoutAlgorithm Task that does some bookkeeping, but primarily delegates to the doLayout() method.
AbstractLayoutTask(String, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutTask: Constructor.
AbstractNetworkCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyNetworks.
AbstractNetworkCollectionTask(Collection<CyNetwork>) - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTask: Base Constructor for a task that will operate on a collection of networks
AbstractNetworkCollectionTaskFactory - Class in org.cytoscape.task: An NetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTaskFactory
AbstractNetworkSearchTaskFactory - Class in org.cytoscape.application.swing.search: This abstract implementation of NetworkSearchTaskFactory makes the method AbstractNetworkSearchTaskFactory.getQueryComponent() optional.
AbstractNetworkSearchTaskFactory(String, String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
AbstractNetworkSearchTaskFactory(String, String, String, Icon, URL) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
AbstractNetworkSearchTaskFactory(String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
AbstractNetworkTask - Class in org.cytoscape.task: Base class for all tasks that need to operate on a CyNetwork.
AbstractNetworkTask(CyNetwork) - Constructor for class org.cytoscape.task.AbstractNetworkTask: Base class for tasks that need to operate on a CyNetwork
AbstractNetworkTaskFactory - Class in org.cytoscape.task: A NetworkTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkTaskFactory
AbstractNetworkViewCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyNetworkViews.
AbstractNetworkViewCollectionTask(Collection<CyNetworkView>) - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTask: Base class for any tasks that need to operate on a collection of network views.
AbstractNetworkViewCollectionTaskFactory - Class in org.cytoscape.task: A NetworkViewCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory
AbstractNetworkViewLocationTaskFactory - Class in org.cytoscape.task: A base class for task factories that need to add a functionality to the network view considering a given location (for example adding a node where a mouse was clicked).
AbstractNetworkViewLocationTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory
AbstractNetworkViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a network view.
AbstractNetworkViewTask(CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNetworkViewTask: A base class for tasks that need to operate on a network view.
AbstractNetworkViewTaskFactory - Class in org.cytoscape.task: A NetworkViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewTaskFactory
AbstractNode - Class in org.cytoscape.equations: A node in the parse tree.
AbstractNode(int) - Constructor for class org.cytoscape.equations.AbstractNode: Base class constructor for any Node type.
AbstractNodeViewTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTask(View<CyNode>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNodeViewTask: Base class constructor for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTaskFactory - Class in org.cytoscape.task: A NodeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNodeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNodeViewTaskFactory
AbstractParallelPartitionLayoutTask - Class in org.cytoscape.view.layout: This is an even more helpful implementation of a LayoutAlgorithm Task that extends AbstractPartitionLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractParallelPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractParallelPartitionLayoutTask: Creates a new AbstractPartitionLayoutTask object.
AbstractPartitionLayoutTask - Class in org.cytoscape.view.layout: This is a more helpful implementation of a LayoutAlgorithm Task that extends AbstractBasicLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractPartitionLayoutTask: Creates a new AbstractPartitionLayoutTask object.
AbstractRootNetworkCollectionTask - Class in org.cytoscape.task: The base class for all tasks that need to operate on a Collection of CyRootNetworks.
AbstractRootNetworkCollectionTask(Collection<CyRootNetwork>) - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTask
AbstractRootNetworkCollectionTaskFactory - Class in org.cytoscape.task: A RootNetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractRootNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTaskFactory
AbstractRowTask - Class in org.cytoscape.task: Base class for all tasks that need to operate on a CyRow.
AbstractRowTask(CyRow) - Constructor for class org.cytoscape.task.AbstractRowTask: Base class constructor for all tasks that need to be provisioned with a CyRow.
AbstractStringTunableHandler - Class in org.cytoscape.command
AbstractStringTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
AbstractStringTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
AbstractTableCellTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on a single CyTable cell.
AbstractTableCellTask(CyColumn, Object) - Constructor for class org.cytoscape.task.AbstractTableCellTask: Initializes a Task that needs to operate on a CyTable cell entry.
AbstractTableCellTaskFactory - Class in org.cytoscape.task: A TableCellTaskFactory that is always ready to produce a TaskIterator.
AbstractTableCellTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableCellTaskFactory
AbstractTableColumnTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on an entire CyTable column.
AbstractTableColumnTask(CyColumn) - Constructor for class org.cytoscape.task.AbstractTableColumnTask: Initializes a Task that needs to operate on a CyTable column.
AbstractTableColumnTaskFactory - Class in org.cytoscape.task: A TableColumnTaskFactory that is always ready to produce a TaskIterator.
AbstractTableColumnTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableColumnTaskFactory
AbstractTableTask - Class in org.cytoscape.task: A base class for Tasks that need to operate on an entire CyTable.
AbstractTableTask(CyTable) - Constructor for class org.cytoscape.task.AbstractTableTask: Initializes a Task that needs to operate on a CyTable.
AbstractTableTaskFactory - Class in org.cytoscape.task: A TableTaskFactory that is always ready to produce a TaskIterator.
AbstractTableTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableTaskFactory
AbstractTask - Class in org.cytoscape.work: A base class for tasks that need to be able to access the TaskIterator that contains them.
AbstractTask() - Constructor for class org.cytoscape.work.AbstractTask
AbstractTaskFactory - Class in org.cytoscape.work: A TaskFactory that is always ready to produce a TaskIterator.
AbstractTaskFactory() - Constructor for class org.cytoscape.work.AbstractTaskFactory
AbstractTaskManager<T,C> - Class in org.cytoscape.work: Provides access to a TunableInterceptor to all derived classes and a utility method to determine if an object has been annotated with Tunables.
AbstractTaskManager(TunableMutator) - Constructor for class org.cytoscape.work.AbstractTaskManager: Initializes an AbstractTaskManager object by setting its TunableInterceptor.
AbstractToolBarComponent - Class in org.cytoscape.application.swing: An abstract, convenience implementation of ToolBarComponent.
AbstractToolBarComponent() - Constructor for class org.cytoscape.application.swing.AbstractToolBarComponent
AbstractTransformer<C,E> - Class in org.cytoscape.filter.model: A convenience base class for Transformers.
AbstractTransformer() - Constructor for class org.cytoscape.filter.model.AbstractTransformer: Creates a new AbstractTransformer.
AbstractTreeTableModel - Class in org.cytoscape.util.swing: An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class org.cytoscape.util.swing.AbstractTreeTableModel: Creates a new AbstractTreeTableModel object.
AbstractTunableHandler - Class in org.cytoscape.work: Provides the standard implementation for most of the methods declared by the TunableHandler interface.
AbstractTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler: Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractTunableInterceptor<T extends TunableHandler> - Class in org.cytoscape.work: An abstract base class for TunableRecorder and TunableMutator implementations.
AbstractTunableInterceptor() - Constructor for class org.cytoscape.work.AbstractTunableInterceptor: Creates a new AbstractTunableInterceptor object.
AbstractValidatableTransformer<C,E> - Class in org.cytoscape.filter.model: A convenience base class for ValidatableTransformers.
AbstractValidatableTransformer() - Constructor for class org.cytoscape.filter.model.AbstractValidatableTransformer: Creates a new AbstractValidatableTransformer.
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.
AbstractVisualLexicon - Class in org.cytoscape.view.presentation.property: Reusable template implementation of VisualLexicon.
AbstractVisualLexicon(VisualProperty<NullDataType>) - Constructor for class org.cytoscape.view.presentation.property.AbstractVisualLexicon
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(InputStream, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter: This method always returns false in this particular implementation.
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.
accepts(URI, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
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.
acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor: Returns true if this ArgDescriptor accepts multiple arguments, otherwise false.
acceptsMultipleArgs() - Method in enum class 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(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.
ActionEnableSupport(DynamicSubmenuListener, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport: Constructor.
actuallyShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent: Returns true if no reason is provided to abort the shutdown and false if anyone processing this event wants to prevent shutdown.
adapter - Variable in class org.cytoscape.app.AbstractCyApp: Deprecated.

Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.
add(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.
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.
addAction(CyAction) - Method in interface org.cytoscape.application.swing.CySwingApplication: Add a CyAction to application.
addAggregator(Aggregator<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Add a new aggregator to the available aggregators.
addAnnotation(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Add an annotation to the specified network view.
addAnnotations(Collection<? extends Annotation>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Adds annotations to the specified network view.
addAppFiles(String, List<File>) - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent: A method that allows apps to specify a list of files that should be stored in the session.
addArrow(ArrowAnnotation) - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Add an arrow annotation to this annotation.
addBasicVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil: Deprecated.
addBendFactory(BendFactory, Map<?, ?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
addCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
addChangeListener(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Adds the argument as a new dependency to this GUITunableHandler.
addChangeListener(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler: Adds a GUITunableHandler that listens to THIS tunable handler.
addCollapseListener(BasicCollapsiblePanel.CollapseListener) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
addData(CyJobData, String, Object) - Method in interface org.cytoscape.jobs.CyJobDataService: Add a single data item to a CyJobData object.
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, 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.
AddedColumnViewEvent - Class in org.cytoscape.view.model.events: When column View is added to a CyTableView, this event will be fired.
AddedColumnViewEvent(CyTableView, View<CyColumn>) - Constructor for class org.cytoscape.view.model.events.AddedColumnViewEvent
AddedColumnViewListener - Interface in org.cytoscape.view.model.events: Listener for AddedColumnViewEvent.
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(CyEdge) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Adds an edge to this CySubNetwork.
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.
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(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.
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.
AddedRowViewsEvent - Class in org.cytoscape.view.model.events: When row View is added to a CyTableView, this event will be fired.
AddedRowViewsEvent(CyTableView, Collection<View<CyRow>>) - Constructor for class org.cytoscape.view.model.events.AddedRowViewsEvent
AddedRowViewsListener - Interface in org.cytoscape.view.model.events: Listener for AddedRowViewsEvent.
addEventPayload(S, P, Class<E>) - Method in interface org.cytoscape.event.CyEventHelper: Adds a payload object to be accumulated in a CyPayloadEvent.
addGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager: Registers a group with the group manager.
addGroups(List<CyGroup>) - Method in interface org.cytoscape.group.CyGroupManager: Registers a list of groups with the group manager.
addGroupToNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup: Add a group to an additional network.
addIcon(String, Icon) - Method in interface org.cytoscape.util.swing.IconManager
addIconFont(Font) - Method in interface org.cytoscape.util.swing.IconManager
addIdentifierMapping(Class<?>, String, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
addJob(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager: Add a job to be managed by the job manager.
addListener(TransformerListener) - Method in class org.cytoscape.filter.model.AbstractTransformer
addListener(TransformerListener) - Method in interface org.cytoscape.filter.model.Transformer: Subscribes the given listener to changes in this Transformer's parameters.
addListener(BoundedChangeListener<N>) - Method in class org.cytoscape.work.util.AbstractBounded: Adds a listener that will listen for changes to this object
addListener(ListChangeListener<T>) - Method in class org.cytoscape.work.util.ListSelection: Adds a listener that will listen for changes to this object
addMember(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: Add a new annotation to the group.
addMenu(JMenu, double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a new submenu into a position based on "gravity" of the new item.
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addMenuItem(JMenuItem, double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a new menu item into a position based on "gravity" of the new item.
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addMenuSeparator(double) - Method in interface org.cytoscape.util.swing.GravityTracker: Adds a separator into a position based on "gravity" of the new item.
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
addNamedTransformer(NamedTransformer<C, E>) - Method in interface org.cytoscape.filter.TransformerContainer: Add a NamedTransformer to this container.
addNeighbor(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Convenience function to keep track of neighbors of this node.
addNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager: Registers a network with the network manager and sets the network as current.
addNetwork(CyNetwork, boolean) - Method in interface org.cytoscape.model.CyNetworkManager: Registers a network with the network manager.
addNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Registers a network view with the network view manager and sets the new view as current.
addNetworkView(CyNetworkView, boolean) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Registers a network view with the network view manager.
addNetworkViewListener(CyNetworkViewListener) - Method in interface org.cytoscape.view.model.CyNetworkView: Adds a CyNetworkViewListener (optional operation).
addNode() - Method in interface org.cytoscape.model.CyNetwork: This method is used to create and add a node to this network.
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.
addNode(CyNode) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Adds a node to this CySubNetwork.
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.
addNonClearableVisualProperty(VisualProperty<?>) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig: Add a VisualProperty that will not have its value cleared when View.clearVisualProperties() is called.
addPaletteProvider(PaletteProvider) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Add a palette provider to the manager.
addPoint(K, BoundaryRangeValues<V>) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Adds a New Data Point.
addRangeValue(T) - Method in class org.cytoscape.view.model.DiscreteRange: Add a value to this DiscreteRange.
addRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Add new RenderingEngine to this manager.
addScalarArgumentTypes(List<Class>) - Static method in class org.cytoscape.equations.FunctionUtil: Adds the scalar types that equations use internally to the argument, i.e.
addSubNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Create an empty CySubNetwork.
addSubNetwork(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.
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.
addTable(CyTable) - Method in interface org.cytoscape.model.CyTableManager: Registers a new table with the manager and fires a TableAddedEvent event.
addTrackedVisualProperty(Object, VisualProperty<? extends T>, Predicate<V>) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig: Turns on tracking of the given VisualProperty such that nodes/edge that have the VisualProperty set to a value that satisfies the given Predicate are returned by the CyNetworkViewSnapshot.getTrackedNodes(Object) or CyNetworkViewSnapshot.getTrackedEdges(Object) method .
addTrackedVisualProperty(Object, VisualProperty<? extends T>, V) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig: Turns on tracking of the given VisualProperty such that nodes/edge that have the VisualProperty set to a value that is equal to the given value are returned by the CyNetworkViewSnapshot.getTrackedNodes(Object) or CyNetworkViewSnapshot.getTrackedEdges(Object) method .
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.
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
addVisualProperty(VisualProperty<?>, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon: 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 - Enum constant in enum class org.cytoscape.filter.model.CompositeFilter.Type: Use set-intersection semantics (logical AND) to combine the results.
ALL - Static variable in class org.cytoscape.view.presentation.property.table.TableModeVisualProperty
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.
AMPERSAND - Enum constant in enum class org.cytoscape.equations.Token.Type
AnalyzeNetworkCollectionTaskFactory - Interface in org.cytoscape.task.analyze: Provides a TaskIterator to analyze a collection of networks.
ANCHOR - Enum constant in enum class org.cytoscape.view.presentation.annotations.ArrowAnnotation.AnchorType
AND - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType: Aggregated as a logical AND of all values.
ANGLE_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
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.
ANY - Enum constant in enum class org.cytoscape.equations.ArgType: Any scalar argument.
ANY - Enum constant in enum class org.cytoscape.filter.model.CompositeFilter.Type: Use set-union semantics (logical OR) to combine the results.
ANY - Enum constant in enum class org.cytoscape.model.CyEdge.Type: matches any edge
ANY - Enum constant in enum class org.cytoscape.util.color.BrewerType: Any (or all) palettes
ANY_LIST - Enum constant in enum class org.cytoscape.equations.ArgType: One or more lists with arbitrary member element types and/or one or more scalars.
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(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).
apply(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Apply Visual Style to the entire network view.
apply(View<CyColumn>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Apply Visual Style to the entire table view.
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.AbstractVisualLexicon
ARBITRARY_STRING_RANGE - Static variable in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
ARCHIVE - Enum constant in enum class org.cytoscape.io.DataCategory: Data to be exported is an archive file
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 Class in org.cytoscape.equations: An enum specifying a function argument type.
argTypesAreValid(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
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 Class 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 Class 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, String, int) - Method in interface org.cytoscape.jobs.CyJobManager: Associate a handler with a job.
associateMonitor(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager: Associate a monitor with a job.
attribNameAsReference(String) - Static method in class org.cytoscape.equations.EquationUtil: Converts a bare name to a variable reference.
