Cytoscape 3.1.0 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.
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
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
AbstractBounded<N extends Comparable<N>> - Class in org.cytoscape.work.util
A bounded number object whose bounds values cannot be modified
AbstractBounded(N, N, N, boolean, boolean) - Constructor for class org.cytoscape.work.util.AbstractBounded
Creates a new Bounded object.
AbstractCellEditor - Class in org.cytoscape.util.swing
An abstract, convenience implementation of a Cell Editor that really only adds event listener support.
AbstractCellEditor() - Constructor for class org.cytoscape.util.swing.AbstractCellEditor
 
AbstractConfigDirPropsReader - Class in org.cytoscape.property
An abstract implementation of CyProperty<Properties> that attempts to read the specified properties file first from the jar file running this code and then appends any properties found in the local configuration directory to that properties object.
AbstractConfigDirPropsReader(String, String, CyProperty.SavePolicy) - Constructor for class org.cytoscape.property.AbstractConfigDirPropsReader
Creates a new AbstractConfigDirPropsReader object.
AbstractCyAction - Class in org.cytoscape.application.swing
An abstract implementation of the CyAction interface.
AbstractCyAction(String) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object that is always enabled.
AbstractCyAction(String, CyApplicationManager, String, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object that is enabled for the specific "enableFor" state.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyActivator - Class in org.cytoscape.service.util
A simple BundleActivator with convenience methods for registering OSGi services and either getting references to single services or registering interest in all services of a specified type.
AbstractCyActivator() - Constructor for class org.cytoscape.service.util.AbstractCyActivator
Constructor.
AbstractCyApp - Class in org.cytoscape.app
The primary app interface for Cytoscape that all apps must extend.
AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp
The constructor that all apps must call using "super(adapter);" where the "adapter" is a CyAppAdapter reference provided as an argument to the constructor.
AbstractCyEdit - Class in org.cytoscape.work.undo
A small class used to create new undoable edits.
AbstractCyEdit(String) - Constructor for class org.cytoscape.work.undo.AbstractCyEdit
Constructor.
AbstractCyEvent<T> - Class in org.cytoscape.event
A base implementation of CyEvent that can be used by events.
AbstractCyEvent(T, Class<?>) - Constructor for class org.cytoscape.event.AbstractCyEvent
Constructor.
AbstractCyNetworkReader - Class in org.cytoscape.io.read
 
AbstractCyNetworkReader(InputStream, CyNetworkViewFactory, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
 
AbstractCyPayloadEvent<T,P> - Class in org.cytoscape.event
A base implementation of CyPayloadEvent that can be used by events.
AbstractCyPayloadEvent(T, Class<?>, Collection<P>) - Constructor for class org.cytoscape.event.AbstractCyPayloadEvent
Constructor.
AbstractCySwingApp - Class in org.cytoscape.app.swing
The primary Swing-based app interface for Cytoscape that all Swing-based apps must extend.
AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp
The constructor that all apps must call using "super(adapter);" where the "adapter" is a CySwingAppAdapter reference provided as an argument to the constructor.
AbstractEdgeViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on an edge view and possibly its associated network view.
AbstractEdgeViewTask(View<CyEdge>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractEdgeViewTask
Base constructor for all tasks that need an edge view to operate on.
AbstractEdgeViewTaskFactory - Class in org.cytoscape.task
An EdgeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractEdgeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractEdgeViewTaskFactory
 
AbstractFunction - Class in org.cytoscape.equations
Base class for all Function implementations.
AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction
Base class constructor for easy creation of Functions from function argument descriptors.
AbstractGUITunableHandler - Class in org.cytoscape.work.swing
Base class for the various Swing implementations of TunableHandler.
AbstractGUITunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractGUITunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractInputStreamTaskFactory - Class in org.cytoscape.io.read
TODO: Missing documentation
AbstractInputStreamTaskFactory(CyFileFilter) - Constructor for class org.cytoscape.io.read.AbstractInputStreamTaskFactory
 
AbstractLayoutAlgorithm - Class in org.cytoscape.view.layout
The AbstractLayoutAlgorithm provides a basic implementation of a layout TaskFactory.
AbstractLayoutAlgorithm(String, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutAlgorithm
The Constructor.
AbstractLayoutTask - Class in org.cytoscape.view.layout
This is a basic implementation of a LayoutAlgorithm Task that does some bookkeeping, but primarily delegates to the doLayout() method.
AbstractLayoutTask(String, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutTask
Constructor.
AbstractNetworkCollectionTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a Collection of CyNetworks.
AbstractNetworkCollectionTask(Collection<CyNetwork>) - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTask
Base Constructor for a task that will operate on a collection of networks
AbstractNetworkCollectionTaskFactory - Class in org.cytoscape.task
An NetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTaskFactory
 
AbstractNetworkTask - Class in org.cytoscape.task
Base class for all tasks that need to operate on a CyNetwork.
AbstractNetworkTask(CyNetwork) - Constructor for class org.cytoscape.task.AbstractNetworkTask
Base class for tasks that need to operate on a CyNetwork
AbstractNetworkTaskFactory - Class in org.cytoscape.task
A NetworkTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkTaskFactory
 
AbstractNetworkViewCollectionTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a Collection of CyNetworkViews.
AbstractNetworkViewCollectionTask(Collection<CyNetworkView>) - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTask
Base class for any tasks that need to operate on a collection of network views.
AbstractNetworkViewCollectionTaskFactory - Class in org.cytoscape.task
A NetworkViewCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory
 
AbstractNetworkViewLocationTaskFactory - Class in org.cytoscape.task
A base class for task factories that need to add a functionality to the network view considering a given location (for example adding a node where a mouse was clicked).
AbstractNetworkViewLocationTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory
 
AbstractNetworkViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a network view.
AbstractNetworkViewTask(CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNetworkViewTask
A base class for tasks that need to operate on a network view.
AbstractNetworkViewTaskFactory - Class in org.cytoscape.task
A NetworkViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewTaskFactory
 
AbstractNode - Class in org.cytoscape.equations
A node in the parse tree.
AbstractNode(int) - Constructor for class org.cytoscape.equations.AbstractNode
Base class constructor for any Node type.
AbstractNodeViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTask(View<CyNode>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNodeViewTask
Base class constructor for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTaskFactory - Class in org.cytoscape.task
A NodeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNodeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNodeViewTaskFactory
 
AbstractPartitionLayoutTask - Class in org.cytoscape.view.layout
This is a more helpful implementation of a LayoutAlgorithm Task that extends AbstractBasicLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Creates a new AbstractPartitionLayoutTask object.
AbstractRowTask - Class in org.cytoscape.task
Base class for all tasks that need to operate on a CyRow.
AbstractRowTask(CyRow) - Constructor for class org.cytoscape.task.AbstractRowTask
Base class constructor for all tasks that need to be provisioned with a CyRow.
AbstractStringTunableHandler - Class in org.cytoscape.command
 
AbstractStringTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
 
AbstractStringTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
 
AbstractTableCellTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on a single CyTable cell.
AbstractTableCellTask(CyColumn, Object) - Constructor for class org.cytoscape.task.AbstractTableCellTask
Initializes a Task that needs to operate on a CyTable cell entry.
AbstractTableCellTaskFactory - Class in org.cytoscape.task
A TableCellTaskFactory that is always ready to produce a TaskIterator.
AbstractTableCellTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableCellTaskFactory
 
AbstractTableColumnTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on an entire CyTable column.
AbstractTableColumnTask(CyColumn) - Constructor for class org.cytoscape.task.AbstractTableColumnTask
Initializes a Task that needs to operate on a CyTable column.
AbstractTableColumnTaskFactory - Class in org.cytoscape.task
A TableColumnTaskFactory that is always ready to produce a TaskIterator.
AbstractTableColumnTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableColumnTaskFactory
 
AbstractTableTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on an entire CyTable.
AbstractTableTask(CyTable) - Constructor for class org.cytoscape.task.AbstractTableTask
Initializes a Task that needs to operate on a CyTable.
AbstractTableTaskFactory - Class in org.cytoscape.task
A TableTaskFactory that is always ready to produce a TaskIterator.
AbstractTableTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableTaskFactory
 
AbstractTask - Class in org.cytoscape.work
A base class for tasks that need to be able to access the TaskIterator that contains them.
AbstractTask() - Constructor for class org.cytoscape.work.AbstractTask
 
AbstractTaskFactory - Class in org.cytoscape.work
A TaskFactory that is always ready to produce a TaskIterator.
AbstractTaskFactory() - Constructor for class org.cytoscape.work.AbstractTaskFactory
 
AbstractTaskManager<T,C> - Class in org.cytoscape.work
Provides access to a TunableInterceptor to all derived classes and a utility method to determine if an object has been annotated with Tunables.
AbstractTaskManager(TunableMutator) - Constructor for class org.cytoscape.work.AbstractTaskManager
Initializes an AbstractTaskManager object by setting its TunableInterceptor.
AbstractToolBarComponent - Class in org.cytoscape.application.swing
An abstract, convenience implementation of ToolBarComponent.
AbstractToolBarComponent() - Constructor for class org.cytoscape.application.swing.AbstractToolBarComponent
 
AbstractTransformer<C,E> - Class in org.cytoscape.filter.model
A convenience base class for Transformers.
AbstractTransformer() - Constructor for class org.cytoscape.filter.model.AbstractTransformer
Creates a new AbstractTransformer.
AbstractTreeTableModel - Class in org.cytoscape.util.swing
An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class org.cytoscape.util.swing.AbstractTreeTableModel
Creates a new AbstractTreeTableModel object.
AbstractTunableHandler - Class in org.cytoscape.work
Provides the standard implementation for most of the methods declared by the TunableHandler interface.
AbstractTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractTunableInterceptor<T extends TunableHandler> - Class in org.cytoscape.work
An abstract base class for TunableRecorder and TunableMutator implementations.
AbstractTunableInterceptor() - Constructor for class org.cytoscape.work.AbstractTunableInterceptor
Creates a new AbstractTunableInterceptor object.
AbstractViewUpdater<S> - Class in org.cytoscape.application.swing
A utility class that provides an implementation of RowsSetListener for a particular column and VisualProperty.
AbstractViewUpdater(VisualProperty<S>, String, Map<CyRow, View<?>>) - Constructor for class org.cytoscape.application.swing.AbstractViewUpdater
Constructor.
AbstractVisualMappingFunction<K,V> - Class in org.cytoscape.view.vizmap.mappings
A base class for visual mapping functions where all fields are immutable.
AbstractVisualMappingFunction(String, Class<K>, VisualProperty<V>, CyEventHelper) - Constructor for class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Constructs this AbstractVisualMappingFunction.
AbstractVisualProperty<T> - Class in org.cytoscape.view.model
An abstract implementation of VisualProperty that omits the methods dealing with serializing data.
AbstractVisualProperty(T, Range<T>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.model.AbstractVisualProperty
Constructor to set all immutable fields.
AbstractVisualPropertyEditor<T> - Class in org.cytoscape.view.vizmap.gui.editor
Abstract implementation of Visual Property Editor.
AbstractVisualPropertyEditor(Class<T>, PropertyEditor, ContinuousEditorType, ContinuousMappingCellRendererFactory) - Constructor for class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
Creates a new AbstractVisualPropertyEditor object.
AbstractVisualPropertyValue - Class in org.cytoscape.view.presentation.property.values
Base class for all VisualPropertyValue.
AbstractVisualPropertyValue(String, String) - Constructor for class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
Constructs an AbstractVisualPropertyValue.
AbstractWebServiceClient - Class in org.cytoscape.io.webservice.client
Abstract class for all web service clients.
AbstractWebServiceClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.client.AbstractWebServiceClient
Constructs this AbstractWebServiceClient.
AbstractWebServiceGUIClient - Class in org.cytoscape.io.webservice.swing
Abstract base class for web service clients with Swing GUI.
AbstractWebServiceGUIClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
Constructor.
ACCELERATOR - Static variable in interface org.cytoscape.work.ServiceProperties
Shortcut key combination for desktop app.
acceleratorKeyStroke - Variable in class org.cytoscape.application.swing.AbstractCyAction
The accelerator keystroke, if set.
acceleratorSet - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether accelerator keys have been set for the action.
accept(File) - Method in class org.cytoscape.util.swing.FileChooserFilter
Accept or not the file from JFileChooser.
accepts(C, E) - Method in interface org.cytoscape.filter.model.Filter
Returns true if this filter accepts the given element from context.
accepts(URI, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
accepts(InputStream, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
This method always returns false in this particular implementation.
accepts(URI, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter
A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
accepts(InputStream, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter
A method that attempts to determine whether the specified InputStream can be read by the Reader using this filter.
acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor
Returns true if this ArgDescriptor accepts multiple arguments, otherwise false.
acceptsMultipleArgs() - Method in enum org.cytoscape.equations.ArgType
Returns true if this type accepts multiple args.
ActionEnableSupport - Class in org.cytoscape.application.swing
A class that allows the enabled state of an Action of JMenuItem to managed in a consistent way.
ActionEnableSupport(DynamicSubmenuListener, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
ActionEnableSupport(Action, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
ActionEnableSupport(JMenuItem, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
actuallyShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent
Returns true if no reason is provided to abort the shutdown and false if anyone processing this event wants to prevent shutdown.
adapter - Variable in class org.cytoscape.app.AbstractCyApp
Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.
add(URL) - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Adds "newURL" to the list of recently opened file names and trims the list if it has exceeded its maximum length.
add(Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, Object) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, Object, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(String, Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
addAction(CyAction) - Method in interface org.cytoscape.application.swing.CySwingApplication
Add a CyAction to application.
addAggregator(Aggregator) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Add a new aggregator to the available aggregators.
addAnnotation(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Add an annotation to the specified network view.
addAppFiles(String, List<File>) - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent
A method that allows apps to specify a list of files that should be stored in the session.
addArrow(ArrowAnnotation) - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Add an arrow annotation to this annotation.
addBasicVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
Deprecated.
addBendFactory(BendFactory, Map<?, ?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
addCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
addChangeListener(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Adds the argument as a new dependency to this GUITunableHandler.
addChangeListener(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler
Adds a GUITunableHandler that listens to THIS tunable handler.
addDependent(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Adds the argument as a new dependency to this GUITunableHandler.
addDependent(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler
Adds a GUITunableHandler that depends on THIS tunable handler.
AddedEdgesEvent - Class in org.cytoscape.model.events
An event fired when an edge is added to a network.
AddedEdgesEvent(CyNetwork, Collection<CyEdge>) - Constructor for class org.cytoscape.model.events.AddedEdgesEvent
Constructs event.
AddedEdgesListener - Interface in org.cytoscape.model.events
Listener for AddedEdgesEvents.
AddedEdgeViewsEvent - Class in org.cytoscape.view.model.events
When edge View is added to a CyNetworkView, this event will be fired.
AddedEdgeViewsEvent(CyNetworkView, Collection<View<CyEdge>>) - Constructor for class org.cytoscape.view.model.events.AddedEdgeViewsEvent
Creates the event for new edge views.
AddedEdgeViewsListener - Interface in org.cytoscape.view.model.events
Listener for AddedEdgeViewsEvent.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.CyNetwork
This method is used to create and add an edge to this network.
addEdge(CyEdge) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Adds an edge to this CySubNetwork.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
A shortcut method that Creates a new CyEdge in both this subnetwork AND in the CyRootNetwork.
addEdge(CyEdge, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition
Add an edge to this partition assuming that the source and target nodes are not yet known.
addEdge(CyEdge, LayoutNode, LayoutNode, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition
Add an edge to this partition assuming that the source and target nodes are known.
addEdges(List<CyEdge>) - Method in interface org.cytoscape.group.CyGroup
Add a list of edges to a group.
AddedNodesEvent - Class in org.cytoscape.model.events
Event for upper layers.
AddedNodesEvent(CyNetwork, Collection<CyNode>) - Constructor for class org.cytoscape.model.events.AddedNodesEvent
Constructs event.
AddedNodesListener - Interface in org.cytoscape.model.events
Listener for AddedNodesEvents.
AddedNodeViewsEvent - Class in org.cytoscape.view.model.events
When node View is added to a CyNetworkView, this event will be fired.
AddedNodeViewsEvent(CyNetworkView, Collection<View<CyNode>>) - Constructor for class org.cytoscape.view.model.events.AddedNodeViewsEvent
Creates the event for a new node view.
AddedNodeViewsListener - Interface in org.cytoscape.view.model.events
Listener for AddedNodeViewsEvent.
addEventPayload(S, P, Class<E>) - Method in interface org.cytoscape.event.CyEventHelper
Adds a payload object to be accumulated in a CyPayloadEvent.
addGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager
Registers a group with the group manager.
addGroups(List<CyGroup>) - Method in interface org.cytoscape.group.CyGroupManager
Registers a list of groups with the group manager.
addGroupToNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Add a group to an additional network.
addIdentifierMapping(Class<?>, String, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
#ASKMIKE
addListener(TransformerListener) - Method in class org.cytoscape.filter.model.AbstractTransformer
 
addListener(TransformerListener) - Method in interface org.cytoscape.filter.model.Transformer
Subscribes the given listener to changes in this Transformer's parameters.
addListener(BoundedChangeListener<N>) - Method in class org.cytoscape.work.util.AbstractBounded
Adds a listener that will listen for changes to this object
addListener(ListChangeListener<T>) - Method in class org.cytoscape.work.util.ListSelection
Adds a listener that will listen for changes to this object
addMember(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation
Add a new annotation to the group
addMenu(JMenu, double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a new submenu into a position based on "gravity" of the new item.
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addMenuItem(JMenuItem, double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a new menu item into a position based on "gravity" of the new item.
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addMenuSeparator(double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a separator into a position based on "gravity" of the new item.
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addNeighbor(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
Convenience function to keep track of neighbors of this node.
addNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager
Registers a network with the network manager.
addNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Registers a network view with the network view manager.
addNode() - Method in interface org.cytoscape.model.CyNetwork
This method is used to create and add a node to this network.
addNode(CyNode) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Adds a node to this CySubNetwork.
addNode() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
A shortcut method that Creates a new CyNode in both this subnetwork AND in the CyRootNetwork.
addNode(CyNetwork, View<CyNode>, boolean) - Method in class org.cytoscape.view.layout.LayoutPartition
Add a node to this partition.
addNodes(List<CyNode>) - Method in interface org.cytoscape.group.CyGroup
Add a list of nodes and their edges
addNodes(LayoutNode, LayoutNode) - Method in class org.cytoscape.view.layout.LayoutEdge
Set the nodes associated with this edge.
addPoint(K, BoundaryRangeValues<V>) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Adds a New Data Point.
addRangeValue(T) - Method in class org.cytoscape.view.model.DiscreteRange
Add a value to this DiscreteRange.
addRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Add new RenderingEngine to this manager.
addScalarArgumentTypes(List<Class>) - Static method in class org.cytoscape.equations.FunctionUtil
Adds the scalar types that equations use internally to the argument, i.e.
addSubNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create an empty CySubNetwork.
addSubNetwork(SavePolicy) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create an empty CySubNetwork which can have a different save policy from that of this root network, as long as the root network's policy is not SavePolicy.DO_NOT_SAVE.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create a CySubNetwork containing the specified CyNodes and CyEdges.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>, SavePolicy) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create a CySubNetwork containing the specified CyNodes and CyEdges.
addTable(CyTable) - Method in interface org.cytoscape.model.CyTableManager
Registers a new table with the manager and fires a TableAddedEvent event.
addTreeModelListener(TreeModelListener) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
 
addTunableHandlerFactory(TunableHandlerFactory<T>, Map) - Method in class org.cytoscape.work.AbstractTunableInterceptor
Allows TunableHandlerFactory services to be added to the list of factories used to process Tunables.
addTunableRecorder(TunableRecorder, Map) - Method in class org.cytoscape.work.AbstractTaskManager
Adds the specified TunableRecorder service to the task manager.
addValueEditor(ValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Add value editor OSGi services.
addVirtualColumn(String, String, CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable
Adds a "virtual" column to the the current table.
addVirtualColumns(CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable
Adds all columns in another table as "virtual" columns to the the current table.
addVisualMappingFunction(VisualMappingFunction<?, ?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Add a new VisualMappingFunction to this VisualStyle.
addVisualProperty(VisualProperty<?>, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
Insert a VisualProperty to the tree.
addVisualPropertyDependency(VisualPropertyDependency<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
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.
adjustColumnPreferredWidths(JTable) - Static method in class org.cytoscape.util.swing.ColumnResizer
Adjust the columns in the table to their preferred widths.
aggregate(CyTable, CyGroup, CyColumn) - Method in interface org.cytoscape.group.data.Aggregator
Aggregate the column for the members of the specified group into the group.
Aggregator<T> - Interface in org.cytoscape.group.data
The Aggregator interface acts as a service interface for different methods of aggregating attribute data for the nodes in a CyGroup.
ALL_NODE_VIEWS - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithm
A convenience declaration for an empty set signifying that all node views should be laid out when creating the task iterator.
allFinished(FinishStatus) - Method in interface org.cytoscape.work.TaskObserver
Called by a TaskManager to tell us that the task iterator has completed.
AnalyzeNetworkCollectionTaskFactory - Interface in org.cytoscape.task.analyze
Provides a TaskIterator to analyze a collection of networks.
Annotation - Interface in org.cytoscape.view.presentation.annotations
This is the base interface for all Annotations.
AnnotationFactory<T extends Annotation> - Interface in org.cytoscape.view.presentation.annotations
An interface describing a factory used to create Annotations.
AnnotationManager - Interface in org.cytoscape.view.presentation.annotations
The annotation manager is responsible for managing all of the annotations currently assigned to a particular org.cytoscape.view.model.NetworkView.
append(Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter
Appends filter to the list of children.
append(Task) - Method in class org.cytoscape.work.TaskIterator
Adds the given task to the end of this iterator.
append(TaskIterator) - Method in class org.cytoscape.work.TaskIterator
Adds the tasks in the given TaskIterator to the end of this iterator.
appFileListMap(Map<String, List<File>>) - Method in class org.cytoscape.session.CySession.Builder
Returns an instance of Builder that has at least been configured with the specified app file list map.
The app name should follow the java class namespace convention (e.g.
apply(C, E, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.ElementTransformer
Transforms the given element.
apply(C, TransformerSource<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.HolisticTransformer
Transforms the elements in source from context.
apply(CyRow, View<? extends CyIdentifiable>) - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Apply mapping to the view model.
apply(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Apply Visual Style to the entire network view.
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Apply Visual Property values only to the given View Object (node or edge).
ApplyPreferredLayoutTaskFactory - Interface in org.cytoscape.task.visualize
This interface provides a task iterator for applying the preferred layout.
applyTunables(Object, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter
Applies each value from the key-value pairs in tunableValues to the tunable in the given object whose name matches the corresponding key.
ApplyVisualStyleTaskFactory - Interface in org.cytoscape.task.visualize
Marker interface which provides a task iterator for applying a visual style to views.
APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
Define standard context menus.
AppsFinishedStartingEvent - Class in org.cytoscape.app.event
An event that occurs when apps that are installed prior to launch have all successfully finished starting up.
AppsFinishedStartingEvent(Object) - Constructor for class org.cytoscape.app.event.AppsFinishedStartingEvent
Create a new event with the given source.
AppsFinishedStartingListener - Interface in org.cytoscape.app.event
Listener for the AppsFinishedStartingEvent.
ARBITRARY_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
ARBITRARY_STRING_RANGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
ArgDescriptor - Class in org.cytoscape.equations
A class describing a function argument.
ArgDescriptor(ArgType, String, String) - Constructor for class org.cytoscape.equations.ArgDescriptor
 
ArgType - Enum in org.cytoscape.equations
An enum specifying a function argument type.
argTypesAreValid(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
Returns true of false if the args passed in had arity of a type mismatch.
arrangeWindows(CyNetworkViewDesktopMgr.ArrangeType) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Request the desktop view manager to tile (or untile) the current network windows.
ARROW - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Pointy triangle shaped arrow
ArrowAnnotation - Interface in org.cytoscape.view.presentation.annotations
This is the interface for an arrow annotation.
ArrowAnnotation.AnchorType - Enum in org.cytoscape.view.presentation.annotations
This enum is used to indicate how the arrow is anchored to the source or target.
ArrowAnnotation.ArrowEnd - Enum in org.cytoscape.view.presentation.annotations
This enum is used to indicate which end of the arrow the operation is referring to.
ArrowShape - Interface in org.cytoscape.view.presentation.property.values
Marker interface representing edge end shape (arrow).
ArrowShapeVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for ArrowShape values.
ArrowShapeVisualProperty(ArrowShape, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Constructor.
attribNameAsReference(String) - Static method in class org.cytoscape.equations.EquationUtil
Converts a bare name to a variable reference.
Attribute - Class in org.cytoscape.property.bookmark
Java class for anonymous complex type.
Attribute() - Constructor for class org.cytoscape.property.bookmark.Attribute
 
attribute - Variable in class org.cytoscape.property.bookmark.DataSource
 
AttributeHandlingType - Enum in org.cytoscape.group.data
The AttributeHandlingType enum contains the list of all of the different ways that attributes can be aggregated.
AvailableCommands - Interface in org.cytoscape.command
TODO: Missing documentation

B

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

C

calcSampleVariance(double[]) - Static method in class org.cytoscape.equations.FunctionUtil
Calculates the sample variance of some numbers.
calculateEdgeWeights() - Method in class org.cytoscape.view.layout.LayoutPartition
Calculate and set the edge weights.
calculateHandleLocation(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.view.presentation.property.values.Handle
Calculate absolute position of this handle for the given edge view.
cancel() - Method in class org.cytoscape.work.AbstractTask
Calling this attempts to abort the current Task.
cancel() - Method in interface org.cytoscape.work.Task
This method is called by the TaskManager when the user chooses to cancel the Task.
cancelCellEditing() - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
 
cancelled - Variable in class org.cytoscape.work.AbstractTask
If this is true, we should abort whatever the Task is currently doing in the run() method.
CANVAS - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation
Arg map key to initialize the canvas to draw this annotation on
category - Variable in class org.cytoscape.io.BasicCyFileFilter
Type of data that this filter applies to.
category - Variable in class org.cytoscape.property.bookmark.Bookmarks
 
Category - Class in org.cytoscape.property.bookmark
Java class for anonymous complex type.
Category() - Constructor for class org.cytoscape.property.bookmark.Category
 
categoryOrDataSource - Variable in class org.cytoscape.property.bookmark.Category
 
changeOccurred(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
This is called when a GUITunableHandler that this tunable handler listens to makes a change.
changeOccurred(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler
This is called when a GUITunableHandler that this tunable handler listens to makes a change.
CheckBoxJList - Class in org.cytoscape.util.swing
This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 By Joshua Marinacci, Chris Adamson
CheckBoxJList() - Constructor for class org.cytoscape.util.swing.CheckBoxJList
Creates a new CheckBoxJList object.
checkDependency(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
To check the dependencies of this GUITunableHandler with the others.
checkDependency(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler
To check the dependencies of this GUITunableHandler with the others.
CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Circle shaped arrow
clamp(N) - Method in class org.cytoscape.work.util.AbstractBounded
Clamps the value of the Bounded object.
clamp(Double) - Method in class org.cytoscape.work.util.BoundedDouble
Clamp the value to be within the range.
clamp(Float) - Method in class org.cytoscape.work.util.BoundedFloat
Clamp the value to be within the range.
clamp(Integer) - Method in class org.cytoscape.work.util.BoundedInteger
Clamp the value to be within the range.
clamp(Long) - Method in class org.cytoscape.work.util.BoundedLong
Clamp the value to be within the range.
clearValueLock(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View
Clear value lock for given VisualProperty.
clearVisualProperties() - Method in interface org.cytoscape.view.model.View
Clear all VisualProperty values previously set to this view.
CloneNetworkTaskFactory - Interface in org.cytoscape.task.create
This interface provides a task iterator for network cloning.
CodeAndSourceLocation - Class in org.cytoscape.equations
Encapsulates compiled code with the location in the original source equation.
CodeAndSourceLocation(Object, int) - Constructor for class org.cytoscape.equations.CodeAndSourceLocation
 
collapse(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Collapse this group in the designated network.
collapsed() - Method in class org.cytoscape.group.events.GroupCollapsedEvent
Is the group collapsed or expanded?
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.
column - Variable in class org.cytoscape.task.AbstractTableCellTask
The CyColumn of the CyTable cell
column - Variable in class org.cytoscape.task.AbstractTableColumnTask
The CyColumn that descendants will operate on.
COLUMN_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers
The id of the core Column Filter, which finds nodes and edges based on their column values.
ColumnCreatedEvent - Class in org.cytoscape.model.events
This event signals that a column has been created.
ColumnCreatedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnCreatedEvent
Constructs event.
ColumnCreatedListener - Interface in org.cytoscape.model.events
Listener for ColumnCreatedEvents.
ColumnDeletedEvent - Class in org.cytoscape.model.events
This event signals that a column has been deleted.
ColumnDeletedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnDeletedEvent
Constructs event.
ColumnDeletedListener - Interface in org.cytoscape.model.events
Listener for ColumnDeletedEvents.
columnName - Variable in class org.cytoscape.application.swing.AbstractViewUpdater
The name of the column that the RowsSetListener is provided for.
columnName - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Mapping attribute name.
ColumnNameChangedEvent - Class in org.cytoscape.model.events
This event signals that a columns name has been changed.
ColumnNameChangedEvent(CyTable, String, String) - Constructor for class org.cytoscape.model.events.ColumnNameChangedEvent
Constructs event.
ColumnNameChangedListener - Interface in org.cytoscape.model.events
Listener for ColumnNameChangedEvents.
ColumnResizer - Class in org.cytoscape.util.swing
Automatically resize column based on the objects in the cell.
columnType - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Type of attribute.
COMMAND - Static variable in interface org.cytoscape.work.ServiceProperties
Name of command used by Command Executor
COMMAND_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties
Name space for a command
CommandExecutorTaskFactory - Interface in org.cytoscape.command
TODO: Missing documentation
compare(TunableHandler, TunableHandler) - Method in class org.cytoscape.work.TunableGravityOrderer
 