AttributeHandlingType - Enum Class in org.cytoscape.group.data: The AttributeHandlingType enum contains the list of all of the different ways that attributes can be aggregated.
AUTO - Static variable in class org.cytoscape.view.presentation.property.table.TableModeVisualProperty
AUTO_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeStackingVisualProperty
AvailableCommands - Interface in org.cytoscape.command: TODO: Missing documentation
AVG - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType: Aggregated as the average of all values.

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(String) - Constructor for class org.cytoscape.util.swing.BasicCollapsiblePanel: Constructor for a label/button controlled collapsible panel.
BasicCollapsiblePanel(JRadioButton) - Constructor for class org.cytoscape.util.swing.BasicCollapsiblePanel: Constructor for an option 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(String[], String[], String, DataCategory, StreamUtil) - Constructor for class org.cytoscape.io.BasicCyFileFilter: Creates a file filter from the specified arguments.
BasicCyFileFilter(Set<String>, Set<String>, String, DataCategory, StreamUtil) - Constructor for class org.cytoscape.io.BasicCyFileFilter: Creates a file filter from the specified arguments.
BasicTableVisualLexicon - Class in org.cytoscape.view.presentation.property.table
BasicTableVisualLexicon(VisualProperty<NullDataType>) - Constructor for class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
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.
batch(Consumer<View<S>>) - Method in interface org.cytoscape.view.model.View: Performs the given action on this View object.
batch(Consumer<View<S>>, boolean) - Method in interface org.cytoscape.view.model.View: Performs the given action on this View object.
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.
BETWEEN - Enum constant in enum class org.cytoscape.filter.predicates.Predicate: A ternary predicate that tests whether the first parameter is greater than or equal to the second parameter, and less than or equal to the third parameter.
BIRDS_EYE_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
BookmarksUtil - Interface in org.cytoscape.property.bookmark: A set of utility methods to manipulate the bookmarks.
BOOL - Enum constant in enum class org.cytoscape.equations.ArgType: An argument that can be converted to a boolean.
BOOLEAN_CONSTANT - Enum constant in enum class org.cytoscape.equations.Token.Type
BooleanVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Boolean values.
BooleanVisualProperty(Boolean, String, String, Boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.BooleanVisualProperty: Constructor.
BooleanVisualProperty(Boolean, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.BooleanVisualProperty: Constructor.
BOOLS - Enum constant in enum class org.cytoscape.equations.ArgType: An non-empty sequence of arguments that consist of lists of booleans and scalars that can be converted to a boolean.
BOTH_CONTEXT - Static variable in annotation interface 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(BoundaryRangeValues<T>) - Constructor for class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
BoundaryRangeValues(T, T, T) - Constructor for class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Creates a new BoundaryRangeValues object.
BoundedChangeListener<N> - Interface in org.cytoscape.work.util: Classes which wish to listen for changes in AbstractBounded objects (BoundedDouble, BoundedFloat, etc.) should implement this interface and add themselves as observers (listeners) to the object.
BoundedDouble - Class in org.cytoscape.work.util: A Double object which has low and up bounds
BoundedDouble(Double, Double, Double, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedDouble: Creates a new Bounded Double object.
BoundedFloat - Class in org.cytoscape.work.util: A Float object which has low and up bounds.
BoundedFloat(Float, Float, Float, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedFloat: Creates a new Bounded Float object.
BoundedInteger - Class in org.cytoscape.work.util: An Integer object which has low and up bounds.
BoundedInteger(Integer, Integer, Integer, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedInteger: Creates a new Bounded Integer object.
BoundedLong - Class in org.cytoscape.work.util: A Long object which has low and up bounds.
BoundedLong(Long, Long, Long, boolean, boolean) - Constructor for class org.cytoscape.work.util.BoundedLong: Creates a new Bounded Long object.
BoundedTextAnnotation - Interface in org.cytoscape.view.presentation.annotations: The BoundedText annotation is a ShapeAnnotation that also implements Text.
boundsChanged(AbstractBounded) - Method in interface org.cytoscape.work.util.BoundedChangeListener
BrewerType - Enum Class in org.cytoscape.util.color
build() - Method in class org.cytoscape.session.CySession.Builder: Returns a complete instance of CySession based upon the methods called on this instance of Builder.
buildConfiguration(Object) - Method in interface org.cytoscape.work.TunableMutator: Returns the configuration object used to mutate the tunables.
buildCyNetworkView(CyNetwork) - Method in interface org.cytoscape.io.read.CyNetworkReader: A method to build a CyNetworkView from one of the networks just read.
Builder() - Constructor for class org.cytoscape.session.CySession.Builder

C

calcSampleVariance(double[]) - Static method in class org.cytoscape.equations.FunctionUtil: Calculates the sample variance of some numbers.
calculate_max_dimension(double, double, double, double, List<LayoutPartition>) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
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
CANCELED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
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.
CANCELLED - Enum constant in enum class org.cytoscape.work.FinishStatus.Type: Indicates that the task iterator did not complete because one of its tasks was cancelled by the user.
CANVAS - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: Arg map key to initialize the canvas to draw this annotation on
CARET - Enum constant in enum class org.cytoscape.equations.Token.Type
CASCADE - Enum constant in enum class org.cytoscape.application.swing.CyNetworkViewDesktopMgr.ArrangeType
category - Variable in class org.cytoscape.io.BasicCyFileFilter: Type of data that this filter applies to.
CELL - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CELL_BACKGROUND_PAINT - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CELL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CELL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CELL_TEXT_COLOR - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CELL_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
CellFormat - Class in org.cytoscape.view.presentation.property.table
CellFormat(String) - Constructor for class org.cytoscape.view.presentation.property.table.CellFormat
CellFormatVisualProperty - Class in org.cytoscape.view.presentation.property.table: Visual Property for CellFormat values.
CellFormatVisualProperty(CellFormat, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.table.CellFormatVisualProperty
CENTER - Enum constant in enum class org.cytoscape.view.presentation.annotations.ArrowAnnotation.AnchorType
CENTER - Enum constant in enum class org.cytoscape.view.presentation.property.values.Position
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(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.
clamp(N) - Method in class org.cytoscape.work.util.AbstractBounded: Clamps the value of the Bounded object.
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.
CLOSE_BRACE - Enum constant in enum class org.cytoscape.equations.Token.Type
CLOSE_PAREN - Enum constant in enum class org.cytoscape.equations.Token.Type
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.
COLON - Enum constant in enum class org.cytoscape.equations.Token.Type
COLOR - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType: Used for mapping continuous attribute values to color visual property types such as Node Color.
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: The basic constructor for a color button without palettes.
ColorButton(CyServiceRegistrar, Palette, PaletteType, Color, boolean) - Constructor for class org.cytoscape.util.swing.ColorButton: The basic constructor for a color button with palettes.
ColorUtils - Class in org.cytoscape.util.color
ColorUtils() - Constructor for class org.cytoscape.util.color.ColorUtils
column - Variable in class org.cytoscape.task.AbstractTableCellTask: The CyColumn of the CyTable cell
column - Variable in class org.cytoscape.task.AbstractTableColumnTask: The CyColumn that descendants will operate on.
COLUMN - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_EDITABLE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
COLUMN_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Column Filter, which finds nodes and edges based on their column values.
COLUMN_FORMAT - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_GRAVITY - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
COLUMN_SELECTED - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_TEXT_WRAPPED - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
COLUMN_WIDTH - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
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: Deprecated.
ColumnCreatedEvent(CyTable, String, Long) - Constructor for class org.cytoscape.model.events.ColumnCreatedEvent
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: Deprecated.
ColumnDeletedEvent(CyTable, String, Long) - Constructor for class org.cytoscape.model.events.ColumnDeletedEvent
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.
ColumnVisualStyleSetEvent - Class in org.cytoscape.view.vizmap.events.table: Event fired when a VisualStyle is set to a column view through TableVisualMappingManager.setVisualStyle(View, VisualStyle).
ColumnVisualStyleSetEvent(TableVisualMappingManager, VisualStyle, View<CyColumn>) - Constructor for class org.cytoscape.view.vizmap.events.table.ColumnVisualStyleSetEvent: Creates the event.
ColumnVisualStyleSetListener - Interface in org.cytoscape.view.vizmap.events.table: Listener for ColumnVisualStyleSetEvent.
COMMA - Enum constant in enum class org.cytoscape.equations.Token.Type
COMMAND - Static variable in interface org.cytoscape.work.ServiceProperties: Name of command used by Command Executor.
COMMAND_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties: Description for a command.
COMMAND_EXAMPLE_JSON - Static variable in interface org.cytoscape.work.ServiceProperties: A valid JSON string representative of the expected JSON output of a command.
COMMAND_LONG_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties: Prose description for a command.
COMMAND_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties: Name space for a command.
COMMAND_SUPPORTS_JSON - Static variable in interface org.cytoscape.work.ServiceProperties: Indicates if the command supports JSON output.
CommandExecutorTaskFactory - Interface in org.cytoscape.command: TODO: Missing documentation
compare(TunableHandler, TunableHandler) - Method in class org.cytoscape.work.TunableGravityOrderer
compareTo(LayoutEdge) - Method in class org.cytoscape.view.layout.LayoutEdge
compareTo(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
compareTo(VisualLexiconNode) - Method in class org.cytoscape.view.model.VisualLexiconNode: Compare by display name of this Visual Property.
comparing(VisualProperty<V>) - Static method in interface org.cytoscape.view.model.VisualProperty: Utility method for sorting collections of Views according to the value of a VisualProperty.
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 Class in org.cytoscape.filter.model: Determines how a CompositeFilter combines the results of its contained Filters.
COMPOUND - Enum constant in enum class org.cytoscape.group.CyGroupSettingsManager.GroupViewType
CONCAT - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType: Aggregated as a concatenation of all values.
CONFIG_DIR - Enum constant in enum class org.cytoscape.property.CyProperty.SavePolicy: These properties are loaded from and written to the default config directory and are user defaults.
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.
CONTAINS - Enum constant in enum class org.cytoscape.filter.predicates.Predicate: A binary predicate that tests whether the first parameter is contained within the second parameter.
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 Interface in org.cytoscape.work: An annotation designed to signal that the annotated field contains fields and methods that are annotated with the Tunable annotation.
contentTypes - Variable in class org.cytoscape.io.BasicCyFileFilter
context() - Element in annotation interface org.cytoscape.work.Tunable: Returns the context that this Tunable is meant for.
CONTEXT - Static variable in class org.cytoscape.work.AbstractTunableHandler
CONTINUOUS - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType: Used for mapping continuous attribute values to continuous visual property types such as Node Size.
CONTINUOUS - Static variable in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: A label string for this mapping.
ContinuousEditorType - Enum Class in org.cytoscape.view.vizmap.gui.editor: An enum describing the possible types of continuous editors.
ContinuousMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings: An interface describing a continuous mapping from attribute value to visual property.
ContinuousMappingCellRendererFactory - Interface in org.cytoscape.view.vizmap.gui.editor: A factory for creating TableCellRenderers for a particular ContinuousMappingEditor.
ContinuousMappingEditor<K extends Number,V> - Interface in org.cytoscape.view.vizmap.gui.editor: A basic interface used to display continuous mapping editors.
ContinuousMappingPoint<K,V> - Class in org.cytoscape.view.vizmap.mappings: Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(K, BoundaryRangeValues<V>, ContinuousMapping<K, V>, CyEventHelper) - Constructor for class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Constructor.
ContinuousRange<T> - Class in org.cytoscape.view.model: Defines a continuous range of values for VisualPropertys.
ContinuousRange(Class<T>, T, T, Boolean, Boolean) - Constructor for class org.cytoscape.view.model.ContinuousRange: Constructs this ContinuousRange.
CONTRAST - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: This value allows the image contrast to be adjusted
controlsMutuallyExclusiveNestedChildren() - Method in class org.cytoscape.work.AbstractTunableHandler
controlsMutuallyExclusiveNestedChildren() - Method in interface org.cytoscape.work.TunableHandler: Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
CORE_PROPRERTY_NAME - Static variable in class org.cytoscape.property.SimpleCyProperty: Core Cytoscape Property (Cytoscape System Property)
countMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable: Returns the number of rows with the in the specified column with the specified value in the user namespace.
countMatchingRows(String, String, Object) - Method in interface org.cytoscape.model.CyTable: Returns the number of rows with the in the specified column with the specified value.
createAnnotation(Class<? extends T>, CyNetworkView, Map<String, String>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: Create an annotation.
createBend() - Method in interface org.cytoscape.view.presentation.property.values.BendFactory: Creates an instance of edge bend.
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.
createColumn(String, String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type in the specified namespace.
createColumn(String, String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable: Create a column of the specified name and the specified type in the specified namespace.
createColumnIdentifier(String) - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifierFactory: Returns a CyColumnIdentifier that represents a CyColumn from a default network CyTable (a table associated with a CyNetwork, CyNode or CyEdge).
createCompositeFilter(Class<C>, Class<E>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a new empty CompositeFilter that selects elements of type elementType from an object of type contextType.
createConfig(VisualLexicon) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider: Create a default configuration object for the given VisualLexicon.
createCyJob(String) - Method in interface org.cytoscape.jobs.CyJobExecutionService: Create an empty (unsubmitted) CyJob
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(NetworkCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkViewCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(NetworkViewTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(RowTaskFactory, CyRow) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(TableCellTaskFactory, CyColumn, Object) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
createFor(TableColumnTaskFactory, CyColumn) - 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, boolean) - Method in interface org.cytoscape.group.CyGroupFactory: Creates a CyGroup object in the referenced network from an existing CyNode.
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.
createHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.HandleFactory: Creates a new instance of the Handle.
createHelpButton(String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
createHolisticTransformer() - Method in interface org.cytoscape.filter.model.HolisticTransformerFactory
createIcon(VisualProperty<V>, V, int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine: Create Icon object for the given VisualProperty value.
createImage(int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine: Render an Image object from current visualization.
createImage(CyNetworkView, int, int) - Method in interface org.cytoscape.view.presentation.NetworkImageFactory: Creates a network image thumbnail with the given width and height.
createImage(CyNetworkView, Collection<Annotation>, Map<String, Object>) - Method in interface org.cytoscape.view.presentation.NetworkImageFactory: Creates a network image thumbnail with the given properties.
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.
createListColumn(String, String, Class<T>, boolean) - Method in interface org.cytoscape.model.CyTable: Create a column of Lists with the specified name and the specified element type in the specified namespace.
createListColumn(String, String, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable: Create a column of Lists with the specified name and the specified element type in the specified namespace.
createMenuItem(CyNetworkView) - 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<CyEdge>) - Method in interface org.cytoscape.application.swing.CyEdgeViewContextMenuFactory: This method should return a CyMenuItem to be added to the context menu of the specified edge view.
createMenuItem(CyNetworkView, View<CyNode>) - Method in interface org.cytoscape.application.swing.CyNodeViewContextMenuFactory: This method should return a CyMenuItem to be added to the context menu of the specified node view.
createNamedTransformer(String, List<Transformer<C, E>>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a new NamedTransformer with the given name and list of transformers.
createNetwork() - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object.
createNetwork(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object.
createNetworkView(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewFactory: Create a CyNetworkView from a CyNetwork object.
createNetworkViewFactory(VisualLexicon, String) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider: Creates a CyNetworkViewFactory with a default CyNetworkViewConfig that supports standard 2D rendering.
createNetworkViewFactory(VisualLexicon, String, CyNetworkViewFactoryConfig) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider: Creates a CyNetworkViewFactory.