compareTo(LayoutEdge) - Method in class org.cytoscape.view.layout.LayoutEdge
 
compareTo(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
 
compareTo(VisualLexiconNode) - Method in class org.cytoscape.view.model.VisualLexiconNode
Compare by display name of this Visual Property.
compile(String, Map<String, Class<?>>) - Method in interface org.cytoscape.equations.EquationCompiler
Compiles a string to byte code plus some metadata as encapsulated by the Equation class
CompositeFilter<C,E> - Interface in org.cytoscape.filter.model
A Filter that computes the set-union or set-intersection of the Filters it contains.
CompositeFilter.Type - Enum in org.cytoscape.filter.model
Determines how a CompositeFilter combines the results of its contained Filters.
configurationProperties - Variable in class org.cytoscape.application.swing.AbstractCyAction
The configuration properties.
ConnectSelectedNodesTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for connecting selected nodes.
containsBookmarks(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Check if a bookmark is in the bookmarks.
containsColumn(String) - Method in class org.cytoscape.model.events.RowsSetEvent
Returns true if any of the changed records' column name is colName
containsDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Check if a DataSource already existed in the DataSourceManager
containsEdge(CyEdge) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains a particular edge.
containsEdge(CyNode, CyNode) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains an edge between two nodes.
containsNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns true if the network to be checked is a subnetwork of this root network and returns false otherwise.
containsNode(CyNode) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains a particular node.
ContainsTunables - Annotation Type in org.cytoscape.work
An annotation designed to signal that the annotated field contains fields and methods that are annotated with the Tunable annotation.
content - Variable in class org.cytoscape.property.bookmark.Attribute
 
contentTypes - Variable in class org.cytoscape.io.BasicCyFileFilter
 
CONTEXT - Static variable in class org.cytoscape.work.AbstractTunableHandler
 
CONTINUOUS - Static variable in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
A label string for this mapping.
ContinuousEditorType - Enum in org.cytoscape.view.vizmap.gui.editor
An enum describing the possible types of continuous editors.
ContinuousMapping<K,V> - Interface in org.cytoscape.view.vizmap.mappings
An interface describing a continuous mapping from attribute value to visual property.
ContinuousMappingCellRendererFactory - Interface in org.cytoscape.view.vizmap.gui.editor
A factory for creating TableCellRenderers for a particular ContinuousMappingEditor.
ContinuousMappingEditor<K extends Number,V> - Interface in org.cytoscape.view.vizmap.gui.editor
A basic interface used to display continuous mapping editors.
ContinuousMappingPoint<K,V> - Class in org.cytoscape.view.vizmap.mappings
Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(K, BoundaryRangeValues<V>, ContinuousMapping<K, V>, CyEventHelper) - Constructor for class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Constructor.
ContinuousRange<T> - Class in org.cytoscape.view.model
Defines a continuous range of values for VisualPropertys.
ContinuousRange(Class<T>, T, T, Boolean, Boolean) - Constructor for class org.cytoscape.view.model.ContinuousRange
Constructs this ContinuousRange.
controlsMutuallyExclusiveNestedChildren() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
controlsMutuallyExclusiveNestedChildren() - Method in interface org.cytoscape.work.TunableHandler
Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
CORE_PROPRERTY_NAME - Static variable in class org.cytoscape.property.SimpleCyProperty
Core Cytoscape Property (Cytoscape System Property)
countMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable
Returns the number of rows with the in the specified column with the specified value.
createAnnotation(Class<? extends T>, CyNetworkView, Map<String, String>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
Create an annotation.
createAttribute() - Method in class org.cytoscape.property.bookmark.ObjectFactory
Create an instance of Attribute
createBend() - Method in interface org.cytoscape.view.presentation.property.values.BendFactory
Creates an instance of edge bend.
createBookmarks() - Method in class org.cytoscape.property.bookmark.ObjectFactory
Create an instance of Bookmarks
createCategory() - Method in class org.cytoscape.property.bookmark.ObjectFactory
Create an instance of Category
createColumn(String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type.
createColumn(String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type.
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.
createDataSource() - Method in class org.cytoscape.property.bookmark.ObjectFactory
Create an instance of DataSource
createDescription(String) - Method in class org.cytoscape.property.bookmark.ObjectFactory
Create an instance of JAXBElement<String>}
createElementTransformer() - Method in interface org.cytoscape.filter.model.ElementTransformerFactory
Returns a new ElementTransformer with the same id as this factory.
createFilter() - Method in interface org.cytoscape.filter.model.FilterFactory
Returns a new Filter with the same id as this factory.
createFor(NetworkTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkViewTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkViewCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(TableTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createGroup(CyNetwork, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network.
createGroup(CyNetwork, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network initially populated with the supplied nodes.
createGroup(CyNetwork, CyNode, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network from an existing CyNode.
createGroup(CyNetwork, CyNode, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network from an existing CyNode.
createHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.HandleFactory
Creates a new instance of the Handle.
createHolisticTransformer() - Method in interface org.cytoscape.filter.model.HolisticTransformerFactory
 
createIcon(VisualProperty<V>, V, int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine
Create Icon object for the given VisualProperty value.
createImage(int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine
Render an Image object from current visualization.
createLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
createLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns a new layout context object.
createListColumn(String, Class<T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type.
createListColumn(String, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type.
createMenuItem(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.application.swing.CyEdgeViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified edge view.
createMenuItem(CyNetworkView) - Method in interface org.cytoscape.application.swing.CyNetworkViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified network view.
createMenuItem(CyNetworkView, View<CyNode>) - Method in interface org.cytoscape.application.swing.CyNodeViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified node view.
createNetwork() - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object.
createNetwork(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object.
createNetworkView(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewFactory
Create a CyNetworkView from a CyNetwork object.
CreateNetworkViewTaskFactory - Interface in org.cytoscape.task.create
This interface provides a task iterator for creating network views.
createNetworkWithPrivateTables() - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object where the associated default tables are private.
createNetworkWithPrivateTables(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object where the associated default tables are private.
createNewEmptyNetworkView() - Method in interface org.cytoscape.task.create.NewEmptyNetworkViewFactory
Returns a new, empty CyNetworkView.
createPrintable() - Method in interface org.cytoscape.view.presentation.RenderingEngine
For export image function.
createRenderingEngine(Object, View<T>) - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory
A view model can have multiple presentations.
createTable(String, String, Class<?>, boolean, boolean, CyTableFactory.InitialTableSize) - Method in interface org.cytoscape.model.CyTableFactory
Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTable(String, String, Class<?>, boolean, boolean) - Method in interface org.cytoscape.model.CyTableFactory
Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTableCellRenderer(ContinuousMappingEditor<? extends Number, ?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingCellRendererFactory
 
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskIterator(TaskObserver, String...) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskIterator(List<String>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskIterator(String, String, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified command.
createTaskIterator(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory
Sets the input stream that will be read by the Reader created from this factory.
createTaskIterator(Object) - Method in interface org.cytoscape.io.webservice.WebServiceClient
Set query for the tasks to be executed.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.CloneNetworkTaskFactory
Returns a TaskIterator that clones the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFactory
Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesOnlyTaskFactory
Returns a TaskIterator that creates a new network from the selected nodes in the given network.
createTaskIterator(boolean) - Method in interface org.cytoscape.task.create.NewSessionTaskFactory
Creates a task iterator for creating a new session and destroying the current session based on the input.
createTaskIterator(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory
Creates a new TaskIterator using the given edge view and network view.
createTaskIterator(CyNetwork, String) - Method in interface org.cytoscape.task.edit.EditNetworkTitleTaskFactory
Creates a task iterator for editing a network's title.
createTaskIterator(CyTable, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory
Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyTableReader) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory
Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyTable, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.JoinTablesTaskTaskFactory
 
createTaskIterator(CyTable, Collection<CyTable>) - Method in interface org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory
Creates a task iterator for mapping a selected global table to a selected local table.
createTaskIterator(CyTable, boolean, List<CyNetwork>, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory
 
createTaskIterator(CyTable, CyTable, List<String>, String, boolean, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MergeTablesTaskFactory
Creates a task iterator for merging two data tables.
createTaskIterator(CyColumn, String) - Method in interface org.cytoscape.task.edit.RenameColumnTaskFactory
Create a task iterator for renaming a selected column.
createTaskIterator(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory
Provisions this factory with the collection of networks that will be passed into any task created by it.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory
Provisions this factory with the CyNetwork that will be passed into any task created by it.
createTaskIterator(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory
Provisions this factory with the collection of network views that will be passed into any task created by it.
createTaskIterator(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory
Creates a task iterator using the specified network view and points.
createTaskIterator(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory
Creates a new TaskIterator using the given CyNetworkView
createTaskIterator(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory
Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory
Create a task iterator for loading a network from a file.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory
Create a task iterator for loading a network from a file.
createTaskIterator(URL, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkURLTaskFactory
Creates a task iterator for loading a URL into a network.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadTableFileTaskFactory
Creates the task iterator for importing an attribute file to a table.
createTaskIterator(URL) - Method in interface org.cytoscape.task.read.LoadTableURLTaskFactory
Creates the task iterator for importing an attribute file to a table.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory
Creates a task iterator for loading files into visual styles.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory
Creates a task iterator for loading files into visual styles.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory
Creates a task iterator for loading a session from a file.
createTaskIterator(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory
Provisions this factory with the CyRow that will be passed into any task created by it.
createTaskIterator(CyNetwork, File) - Method in interface org.cytoscape.task.select.SelectFromFileListTaskFactory
Creates a task iterator for selecting items of a network based on a file.
createTaskIterator(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory
Used to provision this factory with a CyColumn and a primary key that will be used to create tasks.
createTaskIterator(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory
Used to provision this factory with a CyColumn that will be used to create tasks.
createTaskIterator(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory
Used to provision this factory with a CyTable that will be used to create tasks.
createTaskIterator(CyNetwork, File) - Method in interface org.cytoscape.task.write.ExportNetworkTaskFactory
Creates the task iterator for exporting networks.
createTaskIterator(CyNetworkView, File) - Method in interface org.cytoscape.task.write.ExportNetworkViewTaskFactory
Creates the task iterator for exporting network views.
createTaskIterator(CyTable, File) - Method in interface org.cytoscape.task.write.ExportTableTaskFactory
Returns a task factory that write the specified table to the specified file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportVizmapTaskFactory
Creates a task iterator for exporting the vizmap file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.SaveSessionAsTaskFactory
Creates a task iterator for saving the session in a specified file.
createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Creates a task iterator containing the layout tasks.
createTaskIterator() - Method in interface org.cytoscape.work.TaskFactory
Returns an iterator containing a sequence of Tasks.
createTaskIterator(TaskIterator, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter
This method takes as input a TaskIterator and a map of tunable names to tunable values and applies those values to any tunables found in the Tasks found in the TaskIterator.
createTaskIterator(TaskIterator, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.work.TunableSetter
This version of createTaskIterator adds a TaskObserver argument.
createTaskStatusPanel() - Method in interface org.cytoscape.work.swing.TaskStatusPanelFactory
 
createTransformer(String) - Method in interface org.cytoscape.filter.TransformerManager
Returns a new Transformer with the given id.
createTunableHandler(Field, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
 
createTunableHandler(Method, Method, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
 
createTunableHandler(Field, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory
This method returns a TunableHandler for a field annotated as a Tunable if this factory can produce an appropriate handler for this type of field.
createTunableHandler(Method, Method, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory
This method returns a TunableHandler for a method annotated as a Tunable if this factory can produce an appropriate handler for this type of method.
createView(Transformer<?, ?>) - Method in interface org.cytoscape.filter.view.TransformerViewFactory
Creates a UI panel that configures the given transformer.
createVisualMappingFunction(String, Class<K>, VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory
Create a new VisualMappingFunction.
createVisualPropertyDependency() - Method in interface org.cytoscape.view.vizmap.VisualPropertyDependencyFactory
 
createVisualStyle(String) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory
Create a new VisualStyle.
createVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory
Create a copy of given VisualStyle.
createWriter(OutputStream, CyNetworkView) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory
Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, CyNetwork) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory
Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, Object) - Method in interface org.cytoscape.io.write.CyPropertyWriterFactory
Creates a single Task that will write the specified property object to the specified OutputStream.
createWriter(OutputStream, CySession) - Method in interface org.cytoscape.io.write.CySessionWriterFactory
Creates a single Task that will write the specified CySession object to the specified OutputStream.
createWriter(OutputStream, CyTable) - Method in interface org.cytoscape.io.write.CyTableWriterFactory
Creates a single Task that will write the specified CyTable object to the specified OutputStream.
createWriter(OutputStream, RenderingEngine<?>) - Method in interface org.cytoscape.io.write.PresentationWriterFactory
Creates a single Task that will write the contents of the specified RenderingEngine object to the specified OutputStream.
createWriter(OutputStream, Set<VisualStyle>) - Method in interface org.cytoscape.io.write.VizmapWriterFactory
Creates a single Task that will write the specified set of VisualStyle objects to the specified OutputStream.
current_size - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Partition size used for taskMonitor.
current_start - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Starting node number used for taskMonitor.
CUSTOM - Static variable in interface org.cytoscape.util.swing.FileUtil
Equal to FileDialog.LOAD + FileDialog.SAVE.
CustomGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics
This interface defines a the mimimum interface to add a custom graphics to a CyNode.
CyAction - Interface in org.cytoscape.application.swing
An interface that describes how an action should be placed within the menus and/or toolbars of the Swing application.
CyAppAdapter - Interface in org.cytoscape.app
A Java-only api providing access to Cytoscape functionality.
CyApplicationConfiguration - Interface in org.cytoscape.application
Application-wide setting will be accessible through this interface.
CyApplicationManager - Interface in org.cytoscape.application
Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.
CyColorChooser - Class in org.cytoscape.util.swing
This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColumn - Interface in org.cytoscape.model
This class describes a column in a CyTable.
CyCustomGraphics<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
Base interface for all Custom Graphics.
CyCustomGraphicsFactory<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
This interface provides the factory to create CyCustomGraphics objects.
CyDisposable - Interface in org.cytoscape.model
An interface for objects that require an explicit clean up at the end of their lifecycle.
CyEdge - Interface in org.cytoscape.model
An object that represents an edge within a network of nodes (vertices) and edges.
CyEdge.Type - Enum in org.cytoscape.model
The Type enum is used by methods in CyNetwork to restrict the edges that match a query.
CyEdgeViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified edge view.
CyEvent<T> - Interface in org.cytoscape.event
All Cytoscape events should extend this interface.
CyEventHelper - Interface in org.cytoscape.event
The basic event handling interface for Cytoscape.
CyFileFilter - Interface in org.cytoscape.io
An interface that captures the metadata description of a file type so that files of the specified type can be handled correctly by the application and the user interface.
CyFileFilterProvider - Interface in org.cytoscape.io
An interface extended by various reader and writer factories.
CyGroup - Interface in org.cytoscape.group
An object that represents a group of nodes and edges.
CyGroupAggregationManager - Interface in org.cytoscape.group.data
The CyGroupAggregationManager provides a mechanism to add new Aggregators to the group aggregation mechanism.
CyGroupFactory - Interface in org.cytoscape.group
An interface describing a factory used for creating CyGroup objects.
CyGroupManager - Interface in org.cytoscape.group
The CyGroupManager maintains information about all of the groups an instance of Cytoscape.
CyHelpBroker - Interface in org.cytoscape.application.swing
This interface provides access to the Cytoscape Help Broker and Help Set for managing the JavaHelp system.
CyIdentifiable - Interface in org.cytoscape.model
CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyLayoutAlgorithm - Interface in org.cytoscape.view.layout
A task factory specifically for layout algorithms.
CyLayoutAlgorithmManager - Interface in org.cytoscape.view.layout
This class provides access to the available layout algorithms.
CyListener - Interface in org.cytoscape.event
The basic interface that any class interested in a particular type of event should implement.
CyMenuItem - Class in org.cytoscape.application.swing
A simple wrapper class that allows a JMenuItem to be associated with a gravity value which defines where in a menu the item should fall.
CyMenuItem(JMenuItem, float) - Constructor for class org.cytoscape.application.swing.CyMenuItem
Constructor.
CyNetwork - Interface in org.cytoscape.model
CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
cyNetworkFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.
CyNetworkFactory - Interface in org.cytoscape.model
A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager - Interface in org.cytoscape.model
Basic access to networks and view in an instance of Cytoscape.
CyNetworkNaming - Interface in org.cytoscape.session
A utility that helps with the creation of unique network names.
CyNetworkReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns an array of CyNetwork objects that are read as part of the Task.
CyNetworkReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyNetworkReader for the input.
CyNetworkTableManager - Interface in org.cytoscape.model
Provides access to all network-table relationships.
CyNetworkView - Interface in org.cytoscape.view.model
Additional methods for CyNetworkView.
CyNetworkViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified network view.
CyNetworkViewDesktopMgr - Interface in org.cytoscape.application.swing
Interface for managing CyNetworkViews within the desktop where they reside.
CyNetworkViewDesktopMgr.ArrangeType - Enum in org.cytoscape.application.swing
 
cyNetworkViewFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
Will be used for creating network views.
CyNetworkViewFactory - Interface in org.cytoscape.view.model
Factory for CyNetworkView objects.
CyNetworkViewManager - Interface in org.cytoscape.view.model
Basic access to network views in an instance of Cytoscape.
CyNetworkViewWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CyNetworkView or CyNetwork to be specified and written to an OutputStream.
CyNetworkViewWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CyNetworkView objects.
CyNode - Interface in org.cytoscape.model
An object that represents a node (vertex) within a network of nodes and edges.
CyNodeViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified node view.
CyPayloadEvent<S,P> - Interface in org.cytoscape.event
An extension of CyEvent specifically for payload events.
CyProperty<P> - Interface in org.cytoscape.property
A general property service interface for providing access to different types of property objects as OSGi services.
CyProperty.SavePolicy - Enum in org.cytoscape.property
SavePolicy specifies how the CyProperty will be saved, or if it will not be saved.
CyPropertyReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns a property object.
CyPropertyReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyPropertyReader for the input.
CyPropertyWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a property Object to be specified and written.
CyPropertyWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing property objects.
CyRootNetwork - Interface in org.cytoscape.model.subnetwork
CyRootNetwork is an interface for managing Cytoscape's meta-network implementation.
CyRootNetworkManager - Interface in org.cytoscape.model.subnetwork
A manager that provides access to the CyRootNetwork objects associated with CyNetwork objects.
CyRow - Interface in org.cytoscape.model
This interface represents one row in a CyTable.
CyServiceRegistrar - Interface in org.cytoscape.service.util
An interface to hide the OSGi dependencies needed to register services dynamically at runtime.
CySession - Class in org.cytoscape.session
A session is an immutable snapshot of the data contents of Cytoscape.
CySession.Builder - Class in org.cytoscape.session
A implementation of the builder pattern used to construct immutable instances of CySession objects.
CySession.Builder() - Constructor for class org.cytoscape.session.CySession.Builder
 
CySessionManager - Interface in org.cytoscape.session
This class primarily acts as a listener and tracks the state of the Cytoscape application.
CySessionReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns a org.cytoscape.property.session.Cysession object.
CySessionReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CySessionReader for the input.
CySessionWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CySession to be specified and written.
CySessionWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CySession objects.
CyShutdown - Interface in org.cytoscape.application
A service that will shutdown Cytoscape cleanly.
CyShutdownEvent - Class in org.cytoscape.application.events
An event fired immediately before Cytoscape will be shutdown.
CyShutdownEvent(Object, boolean) - Constructor for class org.cytoscape.application.events.CyShutdownEvent
Constructor.
CyShutdownEvent(Object) - Constructor for class org.cytoscape.application.events.CyShutdownEvent
Constructor.
CyShutdownListener - Interface in org.cytoscape.application.events
The listener for the CyShutdownEvent.
CyStartEvent - Class in org.cytoscape.application.events
An event fired after Cytoscape startup mostly complete (but not necessarily 100 percent).
CyStartEvent(Object) - Constructor for class org.cytoscape.application.events.CyStartEvent
Constructor.
CyStartListener - Interface in org.cytoscape.application.events
The listener for the CyStartEvent.
CySubNetwork - Interface in org.cytoscape.model.subnetwork
A CySubNetwork is a CyNetwork that is contained within a parent CyNetwork.
CySwingAppAdapter - Interface in org.cytoscape.app.swing
A Swing-specific extension of CyAppAdapter that serves as a Java-only api providing access to core Cytoscape functionality.
CySwingApplication - Interface in org.cytoscape.application.swing
This interface provides basic access to the Swing objects that constitute this application.
CyTable - Interface in org.cytoscape.model
A simple representation of a table object consisting of rows and columns.
CyTable.Mutability - Enum in org.cytoscape.model
Mutability of the table specifies whether or not it is able to be deleted..
CyTableFactory - Interface in org.cytoscape.model
An interface describing a factory used for creating CyTable objects.
CyTableFactory.InitialTableSize - Enum in org.cytoscape.model
A description of the initial size of the table.
CyTableManager - Interface in org.cytoscape.model
A singleton object for managing registered CyTables.
CyTableMetadata - Interface in org.cytoscape.model
A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.
CyTableReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns an array of CyTable objects.
CyTableReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyTableReader for the input.
CyTableUtil - Class in org.cytoscape.model
A collection of state-less, static utility methods provided to simplify querying of table objects.
CyTableWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CyTable to be specified and written.
CyTableWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CyTable objects.
CytoPanel - Interface in org.cytoscape.application.swing
Interface to a CytoPanel.
CytoPanelComponent - Interface in org.cytoscape.application.swing
An interface that allows a component to be registered as a service that will then be added to the appropriate CytoPanel.
CytoPanelComponent2 - Interface in org.cytoscape.application.swing
Implement this interface rather than CytoPanelComponent, if you want to allow your component to be retrieved from the CytoPanel by its identifier.
CytoPanelComponentSelectedEvent - Class in org.cytoscape.application.swing.events
The event fired to indicate that a CytoPanelComponent has been selected.
CytoPanelComponentSelectedEvent(Object, CytoPanel, int) - Constructor for class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Constructor.
CytoPanelComponentSelectedListener - Interface in org.cytoscape.application.swing.events
The listener for handling CytoPanelComponentSelectedEvent.
CytoPanelName - Enum in org.cytoscape.application.swing
An enum that describes CytoPanels uses compass directions to describe their location within the application.
CytoPanelState - Enum in org.cytoscape.application.swing
The different display states available for a CytoPanel.
CytoPanelStateChangedEvent - Class in org.cytoscape.application.swing.events
An event to indicate that a CytoPanel has changed state.
CytoPanelStateChangedEvent(Object, CytoPanel, CytoPanelState) - Constructor for class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Constructor.
CytoPanelStateChangedListener - Interface in org.cytoscape.application.swing.events
A listener for handling CytoPanelStateChangedEvents.
CyTransformerReader - Interface in org.cytoscape.io.read
 
CyTransformerWriter - Interface in org.cytoscape.io.write
 
CyVersion - Interface in org.cytoscape.application
An interface providing access to version information about this version of the Cytoscape application.
CyWriter - Interface in org.cytoscape.io.write
A marker interface used to identify tasks involved in writing data.
CyWriterFactory - Interface in org.cytoscape.io.write
A marker interface used to identify factories that create CyWriter instances.
CyWriterManager<W extends CyWriterFactory> - Interface in org.cytoscape.io.write
A CyWriterManager aggregates CyWriterFactory services for specific DataCategories and provides a mechanism for choosing the CyWriterFactory given a particular file type.

D

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

E

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

F

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.
Filter<C,E> - Interface in org.cytoscape.filter.model
A transformer that decides whether to accept or reject elements.
FilterFactory<C,E> - Interface in org.cytoscape.filter.model
A factory for creating Filters.
FinishStatus - Class in org.cytoscape.work
Indicates the status of a task iterator when it has finished for TaskObservers.
FinishStatus(FinishStatus.Type, Task, Exception) - Constructor for class org.cytoscape.work.FinishStatus
 
FinishStatus.Type - Enum in org.cytoscape.work
 
fireEditingCanceled() - Method in class org.cytoscape.util.swing.AbstractCellEditor
Notify all listeners that have registered interest for notification on this event type.
fireEditingStopped() - Method in class org.cytoscape.util.swing.AbstractCellEditor
Notify all listeners that have registered interest for notification on this event type.
fireEvent(E) - Method in interface org.cytoscape.event.CyEventHelper
Calls each listener found in the Service Registry identified by the listenerClass interface by the supplied CyEvent.
fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fitContent() - Method in interface org.cytoscape.view.model.CyNetworkView
Utility method to fit content to the presentation container (usually a Swing Window).
FitContentEvent - Class in org.cytoscape.view.model.events
Fit network visualization to the given container.
FitContentEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitContentEvent
Fit the size of network view to the current container.
FitContentListener - Interface in org.cytoscape.view.model.events
Listener for FitContentEvent.
fitSelected() - Method in interface org.cytoscape.view.model.CyNetworkView
Utility method to fit selected graph objects to the presentation container.
FitSelectedEvent - Class in org.cytoscape.view.model.events
Fit only selected graph object views to the container.
FitSelectedEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitSelectedEvent
Fit the selected part of network view to the container.
FitSelectedListener - Interface in org.cytoscape.view.model.events
Listener for FitSelectedEvent.
fitShapeToText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
This method causes the shape to be resized to fit the provided text.
fixEdges() - Method in class org.cytoscape.view.layout.LayoutPartition
Convenience routine to update the source and target for all of the edges in a partition.
flushPayloadEvents() - Method in interface org.cytoscape.event.CyEventHelper
Forces accumulated payload events to be fired.
FontVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for Font values.
FontVisualProperty(Font, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.FontVisualProperty
Constructor.
forceShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent
Returns true if we want to force the shutdown without any user prompt
FOREGROUND - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation
The foreground canvas
format - Variable in class org.cytoscape.property.bookmark.DataSource
 
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, Class<? extends T>) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get(String, Class<? extends T>, T) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get_ApplyPreferredLayoutTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ApplyPreferredLayoutTaskFactory.
get_ApplyVisualStyleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ApplyVisualStyleTaskFactory.
get_CloneNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CloneNetworkTaskFactory.
get_CollapseGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CollapseGroupTaskFactory.
get_ConnectSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ConnectSelectedNodesTaskFactory.
get_CreateNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CreateNetworkViewTaskFactory.
get_DeleteColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DeleteColumnTaskFactory.
get_DeleteSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
get_DeleteTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DeleteTableTaskFactory.
get_DeselectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DeselectAllEdgesTaskFactory.
get_DeselectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DeselectAllNodesTaskFactory.
get_DeselectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DeselectAllTaskFactory.
get_DestroyNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DestroyNetworkTaskFactory.
get_DestroyNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DestroyNetworkViewTaskFactory.
get_EditNetworkTitleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of EditNetworkTitleTaskFactory.
get_ExpandGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExpandGroupTaskFactory.
get_ExportNetworkImageTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExportNetworkImageTaskFactory.
get_ExportNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExportNetworkViewTaskFactory.
get_ExportSelectedTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExportSelectedTableTaskFactory.
get_ExportTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExportTableTaskFactory.
get_ExportVizmapTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of ExportVizmapTaskFactory.
get_GroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of GroupNodesTaskFactory.
get_HideSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of HideSelectedEdgesTaskFactory.
get_HideSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of HideSelectedNodesTaskFactory.
get_HideSelectedTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of HideSelectedTaskFactory.
get_InvertSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of InvertSelectedEdgesTaskFactory.
get_InvertSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of InvertSelectedNodesTaskFactory.
get_LoadNetworkFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of LoadNetworkFileTaskFactory.
get_LoadNetworkURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of LoadNetworkURLTaskFactory.
get_LoadTableFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of LoadTableFileTaskFactory.
get_LoadTableURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of LoadTableURLTaskFactory.
get_LoadVizmapFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of LoadVizmapFileTaskFactory.
get_MapGlobalToLocalTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of MapGlobalToLocalTableTaskFactory.
get_MapTableToNetworkTablesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of MapTableToNetworkTablesTaskFactory.
get_NewEmptyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of NewEmptyNetworkViewFactory.
get_NewNetworkSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
get_NewNetworkSelectedNodesOnlyTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
get_NewSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of NewSessionTaskFactory.
get_OpenSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of OpenSessionTaskFactory.
get_RenameColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of RenameColumnTaskFactory.
get_SaveSessionAsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SaveSessionAsTaskFactory.
get_SelectAdjacentEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectAdjacentEdgesTaskFactory.
get_SelectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectAllEdgesTaskFactory.
get_SelectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectAllNodesTaskFactory.
get_SelectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectAllTaskFactory.
get_SelectConnectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectConnectedNodesTaskFactory.
get_SelectFirstNeighborsNodeViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
get_SelectFirstNeighborsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryInEdge() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryOutEdge() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFromFileListTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of SelectFromFileListTaskFactory.
get_UnGroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UnGroupNodesTaskFactory.
get_UnGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UnGroupTaskFactory.
get_UnHideAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UnHideAllEdgesTaskFactory.
get_UnHideAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UnHideAllNodesTaskFactory.
get_UnHideAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UnHideAllTaskFactory.
getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction
Returns the accelerator KeyStroke defined for this action.
getAcceleratorKeyStroke() - Method in interface org.cytoscape.application.swing.CyAction
Returns the accelerator KeyStroke defined for this action.
getAdjacentEdgeIterable(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Gets an Iteable of edges that connect to this node.
getAdjacentEdgeList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of edges that connect to this node.
getAggregators(Class) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of aggregators for a particular Class.
getAggregators() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of aggregators.
getAll() - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping
Gets all map values.
getAllCategories() - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data categories
getAllDataSources() - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources registered as OSGi services
getAllDescendants(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon
Get collection of visual properties for a given object type (node/edge/network).
getAllDescendants(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
getAllHandles() - Method in interface org.cytoscape.view.presentation.property.values.Bend
Get List of all handles on this edge
getAllLayouts() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns a collection of all available layouts.
getAllPoints() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets all Data Points.
getAllRenderingEngines() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Get all RenderingEngines registered in this manager.
getAllRows() - Method in interface org.cytoscape.model.CyTable
Return a list of all the rows stored in this data table.
getAllTables(boolean) - Method in interface org.cytoscape.model.CyTableManager
Returns a Set of all tables with the specified visibility.
getAllValues() - Method in interface org.cytoscape.model.CyRow
Returns a map of column names to Objects that contain the values contained in this Row.
getAllViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of all View including those for Nodes, Edges, and Network.
getAllVisualLexicon() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns a Set of all VisualLexicons.
getAllVisualMappingFunctions() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns all VisualMappingFunctions in this style.
getAllVisualProperties() - Method in interface org.cytoscape.view.model.VisualLexicon
Returns the Set of VisualPropertys supported by this Renderer.
getAllVisualProperties() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
getAllVisualPropertyDependencies() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Get all dependencies for this style.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns all available VisualStyles managed by this object.
getAnchorType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the anchor type for one end of the arrow
getAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Retrieve the list of annotations for a specific network view.
getAppConfigurationDirectoryLocation(Class<?>) - Method in interface org.cytoscape.application.CyApplicationConfiguration
Returns the absolute path to the configuration directory of a particular app.
getAppFileListMap() - Method in class org.cytoscape.session.CySession
Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.
getAppFileListMap() - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent
This method is not meant to be used by listeners for this event, although you can and no harm should come to you.
getArgAsBoolean(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
getArgAsDouble(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgAsLong(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
getArgAsString(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
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.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
 
getArguments(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of arguments for the specified namespace and command in alphabetical order.
getArrowColor(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the color of one end of the arrow
getArrows() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get all arrows that are currently linked to this annotation.
getArrowSize(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the size of one end of the arrow
getArrowType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the type of one end of the arrow
getAttribute(DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Given the attribute name, return the value in a bookmark
getAttribute() - Method in class org.cytoscape.property.bookmark.DataSource
Gets the value of the attribute property.
getAttributeSelectors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns set of selector for available attributes (table columns).
getAvailableCommands() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of AvailableCommands.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyFileFilters known to this CyWriter manager.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyWriterManager
Returns a list of the available CyFileFilters that define the available output types.
getAverageLocation() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the average location of the nodes in this partition
getBaseNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
The initial network of CyNodes and CyEdges.
getBooleans(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of booleans.
getBorderColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the border (stroke) color.
getBorderWidth() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the border (stroke) width.
getBounds(CyNetworkView) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Get the existing bounds of a given CyNetworkView within the desktop view area.
getBounds2D() - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer
Return the bounds of the area covered by this CustomGraphicLayer as a Rectangle2D
getBugFixVersion() - Method in interface org.cytoscape.application.CyVersion
The third of the three numbers defining the version of the software, meaning "5" if the version is "3.2.5".
getCanvasName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Return the canvas that this Annotation is on
getCategory() - Method in class org.cytoscape.property.bookmark.Bookmarks
Gets the value of the category property.
getCategory(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Select specific category from a list of categories.
getCategoryOrDataSource() - Method in class org.cytoscape.property.bookmark.Category
Gets the value of the categoryOrDataSource property.
getCellEditors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns editors for individual cells in discrete mapping editor.
getCellEditorValue() - Method in class org.cytoscape.util.swing.AbstractCellEditor
getChangeSources() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChangeSources() - Method in interface org.cytoscape.work.swing.GUITunableHandler
Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChildKey() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildKey() - Method in interface org.cytoscape.work.TunableHandler
Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildren() - Method in class org.cytoscape.view.model.VisualLexiconNode
Returns collection of all children of this node.
getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation
 
getCode() - Method in class org.cytoscape.equations.Equation
Returns the compiled code (not Java byte code!) for the VM representing this Equation.
getColumn(String) - Method in interface org.cytoscape.model.CyTable
Returns the column for the specified name.
getColumn() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the name of the column of the data that was set.
getColumnClass(int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the class of the column specified in the argument.
getColumnClass(int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the type for column number column.
getColumnClass(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the class of the column at the given column number.
getColumnCount() - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the number of available columns.
getColumnCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the number of columns in the TreeTabelModel.
getColumnName(int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the name for column number column.
getColumnName(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the column name at the given column number.
getColumnNames(CyTable) - Static method in class org.cytoscape.model.CyTableUtil
Returns all the column names of a given table.
getColumnRecords(String) - Method in class org.cytoscape.model.events.RowsSetEvent
Returns all of the RowSetRecords whose specified column value is set.
getColumns() - Method in interface org.cytoscape.model.CyTable
Returns the column types for all columns in this table.
getCommandExecutorTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CommandExecutorTaskFactory which can be used to execute commands.
getCommands(String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of available commands in alphabetical order for the specified namespace.
getCompatibleTypes() - Method in class org.cytoscape.equations.ArgDescriptor
Returns the types that are compatible with this argument.
getCompatibleTypes() - Method in enum org.cytoscape.equations.ArgType
Returns an array of compatible Class types.
getComponent() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the Component to be added to the CytoPanel.
getComponent() - Method in interface org.cytoscape.application.swing.ToolBarComponent
Returns the Component to be added to the ToolBar.
getComponentAt(int) - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the component at index.
getConfiguration(TaskFactory, Object) - Method in interface org.cytoscape.work.TaskManager
Returns a configuration object generated from the Tunables read from the TaskFactory.
getConfigurationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration
Returns absolute path to .cytoscape location.
getConnectingEdgeList(CyNode, CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of edges that connect two nodes.
getContent() - Method in class org.cytoscape.property.bookmark.Attribute
Gets the value of the content property.
getContentPane() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
This class requires that all content be placed within a designated panel, this method returns that panel.
getContentTypes() - Method in class org.cytoscape.io.BasicCyFileFilter
The MIME content types supported by this filter.
getContentTypes() - Method in interface org.cytoscape.io.CyFileFilter
The MIME content types supported by this filter.
getContext() - Method in class org.cytoscape.work.AbstractTunableHandler
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.
getCoreProperties() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyProperty of type Properties.
getCurrentNetwork() - Method in interface org.cytoscape.application.CyApplicationManager
Provides access to the current network.
getCurrentNetworkView() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the current network view.
getCurrentNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the NetworkViewRenderer associated with the current RenderingEngine.
getCurrentRenderingEngine() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the rendering engine associated with the current network view.
getCurrentSession() - Method in interface org.cytoscape.session.CySessionManager
This method returns a CySession object describing the current state of Cytoscape.
getCurrentSessionFileName() - Method in interface org.cytoscape.session.CySessionManager
Returns the name of the current session file.
getCurrentTable() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the currently active table.
getCurrentVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns currently selected Visual Style.
getCyApplicationConfiguration() - Method in interface org.cytoscape.app.CyAppAdapter
 
getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyApplicationManager.
getCyEventHelper() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyEventHelper.
getCyGroupAggregationManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyGroupAggregationManager.
getCyGroupFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyGroupFactory.
getCyGroupManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyGroupManager.
getCyLayoutAlgorithmManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyLayoutAlgorithmManager.
getCyNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkFactory.
getCyNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkManager.
getCyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkViewFactory.
getCyNetworkViewManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkViewManager.
getCyNetworkViewReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkReaderManager.
getCyNetworkViewWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyNetworkViewWriterManager.
getCyPropertyReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyPropertyReaderManager.
getCyPropertyWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyPropertyWriterManager.
getCyRootNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyRootNetworkManager.
getCyServiceRegistrar() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyServiceRegistrar.
getCySessionManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CySessionManager.
getCySessionReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CySessionReaderManager.
getCySessionWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CySessionWriterManager.
getCySwingApplication() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Returns an instance of CySwingApplication.
getCyTableFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyTableFactory.
getCyTableManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyTableManager.
getCyTableReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyTableReaderManager.
getCyTableWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyTableWriterManager.
getCytoPanel(CytoPanelName) - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the appropriate CytoPanel for the specified compass direction.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Returns the CytoPanel on which a component was selected.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Returns the CytoPanel whose state has changed.
getCytoPanelComponentCount() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the number of components in the CytoPanel.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the position in the layout.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the name of the CytoPanel that this component should be added to.
getCyVersion() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of CyVersion.
getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter
The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.CyFileFilter
The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.datasource.DataSource
DataCategory of this data.
getDataCategory() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getDataSourceList(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Traverse bookmark tree and get a list of data sources from the specified category.
getDataSourceManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of DataSourceManager.
getDataSources(DataCategory) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources under the given category.
getDataSources(String) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources from a data provider
getDataTableComboBoxEditor(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Attribute selector for the given table entry type.
getDataType() - Method in interface org.cytoscape.view.vizmap.gui.util.DiscreteMappingGenerator
Returns the type of the visual property.
getDefault() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getDefault() - Method in interface org.cytoscape.view.model.VisualProperty
The default value of this property.
getDefaultComboBoxEditor(String) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Get JComboBox type editor
getDefaultEdgeTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for the edges of this network.
getDefaultIcon(int, int) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getDefaultIcon(int, int) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
This is for default view editor.
getDefaultLayout() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns the default layout.
getDefaultLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getDefaultLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the default instance of the layout context.
getDefaultNetworkTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for this network.
getDefaultNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the NetworkViewRenderer that should be used to create CyNetworkViews.
getDefaultNodeTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for the nodes of this network.
getDefaultValue() - Method in interface org.cytoscape.model.CyColumn
Returns the default value for the column, possibly null.
getDefaultValue(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns default value for the VisualProperty.
getDefaultVariableValues() - Method in class org.cytoscape.equations.Equation
Returns default values for variable references, if any.
getDefaultVariableValues() - Method in interface org.cytoscape.equations.EquationParser
Returns a map of variable names to their default values, if any.
getDefaultView(VisualStyle) - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewEditor
Deprecated.
getDefaultViewEditor() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI
Deprecated.
getDefaultViewPanel() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI
Deprecated.
getDefaultVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Provide default VisualLexicon from a default engine factory.
getDefaultVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Return default VisualStyle.
getDegree() - Method in class org.cytoscape.view.layout.LayoutNode
Return the node's degree (i.e.
getDependency() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDependency() - Method in interface org.cytoscape.work.swing.GUITunableHandler
Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor
Returns the description of the argument.
getDescription() - Method in class org.cytoscape.io.BasicCyFileFilter
A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.CyFileFilter
A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.datasource.DataSource
Description for this data.
getDescription() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getDescription() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getDescription() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Get human-readable description of this client.
getDescription() - Method in class org.cytoscape.property.bookmark.Bookmarks
Gets the value of the description property.
getDescription() - Method in class org.cytoscape.util.swing.FileChooserFilter
Returns the short description of the acceptable file type.
getDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the associated Tunable's description.
getDescription() - Method in interface org.cytoscape.work.TunableHandler
Returns the associated Tunable's description.
getDesktopViewAreaSize() - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Return the size of the desktop view area where all CyNetworkViews reside.
getDialogTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Returns an instance of DialogTaskManager.
getDisabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent
Get set of Visual Properties to be disabled in the lexicon.
getDiscreteTableCellRenderer() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getDiscreteTableCellRenderer() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
A custom cell renderer for Discrete table cells.
getDisplayName() - Method in enum org.cytoscape.io.DataCategory
 
getDisplayName() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getDisplayName() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Returns display name of this client.
getDisplayName() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getDisplayName() - Method in interface org.cytoscape.view.model.VisualProperty
Returns a short string suitable for presentation to humans.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Display name is a simple description of this image object.
getDisplayName() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
 
getDisplayName() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue
Name of this value type.
getDisplayName() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Provides human-readable name of this dependency.
getDoubles(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of doubles.
getEdge(long) - Method in interface org.cytoscape.model.CyNetwork
Return the CyEdge that has the SUID.
getEdge() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the Edge this LayoutEdge represents
getEdgeCount() - Method in interface org.cytoscape.model.CyNetwork
Return the number of edges in this network.
getEdgeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a edgelist into a list of CyEdges.
getEdgeList() - Method in interface org.cytoscape.model.CyNetwork
Return a list of the edges in this network.
getEdgeList() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the list of LayoutEdges within this partition.
getEdges() - Method in class org.cytoscape.model.events.AboutToRemoveEdgesEvent
Returns the collection of edges about to be removed.
getEdgesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil
A utility method that returns a list of edges that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getEdgeView(CyEdge) - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a View for a specified Edge.
getEdgeViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of Views for all CyEdges in the network.
getEdgeViews() - Method in class org.cytoscape.view.model.events.AddedEdgeViewsEvent
Returns new edge view added to the source network view object.
getEditingRow() - Method in class org.cytoscape.util.swing.JTreeTable
Returns the row being edited.
getElementCount(C) - Method in interface org.cytoscape.filter.model.TransformerSource
Returns the number of elements that could be produced from the given context.
getElementList(C) - Method in interface org.cytoscape.filter.model.TransformerSource
Returns a List of elements from the given context.
getElementType() - Method in interface org.cytoscape.filter.model.Transformer
Returns the type of the elements this Transformer is compatible with.
getElementType() - Method in interface org.cytoscape.filter.model.TransformerSource
Returns the type of the elements this TransformerSource is compatible with.
getEnabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent
Get set of Visual Properties to be enabled in the lexicon.
getEquation() - Method in interface org.cytoscape.equations.EquationCompiler
If compile() returns true, this returns the result of the compilation.
getErrorEquation(String, Class<?>, String) - Method in interface org.cytoscape.equations.EquationCompiler
A factory method that returns an Equation that always fails at runtime.
getErrorMsg() - Method in interface org.cytoscape.equations.EquationParser
If parse() failed, this will return the last error messages.
getException() - Method in class org.cytoscape.session.events.SessionLoadCancelledEvent
 
getException() - Method in class org.cytoscape.session.events.SessionSaveCancelledEvent
 
getException() - Method in class org.cytoscape.work.FinishStatus
Returns the exception thrown by the task that failed, or null if the task iterator succeeded or was cancelled.
getExtension(String) - Method in class org.cytoscape.io.BasicCyFileFilter
Returns a string of the characters following the last '.' in the input string, which is to say the file extension assuming that the input string represents a file name.
getExtensions() - Method in class org.cytoscape.io.BasicCyFileFilter
Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in interface org.cytoscape.io.CyFileFilter
Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in class org.cytoscape.util.swing.FileChooserFilter
Returns an array of the extensions associated with this FileChooserFilter.
getExternalEdgeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of exterior edges connected to the nodes within this group.
getFactories() - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager
Returns all available factories.
getFactory(Class<?>) - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager
Factory for the specific mapping type.
getFile(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileFilter() - Method in interface org.cytoscape.io.CyFileFilterProvider
Return the file filter associated with the IOFactory.
getFileFilter() - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory
Return the file filter associated with the IOFactory.
getFiles(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFillColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the fill color.
getFitRatio() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Get the fit ratio for this custom graphic.
getFont() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font being used
getFont() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font being used
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font family to be used for the text display
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font family to be used for the text display
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the size of the font used to display the text
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the size of the font used to display the text
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font style
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font style
getFormat() - Method in class org.cytoscape.property.bookmark.DataSource
Gets the value of the format property.
getFunction(String) - Method in interface org.cytoscape.equations.EquationParser
Returns the function associated with the name "functionName" or null if no such function exists.
getFunctionSummary() - Method in class org.cytoscape.equations.AbstractFunction
Used to provide help for users.
getFunctionSummary() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getGlobalTables() - Method in interface org.cytoscape.model.CyTableManager
Returns a set of all global tables.
getGravity() - Method in class org.cytoscape.work.AbstractTunableHandler
getGravityTracker(String) - Method in class org.cytoscape.util.swing.JMenuTracker
This method will fetch an existing menu or create a new one if a menu with the specified name does not exist.
getGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Return the group the corresponds to a particular node in a CyNetwork.
getGroupNetwork() - Method in interface org.cytoscape.group.CyGroup
Returns the network referenced by this group.
getGroupNode() - Method in interface org.cytoscape.group.CyGroup
Return the CyNode that represents this group in the network.
getGroups() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the associated Tunable's groups or nesting hierarchy.
getGroups() - Method in interface org.cytoscape.work.TunableHandler
Returns the associated Tunable's groups or nesting hierarchy.
getGroupSet(CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Provides the set of all the groups known to the groups manager in a particular network.
getGroupsForNode(CyNode) - Method in interface org.cytoscape.group.CyGroupManager
Return the list of CyGroups this node is in.
getGroupsForNode(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Return the list of CyGroups this node is in for a particular network.
getHandler(String) - Method in interface org.cytoscape.view.vizmap.gui.event.VizMapEventHandlerManager
Returns handler for the event.
getHandlers(Object) - Method in class org.cytoscape.work.AbstractTunableInterceptor
Returns a 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
Returns the HelpBroker.
getHelpSet() - Method in interface org.cytoscape.application.swing.CyHelpBroker
Returns the HelpSet.
getHref() - Method in class org.cytoscape.property.bookmark.DataSource
Gets the value of the href property.
getIcon() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the Icon to be used along with the title in the tab for this this component.
getId() - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getId() - Method in interface org.cytoscape.filter.model.Transformer
Returns the unique id of this type of Transformer.
getId() - Method in interface org.cytoscape.filter.model.TransformerFactory
Returns the unique id of the Transformer produced by this factory.
getId() - Method in interface org.cytoscape.filter.view.TransformerViewFactory
Returns the unique id of the Transformer this factory produces views for.
getIdentifier() - Method in interface org.cytoscape.application.swing.CytoPanelComponent2
Returns this component's identifier, which should be unique.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the edge's identifier.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutNode
Return the node's identifier.
getIdentifier() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Immutable session-unique identifier of this custom graphic generated by the custom graphics manager.
getIdString() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getIdString() - Method in interface org.cytoscape.view.model.VisualProperty
Returns a short string used to identify this visual property and suitable for serializing to XML and other text formats.
getIdString() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Provides serializable string of this dependency.
getImage() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the image currently assigned to this annotation
getImageBrightness() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the brightness adjustment for this image.
getImageContrast() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the contrast adjustment for this image
getImageOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the current opacity of the image.
getImageURL() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Get the URL for the image to be displayed
getImportedObject() - Method in class org.cytoscape.io.webservice.events.DataImportFinishedEvent
Returns the object that was imported.
getIndex() - Method in class org.cytoscape.view.layout.LayoutNode
Returns the index of this LayoutNode.
getIndex(Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend
Get index of a Handle
getIndexOfChild(Object, Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the index of a child given a parent.
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.
getInstance(URL) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Get a new instance of the CyCustomGraphics based on pulling the data from a URL.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Get a new instance of the CyCustomGraphics.
getInternalEdgeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of edges contained within this group.
getJFrame() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JFrame that contains the application.
getJMenu(String) - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JMenu for the specified name and null if no menu exists for the name.
getJMenuBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JMenuBar object for the application.
getJPanel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns the panel associated with this GUITunableHandler.
getJPanel() - Method in interface org.cytoscape.work.swing.GUITunableHandler
To get the panel that contains the GUI representation (JTextField, JFileChooser, JLabel, JList ...)
getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JToolBar object for the application.
getKeys() - Method in class org.cytoscape.model.events.RowsDeletedEvent
Returns the primary keys of the rows for this event.
getLastErrorMsg() - Method in interface org.cytoscape.equations.EquationCompiler
Returns an error message for an error encountered during a call to compile, if any.
getLastInternalError() - Method in interface org.cytoscape.model.CyTable
Returns a descriptive message for certain internal errors.
getLayers(CyNetworkView, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Get layers that belong to this object.
getLayout(String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns a layout algorithm of the specified name and null if no algorithm exists with that name.
getLeftChild() - Method in class org.cytoscape.equations.AbstractNode
 