CreateNetworkViewTaskFactory - Interface in org.cytoscape.task.create: This interface provides a task iterator for creating network views.
createNetworkWithPrivateTables() - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object where the associated default tables are private.
createNetworkWithPrivateTables(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory: Returns a new, empty CyNetwork object where the associated default tables are private.
createNewEmptyNetworkView() - Method in interface org.cytoscape.task.create.NewEmptyNetworkViewFactory: Returns a new, empty CyNetworkView.
createOkCancelPanel(JButton, JButton) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create a standard Cytoscape panel (usually added to the bottom of a dialog) that contains an "OK" and/or a "Cancel" button.
createOkCancelPanel(JButton, JButton, String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to create OK, Cancel and Help
createOkCancelPanel(JButton, JButton, String, JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Use this method to include a help button in the bottom left corner.
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
createSnapshot() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns an immutable snapshot of this network view (optional operation).
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.
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.
createTableCellRenderer(ContinuousMappingEditor<? extends Number, ?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingCellRendererFactory
createTableView(CyTable) - Method in interface org.cytoscape.view.model.table.CyTableViewFactory: Create a CyTableView from a CyTable object.
createTableViewFactory(VisualLexicon, String) - Method in interface org.cytoscape.view.model.table.CyTableViewFactoryProvider: Returns a CyTableViewFactory for the given lexicon and with the given ID.
createTaskIterator() - Method in interface org.cytoscape.work.TaskFactory: Returns an iterator containing a sequence of Tasks.
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(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory: Creates a task iterator for loading a network from a file.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadTableFileTaskFactory: 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) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory: Creates a task iterator for loading a session from a file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportSelectedNetworkTaskFactory: Creates the task iterator for exporting the selected network.
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(File, boolean) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory: Creates a task iterator for loading a session from a file, with an option to let the user confirm it before disposing the current session if it is not empty.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory: Creates a task iterator for loading a network from a file.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory: Creates a task iterator for loading files into visual styles.
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(String, String, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified command.
createTaskIterator(URL) - Method in interface org.cytoscape.task.read.LoadTableURLTaskFactory: Creates the task iterator for importing an attribute file to a table.
createTaskIterator(URL, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkURLTaskFactory: Creates a task iterator for loading a URL into a network.
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(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(Collection<CyRootNetwork>) - Method in interface org.cytoscape.task.RootNetworkCollectionTaskFactory: Provisions this factory with the collection of root-networks that will be passed into any task created by it.
createTaskIterator(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(List<File>, CyRootNetwork) - Method in interface org.cytoscape.task.read.LoadMultipleNetworkFilesTaskFactory: Creates a task iterator for loading one or more networks from supported files (e.g.
createTaskIterator(List<String>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
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(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory: Used to provision this factory with a CyColumn that will be used to create tasks.
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, String) - Method in interface org.cytoscape.task.edit.RenameColumnTaskFactory: Create a task iterator for renaming a selected column.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.CloneNetworkTaskFactory: Returns a TaskIterator that clones the given network.
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(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(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(CyNetwork, File) - Method in interface org.cytoscape.task.write.ExportNetworkTaskFactory: Creates the task iterator for exporting networks.
createTaskIterator(CyNetwork, String) - Method in interface org.cytoscape.task.edit.EditNetworkTitleTaskFactory: Creates a task iterator for editing a network's title.
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(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory: Used to provision this factory with a CyTable that will be used to create tasks.
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(CyTable, boolean, List<CyNetwork>, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory
createTaskIterator(CyTable, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.JoinTablesTaskTaskFactory
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(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, 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(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory: Creates a new TaskIterator using the given CyNetworkView
createTaskIterator(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory: Creates a task iterator using the specified network view and points.
createTaskIterator(CyNetworkView, File) - Method in interface org.cytoscape.task.write.ExportNetworkViewTaskFactory: Creates the task iterator for exporting network views.
createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Creates a task iterator containing the layout tasks.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.HideTaskFactory: Creates a task iterator that will hide the given nodes and edges.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.UnHideTaskFactory: Creates a task iterator that will show the given nodes and edges.
createTaskIterator(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory: Creates a new TaskIterator using the given edge view and network view.
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(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.
createTaskIterator(TaskObserver, String...) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory: Creates a task iterator that will execute the specified commands.
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(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 class org.cytoscape.work.BasicTunableHandlerFactory
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, 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, 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.
createWriter(OutputStream, Set<VisualStyle>, 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.
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, 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, 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, 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, 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.
CROSS_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Triangle shaped arrow with a cross hatch
CROSS_OPEN_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Unfilled triangle shaped arrow with a cross hatch
CSV - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType: Aggregated as comma-separated values.
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 - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
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
CY_EDGE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_EDGE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_VIEW_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NETWORK_VIEW_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_NODE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
CY_NODE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
CY_ROW_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
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.
CyActivator - Class in org.cytoscape.service.util.internal
CyActivator() - Constructor for class org.cytoscape.service.util.internal.CyActivator
CyAppAdapter - Interface in org.cytoscape.app: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
CyApplicationConfiguration - Interface in org.cytoscape.application: Application-wide setting will be accessible through this interface.
cyApplicationManager - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
CyApplicationManager - Interface in org.cytoscape.application: Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.
CyColorChooser - Class in org.cytoscape.util.swing: This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColorPaletteChooser - Interface in org.cytoscape.util.swing: This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColorPaletteChooserFactory - Interface in org.cytoscape.util.swing: This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColumn - Interface in org.cytoscape.model: This class describes a column in a CyTable.
CyColumnComboBox - Class in org.cytoscape.application.swing: An implementation of JComboBox that displays a list of CyColumns with their namespace icons.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox: Creates a CyColumnComboBox with all entries enabled.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>, Predicate<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox: Creates a CyColumnComboBox.
CyColumnIdentifier - Interface in org.cytoscape.view.presentation.property.values: Interface used to carry and save information that represents a CyColumn (usually from a network CyTable).
CyColumnIdentifierFactory - Interface in org.cytoscape.view.presentation.property.values: A factory for creating CyColumnIdentifier objects.
CyColumnPresentation - Interface in org.cytoscape.application.swing: Service that allows UI presentation to be given for a column namespace.
CyColumnPresentationManager - Interface in org.cytoscape.application.swing: This class provides access to registered CyColumnPresentation service objects.
CyColumnSelector - Class in org.cytoscape.application.swing: An Swing control that allows the user to select a set of CyColumn objects.
CyColumnSelector(IconManager, CyColumnPresentationManager) - Constructor for class org.cytoscape.application.swing.CyColumnSelector: Creates a CyColumnSelector.
cyColumnsToJson(Collection<CyColumn>) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a list of references (via column name) for a collection of CyColumn.
CyColumnView - Interface in org.cytoscape.view.model.table: This interface is meant for internal use, it should not be used by Apps.
CyColumnViewMetadata - Class in org.cytoscape.view.model.table: A snapshot of information about a CyColumn and its associated visual property values.
CyColumnViewMetadata(String, String, Map<String, String>) - Constructor for class org.cytoscape.view.model.table.CyColumnViewMetadata
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 Class 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 Class 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 Class in org.cytoscape.group: The CyGroupSettingsManager.GroupViewType enum provides the options for how to visualize a group.
CyHelpBroker - Interface in org.cytoscape.application.swing: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. This interface provides access to the Cytoscape Help Broker and Help Set for managing the JavaHelp system.
CyIdentifiable - Interface in org.cytoscape.model: CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
cyIdentifiablesToJson(Collection<? extends CyIdentifiable>) - Method in interface org.cytoscape.util.json.CyJSONUtil: Returns a list of references (via SUID) for a collection of CyIdentifiable.
CyJob - Interface in org.cytoscape.jobs: A CyJob represents all of the state information necessary to marshal and unmarshal data, submit jobs, query job status, and fetch results.
CyJobData - Interface in org.cytoscape.jobs: CyJobData presents a general interface to sending data to and receiving data from a job.
CyJobDataService - Interface in org.cytoscape.jobs: The main interface for the marshalling and unmarshalling of data to be exchanged with remote services.
CyJobExecutionService - Interface in org.cytoscape.jobs: The CyJobExecutionService is a stateless service that can be used to provide remote job services, including the execution, cancellation, status checking, and retrieval of results.
CyJobManager - Interface in org.cytoscape.jobs: CyJobManager is responsible for managing all currently running CyJobs, including polling for changes in the Status of the job and notifying the CyJobMonitor provided by the App of the change in status.
CyJobMonitor - Interface in org.cytoscape.jobs: Apps are expected to implement this interface to receive notifications about job completions.
CyJobStatus - Class in org.cytoscape.jobs: This object stores information about the status of a CyJob, including the actual job status (CyJobStatus.Status) and any message returned from the remote execution.
CyJobStatus(CyJobStatus.Status, String) - Constructor for class org.cytoscape.jobs.CyJobStatus
CyJobStatus.Status - Enum Class in org.cytoscape.jobs: This enum contains the primary status returned from the remote execution.
CyJSONUtil - Interface in org.cytoscape.util.json: This interface provides some very basic JSON representations of Cytoscape objects.
CyLayoutAlgorithm - Interface in org.cytoscape.view.layout: A task factory specifically for layout algorithms.
CyLayoutAlgorithmManager - Interface in org.cytoscape.view.layout: This class provides access to the available layout algorithms.
CyListener - Interface in org.cytoscape.event: The basic interface that any class interested in a particular type of event should implement.
CyMenuItem - Class in org.cytoscape.application.swing: A simple wrapper class that allows a JMenuItem to be associated with a gravity value which defines where in a menu the item should fall.
CyMenuItem(JMenuItem, float) - Constructor for class org.cytoscape.application.swing.CyMenuItem: Constructor.
CyNetwork - Interface in org.cytoscape.model: CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
cyNetworkFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader: Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.
CyNetworkFactory - Interface in org.cytoscape.model: A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager - Interface in org.cytoscape.model: Basic access to networks and view in an instance of Cytoscape.
CyNetworkNaming - Interface in org.cytoscape.session: A utility that helps with the creation of unique network names.
CyNetworkReader - Interface in org.cytoscape.io.read: An extension of the Task interface that returns an array of CyNetwork objects that are read as part of the Task.
CyNetworkReaderManager - Interface in org.cytoscape.io.read: An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyNetworkReader for the input.
CyNetworkTableManager - Interface in org.cytoscape.model: Provides access to all network-table relationships.
CyNetworkView - Interface in org.cytoscape.view.model: Additional methods for CyNetworkView.
CyNetworkViewContextMenuFactory - Interface in org.cytoscape.application.swing: A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified network view.
CyNetworkViewDesktopMgr - Interface in org.cytoscape.application.swing: Interface for managing CyNetworkViews within the desktop where they reside.
CyNetworkViewDesktopMgr.ArrangeType - Enum Class 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.
CyNetworkViewFactoryConfig - Interface in org.cytoscape.view.model: Used to configure the behavior of CyNetworkView objects created using the CyNetworkViewFactoryFactory service.
CyNetworkViewFactoryProvider - Interface in org.cytoscape.view.model: A singleton factory that is used to create CyNetworkViewFactory objects.
CyNetworkViewListener - Interface in org.cytoscape.view.model: Callback interface for use with CyNetworkView instances that are created from CyNetworkViewFactoryProvider factories.
CyNetworkViewManager - Interface in org.cytoscape.view.model: Basic access to network views in an instance of Cytoscape.
CyNetworkViewSnapshot - Interface in org.cytoscape.view.model: An immutable snapshot of a CyNetworkView created using the CyNetworkView.createSnapshot() method.
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 Class 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.
CyRowViewMetadata - Class in org.cytoscape.view.model.table: A snapshot of information about a CyRow and its associated visual property values.
CyRowViewMetadata(Object, Map<String, String>) - Constructor for class org.cytoscape.view.model.table.CyRowViewMetadata
CyServiceRegistrar - Interface in org.cytoscape.service.util: An interface to hide the OSGi dependencies needed to register services dynamically at runtime.
CyServiceRegistrarFactory - Class in org.cytoscape.service.util.internal
CyServiceRegistrarFactory() - Constructor for class org.cytoscape.service.util.internal.CyServiceRegistrarFactory
CyServiceRegistrarImpl - Class in org.cytoscape.service.util.internal: Implementation of CyServiceRegistrar.
CyServiceRegistrarImpl(BundleContext) - Constructor for class org.cytoscape.service.util.internal.CyServiceRegistrarImpl
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) - Constructor for class org.cytoscape.application.events.CyShutdownEvent: Constructor.
CyShutdownEvent(Object, boolean) - Constructor for class org.cytoscape.application.events.CyShutdownEvent: Constructor.
CyShutdownListener - Interface in org.cytoscape.application.events: The listener for the CyShutdownEvent.
CyStartEvent - Class in org.cytoscape.application.events: An event fired after Cytoscape startup mostly complete (but not necessarily 100 percent).
CyStartEvent(Object) - Constructor for class org.cytoscape.application.events.CyStartEvent: Constructor.
CyStartListener - Interface in org.cytoscape.application.events: The listener for the CyStartEvent.
CySubNetwork - Interface in org.cytoscape.model.subnetwork: A CySubNetwork is a CyNetwork that is contained within a parent CyNetwork.
CySwingAppAdapter - Interface in org.cytoscape.app.swing: Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
CySwingApplication - Interface in org.cytoscape.application.swing: This interface provides basic access to the Swing objects that constitute this application.
CyTable - Interface in org.cytoscape.model: A simple representation of a table object consisting of rows and columns.
CyTable.Mutability - Enum Class 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 Class 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.
CyTableView - Interface in org.cytoscape.view.model.table: Additional methods for table views.
CyTableViewFactory - Interface in org.cytoscape.view.model.table: Factory for CyTableView objects.
CyTableViewFactoryProvider - Interface in org.cytoscape.view.model.table: A singleton factory that is used to create CyTableViewFactory objects.
CyTableViewManager - Interface in org.cytoscape.view.model.table: Basic access to table views in an instance of Cytoscape.
CyTableViewMetadata - Class in org.cytoscape.view.model.table: A snapshot of information about a CyTable and its associated visual property values.
CyTableViewMetadata(long, String, String, Map<String, String>, List<CyColumnViewMetadata>, List<CyRowViewMetadata>, Class<?>, Class<?>) - Constructor for class org.cytoscape.view.model.table.CyTableViewMetadata
CyTableWriterFactory - Interface in org.cytoscape.io.write: A specialization of CyWriterFactory that allows a CyTable to be specified and written.
CyTableWriterManager - Interface in org.cytoscape.io.write: A CyWriterManager specific to writing CyTable objects.
CyToolTip - Class in org.cytoscape.util.swing
CyToolTip(JComponent, String, String, Icon) - Constructor for class org.cytoscape.util.swing.CyToolTip
CytoPanel - Interface in org.cytoscape.application.swing: Interface to a CytoPanel.
CytoPanelComponent - Interface in org.cytoscape.application.swing: An interface that allows a component to be registered as a service that will then be added to the appropriate CytoPanel.
CytoPanelComponent2 - Interface in org.cytoscape.application.swing: Implement this interface rather than CytoPanelComponent, if you want to allow your component to be retrieved from the CytoPanel by its identifier.
CytoPanelComponentSelectedEvent - Class in org.cytoscape.application.swing.events: The event fired to indicate that a CytoPanelComponent has been selected.
CytoPanelComponentSelectedEvent(Object, CytoPanel, int) - Constructor for class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent: Constructor.
CytoPanelComponentSelectedListener - Interface in org.cytoscape.application.swing.events: The listener for handling CytoPanelComponentSelectedEvent.
CytoPanelName - Enum Class in org.cytoscape.application.swing: An enum that describes CytoPanels uses compass directions to describe their location within the application.
CytoPanelState - Enum Class 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 Class 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.
DataSourceManager - Interface in org.cytoscape.io.datasource: Entry point to access all data sources implemented as OSGi services.
debounce(Object, Runnable) - Method in class org.cytoscape.event.DebounceTimer: Starts a timer that will run the runnable after a short delay (on a separate thread).
debounce(Runnable) - Method in class org.cytoscape.event.DebounceTimer: Starts a timer that will run the runnable after a short delay (on a separate thread).
DebounceTimer - Class in org.cytoscape.event: A timer that can be used to ensure that time-consuming tasks, usually triggered by events, do not run too often.
DebounceTimer() - Constructor for class org.cytoscape.event.DebounceTimer: Creates a new DebounceTimer with the default delay.
DebounceTimer(int) - Constructor for class org.cytoscape.event.DebounceTimer: Creates a new DebounceTimer with the given delay (in milliseconds).
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 - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType: Default, no aggregation.
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_CONTEXT - Static variable in interface org.cytoscape.application.TableViewRenderer
DEFAULT_DELAY_MILLISECONDS - Static variable in class org.cytoscape.event.DebounceTimer
DEFAULT_EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: The default edge bend.
DEFAULT_FONT_NAME - Static variable in interface org.cytoscape.util.swing.IconManager
DEFAULT_LAYOUT_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: The name of the default layout.
DEFAULT_LAYOUT_PROPERTY_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: The name of the default layout property.
DEFAULT_PAYLOAD_INTERVAL_MILLIS - Static variable in interface org.cytoscape.event.CyEventHelper: The default number of milliseconds to wait before the next time that we will check for payload events to fire.
DEFAULT_POSITION - Static variable in class org.cytoscape.view.presentation.property.values.ObjectPosition
DEFAULT_PROPS_CONFIG_DIR - Static variable in interface org.cytoscape.property.CyProperty: The name of the default directory where we will look for properties files.
DefaultDataSource - Class in org.cytoscape.io.datasource: Basic implementation of DataSource.
DefaultDataSource(String, String, String, DataCategory, URL) - Constructor for class org.cytoscape.io.datasource.DefaultDataSource: Constructor for the default data source.
defaultEdgeWeight - Variable in class org.cytoscape.view.layout.EdgeWeighter
DefaultViewEditor - Interface in org.cytoscape.view.vizmap.gui: Deprecated.
DefaultViewPanel - Interface in org.cytoscape.view.vizmap.gui: Deprecated.
DefaultVisualizableVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property to represent abstract concept such as Node or Edge.
DefaultVisualizableVisualProperty(String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty
defineHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.Handle: Define this handle.
DEGREE_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers: The id of the core Degree Filter, which finds nodes based on their degree.
delayedFireTableDataChanged() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Invokes fireTableDataChanged after all the pending events have been processed.
deleteBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Delete a bookmark (pDataSource) from the category (pCategoryName) in the bookmarks object (pBookmarks)
deleteColumn(String) - Method in interface org.cytoscape.model.CyTable: Will delete the column with the specified fully-qualified name.
deleteColumn(String, String) - Method in interface org.cytoscape.model.CyTable: Will delete the column of the specified name in the specified namespace.
DeleteColumnTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting a column.
deleteDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Remove a DataSource from the DataSourceManager
deleteRows(Collection<?>) - Method in interface org.cytoscape.model.CyTable: Deletes the rows corresponding to the given primary keys and returns true if at least one row was deleted.
DeleteSelectedNodesAndEdgesTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting selected nodes and edges.
deleteTable(long) - Method in interface org.cytoscape.model.CyTableManager: Deletes a mutable table.
DeleteTableTaskFactory - Interface in org.cytoscape.task.destroy: This interface provides a task iterator for deleting a table.
DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Triangle shaped arrow
DELTA_SHORT_1 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Shorter triangle shaped arrow
DELTA_SHORT_2 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty: Even shorter triangle shaped arrow
dependsOn() - Method in class org.cytoscape.work.AbstractTunableHandler
dependsOn() - Element in annotation interface org.cytoscape.work.Tunable: To add a dependency between two or more Tunables, where the display of one Tunable depends on the the state of another.
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() - Element in annotation interface org.cytoscape.work.Tunable: Mandatory, human-readable label identifying the Tunable as displayed to a user.
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(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.
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(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.
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.
destroyTableView(CyTableView) - Method in interface org.cytoscape.view.model.table.CyTableViewManager: Destroys the given table 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 - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
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
DIRECTED - Enum constant in enum class org.cytoscape.model.CyEdge.Type: matches directed edges regardless of whether this node is the source or the target
DirectlyPresentableTunableHandler - Interface in org.cytoscape.work.swing: TODO: Missing documentation
dirty(boolean) - Method in interface org.cytoscape.view.model.CyNetworkView: If this network view supports creating snapshots using the CyNetworkView.createSnapshot() method, then this method will return true if the state of the network has changed since last clearing the dirty flag.
DISCRETE - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType: Used for mapping continuous attribute values to discrete visual property types such as Node Shape.
DISCRETE - Static variable in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: A label string describing the mapping.
DiscreteMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings: An interface describing a discrete mapping from attribute value to visual property.
DiscreteMappingGenerator<V> - Interface in org.cytoscape.view.vizmap.gui.util: Generates Discrete mapping for a set of attribute values and a Visual Property.
DiscreteRange<T> - Class in org.cytoscape.view.model: Defines a discrete range of values for VisualPropertys.
DiscreteRange(Class<T>, Set<T>) - Constructor for class org.cytoscape.view.model.DiscreteRange: Constructor for this DiscreteRange.
discreteTableCellRenderer - Variable in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor: The cell renderer for discrete mappings.
dispose() - Method in interface org.cytoscape.model.CyDisposable: Free up any memory or resources used by this object.
disposeCurrentSession() - Method in interface org.cytoscape.session.CySessionManager: Disposes the current session.
distance(double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 2D) between this node and a location.
distance(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 2D) between this node and another node.
DISTANCE - Enum constant in enum class org.cytoscape.view.layout.WeightTypes: Use 1 minus the normalized value.
distance3D(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode: Return the Euclidean distance (in 3D) 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.
DIV - Enum constant in enum class org.cytoscape.equations.Token.Type
DIVERGING - Enum constant in enum class org.cytoscape.util.color.BrewerType: Diverging palettes -- typically used to represent centered data with extremes in either direction.
DO_NOT_SAVE - Enum constant in enum class org.cytoscape.model.SavePolicy: The object should not be saved.
DO_NOT_SAVE - Enum constant in enum class org.cytoscape.property.CyProperty.SavePolicy: These properties are preset by Cytoscape to some default value and are never written out.
DOCK - Enum constant in enum class org.cytoscape.application.swing.CytoPanelState: The CytoPanel will be open and appear as a nested frame within the application.
DOES_NOT_CONTAIN - Enum constant in enum class org.cytoscape.filter.predicates.Predicate: A binary predicate that tests whether the first parameter does not contain the second parameter.
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.
DOLLAR - Enum constant in enum class org.cytoscape.equations.Token.Type
dontMove(boolean) - Method in class org.cytoscape.view.layout.LayoutPartition
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, boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DoubleVisualProperty: Constructor.
DoubleVisualProperty(Double, Range<Double>, String, String, 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.
draw(Graphics2D, CyTableView, CyColumn, CyRow) - Method in interface org.cytoscape.view.presentation.customgraphics.Cy2DGraphicLayer: This method is called by Cytoscape when a CyTableView is being updated in order to let the custom graphics draw onto its cells.
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() - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
DropDownMenuButton(AbstractAction) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton: Creates a new DropDownMenuButton object.
DropDownMenuButton(JPopupMenu) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
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

EAST - Enum constant in enum class org.cytoscape.application.swing.CytoPanelName: The east or right-hand panel.
EAST - Enum constant in enum class org.cytoscape.view.presentation.property.values.Position
EDGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
EDGE_APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: If Edge Bend is defined, edges will be rendered as straight or curved lines.
EDGE_DYNAMIC_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_EDIT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text used for the edge label.
EDGE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The font used for the edge label.
EDGE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The size of the font used for the edge label.
EDGE_LABEL_ROTATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: A value used to rotate the edge label about its center, in degrees.
EDGE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The opacity of the color of the edge label.
EDGE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The type of stoke used to render the line (solid, dashed, etc.)
EDGE_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (including the stroke and arrows) when it is selected or unselected.
EDGE_PREFERENCES_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
EDGE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (stroke and arrows) when selected.
EDGE_SOURCE_ARROW_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge source arrow when selected.
EDGE_SOURCE_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The shape of the arrow on the source node end of the edge.
EDGE_SOURCE_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_SOURCE_ARROW_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge source arrow when unselected.
EDGE_STACKING - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The strategy to use to render edges when there are more than one edge between a pair of nodes.
EDGE_STACKING_DENSITY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Controls how tightly packed edges are when there are more than one edge between a pair of nodes.
EDGE_STROKE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge line when selected.
EDGE_STROKE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge line.
EDGE_TARGET_ARROW_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge target arrow when selected.
EDGE_TARGET_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The shape of the arrow on the target node end of the edge.
EDGE_TARGET_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: TODO Documentation
EDGE_TARGET_ARROW_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the edge target arrow when unselected.
EDGE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The text of the tooltip that appears when a mouse hovers over the edge.
EDGE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The opacity of the of the edge.
EDGE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The color of the whole edge (stroke and arrows) when it is not selected.
EDGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: Hides the edge if set to false.
EDGE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: The width of the edge line.
EDGE_Z_ORDER - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon: When rendering edges in 2D, edges with a higher Z-order will be rendered on top of edges with lower Z-order.
EdgeBendVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Edge Bend values.
EdgeBendVisualProperty(Bend, String, String) - Constructor for class org.cytoscape.view.presentation.property.EdgeBendVisualProperty: Constructor.
EDGECOLOR - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The color of the border
edgeCount() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the number of edges in this partition
edgeIterator() - Method in class org.cytoscape.view.layout.LayoutPartition: Return an iterator over all of the LayoutEdges in this partition
EdgeList - Class in org.cytoscape.command.util: This class implements a wrapper for a List of CyEdges that can be used by the Tunables mechanism.
EdgeList() - Constructor for class org.cytoscape.command.util.EdgeList: Empty constructor for an EdgeList.
EdgeList(CyNetwork) - Constructor for class org.cytoscape.command.util.EdgeList: Constructor for EdgeList when the network is known at time of creation.
EDGEOPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: The opacity of the border
edgesChanged() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns true if the selection stated of edges has changed.
EdgeSpacialIndex2DEnumerator - Interface in org.cytoscape.view.model.spacial: Enumerator returned when querying a NetworkSpacialIndex2D, used to iterate over the results of the query.
EdgeStacking - Interface in org.cytoscape.view.presentation.property.values: Marker interface for edge stacking.
EdgeStackingVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for EdgeStacking values.
EdgeStackingVisualProperty(EdgeStacking, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.EdgeStackingVisualProperty
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 - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
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.
EOS - Enum constant in enum class org.cytoscape.equations.Token.Type
eqnTypeIsCompatible(Class<?>, Class<?>, Class<?>) - Static method in class org.cytoscape.equations.EquationUtil: Returns whether the given column type is compatible with an equation type
EQUAL - Enum constant in enum class org.cytoscape.equations.Token.Type
EQUAL_DASH - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty: Equal dash and space
equalizeSize(JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil: Resizes the given components making them equal in size.
equals(Object) - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
equals(Object) - Method in class org.cytoscape.equations.Equation: Compares one Equation to another.
equals(Object) - Method in class org.cytoscape.equations.Token
equals(Object) - Method in class org.cytoscape.util.swing.FileChooserFilter
equals(Object) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Compare two ObjectPositions
equals(Object) - Method in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
equals(Object) - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
equalValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues: Will be used when the domain value is exactly equal to the associated boundary domain value
Equation - Class in org.cytoscape.equations: The class representing an equation.
Equation(String, Set<String>, Map<String, Object>, Object[], int[], Class<?>) - Constructor for class org.cytoscape.equations.Equation: Constructs an Equation.
EquationCompiler - Interface in org.cytoscape.equations: Compiler that compiles equations to byte (non-Java) code.
EquationFunctionAddedEvent - Class in org.cytoscape.equations.event
EquationFunctionAddedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionAddedEvent
EquationFunctionAddedListener - Interface in org.cytoscape.equations.event
EquationFunctionRemovedEvent - Class in org.cytoscape.equations.event
EquationFunctionRemovedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionRemovedEvent
EquationFunctionRemovedListener - Interface in org.cytoscape.equations.event
EquationParser - Interface in org.cytoscape.equations: Parser for a string representing an equation.
EquationTokeniser - Interface in org.cytoscape.equations: Tokeniser for a string representing an equation.
EquationUtil - Class in org.cytoscape.equations: Various static utility methods relating to equations.
ERROR - Enum constant in enum class org.cytoscape.equations.Token.Type
ERROR - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
ERROR - Enum constant in enum class org.cytoscape.work.TaskMonitor.Level: A message that informs the user that a non-recoverable error has occured.
evaluateFunction(Object[]) - Method in interface org.cytoscape.equations.Function: Used to invoke this function.
eventHelper - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
exampleStringValue() - Element in annotation interface org.cytoscape.work.Tunable: Optional example string for use in scripting environments.
execService - Variable in class org.cytoscape.jobs.AbstractCyJob
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, Transformer<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager: Applies transformer 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(Equation, Map<String, IdentDescriptor>) - Method in interface org.cytoscape.equations.Interpreter: Executes the code represented by "equation".
execute(TaskIterator) - Method in interface org.cytoscape.work.TaskManager: This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
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.
exists(K) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D: Returns true if an object with the given key is stored in this SpacialIndex2D.
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.
EXPANDCONTRACT - Enum constant in enum class org.cytoscape.group.CyGroupSettingsManager.DoubleClickAction
expanded() - Method in interface org.cytoscape.util.swing.BasicCollapsiblePanel.CollapseListener
ExpandGroupTaskFactory - Interface in org.cytoscape.task.edit: This interface provides a task iterator expanding a group from a node view.
ExportNetworkImageTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting networks as image.
ExportNetworkTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting network views.
ExportNetworkViewTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting network views.
ExportSelectedNetworkTaskFactory - Interface in org.cytoscape.task.write
ExportSelectedTableTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting the current table.
ExportTableTaskFactory - Interface in org.cytoscape.task.write: This task factory provides a task iterator for writing a specified table to a specified file.
ExportVizmapTaskFactory - Interface in org.cytoscape.task.write: This interface provides a task iterator for exporting the vizmap visual style.
extensions - Variable in class org.cytoscape.io.BasicCyFileFilter

F

FAILED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
FAILED - Enum constant in enum class org.cytoscape.work.FinishStatus.Type: Indicates that the task iterator did not complete because one of its tasks failed by throwing an exception.
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.
FINISHED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
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 Class 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.
FIT_CONTENT - Static variable in interface org.cytoscape.view.presentation.NetworkImageFactory: If true the network will be automatically centered and scaled to fit inside the image bounds.
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.
FLOAT - Enum constant in enum class org.cytoscape.application.swing.CytoPanelState: The CytoPanel will be open and appear as a separate frame independent of the application.
FLOAT - Enum constant in enum class org.cytoscape.equations.ArgType: An argument that can be converted to a floating point value.