getLeftChild() - Method in interface org.cytoscape.equations.TreeNode
Returns the left child if it exists or null if it doesn't.
getLength() - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the number of direct children Filters contained by this CompositeFilter.
getLineColor() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Set the line color for this arrow
getLineWidth() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the line width for this arrow
getList(String, Class<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getList(String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getListElementType() - Method in interface org.cytoscape.model.CyColumn
Returns the data type of the list elements if the column type is List.class otherwise null.
getListenerClass() - Method in class org.cytoscape.event.AbstractCyEvent
The Class of the listener that is expected to handle this event.
getListenerClass() - Method in interface org.cytoscape.event.CyEvent
The Class of the listener that is expected to handle this event.
getLoadedFileName() - Method in class org.cytoscape.session.events.SessionLoadedEvent
Returns the file name of the session just loaded.
getLoadedSession() - Method in class org.cytoscape.session.events.SessionLoadedEvent
Returns the session that was just loaded.
getLocalTables(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyTableManager
Returns set of all local tables for the given data type.
getLocation() - Method in interface org.cytoscape.io.datasource.DataSource
Location of this data file.
getLocation() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getLogWeight() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the current value for this edge's logWeight (-log(weight)).
getLongs(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of longs.
getLowerBound() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the lower limit of the object.
getMajorVersion() - Method in interface org.cytoscape.application.CyVersion
The first of the three numbers defining the version of the software, meaning "3" if the version is "3.2.5".
getMappedValue(CyRow) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns the mapped value for a CyRow.
getMappingColumnName() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getMappingColumnName() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns attribute name used in this mapping.
getMappingColumnType() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getMappingColumnType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns data type of mapping attribute.
getMappingFunctionSelector() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns selector for Mapping Type.
getMappingFunctionType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory
Returns the type of this VisualMappingFunctionFactory.
getMapValue(K) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping
Gets Value for Specified Key.
getMatchingFactory(CyFileFilter) - Method in interface org.cytoscape.io.write.CyWriterManager
Returns a CyWriterFactory for the appropriate filter.
getMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable
Returns all the rows of a specified column that contain a certain value for that column.
getMax() - Method in class org.cytoscape.view.model.ContinuousRange
Returns the maximum value of this range.
getMaxX() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the maximum X location of all of the LayoutNodes
getMaxY() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the maximum Y location of all of the LayoutNodes
getMembers() - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation
Return the list of members for this group
getMenu() - Method in interface org.cytoscape.util.swing.GravityTracker
Returns the JPopupMenu or JMenu that this gravity tracker tracks.
getMenu() - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
getMenu() - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
getMenuGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in interface org.cytoscape.application.swing.CyAction
Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in class org.cytoscape.application.swing.CyMenuItem
Returns the gravity used to place the menu item in a menu.
getMenuItem() - Method in class org.cytoscape.application.swing.CyMenuItem
Returns the menu item to be placed in a menu according to the specified menu gravity.
getMin() - Method in class org.cytoscape.view.model.ContinuousRange
Returns the minimum value of this range.
getMinorVersion() - Method in interface org.cytoscape.application.CyVersion
The second of the three numbers defining the version of the software, meaning "2" if the version is "3.2.5".
getMinX() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the minimum X location of all of the LayoutNodes
getMinY() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the minimum Y location of all of the LayoutNodes
getModel() - Method in interface org.cytoscape.view.model.View
Get source data structure, such as CyNode, CyEdge, etc.
getMostRecentlyOpenedURL() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Returns the last addition or null if there are no URLs.
getMutability() - Method in interface org.cytoscape.model.CyTable
The table can be deleted if this returns Mutability.MUTABLE, otherwise it cannot be deleted!
getName() - Method in class org.cytoscape.application.swing.AbstractCyAction
Returns the name of the action.
getName() - Method in interface org.cytoscape.application.swing.CyAction
Returns the name of the action.
getName() - Method in class org.cytoscape.equations.AbstractFunction
Used to parse the function string.
getName() - Method in interface org.cytoscape.equations.Function
Used to parse the function string.
getName() - Method in interface org.cytoscape.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 interface org.cytoscape.model.CyColumn
Returns the name of the column.
getName() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.bookmark.Attribute
Gets the value of the name property.
getName() - Method in class org.cytoscape.property.bookmark.Category
Gets the value of the name property.
getName() - Method in class org.cytoscape.property.bookmark.DataSource
Gets the value of the name property.
getName() - Method in interface org.cytoscape.property.CyProperty
Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getName() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the computer-readable name of the layout.
getName() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns a name representing a tunable property.
getName() - Method in interface org.cytoscape.work.TunableHandler
Returns a name representing a tunable property.
getNamespace() - Method in interface org.cytoscape.model.CyTableMetadata
getNamespaces() - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of available command namespaces in alphabetical order.
getNeighborList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.
getNeighbors() - Method in class org.cytoscape.view.layout.LayoutNode
Convenience function to return the list of neighbors (connected nodes) of this node.
getNetwork() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
Returns the network associated with this event.
getNetwork(String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a network into a CyNetwork.
getNetwork() - Method in class org.cytoscape.command.util.EdgeList
Return the network used by this EdgeList
getNetwork() - Method in class org.cytoscape.command.util.NodeList
Get the network for this nodelist
getNetwork(long) - Method in interface org.cytoscape.model.CyNetworkManager
Returns the network corresponding to the provided ID
getNetwork() - Method in interface org.cytoscape.model.CyTableMetadata
Returns all the networks associated with this object's table.
getNetworkForTable(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the network this table is registered with.
getNetworkPointer() - Method in interface org.cytoscape.model.CyNode
Returns the network referenced by this node.
getNetworks() - Method in class org.cytoscape.application.events.SetSelectedNetworksEvent
Returns the list of networks selected.
getNetworks() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getNetworks() - Method in interface org.cytoscape.io.read.CyNetworkReader
Returns an array of networks read after executing the run() method of Task.
getNetworks() - Method in class org.cytoscape.session.CySession
Returns a set of all CyNetwork objects contained in this Session.
getNetworkSet() - Method in interface org.cytoscape.group.CyGroup
Return the list of CyNetworks this group is in.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkManager
Provides the set of all the networks known to the network manager.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns a read-only set of all networks managed by this instance.
getNetworkView() - Method in class org.cytoscape.application.events.SetCurrentNetworkViewEvent
Returns the network view associated with this event.
getNetworkView() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Return the view that this Annotation is for
getNetworkView() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
Get the The target network view model.
getNetworkViewFactory() - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getNetworkViews() - Method in class org.cytoscape.application.events.SetSelectedNetworkViewsEvent
Returns the list of network views that have been selected.
getNetworkViews() - Method in class org.cytoscape.session.CySession
Returns a set of all CyNetworkView objects contained in this Session.
getNetworkViews(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Returns a collection of network views corresponding to the specified network, if found.
getNetworkViewSet() - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Provides the set of network views that are currently known to the network manager.
getNewColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the new name of the column.
getNewProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent
The new properties after being modified.
getNewState() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Returns the new state of the CytoPanel.
getNextSUID() - Static method in class org.cytoscape.model.SUIDFactory
Returns the next available SUID.
getNode(long) - Method in interface org.cytoscape.model.CyNetwork
Return the CyNode that has the SUID.
getNode() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the Node associated with this LayoutNode.
getNodeCount() - Method in interface org.cytoscape.model.CyNetwork
Return the number of nodes in this network.
getNodeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a nodelist into a list of CyNodes.
getNodeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of nodes contained within this group.
getNodeList() - Method in interface org.cytoscape.model.CyNetwork
Return a list of the nodes in this network.
getNodeList() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the list of LayoutNodes within this partition.
getNodeMap() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
Returns map from key value to existing CyNode.
getNodes() - Method in class org.cytoscape.model.events.AboutToRemoveNodesEvent
Returns the collection of nodes about to be removed.
getNodesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil
A utility method that returns a list of nodes that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getNodeView() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the View associated with this LayoutNode.
getNodeView(CyNode) - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a View for a specified Node.
getNodeViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of Views for all CyNodes in the network.
getNodeViews() - Method in class org.cytoscape.view.model.events.AddedNodeViewsEvent
Returns new node view object.
getNumTasks() - Method in class org.cytoscape.work.TaskIterator
Returns the current total number of tasks in the iterator.
getObject(Long, Class<T>) - Method in class org.cytoscape.session.CySession
When a session is restored, Cytoscape automatically generates new SUIDs.
getObject(String, Class<T>) - Method in class org.cytoscape.session.CySession
When a session is restored, Cytoscape automatically generates new SUIDs.
getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the old name of the column.
getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent
The old properties before they were modified.
getOldTitle() - Method in class org.cytoscape.model.events.TableTitleChangedEvent
 
getOrdinal(int) - Static method in class org.cytoscape.equations.FunctionUtil
Converts an integer to an ordinal string.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer
Return the Paint to be used to fill the Shape.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.ImageCustomGraphicLayer
Return the TexturePaint to be used as an image to fill a node
getPaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Paint to fill the shape with.
getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Returns an instance of PanelTaskManager.
getParams() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the parsed result from Tunable.getParams().
getParams() - Method in interface org.cytoscape.work.TunableHandler
Returns the parsed result from Tunable.getParams().
getParent() - Method in class org.cytoscape.view.model.VisualLexiconNode
Get the parent of this VP node.
getParent() - Method in interface org.cytoscape.work.swing.TunableUIHelper
Get the parent of the current Tunable dialog.
getParentVisualProperty() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Returns the parent visual property for this dependency.
getParser() - Method in interface org.cytoscape.equations.EquationCompiler
Returns the parser which can be used for checking the syntax of equations.
getParseTree() - Method in interface org.cytoscape.equations.EquationParser
Returns the parse tree.
getPartitionNumber() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the partition number of this partition
getPayloadCollection() - Method in class org.cytoscape.event.AbstractCyPayloadEvent
Returns an unmodifiable collection of payload objects.
getPayloadCollection() - Method in interface org.cytoscape.event.CyPayloadEvent
Returns a collection of payload objects.
getPoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets Specified Point.
getPointCount() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets Total Point Count.
getPossibleArgTypes(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
Used with the equation builder.
getPossibleArgTypes(Class<?>[]) - Method in interface org.cytoscape.equations.Function
Used with the equation builder.
getPossibleValues() - Method in class org.cytoscape.work.util.ListSelection
To get all the items of the List values.
getPreferredMenu() - Method in class org.cytoscape.application.swing.AbstractCyAction
This method returns a Menu specification string.
getPreferredMenu() - Method in interface org.cytoscape.application.swing.CyAction
This method returns a Menu specification string.
getPrefix() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Return the prefix to identify this custom graphics factory.
getPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in logs and other descriptions of the edit.
getPresentationWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of PresentationWriterManager.
getPrimaryKey() - Method in interface org.cytoscape.model.CyTable
Returns the column type of the primary key for this table.
getProperties() - Method in class org.cytoscape.application.swing.AbstractCyAction
Return the config props.
getProperties() - Method in interface org.cytoscape.application.swing.CyAction
Returns the configuration properties that were passed to the CyAction when it was created.
getProperties() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Return a property object.
getProperties() - Method in interface org.cytoscape.property.CyProperty
Return a property object.
getProperties() - Method in class org.cytoscape.property.SimpleCyProperty
Return a property object.
getProperties() - Method in class org.cytoscape.session.CySession
Returns a set of CyProperty objects defined for this session.
getProperties() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Get property values for the rendering engine, like LOD.
getProperty() - Method in interface org.cytoscape.io.read.CyPropertyReader
Return a property object.
getPropertyEditor() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getPropertyEditor() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
Returns PropertyEditor object for this data type.
getPropertyEditor(VisualProperty<T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor2
Returns PropertyEditor object for this data type.
getPropertyType() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the type of the property object.
getPropertyType() - Method in interface org.cytoscape.property.CyProperty
Returns the type of the property object.
getPropertyType() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the type of the property object.
getProvider() - Method in interface org.cytoscape.io.datasource.DataSource
Name of this data provider for this source.
getProvider() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getProvider(DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Get the provider name from DataSource object
getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifiedName() - Method in interface org.cytoscape.work.TunableHandler
Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifier() - Method in interface org.cytoscape.application.CyVersion
Any text following the last digit of the bug fix version.
getQueryBuilderGUI() - Method in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
Returns query builder UI.
getQueryBuilderGUI() - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUIClient
Returns query builder UI.
getRange() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getRange() - Method in interface org.cytoscape.view.model.VisualProperty
Returns the Range of this VisualProperty.
getRange() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Gets BoundaryRangeValues.
getRaw(String) - Method in interface org.cytoscape.model.CyRow
Returns the Object that contains the value for the specified column.
getRawValue() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the raw value that the data was set as.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader task.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader task.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getRecentlyOpenedURLs() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Returns the current list of recently opened file names.
getRedoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in redo menu items.
getRegisteredFunctions() - Method in interface org.cytoscape.equations.EquationParser
Returns the set of currently registered functions.
getRenderedImage() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
From layers of graphics objects, render a composite scaled Image object.
getRendererId() - Method in interface org.cytoscape.view.presentation.RenderingEngine
 