FLOAT_CONSTANT - Enum constant in enum class org.cytoscape.equations.Token.Type
FLOATS - Enum constant in enum class org.cytoscape.equations.ArgType: An non-empty sequence of arguments that consist of lists of floating point numbers and scalars that can be converted to a floating point number.
flushPayloadEvents() - Method in interface org.cytoscape.event.CyEventHelper: Forces accumulated payload events to be fired.
flushPayloadEvents(Object) - Method in interface org.cytoscape.event.CyEventHelper: Forces accumulated payload events to be fired.
FONTFAMILY - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font family
FONTSIZE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font size
FONTSTYLE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Arg string to set the font style
FontVisualProperty - Class in org.cytoscape.view.presentation.property: Visual Property for Font values.
FontVisualProperty(Font, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.FontVisualProperty: Constructor.
forceShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent: Returns true if we want to force the shutdown without any user prompt
FOREGROUND - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation: The foreground canvas
format() - Element in annotation interface org.cytoscape.work.Tunable: Provides a decimal format string suitable for DecimalFormat.
FORMAT - Static variable in class org.cytoscape.work.AbstractTunableHandler
FORMAT_RANGE - Static variable in class org.cytoscape.view.presentation.property.table.CellFormatVisualProperty
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(String, String, Class<? extends T>) - Method in interface org.cytoscape.model.CyRow: Returns the value found for this row in the specified column with the specified type.
get(String, 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(K, double[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D: Retrieves the extents of the rectangle with the given key.
get(K, float[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D: Retrieves the extents of the rectangle with the given key.
get_ApplyPreferredLayoutTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Returns an instance of UnHideAllTaskFactory.
getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction
getAcceleratorKeyStroke() - Method in interface org.cytoscape.application.swing.CyAction: Returns the accelerator KeyStroke defined for this action.
getActionListener() - Method in class org.cytoscape.work.swing.util.UserAction
getAdjacentEdgeIterable(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns an Iterable that contains the edges that are adjacent (connected) to the given node.
getAdjacentEdgeIterable(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Gets an Iteable of edges that connect to this node.
getAdjacentEdgeIterable(View<CyNode>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns an Iterable that contains the edges that are adjacent (connected) to the given 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() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators.
getAggregators(Class<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators for a particular Class.
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.AbstractVisualLexicon
getAllHandles() - Method in interface org.cytoscape.view.presentation.property.values.Bend: Get List of all handles on this edge
getAllLayouts() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Returns a collection of all available layouts.
getAllPoints() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets all Data Points.
getAllRenderingEngines() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Get all RenderingEngines registered in this manager.
getAllRows() - Method in interface org.cytoscape.model.CyTable: Return a list of all the rows stored in this data table.
getAllTables(boolean) - Method in interface org.cytoscape.model.CyTableManager: Returns a Set of all tables with the specified visibility.
getAllValues() - Method in interface org.cytoscape.jobs.CyJobData: Return all of the values in this CyJobData
getAllValues() - Method in interface org.cytoscape.model.CyRow: Returns a map of fully-qualified column names to Objects that contain the values contained in this Row.
getAllViews() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns a list of all View including those for Nodes, Edges, and Network.
getAllVisualLexicon() - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager: Returns a Set of all VisualLexicons.
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.AbstractVisualLexicon
getAllVisualPropertyDependencies() - Method in interface org.cytoscape.view.vizmap.VisualStyle: Get all dependencies for this style.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager: Returns all available VisualStyles managed by this object.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Returns all available VisualStyles managed by this object.
getAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the anchor of the label (or other object).
getAnchorType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the anchor type for one end of the arrow
getAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Retrieve the list of annotations for a specific network view.
getAppConfigurationDirectoryLocation(Class<?>) - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns the absolute path to the configuration directory of a particular app.
getAppFileListMap() - Method in class org.cytoscape.session.CySession: Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.
getAppFileListMap() - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent: This method is not meant to be used by listeners for this event, although you can and no harm should come to you.
getArea() - Method in class org.cytoscape.view.layout.LayoutPartition
getArgAsBoolean(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
getArgAsDouble(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgAsLong(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
getArgAsString(Object) - Static method in class org.cytoscape.equations.FunctionUtil: Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
getArgDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the description field for this argument.
getArgExampleStringValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the defaultStringValue field for this argument.
getArgLongDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the longDescription field for this argument.
getArgMap() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the argument map that is used to serialize this annotation.
getArgName() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the name of the argument.
getArgNumber() - Method in exception org.cytoscape.equations.FunctionError: Returns the argument number the error is associated with.
getArgRequired(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the required field for this argument.
getArgTooltip(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the value of the tooltip field for this argument.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
getArgType(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the type of the argument.
getArgTypeString(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a human-readable string for this argument of the form: argument=<type>
getArgumentDescriptors() - Method in class org.cytoscape.equations.AbstractFunction: Returns the usage descriptions for the function's arguments.
getArgumentDescriptors() - Method in interface org.cytoscape.equations.Function: Returns the usage descriptions for the function's arguments.
getArguments(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of arguments for the specified namespace and command in alphabetical order.
getArgValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands: Deprecated.
getArrowColor(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the color of one end of the arrow
getArrows() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get all arrows that are currently linked to this annotation.
getArrowSize(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the size of one end of the arrow
getArrowType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Get the type of one end of the arrow
getAttribute(DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Given the attribute name, return the value in a bookmark
getAttributeSelectors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns set of selector for available attributes (table columns).
getAvailableCommands() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of AvailableCommands.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyPropertyWriterManager: Returns the CyFileFilters known to this CyWriter manager.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyWriterManager: Returns a list of the available CyFileFilters that define the available output types.
getAverageLocation() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the average location of the nodes in this partition
getBaseNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: The initial network of CyNodes and CyEdges.
getBooleans(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of booleans.
getBorderColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) color.
getBorderOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) opacity.
getBorderWidth() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the border (stroke) width.
getBounds() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Returns the bounds of the annotation.
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 java.awt.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".
getBypassValues() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
getBypassValues() - Method in class org.cytoscape.view.model.table.CyRowViewMetadata
getBypassValues() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
getCanvasName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Return the canvas that this Annotation is on
getCategory(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Select specific category from a list of categories.
getCategoryName() - Method in interface org.cytoscape.equations.Function: Used to provide help for users.
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
getCellVisualProperty(VisualProperty<? extends T>) - Method in interface org.cytoscape.view.model.table.CyColumnView
getChangeSources() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
getChangeSources() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChildKey() - Method in class org.cytoscape.work.AbstractTunableHandler
getChildKey() - Method in interface org.cytoscape.work.TunableHandler: Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildren() - Method in class org.cytoscape.view.model.VisualLexiconNode: Returns collection of all children of this node.
getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation
getCode() - Method in class org.cytoscape.equations.Equation: Returns the compiled code (not Java byte code!) for the VM representing this Equation.
getColor() - Method in class org.cytoscape.util.swing.ColorButton
getColorPaletteChooser(PaletteType, boolean) - Method in interface org.cytoscape.util.swing.CyColorPaletteChooserFactory
getColors() - Method in interface org.cytoscape.util.color.Palette: Return the palette as an array of colors
getColors(int) - Method in interface org.cytoscape.util.color.Palette: Return the palette as an array of colors of the requested length.
getColumn() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the name of the column of the data that was set.
getColumn(String) - Method in interface org.cytoscape.model.CyTable: Returns the column with the specified fully-qualified name.
getColumn(String, String) - Method in interface org.cytoscape.model.CyTable: Returns the column for the specified name in the specified namespace.
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() - Method in class org.cytoscape.model.events.ColumnDeletedEvent: Returns the fully-qualified name of the column for this event.
getColumnName() - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifier
getColumnName(int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the name for column number column.
getColumnName(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the column name at the given column number.
getColumnNames(CyTable) - Static method in class org.cytoscape.model.CyTableUtil: Returns all the column names of a given table.
getColumnPresentation(String) - Method in interface org.cytoscape.application.swing.CyColumnPresentationManager: Returns a CyColumnPresentation for the given namespace.
getColumnRecords(String) - Method in class org.cytoscape.model.events.RowsSetEvent: Returns all of the RowSetRecords whose specified column value is set.
getColumns() - Method in interface org.cytoscape.model.CyTable: Returns the column types for all columns in this table.
getColumns() - Method in class org.cytoscape.model.events.RowsSetEvent: Returns a unmodifiable Set of the names of the columns that are contained in this event.
getColumns(String) - Method in interface org.cytoscape.model.CyTable: Returns the column types for all columns in this table in the given namespace.
getColumnView() - Method in class org.cytoscape.view.model.events.AboutToRemoveColumnViewEvent
getColumnView() - Method in class org.cytoscape.view.model.events.AddedColumnViewEvent
getColumnView() - Method in class org.cytoscape.view.vizmap.events.table.ColumnVisualStyleSetEvent: Get the The target column view model.
getColumnView(long) - Method in interface org.cytoscape.view.model.table.CyTableView: Returns the View for the specified column using its view SUID as key.
getColumnView(String) - Method in interface org.cytoscape.view.model.table.CyTableView: Returns the View for a specified column.
getColumnView(CyColumn) - Method in interface org.cytoscape.view.model.table.CyTableView: Returns the View for a specified column.
getColumnViews() - Method in interface org.cytoscape.view.model.table.CyTableView: Returns all column views in this table view, in the same order as CyTable.getColumns().
getColumnViews() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
getCommandExecutorTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CommandExecutorTaskFactory which can be used to execute commands.
getCommands(String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of available commands in alphabetical order for the specified namespace.
getCompatibleTypes() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the types that are compatible with this argument.
getCompatibleTypes() - Method in enum class org.cytoscape.equations.ArgType: Returns an array of compatible Class types.
getComponent() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the Component to be added to the CytoPanel.
getComponent() - Method in interface org.cytoscape.application.swing.ToolBarComponent: Returns the Component to be added to the ToolBar.
getComponentAt(int) - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the component at the passed index.
getCompositeFilter() - Method in interface org.cytoscape.filter.model.SubFilterTransformer
getConfiguration(TaskFactory, Object) - Method in interface org.cytoscape.work.TaskManager: Returns a configuration object generated from the Tunables read from the TaskFactory.
getConfigurationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns absolute path to CytoscapeConfiguration location.
getConnectingEdgeList(CyNode, CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Get the list of edges that connect two nodes.
getContentPane() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel: This class requires that all content be placed within a designated panel, this method returns that panel.
getContentTypes() - Method in class org.cytoscape.io.BasicCyFileFilter
getContentTypes() - Method in interface org.cytoscape.io.CyFileFilter: The MIME content types supported by this filter.
getContext() - Method in class org.cytoscape.work.AbstractTunableHandler: This returns the context of the Tunable.
getContextType() - Method in interface org.cytoscape.filter.model.Transformer: Returns the type of the context object this Transformer is compatible with.
getContextType() - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the type of the context object this TransformerSource is compatible with.
getContinuousEditor(VisualProperty<?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns the continuous editor for the specified visual property.
getContinuousEditorType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getContinuousEditorType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns type of Continuous Editor.
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: A custom cell renderer for Continuous table cells.
getControl() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
getCoreProperties() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyProperty of type Properties.
getCurrentDirectory() - Method in interface org.cytoscape.application.CyApplicationManager: Get the current working directory.
getCurrentNetwork() - Method in interface org.cytoscape.application.CyApplicationManager: Provides access to the current network.
getCurrentNetworkView() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the current network view.
getCurrentNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the NetworkViewRenderer associated with the current RenderingEngine.
getCurrentRenderingEngine() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the rendering engine associated with the current network view.
getCurrentSession() - Method in interface org.cytoscape.session.CySessionManager: This method returns a CySession object describing the current state of Cytoscape.
getCurrentSessionFileName() - Method in interface org.cytoscape.session.CySessionManager: Returns the name of the current session file.
getCurrentTable() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the currently active table.
getCurrentVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Returns currently selected Visual Style.
getCyApplicationConfiguration() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.
getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Returns an instance of CyTableWriterManager.
getCytoPanel() - 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.
getCytoPanel(CytoPanelName) - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the appropriate CytoPanel for the specified compass direction.
getCytoPanelComponentCount() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the number of components in the CytoPanel.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the position in the layout.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the name of the CytoPanel that this component should be added to.
getCyVersion() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of CyVersion.
getData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Extract data from a CyJobData object.
getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter
getDataCategory() - Method in interface org.cytoscape.io.CyFileFilter: The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.datasource.DataSource: DataCategory of this data.
getDataCategory() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getDataInstance() - Method in interface org.cytoscape.jobs.CyJobDataService: Returns an empty instance of CyJobData that may be used with this service.
getDataService() - Method in interface org.cytoscape.jobs.CyJobExecutionService: Return the CyJobDataService that is used by service to marshall and unmarshall data for the remote service.
getDataSourceList(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Traverse bookmark tree and get a list of data sources from the specified category.
getDataSourceManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of DataSourceManager.
getDataSources(String) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data sources from a data provider
getDataSources(DataCategory) - Method in interface org.cytoscape.io.datasource.DataSourceManager: Returns all data sources under the given category.
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.
getDefaultTableViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the TableViewRenderer that should be used to create CyTableViews.
getDefaultTableVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Provide default table VisualLexicon from a default engine factory.
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 network VisualLexicon from a default engine factory.
getDefaultVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager: Return default VisualStyle.
getDegree() - Method in class org.cytoscape.view.layout.LayoutNode: Return the node's degree (i.e.
getDependency() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
getDependency() - Method in interface org.cytoscape.work.swing.GUITunableHandler: Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDepth() - Method in class org.cytoscape.view.layout.LayoutNode: Return the height of this node
getDepth() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total depth of all of the LayoutNodes
getDescription() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getDescription() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An optional short text describing what this search provider does.
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor: Returns the description of the argument.
getDescription() - Method in class org.cytoscape.io.BasicCyFileFilter
getDescription() - Method in interface org.cytoscape.io.CyFileFilter: A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.datasource.DataSource: Description for this data.
getDescription() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getDescription() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getDescription() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Get human-readable description of this client.
getDescription() - Method in class org.cytoscape.util.swing.FileChooserFilter: Returns the short description of the acceptable file type.
getDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
getDescription() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's description.
getDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the description of the specified command in the specified namespace.
getDesktopViewAreaSize() - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr: Deprecated.
This method has been deprecated in version 3.4.
getDialogTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Deprecated.

Returns an instance of DialogTaskManager.
getDisabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Get set of Visual Properties to be disabled in the lexicon.
getDiscreteTableCellRenderer() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getDiscreteTableCellRenderer() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: A custom cell renderer for Discrete table cells.
getDisplayName() - Method in enum class org.cytoscape.io.DataCategory
getDisplayName() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getDisplayName() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Returns display name of this client.
getDisplayName() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getDisplayName() - Method in interface org.cytoscape.view.model.VisualProperty: Returns a short string suitable for presentation to humans.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Display name is a simple description of this image object.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Return the CyCustomGraphics2 name which is will be displayed to the user.
getDisplayName() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
getDisplayName() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue: Name of this value type.
getDisplayName() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Provides human-readable name of this dependency.
getDisplayNames() - Static method in enum class org.cytoscape.view.presentation.property.values.Position: Return a sorted list containing all of the display names for all of the Position anchors.
getDoubleClickAction() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current default CyGroupSettingsManager.DoubleClickAction.
getDoubleClickAction(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current CyGroupSettingsManager.DoubleClickAction for the specified group.
getDoubles(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of doubles.
getEdge() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the Edge this LayoutEdge represents
getEdge(long) - Method in interface org.cytoscape.model.CyNetwork: Return the CyEdge that has the SUID.
getEdgeCount() - Method in interface org.cytoscape.model.CyNetwork: Return the number of edges in this network.
getEdgeCount() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the number of edges in the network view.
getEdgeInfo(View<CyEdge>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns an object that provides more information about the given edge.
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.
getEdgeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a edgelist into a list of CyEdges.
getEdges() - Method in class org.cytoscape.group.events.GroupEdgesRemovedEvent: Returns the list of edges associated with this event.
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(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the immutable edge View for the given view SUID.
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.
getEdgeViewsIterable() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns an Iterable for all edge views in the network.
getEditingRow() - Method in class org.cytoscape.util.swing.JTreeTable: Returns the row being edited.
getElementCount(C) - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the number of elements that could be produced from the given context.
getElementList(C) - Method in interface org.cytoscape.filter.model.TransformerSource: Returns a List of elements from the given context.
getElementType() - Method in interface org.cytoscape.filter.model.Transformer: Returns the type of the elements this Transformer is compatible with.
getElementType() - Method in interface org.cytoscape.filter.model.TransformerSource: Returns the type of the elements this TransformerSource is compatible with.
getEnableAttributeAggregation() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not we're enabling aggregation.
getEnableAttributeAggregation(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not we're enabling aggregation for a specific group.
getEnabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent: Get set of Visual Properties to be enabled in the lexicon.
getEnabled() - Method in class org.cytoscape.work.swing.util.UserAction
getEnd() - Method in class org.cytoscape.equations.Token
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.
getErrorLocation() - Method in interface org.cytoscape.equations.EquationCompiler: If compile() failed, this will return the index in the equation where the error was encountered.
getErrorLocation() - Method in interface org.cytoscape.equations.EquationParser: If parse() failed, this will return the index in the equation where the error was encountered.
getErrorMsg() - Method in interface org.cytoscape.equations.EquationParser: If parse() failed, this will return the last error messages.
getExampleJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns a valid JSON string representative of the expected JSON output of the command.
getExampleStringValue() - Method in class org.cytoscape.work.AbstractTunableHandler
getExampleStringValue() - Method in interface org.cytoscape.work.TunableHandler: Returns the exampleStringValue property of the associated Tunable.
getException() - Method in class org.cytoscape.session.events.SessionLoadCancelledEvent: Deprecated.
getException() - Method in class org.cytoscape.session.events.SessionSaveCancelledEvent
getException() - Method in class org.cytoscape.work.FinishStatus: Returns the exception thrown by the task that failed, or null if the task iterator succeeded or was cancelled.
getExtension(String) - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a string of the characters following the last '.' in the input string, which is to say the file extension assuming that the input string represents a file name.
getExtensions() - Method in class org.cytoscape.io.BasicCyFileFilter
getExtensions() - Method in interface org.cytoscape.io.CyFileFilter: Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in class org.cytoscape.util.swing.FileChooserFilter: Returns an array of the extensions associated with this FileChooserFilter.
getExternalEdgeList() - Method in interface org.cytoscape.group.CyGroup: Returns the list of exterior edges connected to the nodes within this group.
getFactories() - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager: Returns all available factories.
getFactory(Class<?>) - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager: Factory for the specific mapping type.
getFile(Component, String, int, String, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, 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, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
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, 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.
getFillColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the fill color.
getFillOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Return the fill opacity, a value between 0.0 (fully transparent) and 100.0 (fully opaque).
getFitRatio() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Get the fit ratio for this custom graphic.
getFolder(Component, String, String) - Method in interface org.cytoscape.util.swing.FileUtil: Returns a File object representing a folder, this method should be used instead of rolling your own JFileChooser.
getFont() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font being used
getFont() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font being used
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font family to be used for the text display
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font family to be used for the text display
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the size of the font used to display the text
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the size of the font used to display the text
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the font style
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the font style
getFormat() - Method in class org.cytoscape.view.presentation.property.table.CellFormat
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 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() - Method in class org.cytoscape.group.events.GroupAddedEvent
getGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Return the group the corresponds to a particular node in a CyNetwork.
getGroupNetwork() - Method in interface org.cytoscape.group.CyGroup: Returns the network referenced by this group.
getGroupNode() - Method in interface org.cytoscape.group.CyGroup: Return the CyNode that represents this group in the network.
getGroups() - Method in class org.cytoscape.work.AbstractTunableHandler
getGroups() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's groups or nesting hierarchy.
getGroupSet(CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Provides the set of all the groups known to the groups manager in a particular network.
getGroupsForNode(CyNode) - Method in interface org.cytoscape.group.CyGroupManager: Return the list of CyGroups this node is in.
getGroupsForNode(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager: Return the list of CyGroups this node is in for a particular network.
getGroupViewType() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current default CyGroupSettingsManager.GroupViewType.
getGroupViewType(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the current CyGroupSettingsManager.GroupViewType for the specified group.
getHandler(String) - Method in interface org.cytoscape.view.vizmap.gui.event.VizMapEventHandlerManager: Returns handler for the event.
getHandlers(Object) - Method in class org.cytoscape.work.AbstractTunableInterceptor: Returns a list of TunableHandler objects that have been found to process the fields and methods annotated with Tunable.
getHeader(InputStream, int) - Method in class org.cytoscape.io.BasicCyFileFilter: Returns a string containing the specified number of lines from the beginning of the file.
getHeight() - Method in class org.cytoscape.view.layout.LayoutNode: Return the height of this node
getHeight() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total height of all of the LayoutNodes
getHeight() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Returns height of current object.
getHelpBroker() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpBroker.
getHelpSet() - Method in interface org.cytoscape.application.swing.CyHelpBroker: Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpSet.
getIcon() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the Icon to be used along with the title in the tab for this this component.
getIcon() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getIcon() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An icon that represents this search provider.
getIcon() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: An icon that represents this AnnotationFactory.
getIcon(int, int) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
getIcon(String) - Method in interface org.cytoscape.util.swing.IconManager
getIconFont(float) - Method in interface org.cytoscape.util.swing.IconManager: Returns the font that renders the text as an icon.
getIconFont(String, float) - Method in interface org.cytoscape.util.swing.IconManager
getIconHeight() - Method in class org.cytoscape.util.swing.TextIcon
getIconWidth() - Method in class org.cytoscape.util.swing.TextIcon
getId() - Method in interface org.cytoscape.application.NetworkViewRenderer
getId() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getId() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Returns the unique id of this network search provider.
getId() - Method in interface org.cytoscape.application.TableViewRenderer
getId() - Method in interface org.cytoscape.filter.model.Transformer: Returns the unique id of this type of Transformer.
getId() - Method in interface org.cytoscape.filter.model.TransformerFactory: Returns the unique id of the Transformer produced by this factory.
getId() - Method in interface org.cytoscape.filter.view.TransformerViewFactory: Returns the unique id of the Transformer this factory produces views for.
getId() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: Returns the unique id of the AnnotationFactory implementation.
getId() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Return the prefix to identify this Custom Graphics factory.
getIdentifier() - Method in interface org.cytoscape.application.swing.CytoPanelComponent2: Returns this component's identifier, which should be unique.
getIdentifier() - Method in interface org.cytoscape.util.color.Palette: Return the internal identifier of this palette.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the edge's identifier.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutNode: Return the node's identifier.
getIdentifier() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Immutable session-unique identifier of this custom graphic generated by the custom graphics manager.
getIdString() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getIdString() - Method in interface org.cytoscape.view.model.VisualProperty: Returns a short string used to identify this visual property and suitable for serializing to XML and other text formats.
getIdString() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Provides serializable string of this dependency.
getImage() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the image currently assigned to this annotation.
getImageBrightness() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the brightness adjustment for this image.
getImageContrast() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the contrast adjustment for this image.
getImageOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the current opacity of the image.
getImageURL() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Get the URL for the image to be displayed.
getImportedObject() - Method in class org.cytoscape.io.webservice.events.DataImportFinishedEvent: Returns the object that was imported.
getIndex() - Method in class org.cytoscape.view.layout.LayoutNode: Returns the index of this LayoutNode.
getIndex(Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend: Get index of a Handle
getIndexOfChild(Object, Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel: Returns the index of a child given a parent.
getInfoColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
getInputStream(String) - Method in interface org.cytoscape.io.util.StreamUtil: Gets the input stream from given a string.
getInputStream(URL) - Method in interface org.cytoscape.io.util.StreamUtil: Gets the input stream from given URL.
getInstallationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration: Returns absolute path to Cytoscape installation directory location.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Get a new instance of a CyCustomGraphics2.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Get a new instance of the CyCustomGraphics.
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(Map<String, Object>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Get a new instance of a CyCustomGraphics2 with the passed properties.
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.
getInternalEdgeList() - Method in interface org.cytoscape.group.CyGroup: Returns the list of edges contained within this group.
getJFrame() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JFrame that contains the application.
getJMenu(String) - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JMenu for the specified name and null if no menu exists for the name.
getJMenuBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JMenuBar object for the application.
getJobDataService() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobDataService() - Method in interface org.cytoscape.jobs.CyJob: Return the CyJobDataService that was used to create this job.
getJobExecutionService() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobExecutionService() - Method in interface org.cytoscape.jobs.CyJob: Return the CyJobExecutionService that created this job.
getJobId() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobId() - Method in interface org.cytoscape.jobs.CyJob: Return the ID for this job.
getJobMonitor() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobMonitor() - Method in interface org.cytoscape.jobs.CyJob: Return the service that handles status changes for this job.
getJobName() - Method in class org.cytoscape.jobs.AbstractCyJob
getJobName() - Method in interface org.cytoscape.jobs.CyJob: Return the name for this job
getJobs() - Method in interface org.cytoscape.jobs.CyJobManager: Return the list of CyJobs currently managed by the CyJobManager.
getJPanel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns the panel associated with this GUITunableHandler.
getJPanel() - Method in interface org.cytoscape.work.swing.GUITunableHandler: To get the panel that contains the GUI representation (JTextField, JFileChooser, JLabel, JList ...)
getJSON() - Method in interface org.cytoscape.work.json.JSONResult
getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the JToolBar object for the application.
getJustify() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the justification of the label (or other object).
getKeys() - Method in class org.cytoscape.model.events.RowsDeletedEvent: Returns the primary keys of the rows for this event.
getKeyValue() - Method in class org.cytoscape.view.model.table.CyRowViewMetadata
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.
getLayers(CyTableView, CyColumnView, CyRow) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
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.
getLayoutAttribute(CyLayoutAlgorithm, CyNetworkView) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager: Returns the attribute name that has been associated with the layout, or the empty string if there is no valid attribute associated to the layout for the given view.
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 class org.cytoscape.equations.Token
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.
getList(String, String, Class<T>) - Method in interface org.cytoscape.model.CyRow: Returns a list which is a view on the underlying column value for this row.
getList(String, 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() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of aggregators for List columns.
getListAggregators(Class<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager: Get the list of List aggregators for a particular Class.
getListElementType() - Method in interface org.cytoscape.model.CyColumn: Returns the data type of the list elements if the column type is List.class otherwise null.
getListenerClass() - Method in class org.cytoscape.event.AbstractCyEvent: The Class of the listener that is expected to handle this event.
getListenerClass() - Method in interface org.cytoscape.event.CyEvent: The Class of the listener that is expected to handle this event.
getListeners() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the list of listeners that will listen for changes to this object
getListeners() - Method in class org.cytoscape.work.util.ListSelection: Returns the list of listeners that will listen for changes to this object
getLoadedFileName() - Method in class org.cytoscape.session.events.SessionLoadedEvent: Returns the file name of the session just loaded.
getLoadedSession() - Method in class org.cytoscape.session.events.SessionLoadedEvent: Returns the session that was just loaded.
getLocalTables(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyTableManager: Returns set of all local tables for the given data type.
getLocation() - Method in interface org.cytoscape.io.datasource.DataSource: Location of this data file.
getLocation() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getLogWeight() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the current value for this edge's logWeight (-log(weight)).
getLongDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
getLongDescription() - Method in interface org.cytoscape.work.TunableHandler: Returns the associated Tunable's longDescription
getLongDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns the longDescription of the specified command in the specified namespace.
getLongs(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Attempts to convert all arguments, including Lists to a uniform array of longs.
getLowerBound() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the lower limit of the object.
getMajorVersion() - Method in interface org.cytoscape.application.CyVersion: The first of the three numbers defining the version of the software, meaning "3" if the version is "3.2.5".
getMapData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService: Extract a map from a CyJobData object.
getMappedColumns() - Method in interface org.cytoscape.view.presentation.property.values.MappableVisualPropertyValue
getMappedValue(CyRow) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns the mapped value for a CyRow.
getMappingColumnName() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getMappingColumnName() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns attribute name used in this mapping.
getMappingColumnType() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
getMappingColumnType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction: Returns data type of mapping attribute.
getMappingFunctionSelector() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager: Returns selector for Mapping Type.
getMappingFunctionType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory: Returns the type of this VisualMappingFunctionFactory.
getMapValue(K) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping: Gets Value for Specified Key.
getMatchingFactory(CyFileFilter) - Method in interface org.cytoscape.io.write.CyWriterManager: Returns a CyWriterFactory for the appropriate filter.
getMatchingKeys(String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable: Returns all the keys of a specified column that match the given value.
getMatchingKeys(String, String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable: Returns all the keys of a specified column that match the given value.
getMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable: Returns all the rows of a specified column that contain a certain value for that column.
getMatchingRows(String, String, Object) - Method in interface org.cytoscape.model.CyTable: Returns all the rows of a specified column that contain a certain value for that column.
getMax() - Method in class org.cytoscape.view.model.ContinuousRange: Returns the maximum value of this range.
getMaxX() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum X location of all of the LayoutNodes
getMaxY() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum Y location of all of the LayoutNodes
getMaxZ() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the maximum Z location of all of the LayoutNodes
getMBR(double[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D: Returns the "Minimum Bounding Rectangle", the smallest rectangle that contains all the objects stored in this SpacialIndex2D.
getMBR(float[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D: Returns the "Minimum Bounding Rectangle", the smallest rectangle that contains all the objects stored in this SpacialIndex2D.
getMembers() - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation: Return the list of members for this group
getMenu() - Method in interface org.cytoscape.util.swing.GravityTracker: Returns the JPopupMenu or JMenu that this gravity tracker tracks.
getMenu() - Method in class org.cytoscape.util.swing.MenuGravityTracker
getMenu() - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
getMenuGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
getMenuGravity() - Method in interface org.cytoscape.application.swing.CyAction: Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in class org.cytoscape.application.swing.CyMenuItem: Returns the gravity used to place the menu item in a menu.
getMenuItem() - Method in class org.cytoscape.application.swing.CyMenuItem: Returns the menu item to be placed in a menu according to the specified menu gravity.
getMessage() - Method in class org.cytoscape.jobs.CyJobStatus: Return any message associated with the job status.
getMin() - Method in class org.cytoscape.view.model.ContinuousRange: Returns the minimum value of this range.
getMinorVersion() - Method in interface org.cytoscape.application.CyVersion: The second of the three numbers defining the version of the software, meaning "2" if the version is "3.2.5".
getMinX() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum X location of all of the LayoutNodes
getMinY() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum Y location of all of the LayoutNodes
getMinZ() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the minimum Z location of all of the LayoutNodes
getModel() - Method in interface org.cytoscape.view.model.View: Get source data structure, such as CyNode, CyEdge, etc.
getModelSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the SUID of the underlying model object.
getModelSUID() - Method in interface org.cytoscape.view.model.SnapshotNodeInfo: Returns the SUID of the underlying model object.