getRenderingEngine() - Method in class org.cytoscape.application.events.SetCurrentRenderingEngineEvent
Return the rendering engine (presentation) that has been set as current.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAboutToBeRemovedEvent
Returns the RenderingEngine associated with the deleted presentation.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAddedEvent
Get new rendering engine.
getRenderingEngine() - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewPanel
Deprecated.
getRenderingEngineFactory(String) - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getRenderingEngineManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of RenderingEngineManager.
getRenderingEngines(View<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Get rendering engines for the given view model.
getResults(Class<? extends R>) - Method in interface org.cytoscape.work.ObservableTask
Return the results from this task (if any)
getReturnType() - Method in class org.cytoscape.equations.AbstractFunction
Returns the static return type of this function.
getReturnType() - Method in interface org.cytoscape.equations.Function
 
getRightChild() - Method in class org.cytoscape.equations.AbstractNode
 
getRightChild() - Method in interface org.cytoscape.equations.TreeNode
Returns the right child if it exists or null if it doesn't.
getRoot() - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the root of this AbstractTreeTableModel.
getRootNetwork() - Method in interface org.cytoscape.group.CyGroup
Return the root network for this group.
getRootNetwork() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
Get target network collection, i.e., parent root network for all networks to be loaded.
getRootNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetworkManager
Converts a CyNetwork to a CyRootNetwork
getRootNetwork() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Return the CyRootNetwork that contains this CySubNetwork.
getRootNetworkList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getRootVisualProperty() - Method in interface org.cytoscape.view.model.VisualLexicon
Get root of this tree.
getRootVisualProperty() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
getRow(CyIdentifiable, String) - Method in interface org.cytoscape.model.CyNetwork
Returns the row for the specified table name for this object.
getRow(CyIdentifiable) - Method in interface org.cytoscape.model.CyNetwork
A convenience method that returns the row in the default table for this object.
getRow(Object) - Method in interface org.cytoscape.model.CyTable
Returns the row specified by the primary key object and if a row for the specified key does not yet exist in the table, a new row will be created and the new row will be returned.
getRow() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the CyRow of the data that was set.
getRow() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the CyRow for this LayoutEdge
getRow() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the CyRow associated with this LayoutNode.
getRowCount() - Method in interface org.cytoscape.model.CyTable
Returns the number of rows in this table.
getRowCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the number of rows in the JTree.
getRowList(CyTable, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a rowlist into a list of CyRows.
getSavedFileName() - Method in class org.cytoscape.session.events.SessionSavedEvent
Returns the file name of the session just loaded.
getSavedSession() - Method in class org.cytoscape.session.events.SessionSavedEvent
Returns the session that was just loaded.
getSavePolicy() - Method in interface org.cytoscape.model.CyNetwork
Returns how (or if) this CyNetwork should be saved.
getSavePolicy() - Method in interface org.cytoscape.model.CyTable
Returns how (or if) this CyTable should be saved.
getSavePolicy() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in interface org.cytoscape.property.CyProperty
Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the CyProperty.SavePolicy of the CyProperty.
getSearchResult() - Method in class org.cytoscape.io.webservice.events.SearchFinishedEvent
Returns The search result.
getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the currently selected component.
getSelectedIndex() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the currently selected index.
getSelectedIndex() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Returns the index of the CytoPanelComponent selected.
getSelectedNetworks() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the list of selected networks.
getSelectedNetworkViews() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the list of selected network views.
getSelectedValue() - Method in class org.cytoscape.work.util.ListSingleSelection
Get the item that is currently selected.
getSelectedValues() - Method in class org.cytoscape.work.util.ListMultipleSelection
Get the items that are currently selected.
getSerializableString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
 
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Bend
Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Handle
Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue
Returns serializable representation of this value.
getService(BundleContext, Class<S>) - Method in class org.cytoscape.service.util.AbstractCyActivator
A method that attempts to get a service of the specified type.
getService(BundleContext, Class<S>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator
A method that attempts to get a service of the specified type and that passes the specified filter.
getService(Class<S>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar
A method that attempts to get a service of the specified type.
getService(Class<S>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar
A method that attempts to get a service of the specified type and that passes the specified filter.
getServiceLocation() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getServiceLocation() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Returns resource location of this service, i.e., service URL.
getSession() - Method in interface org.cytoscape.io.read.CySessionReader
Returns a CySession object
getShape() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the current shape as a Shape object
getShape() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Shape
getShapeType() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the current shape type as a String
getSharedEdgeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the edge table shared by all subnetworks.
getSharedNetworkTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the network table shared by all subnetworks.
getSharedNodeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the node table shared by all subnetworks.
getSize() - Method in enum org.cytoscape.model.CyTableFactory.InitialTableSize
Returns the actual size value for the given enum.
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.
getSourceColumnList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getSourceJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the name of the column from the source table used for the join.
getSourceLocation() - Method in class org.cytoscape.equations.AbstractNode
 
getSourceLocation() - Method in class org.cytoscape.equations.CodeAndSourceLocation
 
getSourceLocation() - Method in interface org.cytoscape.equations.TreeNode
Returns the start of the location in the equation where the code was found that was turned into a node in the parse tree.
getSourceLocations() - Method in class org.cytoscape.equations.Equation
Returns the starting points in the original equation for each node in the parse tree that resulted from the original equation.
getSourceTable() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the originating table for this column if this column is virtual.
getSpecificZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the specific zoom for this annotation
getState() - Method in interface org.cytoscape.application.swing.CytoPanel
Gets the state of the CytoPanel.
getState() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns a string representation of the value of the Tunable associated with this GUITunableHandler.
getState() - Method in interface org.cytoscape.work.swing.GUITunableHandler
To get the current value of a Handler (or path for a FileHandler, or selected item(s) for ListMultipleSelection ListSingleSelection, ...)
getStatusToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the status JToolBar of the application.
getStreamUtil() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of StreamUtil.
getStrings(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Converts all arguments, including Lists to a uniform array of strings.
getStroke() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Stroke to use to outline the Shape provided by the PaintedShape.getShape() method above.
getStrokePaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Paint to use to color the Stroke returned by PaintedShape.getStroke().
getSubNetworkList() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Will return A list of all CySubNetworks contained in this root network.
getSucceeded() - Static method in class org.cytoscape.work.FinishStatus
Get a FinishStatus instance that indicates success.
getSuggestedNetworkTitle(String) - Method in interface org.cytoscape.session.CyNetworkNaming
Generates a unique network title based on a provided suggestion.
getSuggestedSubnetworkTitle(CyNetwork) - Method in interface org.cytoscape.session.CyNetworkNaming
Generates a unique title for a subnetwork based on a parent network.
getSUID() - Method in interface org.cytoscape.model.CyIdentifiable
Returns the SUID of the implementing object.
getSupportedArrows() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the list of supported arrow shapes
getSupportedClass() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Return the class that this factory creates.
getSupportedClasses() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of classes for which have aggregators.
getSupportedEdgeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportedEdgeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedNodeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportedNodeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedShapes() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the list of supported shapes.
getSupportedType() - Method in interface org.cytoscape.group.data.Aggregator
Return the Class this aggregator supports
getSupportsSelectedOnly() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportsSelectedOnly() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns true if this algorithm supports being applied to only the currently selected nodes.
getTable(String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a table into a CyTable.
getTable() - Method in class org.cytoscape.command.util.RowList
Get the table for this rowlist
getTable() - Method in interface org.cytoscape.model.CyColumn
Returns the table for this column.
getTable(Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetwork
Returns the table with the specified namespace and type from this network.
getTable(CyNetwork, Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the table with the specified namespace and type from the network.
getTable() - Method in interface org.cytoscape.model.CyRow
Returns the CyTable that this row belongs to.
getTable(long) - Method in interface org.cytoscape.model.CyTableManager
Returns the table with the specified SUID.
getTable() - Method in interface org.cytoscape.model.CyTableMetadata
Returns the table whose metadata is described by this instance.
getTable() - Method in class org.cytoscape.model.events.TableAboutToBeDeletedEvent
Returns the table that is about to be deleted from the table manager.
getTable() - Method in class org.cytoscape.model.events.TableAddedEvent
Returns the table added to the table manager.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
 
getTableNamespace(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the namespace of this table.
getTables() - Method in interface org.cytoscape.io.read.CyTableReader
Return an array of CyTable objects.
getTables(CyNetwork, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns a read-only map of all of the tables for the specified type from the network.
getTables() - Method in class org.cytoscape.session.CySession
Returns a set of all CyTable objects contained in this Session.
getTableType(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.
getTarget() - Method in interface org.cytoscape.model.CyEdge
Returns the target node determining this edge.
getTarget() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the target of this edge
getTarget() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Return the target object for this arrow.
getTargetColumnList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getTargetDataType() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getTargetDataType() - Method in interface org.cytoscape.view.model.VisualProperty
VisualProperty is always associated with a data type.
getTargetJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the name of the column from the target table used for the join.
getTargetObjectType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ListEditor
Type of object managed by this editor.
getTask() - Method in class org.cytoscape.work.FinishStatus
Returns the task that was cancelled or that had failed, or returns null if the task iterator succeeded.
getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of TaskManager.
getText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the text to be displayed as part of the annotation
getText() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the text to be displayed as part of the annotation
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the color of the text to be displayed
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the color of the text to be displayed
getThisComponent() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the Component that is this CytoPanel.
getTitle() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the title of the tab within the CytoPanel for this component.
getTitle() - Method in enum org.cytoscape.application.swing.CytoPanelName
Returns the human readable title used for labeling this CytoPanel.
getTitle() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getTitle() - Method in interface org.cytoscape.model.CyTable
Returns a human readable name for the CyTable.
getTitle() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns name of this visual style.
getToolbarGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
Returns the gravity used to place this action in the toolbar.
getToolBarGravity() - Method in class org.cytoscape.application.swing.AbstractToolBarComponent
Returns the gravity value for this toolbar component.
getToolbarGravity() - Method in interface org.cytoscape.application.swing.CyAction
Returns the gravity used to place this action in the toolbar.
getToolBarGravity() - Method in interface org.cytoscape.application.swing.ToolBarComponent
Returns the gravity used to place this component in the toolbar.
getTooltip() - Method in class org.cytoscape.work.AbstractTunableHandler
getToolTipText(MouseEvent) - Method in class org.cytoscape.util.swing.JTreeTable
The code in this method is copy and pasted from source code to the same method in javax.swing.JTable, except for one value change on one line.
getTransformers() - Method in interface org.cytoscape.filter.model.NamedTransformer
Returns the List of Transformers contained within this NamedTransformer.
getTransformerSource(Class<C>) - Method in interface org.cytoscape.filter.TransformerManager
Returns a TransformerSource for the given contextType.
getTranslatedValueType() - Method in interface org.cytoscape.view.vizmap.mappings.ValueTranslator
Returns compatible input data type.
getTree() - Method in class org.cytoscape.util.swing.JTreeTable
Returns the tree that is being shared between the model.
getType() - Method in class org.cytoscape.equations.AbstractNode
 
getType() - Method in class org.cytoscape.equations.Equation
The overall type of the Equation, e.g.
getType() - Method in interface org.cytoscape.equations.EquationParser
Returns the result type of the parsed equation if the parse succeeded, otherwise null.
getType() - Method in class org.cytoscape.equations.IdentDescriptor
Returns the, possibly adjusted, type of the descriptor as one of the types internally supported by equations.
getType() - Method in interface org.cytoscape.equations.TreeNode
Returns the type of this node.
getType() - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the type of combining semantics used by this filter.
getType() - Method in interface org.cytoscape.model.CyColumn
Returns the data type of the column.
getType() - Method in interface org.cytoscape.model.CyTableMetadata
Returns the type of the data associated with this object's table.
getType() - Method in class org.cytoscape.view.model.ContinuousRange
 