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!
getMutableEdgeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the mutable edge View for the given view SUID, or null if the edge view no longer exists in the mutable network view.
getMutableNetworkView() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the mutable CyNetworkView that was used to create this snapshot.
getMutableNodeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the mutable node View for the given view SUID, or null if the node view no longer exists in the mutable network view.
getName() - Method in class org.cytoscape.application.swing.AbstractCyAction
getName() - Method in interface org.cytoscape.application.swing.CyAction: Returns the name of the action.
getName() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getName() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: A short name to be displayed to the user.
getName() - Method in 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 class org.cytoscape.jobs.CyJobStatus.Status
getName() - Method in interface org.cytoscape.model.CyColumn: Returns the fully-qualified name of the column.
getName() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Returns the name of the CyProperty.
getName() - Method in interface org.cytoscape.property.CyProperty: Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.SimpleCyProperty: Returns the name of the CyProperty.
getName() - Method in interface org.cytoscape.util.color.Palette: Return the name of this palette.
getName() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getName() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns the computer-readable name of the layout.
getName() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
getName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the name for this annotation.
getName() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory: A short name to be displayed to the user.
getName() - Method in enum class org.cytoscape.view.presentation.property.values.Justification: Return the display name of this justification type.
getName() - Method in enum class org.cytoscape.view.presentation.property.values.Position: Return the display name of this anchor position.
getName() - Method in class org.cytoscape.work.AbstractTunableHandler
getName() - Method in interface org.cytoscape.work.TunableHandler: Returns a name representing a tunable property.
getNamedTransformer(String) - Method in interface org.cytoscape.filter.TransformerContainer: Returns the transformer with the given name, or null if a transformer with the given name does not exist in this container.
getNamedTransformers() - Method in interface org.cytoscape.filter.TransformerContainer: Returns the list of transformers contained in this container.
getNameOnly() - Method in interface org.cytoscape.model.CyColumn: Returns the name portion without the namespace.
getNameOnly() - Method in class org.cytoscape.model.events.ColumnDeletedEvent: Returns the name portion without the namespace.
getNameOnly() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the name portion without the namespace.
getNames() - Static method in enum class org.cytoscape.view.presentation.property.values.Justification: Return the display names for all of the Justifcation values
getNamespace() - Method in interface org.cytoscape.model.CyColumn: Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in interface org.cytoscape.model.CyTableMetadata: Returns the namespace used as the key to this object's table in CyNetworkTableManager.getTables(org.cytoscape.model.CyNetwork, java.lang.Class<? extends org.cytoscape.model.CyIdentifiable>).
getNamespace() - Method in class org.cytoscape.model.events.ColumnDeletedEvent: Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
getNamespaceDescription() - Method in interface org.cytoscape.application.swing.CyColumnPresentation: Returns a String description of the namespace.
getNamespaceIcon() - Method in interface org.cytoscape.application.swing.CyColumnPresentation: Returns an icon associated with the namespace.
getNamespaces() - Method in interface org.cytoscape.command.AvailableCommands: Returns a list of available command namespaces in alphabetical order.
getNamespaces() - Method in interface org.cytoscape.model.CyTable: Returns all the namespaces used in the table.
getNeighborList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork: Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.
getNeighbors() - Method in class org.cytoscape.view.layout.LayoutNode: Convenience function to return the list of neighbors (connected nodes) of this node.
getNetwork() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent: Returns the network associated with this event.
getNetwork() - 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() - Method in class org.cytoscape.group.events.GroupCollapsedEvent
getNetwork() - Method in interface org.cytoscape.model.CyTableMetadata: Returns all the networks associated with this object's table.
getNetwork() - Method in class org.cytoscape.model.events.UnsetNetworkPointerEvent: Returns the CyNetwork for this event.
getNetwork() - Method in class org.cytoscape.model.events.NetworkAddedEvent
getNetwork() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns the CyNetwork event source.
getNetwork(long) - Method in interface org.cytoscape.model.CyNetworkManager: Returns the network corresponding to the provided ID
getNetwork(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a network into a CyNetwork.
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 class org.cytoscape.view.model.events.NetworkViewAddedEvent
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.
getNetworkView(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a network view into a CyNetworkView.
getNetworkViewFactory() - Method in interface org.cytoscape.application.NetworkViewRenderer
getNetworkViewFactory() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
getNetworkViewRenderer(String) - Method in interface org.cytoscape.application.CyApplicationManager: Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.
getNetworkViewRendererList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
getNetworkViewRendererSet() - Method in interface org.cytoscape.application.CyApplicationManager: Returns a set with all the NetworkViewRenderer objects that have been registered.
getNetworkViews() - Method in class org.cytoscape.application.events.SetSelectedNetworkViewsEvent: Returns the list of network views that have been selected.
getNetworkViews() - Method in class org.cytoscape.session.CySession: Returns a set of all CyNetworkView objects contained in this Session.
getNetworkViews(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Returns a collection of network views corresponding to the specified network, if found.
getNetworkViewSet() - Method in interface org.cytoscape.view.model.CyNetworkViewManager: Provides the set of network views that are currently known to the network manager.
getNewColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the new name of the column.
getNewNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the name name portion without the namespace.
getNewNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the new namespace of the column, or null if the column does not have a namespace.
getNewProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: The new properties after being modified.
getNewState() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent: Returns the new state of the CytoPanel.
getNextSUID() - Static method in class org.cytoscape.model.SUIDFactory: Returns the next available SUID.
getNode() - Method in class org.cytoscape.model.events.UnsetNetworkPointerEvent: Returns the CyNode for this event.
getNode() - Method in class org.cytoscape.view.layout.LayoutNode: Accessor function to return the Node associated with this LayoutNode.
getNode(long) - Method in interface org.cytoscape.model.CyNetwork: Return the CyNode that has the SUID.
getNodeCount() - Method in interface org.cytoscape.model.CyNetwork: Return the number of nodes in this network.
getNodeCount() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the number of nodes in the network view.
getNodeInfo(View<CyNode>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns an object that provides more information about the given node.
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.
getNodeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a nodelist into a list of CyNodes.
getNodeMap() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader: Returns map from key value to existing CyNode.
getNodes() - Method in class org.cytoscape.group.events.GroupNodesRemovedEvent: Returns the list of nodes associated with this event.
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(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the immutable node View for the given view SUID.
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.
getNodeViewsIterable() - Method in interface org.cytoscape.view.model.CyNetworkView: Returns an Iterable for all node views in the network.
getNumTasks() - Method in class org.cytoscape.work.TaskIterator: Returns the current total number of tasks in the iterator.
getObject(Long, Class<T>) - Method in class org.cytoscape.session.CySession: When a session is restored, Cytoscape automatically generates new SUIDs.
getObject(String, Class<T>) - Method in class org.cytoscape.session.CySession: When a session is restored, Cytoscape automatically generates new SUIDs.
getOffsetX() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the X offset of the object
getOffsetY() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the Y offset of the object
getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old name of the column.
getOldNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old name portion without the namespace.
getOldNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent: Returns the old namespace of the column, or null if the column did not have a namespace.
getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent: The old properties before they were modified.
getOldTitle() - Method in class org.cytoscape.model.events.TableTitleChangedEvent
getOptionsComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: This implementation simply returns null, which means that no options component will be displayed, unless the subclass overwrites this method to return a custom component.
getOptionsComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: You can use this method to return a component that contains extra search parameters.
getOrdinal(int) - Static method in class org.cytoscape.equations.FunctionUtil: Converts an integer to an ordinal string.
getOverrideAggregation(CyGroup, CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the override aggregation setting for a column (if any) in a specific group.
getOverrideAggregation(CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the override aggregation setting for a column (if any).
getPaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Paint to fill the shape with.
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
getPalette() - Method in class org.cytoscape.util.swing.ColorButton
getPalette(Object) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its internal identifier
getPalette(Object, int) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its internal identifier
getPalette(String) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette by its name
getPalette(String, int) - Method in interface org.cytoscape.util.color.PaletteProvider: Get a palette of the specified size by its name
getPaletteProvider() - Method in interface org.cytoscape.util.color.Palette: Return the PaletteProvider for this palette.
getPaletteProvider(String) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the palette provider that matches the name in the argument.
getPaletteProviders() - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the list of currently registered palette providers
getPaletteProviders(PaletteType, boolean) - Method in interface org.cytoscape.util.color.PaletteProviderManager: Return the list of currently registered palette providers that provide palettes of the requested type.
getPaletteTypes() - Method in interface org.cytoscape.util.color.PaletteProvider: Return the list of org.cytoscape.util.color.Palette.PaletteTypes supported by this provider
getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter: Deprecated.

Returns an instance of PanelTaskManager.
getParams() - Method in class org.cytoscape.work.AbstractTunableHandler
getParams() - Method in interface org.cytoscape.work.TunableHandler: Returns the parsed result from Tunable.getParams().
getParent() - Method in class org.cytoscape.view.model.VisualLexiconNode: Get the parent of this VP node.
getParent() - Method in interface org.cytoscape.work.swing.TunableUIHelper: Get the parent of the current Tunable dialog.
getParentVisualProperty() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: Returns the parent visual property for this dependency.
getParser() - Method in interface org.cytoscape.equations.EquationCompiler: Returns the parser which can be used for checking the syntax of equations.
getParseTree() - Method in interface org.cytoscape.equations.EquationParser: Returns the parse tree.
getPartitionNumber() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the partition number of this partition
getPath() - Method in class org.cytoscape.jobs.AbstractCyJob
getPath() - Method in interface org.cytoscape.jobs.CyJob: Return the base path for communicating with the remote service for this job
getPayloadCollection() - Method in class org.cytoscape.event.AbstractCyPayloadEvent: Returns an unmodifiable collection of payload objects.
getPayloadCollection() - Method in interface org.cytoscape.event.CyPayloadEvent: Returns a collection of payload objects.
getPoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets Specified Point.
getPointCount() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping: Gets Total Point Count.
getPollInterval() - Method in class org.cytoscape.jobs.AbstractCyJob
getPollInterval() - Method in interface org.cytoscape.jobs.CyJob: Return the time in seconds between calls to checkJobStatus.
getPossibleArgTypes(Class[]) - Method in class org.cytoscape.equations.AbstractFunction: Used with the equation builder.
getPossibleArgTypes(Class<?>[]) - Method in interface org.cytoscape.equations.Function: Used with the equation builder.
getPossibleValues() - Method in class org.cytoscape.work.util.ListSelection: To get all the items of the List values.
getPreferredMenu() - Method in class org.cytoscape.application.swing.AbstractCyAction
getPreferredMenu() - Method in interface org.cytoscape.application.swing.CyAction: This method returns a Menu specification string.
getPreferredSize() - Method in class org.cytoscape.util.swing.DropDownMenuButton
getPrefix() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Return the prefix to identify this custom graphics factory.
getPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit: Returns a human-readable description of this edit that will be used in logs and other descriptions of the edit.
getPresentationWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of PresentationWriterManager.
getPrimaryKey() - Method in interface org.cytoscape.model.CyTable: Returns the column type of the primary key for this table.
getPrimaryKeyListElementType() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
getPrimaryKeyType() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
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: Note: This is NOT the correct way for Apps to access CyProperty settings.
getProperties() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2: Provides an optional map of key/value properties which define the custom graphics instance.
getProperties() - Method in interface org.cytoscape.view.presentation.RenderingEngine: Get property values for the rendering engine, like LOD.
getProperty() - Method in interface org.cytoscape.io.read.CyPropertyReader: Return a property object.
getPropertyEditor() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getPropertyEditor() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns PropertyEditor object for this data type.
getPropertyEditor(VisualProperty<T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor2: Returns PropertyEditor object for this data type.
getPropertyType() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader: Returns the type of the property object.
getPropertyType() - Method in interface org.cytoscape.property.CyProperty: Returns the type of the property object.
getPropertyType() - Method in class org.cytoscape.property.SimpleCyProperty: Returns the type of the property object.
getProvider() - Method in interface org.cytoscape.io.datasource.DataSource: Name of this data provider for this source.
getProvider() - Method in class org.cytoscape.io.datasource.DefaultDataSource
getProvider(DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil: Get the provider name from DataSource object
getProviderName() - Method in interface org.cytoscape.util.color.PaletteProvider: Return the human-readable string identifier for this PaletteProvider.
getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler
getQualifiedName() - Method in interface org.cytoscape.work.TunableHandler: Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifier() - Method in interface org.cytoscape.application.CyVersion: Any text following the last digit of the bug fix version.
getQuery() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getQueryBuilderGUI() - Method in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient: Returns query builder UI.
getQueryBuilderGUI() - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUIClient: Returns query builder UI.
getQueryComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory: This implementation simply returns null, which means Cytoscape will provide a default query component, unless the subclass overwrites this method to return a custom component.
getQueryComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: Use this method to return a component that contains the main or mandatory search fields.
If this task factory provides its own query component, make sure the returned JComponent fires a PropertyChangeEvent for the property NetworkSearchTaskFactory.QUERY_PROPERTY whenever its fields change in a way that affects the return of the TaskFactory.isReady() method.
getRange() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getRange() - Method in interface org.cytoscape.view.model.VisualProperty: Returns the Range of this VisualProperty.
getRange() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Gets BoundaryRangeValues.
getRaw(String) - Method in interface org.cytoscape.model.CyRow: Returns the Object that contains the value for the specified column.
getRaw(String, String) - Method in interface org.cytoscape.model.CyRow: Returns the Object that contains the value for the specified column.
getRawValue() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the raw value that the data was set as.
getReader(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(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(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(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(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.
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(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(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(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(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.
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.model.table.CyTableView: 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.
getRendererID() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
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
getRenderingEngineFactory(String) - Method in interface org.cytoscape.application.TableViewRenderer
getRenderingEngineManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of RenderingEngineManager.
getRenderingEngines(View<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager: Get rendering engines for the given view model.
getRequired() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns true if this Tunable must be set (i.e.
getResultClasses() - Method in interface org.cytoscape.work.ObservableTask: Return the classes that can be used to query ObservableTask.getResults(Class)
getResults(Class<? extends R>) - Method in interface org.cytoscape.work.ObservableTask: Return the results from this task (if any)
getReturnType() - Method in 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() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork: Return the CyRootNetwork that contains this CySubNetwork.
getRootNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetworkManager: Converts a CyNetwork to a CyRootNetwork
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.AbstractVisualLexicon
getRotatedBounds() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Returns the bounds of the annotation, adjusted for rotation.
getRotation() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the rotation (in degrees) for this annotation
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.
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(CyIdentifiable) - Method in interface org.cytoscape.model.CyNetwork: A convenience method that returns the row in the default table for this object.
getRow(CyIdentifiable, String) - Method in interface org.cytoscape.model.CyNetwork: Returns the row for the specified table name for this object.
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.
getRowView(CyRow) - Method in interface org.cytoscape.view.model.table.CyTableView: Returns the View for the specified row.
getRowViews() - Method in interface org.cytoscape.view.model.table.CyTableView: Returns all row views in the table view.
getRowViews() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
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.
getSavedTableSUID() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
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.
getSelectedAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager: Retrieve the list of selected annotations for a specific network view.
getSelectedColor() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser: Return the Color the user selected
getSelectedColumnNames() - Method in class org.cytoscape.application.swing.CyColumnSelector: Returns the names of the CyColumns that have been selected.
getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the currently selected component.
getSelectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getSelectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the edges in the network that are currently selected.
getSelectedEdges(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil: Equivalent to
getSelectedIndex() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the currently selected index.
getSelectedIndex() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent: Returns the index of the CytoPanelComponent selected.
getSelectedItem() - Method in class org.cytoscape.application.swing.CyColumnComboBox: Override getSelectedItem() and use covariant return type to change return type to CyColumn.
getSelectedNetworks() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the list of selected networks.
getSelectedNetworkViews() - Method in interface org.cytoscape.application.CyApplicationManager: Returns the list of selected network views.
getSelectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getSelectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the nodes in the network that are currently selected.
getSelectedNodes(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil: Equivalent to
getSelectedPalette() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser: Return the palette the user selected
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(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>) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarImpl: 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.
getService(Class<S>, String) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarImpl: A method that attempts to get a service of the specified type and that passes the specified filter.
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(Bundle, ServiceRegistration) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarFactory
getServiceLocation() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
getServiceLocation() - Method in interface org.cytoscape.io.webservice.WebServiceClient: Returns resource location of this service, i.e., service URL.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobDataService: The name of the service.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobExecutionService: The name of the service.
getSession() - Method in interface org.cytoscape.io.read.CySessionReader: Returns a CySession object
getShape() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the current shape as a Shape object
getShape() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Shape
getShapeType() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation: Get the current shape type as a String
getSharedEdgeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the edge table shared by all subnetworks.
getSharedNetworkTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the network table shared by all subnetworks.
getSharedNodeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork: Returns the node table shared by all subnetworks.
getShortName() - Method in enum class org.cytoscape.view.presentation.property.values.Justification: Return the short name of this justification type
getShortName() - Method in enum class org.cytoscape.view.presentation.property.values.Position: Return the short name of this anchor position.
getSize() - Method in enum class 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.
getSourceNodeView() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the source node view;
getSourceTable() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the originating table for this column if this column is virtual.
getSourceViewSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the SUID of the source node view.
getSpacialIndex2D() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns an immutable NetworkSpacialIndex2D object that can be used to query the bounds of nodes in the network view, or null if the SpacialIndex has been turned off.
getSpecificZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Deprecated.
getStart() - Method in class org.cytoscape.equations.Token
getState() - Method in interface org.cytoscape.application.swing.CytoPanel: Gets the state of the CytoPanel.
getState() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler: Returns a string representation of the value of the Tunable associated with this GUITunableHandler.
getState() - Method in interface org.cytoscape.work.swing.GUITunableHandler: To get the current value of a Handler (or path for a FileHandler, or selected item(s) for ListMultipleSelection ListSingleSelection, ...)
getStatus() - Method in class org.cytoscape.jobs.CyJobStatus: Return the CyJobStatus.Status of the remote job
getStatusToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication: Returns the status JToolBar of the application.
getStreamUtil() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of StreamUtil.
getStrings(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil: Converts all arguments, including Lists to a uniform array of strings.
getStroke() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Stroke to use to outline the Shape provided by the PaintedShape.getShape() method above.
getStrokePaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape: Return the Paint to use to color the Stroke returned by PaintedShape.getStroke().
getStyleName() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
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.
getSUID() - Method in class org.cytoscape.model.events.ColumnDeletedEvent
getSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the view SUID of the edge view.
getSUID() - Method in interface org.cytoscape.view.model.SnapshotNodeInfo: Returns the view SUID of the node view.
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: Returns 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.
getSupportedTargetTypes() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory: Returns all the target types supported by this factory, usually CyNode and CyColumn.
getSupportedTargetTypes() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory: Returns all the target types supported by this factory, usually CyNode and CyColumn.
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.AbstractVisualLexicon
getSupportsJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands: Returns true if the command is expected to provide JSON output.
getSupportsSelectedOnly() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
getSupportsSelectedOnly() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm: Returns true if this algorithm supports being applied to only the currently selected nodes.
getSVG() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation: Return the SVG text currently assigned to this annotation.
getTable() - Method in class org.cytoscape.application.events.SetCurrentTableEvent
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() - Method in interface org.cytoscape.model.CyRow: Returns the CyTable that this row belongs to.
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.
getTable(long) - Method in interface org.cytoscape.model.CyTableManager: Returns the table with the specified SUID.
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(String) - Method in interface org.cytoscape.command.StringToModel: Convert a string request for a table into a CyTable.
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.
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() - Method in class org.cytoscape.session.CySession: Returns a set of all CyTable objects contained in this Session.
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.
getTableStyles() - Method in class org.cytoscape.session.CySession: Returns a set containing all table VisualStyles defined for this session.
getTableType() - Method in interface org.cytoscape.application.swing.TableToolBarComponent
getTableType(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager: Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.
getTableView() - Method in class org.cytoscape.view.model.events.TableViewAboutToBeDestroyedEvent
getTableView() - Method in class org.cytoscape.view.model.events.TableViewAddedEvent
getTableView(CyTable) - Method in interface org.cytoscape.view.model.table.CyTableViewManager: Returns the table view for the given table.
getTableViewFactory() - Method in interface org.cytoscape.application.TableViewRenderer
getTableViewRenderer(String) - Method in interface org.cytoscape.application.CyApplicationManager: Returns the TableViewRenderer that has the passed id or null if it doesn't exist.
getTableViewRendererSet() - Method in interface org.cytoscape.application.CyApplicationManager: Returns a set with all the TableViewRenderer objects that have been registered.
getTableViews() - Method in class org.cytoscape.session.CySession: Returns a set of all CyTableView objects contained in this Session.
getTableViewSet() - Method in interface org.cytoscape.view.model.table.CyTableViewManager: Returns all table views known to this manager.
getTableVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader: Returns a list of table VisualStyle objects.
getTarget() - Method in interface org.cytoscape.model.CyEdge: Returns the target node determining this edge.
getTarget() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the target of this edge
getTarget() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation: Return the target object for this arrow.
getTargetAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition: Return the anchor of the target (e.g.
getTargetColumnList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
getTargetDataType() - Method in class org.cytoscape.view.model.AbstractVisualProperty
getTargetDataType() - Method in interface org.cytoscape.view.model.VisualProperty: VisualProperty is always associated with a data type.
getTargetJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo: Returns the name of the column from the target table used for the join.
getTargetNodeView() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the target node view;
getTargetObjectType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ListEditor: Type of object managed by this editor.
getTargetViewSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo: Returns the SUID of the target node view.
getTask() - Method in class org.cytoscape.work.FinishStatus: Returns the task that was cancelled or that had failed, or returns null if the task iterator succeeded.
getTaskIterator() - Method in class org.cytoscape.work.AbstractTask
getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of TaskManager.
getTaskObserver() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getTaskObserver() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: If you want to be notified when the search task is finished, you should return a TaskObserver here.
getText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the text to be displayed as part of the annotation
getText() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the text to be displayed as part of the annotation
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation: Get the color of the text to be displayed
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation: Get the color of the text to be displayed
getThisComponent() - Method in interface org.cytoscape.application.swing.CytoPanel: Returns the Component that is this CytoPanel.
getTitle() - Method in interface org.cytoscape.application.swing.CytoPanelComponent: Returns the title of the tab within the CytoPanel for this component.
getTitle() - Method in enum class 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.
getTokenIterator(String) - Method in interface org.cytoscape.equations.EquationTokeniser: Returns an iterator of Token objects.
getTokenList(String) - Method in interface org.cytoscape.equations.EquationTokeniser: Returns a list of Token objects.
getToolbarGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
getToolbarGravity() - Method in interface org.cytoscape.application.swing.CyAction: 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.ToolBarComponent: Returns the gravity used to place this component in the toolbar.
getTooltip() - Method in class org.cytoscape.work.AbstractTunableHandler: Returns the tooltip annotation for this Tunable if there is one.
getToolTipImage() - Method in class org.cytoscape.application.swing.AbstractCyAction
getToolTipImage() - Method in interface org.cytoscape.application.swing.CyAction: Optional image to be displayed in the target component's tool tip.
getToolTipText(MouseEvent) - Method in class org.cytoscape.util.swing.JTreeTable: The code in this method is copy and pasted from source code to the same method in javax.swing.JTable, except for one value change on one line.
getTrackedEdgeCount(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the number of edges that are being tracked using the given key.
getTrackedEdges(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns edges that were configured to have their VisualProperties tracked using CyNetworkViewFactoryConfig.addTrackedVisualProperty(Object, VisualProperty, java.util.function.Predicate) and pass the predicate.
getTrackedNodeCount(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the number of nodes that are being tracked using the given key.
getTrackedNodes(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns nodes that were configured to have their VisualProperties tracked using CyNetworkViewFactoryConfig.addTrackedVisualProperty(Object, VisualProperty, java.util.function.Predicate) and pass the predicate.
getTransformers() - Method in interface org.cytoscape.filter.model.NamedTransformer: Returns the List of Transformers contained within this NamedTransformer.
getTransformerSource(Class<C>) - Method in interface org.cytoscape.filter.TransformerManager: Returns a TransformerSource for the given contextType.
getTranslatedValueType() - Method in interface org.cytoscape.view.vizmap.mappings.ValueTranslator: Returns compatible input data type.
getTree() - Method in class org.cytoscape.util.swing.JTreeTable: Returns the tree that is being shared between the model.
getTunableHandler() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
getTunableMutator() - Method in class org.cytoscape.work.AbstractTaskManager: Returns the TunableMutator for this TaskManager or null if there is none.
getTunableMutator() - Method in interface org.cytoscape.work.TaskManager: This method returns the TunableMutator that is being used by this TaskManager.
getTunablePropertySerializerFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of TunablePropertySerializerFactory.
getType() - Method in class org.cytoscape.equations.AbstractNode
getType() - Method in class org.cytoscape.equations.Equation: The overall type of the Equation, e.g.
getType() - Method in interface org.cytoscape.equations.EquationParser: Returns the result type of the parsed equation if the parse succeeded, otherwise null.
getType() - Method in class org.cytoscape.equations.IdentDescriptor: Returns the, possibly adjusted, type of the descriptor as one of the types internally supported by equations.
getType() - Method in class org.cytoscape.equations.Token
getType() - Method in interface org.cytoscape.equations.TreeNode: Returns the type of this node.
getType() - Method in interface org.cytoscape.filter.model.CompositeFilter: Returns the type of combining semantics used by this filter.
getType() - Method in interface org.cytoscape.model.CyColumn: Returns the data type of the column.
getType() - Method in interface org.cytoscape.model.CyTableMetadata: Returns the type of the data associated with this object's table.
getType() - Method in interface org.cytoscape.util.color.Palette: This is the type of the palette, using the Cynthia Brewer's classification.
getType() - Method in class org.cytoscape.view.layout.EdgeWeighter
getType() - Method in class org.cytoscape.view.model.ContinuousRange
getType() - Method in class org.cytoscape.view.model.DiscreteRange
getType() - Method in interface org.cytoscape.view.model.Range: Type of object used in this range.
getType() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
getType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
getType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor: Returns the type of object managed in the Visual property.
getType() - Method in class org.cytoscape.work.AbstractTunableHandler
getType() - Method in class org.cytoscape.work.FinishStatus: Specifies how the task iterator completed.
getType() - Method in interface org.cytoscape.work.TunableHandler: Returns the class type of the field or method annotated by Tunable.
getTypes() - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
getTypes() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
getTypes() - Method in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
getUnderlyingTable() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
getUndoableEditSupport() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport: Returns the UndoableEditSupport associated with this UndoSupport instance.
getUndoManager() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport: Returns the UndoManager associated with this UndoSupport instance.
getUndoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit: Returns a human-readable description of this edit that will be used in undo menu items.
getUndoSupport() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of UndoSupport.
getUnqualifiedName(Class<?>) - Static method in class org.cytoscape.equations.EquationUtil: Returns the unqualified name of the given class
getUnselectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getUnselectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the edges in the network that are currently unselected.
getUnselectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
getUnselectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent: Returns all the nodes in the network that are currently unselected.
getUpperBound() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the upper limit of the object.
getURLConnection(URL) - Method in interface org.cytoscape.io.util.StreamUtil: Obtain a URLConnection for a given URL.
getUsageDescription() - Method in class org.cytoscape.equations.AbstractFunction: Used to provide help for users.
getUsageDescription() - Method in interface org.cytoscape.equations.Function: Used to provide help for users.
getUseNestedNetworks() - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the default setting for whether or not to create a nested network view on collapsed nodes.
getUseNestedNetworks(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager: Get the setting for whether or not to create a nested network view on collapsed nodes for the specified CyGroup.
getUUID() - Method in interface org.cytoscape.view.presentation.annotations.Annotation: Get the UUID of this annotation
getValidationState(Appendable) - Method in interface org.cytoscape.work.TunableValidator: Executes the validation test on the annotated Tunables.
getValue() - Method in class org.cytoscape.command.util.EdgeList: Return the edgeList for this tunable
getValue() - Method in class org.cytoscape.command.util.NodeList: Get the list of nodes
getValue() - Method in class org.cytoscape.command.util.RowList: Get the list of rows
getValue() - Method in class org.cytoscape.equations.IdentDescriptor: Returns the value of the descriptor.
getValue() - Method in class org.cytoscape.model.events.RowSetRecord: Returns the value that the data was set as.
getValue() - Method in class org.cytoscape.view.model.events.ViewChangeRecord: Returns the value that the visual property has been changed to.
getValue() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint: Gets Point Value.
getValue() - Method in class org.cytoscape.work.AbstractTunableHandler
getValue() - Method in interface org.cytoscape.work.TunableHandler: Returns an object describing a field / get method annotated with Tunable or null if no field / get method has been associated with this handler.
getValue() - Method in class org.cytoscape.work.util.AbstractBounded: Returns the value.
getValueAt(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter: Returns the value at the given row and column.
getValueAt(Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel: Returns the value to be displayed for node node, at column number 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".
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.
getViewDefault(VisualProperty<T>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot: Returns the default value of the VisualProperty that was set using CyNetworkView.setViewDefault(VisualProperty, 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.AbstractVisualLexicon
getVisualMappingFunction(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle: Get current VisualMappingFunction for the VisualProperty.
getVisualMappingFunctionContinuousFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

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

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

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

Returns an instance of VisualMappingManager.
getVisualProperties() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency: A set of Visual Properties to be set by the parent if locked.
getVisualProperty() - Method in class org.cytoscape.view.model.events.ViewChangeRecord: Returns the visual property that has been changed.
getVisualProperty() - 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.
getVisualProperty(VisualProperty<T>) - Method in interface org.cytoscape.view.model.View: Get the actual value for the given visual property.
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.table.ColumnVisualStyleSetEvent: Get the VisualStyle that was set to the column view.
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.
getVisualStyle(View<CyColumn>) - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager: Returns the VisualStyle associated with the target column view model.
getVisualStyleAdded() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent: Get the newly created VisualStyle.
getVisualStyleFactory() - Method in interface org.cytoscape.app.CyAppAdapter: Deprecated.

Returns an instance of VisualStyleFactory.
getVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader: Returns a list of network VisualStyle objects.
getVisualStyles() - Method in class org.cytoscape.session.CySession: Returns a set containing all network VisualStyles defined for this session.
getVisualStyleToBeRemoved() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent: Returns target VisualStyle to be removed from manager.
getWarnColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
getWarning() - Method in class org.cytoscape.filter.model.ValidationWarning
getWebsite() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
getWebsite() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory: An optional URL the user can use to find more information about this search provider.
getWeight() - Method in class org.cytoscape.view.layout.LayoutEdge: Return the current value for this edge's weight.
getWidth() - Method in class org.cytoscape.view.layout.LayoutNode: Return the width of this node
getWidth() - Method in class org.cytoscape.view.layout.LayoutPartition: Return the total width of all of the LayoutNodes
getWidth() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics: Returns width of current object.
getWindow(Class<?>) - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUI: Returns the Window that contains the unified web service UI.
getWriter(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(Set<VisualStyle>, 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>, 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.
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.
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(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 interf