getType() - Method in class org.cytoscape.view.model.DiscreteRange
 
getType() - Method in interface org.cytoscape.view.model.Range
Type of object used in this range.
getType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
Returns the type of object managed in the Visual property.
getType() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the class type of the field or method annotated by Tunable.
getType() - Method in class org.cytoscape.work.FinishStatus
Specifies how the task iterator completed.
getType() - Method in interface org.cytoscape.work.TunableHandler
Returns the class type of the field or method annotated by Tunable.
getUndoableEditSupport() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport
Returns the UndoableEditSupport associated with this UndoSupport instance.
getUndoManager() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport
Returns the UndoManager associated with this UndoSupport instance.
getUndoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in undo menu items.
getUndoSupport() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of UndoSupport.
getUpperBound() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the upper limit of the object.
getURLConnection(URL) - Method in interface org.cytoscape.io.util.StreamUtil
Obtain a URLConnection for a given URL.
getUsageDescription() - Method in class org.cytoscape.equations.AbstractFunction
Used to provide help for users.
getUsageDescription() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getValidationState(Appendable) - Method in interface org.cytoscape.work.TunableValidator
Executes the validation test on the annotated Tunables.
getValue() - Method in class org.cytoscape.command.util.EdgeList
Return the edgeList for this tunable
getValue() - Method in class org.cytoscape.command.util.NodeList
Get the list of nodes
getValue() - Method in class org.cytoscape.command.util.RowList
Get the list of rows
getValue() - Method in class org.cytoscape.equations.IdentDescriptor
Returns the value of the descriptor.
getValue() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the value that the data was set as.
getValue() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the value that the visual property has been changed to.
getValue() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Gets Point Value.
getValue() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns an object describing a field / get method annotated with Tunable or null if no field / get method has been associated with this handler.
getValue() - Method in interface org.cytoscape.work.TunableHandler
Returns an object describing a field / get method annotated with Tunable or null if no field / get method has been associated with this handler.
getValue() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the value.
getValueAt(Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the value to be displayed for node node, at column number column.
getValueAt(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the value at the given row and column.
getValueEditor(Class<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns value editor for the given data type.
getValues(Class<? extends T>) - Method in interface org.cytoscape.model.CyColumn
Returns all the values, some of which may be null, for this given column.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor
Get type of the value to be edited.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyValueEditor
Get type of the value to be edited.
getVariableReferences() - Method in class org.cytoscape.equations.Equation
Returns all the variable references that occur as part if this Equation.
getVariableReferences() - Method in interface org.cytoscape.equations.EquationParser
Returns all the variable names that have been detected in the most recently parsed equation.
getVersion() - Method in interface org.cytoscape.application.CyVersion
The full version as a string, for example "3.2.5-alpha".
getVersion() - Method in class org.cytoscape.property.bookmark.Bookmarks
Gets the value of the version property.
getView() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the view that has been changed.
getViewModel() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Returns View being rendered.
getViewVisualStyleMap() - Method in class org.cytoscape.session.CySession
Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.
getVirtualColumnInfo() - Method in interface org.cytoscape.model.CyColumn
Returns information about the virtual column definition of this column.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Provide all compatible Visual Properties as a VisualLexicon.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory
Returns supported VisualLexicon supported by this rendering engine implementation.
getVisualLexiconNode(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon
Get a tree node in for the given VisualProperty.
getVisualLexiconNode(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
getVisualMappingFunction(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Get current VisualMappingFunction for the VisualProperty.
getVisualMappingFunctionContinuousFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionDiscreteFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionPassthroughFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingManager() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of VisualMappingManager.
getVisualProperties() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
A set of Visual Properties to be set by the parent if locked.
getVisualProperty() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the visual property that has been changed.
getVisualProperty(VisualProperty<T>) - Method in interface org.cytoscape.view.model.View
Get the actual value for the given visual property.
getVisualProperty() - Method in class org.cytoscape.view.model.VisualLexiconNode
Returns wrapped VisualProperty object.
getVisualProperty() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getVisualProperty() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Visual Property associated with this function.
getVisualPropertyEditor(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns the VisualPropertyEditor for the given VisualProperty.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.SetCurrentVisualStyleEvent
Get the newly selected current Visual Style.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
Get the VisualStyle that was set to the network view.
getVisualStyle(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns the VisualStyle associated with the target network view model.
getVisualStyleAdded() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent
Get the newly created VisualStyle.
getVisualStyleFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Returns an instance of VisualStyleFactory.
getVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader
Returns a list of VisualStyle objects.
getVisualStyles() - Method in class org.cytoscape.session.CySession
Returns a set containing all VisualStyles defined for this session.
getVisualStyleToBeRemoved() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent
Returns target VisualStyle to be removed from manager.
getWeight() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the current value for this edge's weight.
getWidth() - Method in class org.cytoscape.view.layout.LayoutNode
Return the width of this node
getWidth() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the total width of all of the LayoutNodes
getWidth() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Returns width of current object.
getWindow(Class<?>) - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUI
Returns the Window that contains the unified web service UI.
getWriter(CyNetwork, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified network to the specified file of the specified file type.
getWriter(CyNetwork, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified network to the specified output steam of the specified file type.
getWriter(CyNetworkView, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified view to the specified file of the specified file type.
getWriter(CyNetworkView, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified view to the specified output steam of the specified file type.
getWriter(Object, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyWriter Task that will attempt to write the specified property object to the specified file of the specified file type.
getWriter(Object, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyWriter Task that will attempt to write the specified property object to the specified output stream of the specified file type.
getWriter(CySession, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CySessionWriterManager
Returns the CyWriter Task that will attempt to write the specified session to the specified file of the specified file type.
getWriter(CySession, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CySessionWriterManager
Returns the CyWriter Task that will attempt to write the specified session to the specified output stream of the specified file type.
getWriter(CyTable, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyTableWriterManager
Returns the CyWriter Task that will attempt to write the specified table to the specified file of the specified file type.
getWriter(CyTable, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyTableWriterManager
Returns the CyWriter Task that will attempt to write the specified table to the specified output stream of the specified file type.
getWriter(View<?>, RenderingEngine<?>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.PresentationWriterManager
Returns the CyWriter Task that will attempt to write the specified view to the specified file of the specified file type.
getWriter(View<?>, RenderingEngine<?>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.PresentationWriterManager
Returns the CyWriter Task that will attempt to write the specified view to the specified output stream of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified file of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified output stream of the specified file type.
getX() - Method in class org.cytoscape.view.layout.LayoutNode
Return the current X value for this LayoutNode.
getX() - Method in class org.cytoscape.view.layout.LayoutPoint
Returns the X location of the point.
getXDisp() - Method in class org.cytoscape.view.layout.LayoutNode
Return the current X displacement value for this LayoutNode.
getY() - Method in class org.cytoscape.view.layout.LayoutNode
Return the current Y value for this LayoutNode.
getY() - Method in class org.cytoscape.view.layout.LayoutPoint
Returns the Y location of the point.
getYDisp() - Method in class org.cytoscape.view.layout.LayoutNode
Return the current Y displacement value for this LayoutNode.
getZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the current zoom for this annotation
GRAVITY - Static variable in class org.cytoscape.work.AbstractTunableHandler
 
GravityTracker - Interface in org.cytoscape.util.swing
This interface sepecifies a tracker that will be used to insert items (submenus, menu items and separators) into a menu based on their "gravity" or "weight".
greaterValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
Will be used for interpolation upon larger domain values
GroupAboutToBeDestroyedEvent - Class in org.cytoscape.group.events
This event signals that a group is about to be destroyed -- i.e.
GroupAboutToBeDestroyedEvent(CyGroupManager, CyGroup) - Constructor for class org.cytoscape.group.events.GroupAboutToBeDestroyedEvent
Constructs event.
GroupAboutToBeDestroyedListener - Interface in org.cytoscape.group.events
GroupAboutToBeRemovedEvent - Class in org.cytoscape.group.events
This event signals that a group is about to be removed from a network, but not completely deleted.
GroupAboutToBeRemovedEvent(CyGroup, CyNetwork) - Constructor for class org.cytoscape.group.events.GroupAboutToBeRemovedEvent
Constructs event.
GroupAboutToBeRemovedListener - Interface in org.cytoscape.group.events
GroupAboutToCollapseEvent - Class in org.cytoscape.group.events
This event signals that a group is either about to be expanded or collapsed in a particular network.
GroupAboutToCollapseEvent(CyGroup, CyNetwork, boolean) - Constructor for class org.cytoscape.group.events.GroupAboutToCollapseEvent
Constructs event.
GroupAboutToCollapseListener - Interface in org.cytoscape.group.events
GroupAddedEvent - Class in org.cytoscape.group.events
This event signals that a new group has been added.
GroupAddedEvent(CyGroupManager, CyGroup) - Constructor for class org.cytoscape.group.events.GroupAddedEvent
Constructs event.
GroupAddedListener - Interface in org.cytoscape.group.events
Listener for GroupAddedEvent
GroupAddedToNetworkEvent - Class in org.cytoscape.group.events
This event signals that an existing group has been added to a new network.
GroupAddedToNetworkEvent(CyGroup, CyNetwork) - Constructor for class org.cytoscape.group.events.GroupAddedToNetworkEvent
Constructs event.
GroupAddedToNetworkListener - Interface in org.cytoscape.group.events
GroupAnnotation - Interface in org.cytoscape.view.presentation.annotations
The Group annotation is a container for a collextion of annotations that should be grouped together.
GroupCollapsedEvent - Class in org.cytoscape.group.events
This event signals that a group has either been expanded or collapsed in a particular network.
GroupCollapsedEvent(CyGroup, CyNetwork, boolean) - Constructor for class org.cytoscape.group.events.GroupCollapsedEvent
Constructs event.
GroupCollapsedListener - Interface in org.cytoscape.group.events
Listener for GroupCollapsedEvent
GroupEdgesAddedEvent - Class in org.cytoscape.group.events
This event signals that edges have been added to the network.
GroupEdgesAddedEvent(CyGroup, CyEdge) - Constructor for class org.cytoscape.group.events.GroupEdgesAddedEvent
Constructs event.
GroupEdgesAddedEvent(CyGroup, List<CyEdge>) - Constructor for class org.cytoscape.group.events.GroupEdgesAddedEvent
Constructs event.
GroupEdgesAddedListener - Interface in org.cytoscape.group.events
GroupEdgesRemovedEvent - Class in org.cytoscape.group.events
This event signals that edges have been removed from the network.
GroupEdgesRemovedEvent(CyGroup, CyEdge) - Constructor for class org.cytoscape.group.events.GroupEdgesRemovedEvent
Constructs event.
GroupEdgesRemovedEvent(CyGroup, List<CyEdge>) - Constructor for class org.cytoscape.group.events.GroupEdgesRemovedEvent
Constructs event.
GroupEdgesRemovedListener - Interface in org.cytoscape.group.events
GroupNodesAddedEvent - Class in org.cytoscape.group.events
This event signals that edges have been added to the network.
GroupNodesAddedEvent(CyGroup, CyNode) - Constructor for class org.cytoscape.group.events.GroupNodesAddedEvent
Constructs event.
GroupNodesAddedEvent(CyGroup, List<CyNode>) - Constructor for class org.cytoscape.group.events.GroupNodesAddedEvent
Constructs event.
GroupNodesAddedListener - Interface in org.cytoscape.group.events
GroupNodesRemovedEvent - Class in org.cytoscape.group.events
This event signals that edges have been removed from the network.
GroupNodesRemovedEvent(CyGroup, CyNode) - Constructor for class org.cytoscape.group.events.GroupNodesRemovedEvent
Constructs event.
GroupNodesRemovedEvent(CyGroup, List<CyNode>) - Constructor for class org.cytoscape.group.events.GroupNodesRemovedEvent
Constructs event.
GroupNodesRemovedListener - Interface in org.cytoscape.group.events
GroupNodesTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for grouping nodes.
gui - Variable in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
 
GUITunableHandler - Interface in org.cytoscape.work.swing
An extension of TunableHandler with added functionality to support the construction of a Swing-based UI.
GUITunableHandlerFactory<T extends GUITunableHandler> - Interface in org.cytoscape.work.swing
A specialization fo TunableHandlerFactory for GUITunableHandler.

H

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

I

ID - Static variable in interface org.cytoscape.work.ServiceProperties
Unique ID of an OSGi service.
IdentDescriptor - Class in org.cytoscape.equations
Used to hold a current value for an equation's variable reference.
IdentDescriptor(Object) - Constructor for class org.cytoscape.equations.IdentDescriptor
Initializes a new IdentDescriptor and provides minimal type translation (from Integer to Long).
ImageAnnotation - Interface in org.cytoscape.view.presentation.annotations
This annotation positions an image on on the screen.
ImageCustomGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics
This interface defines a CustomGraphicLayer that paints an image on a node.
ImportDataTableTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for importing a table data in a network data table.
IN_CONTEXT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
Action will be added to context menu if this flag is set to true.
IN_MENU_BAR - Static variable in interface org.cytoscape.work.ServiceProperties
Action will be added to menu bar if this flag is set to true
IN_NETWORK_PANEL_CONTEXT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
Action will be added to network panel's context menu if this flag is set to true
IN_TOOL_BAR - Static variable in interface org.cytoscape.work.ServiceProperties
Action will be added to tool bar if this flag is set to true
includeMax() - Method in class org.cytoscape.view.model.ContinuousRange
Returns true if the maximum value is included in this range.
includeMin() - Method in class org.cytoscape.view.model.ContinuousRange
Returns true if the minimum value is included in this range.
incr - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
The value used for spacing nodes.
increment(double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Increment the location of this node by (x,y).
incrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Increment the displacement recorded for this node by (x,y).
indexOf(Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the index of filter within the list of children, or -1 if filter is not in that list.
indexOfComponent(Component) - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the index for the specified component.
indexOfComponent(String) - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the index for the component that has the specified identifier.
inMenuBar - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether the action is in a menu.
inputStream - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
Data stream for the networks to be created.
InputStreamTaskFactory - Interface in org.cytoscape.io.read
A super interface that allows the input stream to be set for reader task factories.
inRange(T) - Method in class org.cytoscape.view.model.ContinuousRange
 
inRange(T) - Method in class org.cytoscape.view.model.DiscreteRange
 
inRange(T) - Method in interface org.cytoscape.view.model.Range
Return true if the given value is in the range defined in this class.
insert(int, Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter
Inserts filter at the given index within the list of children.
INSERT_SEPARATOR_AFTER - Static variable in interface org.cytoscape.work.ServiceProperties
Insert separator after this menu item
INSERT_SEPARATOR_BEFORE - Static variable in interface org.cytoscape.work.ServiceProperties
Insert separator before this menu item
insertHandleAt(int, Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend
Insert a Handle to the specified position in the Bend
insertSeparatorAfter - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether a separator should be inserted after this item
insertSeparatorAfter() - Method in class org.cytoscape.application.swing.AbstractCyAction
Insert a separator after this menu item.
insertSeparatorAfter() - Method in interface org.cytoscape.application.swing.CyAction
Insert a separator after this menu item.
insertSeparatorBefore - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether a separator should be inserted before this item
insertSeparatorBefore() - Method in class org.cytoscape.application.swing.AbstractCyAction
Insert a separator before this menu item.
insertSeparatorBefore() - Method in interface org.cytoscape.application.swing.CyAction
Insert a separator before this menu item.
insertTasksAfter(Task, Task...) - Method in class org.cytoscape.work.TaskIterator
Inserts "newTasks" immediately after "referenceTask".
insertTasksAfter(Task, TaskIterator) - Method in class org.cytoscape.work.TaskIterator
Inserts "newTasks" immediately after "referenceTask".
insertTasksAfterCurrentTask(Task...) - Method in class org.cytoscape.work.AbstractTask
Inserts "newTasks" after the current Task, in the TaskIterator that is being managed by this class.
insertTasksAfterCurrentTask(TaskIterator) - Method in class org.cytoscape.work.AbstractTask
Inserts "newTasks" after the current Task, in the TaskIterator that is being managed by this class.
IntegerVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for Integer values.
IntegerVisualProperty(Integer, Range<Integer>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.IntegerVisualProperty
Constructor.
INTERACTION - Static variable in interface org.cytoscape.model.CyEdge
A String column created by default for every CyEdge that holds the interaction description of the edge.
INTERACTION_TRANSFORMER - Static variable in interface org.cytoscape.filter.transformers.Transformers
The id of the core Interaction Transformer, which finds nodes based on how they are connected to the input edges.
InteractivityChangedListener - Interface in org.cytoscape.filter.view
Listens for changes in the system-level state of interactivity.
Interpreter - Interface in org.cytoscape.equations
Executes the code represented by an equation.
inToolBar - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether the action is in the toolbar.
InvertSelectedEdgesTaskFactory - Interface in org.cytoscape.task.select
This interface provides a task iterator for inverting the selected edges.
InvertSelectedNodesTaskFactory - Interface in org.cytoscape.task.select
This interface provides a task iterator for inverting the selected nodes.
isAdvancedMode() - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
Deprecated.
isBasic(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
Deprecated.
isCellEditable(EventObject) - Method in class org.cytoscape.util.swing.AbstractCellEditor
isCellEditable(Object, int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
By default, make the column with the Tree in it the only editable one.
isCellEditable(EventObject) - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
Overridden to return false, and if the event is a mouse event it is forwarded to the tree.
isCellEditable(Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Indicates whether the the value for node node, at column number column is editable.
isCellEditable(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns whether the cell at the given location is editable.
isChildOf(VisualProperty<?>, VisualProperty<?>, VisualLexicon) - Static method in class org.cytoscape.view.presentation.property.VisualPropertyUtil
Check whether the given VisualProperty is a child of parent vp or not.
isCollapsed(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Return whether this group is expanded or collapsed in the designated network.
isCollapsed() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Returns the current state of the panel, collapsed (true) or expanded (false).
isCompatible(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
Returns true if given VisualProperty is compatible with current rendering engine.
isCompatibleList(Class) - Method in class org.cytoscape.equations.ArgDescriptor
Returns true if "listType", which must be some type of List is a type compatible with this argument descriptor.
isCompatibleWith(Class) - Method in class org.cytoscape.equations.ArgDescriptor
Tests to see if the specified class is compatible with this ArgType.
isDefaultShape(ArrowShape) - Static method in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
 
isDefaultShape(NodeShape) - Static method in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
Returns true if the specified shape is one of the possible default shape values.
isDependencyEnabled() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Returns whether or not this dependency is enabled.
isDirected() - Method in interface org.cytoscape.model.CyEdge
This will return true if the edge is directed and false if the node is undirected.
isDirectlyLocked(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View
Returns true if the given VisualProperty's value has been locked.
isDiscrete() - Method in class org.cytoscape.view.model.ContinuousRange
 
isDiscrete() - Method in class org.cytoscape.view.model.DiscreteRange
 
isDiscrete() - Method in interface org.cytoscape.view.model.Range
If this range is a set of discrete values, return true.
isEnabled - Variable in class org.cytoscape.application.swing.AbstractToolBarComponent
Whether the toolbar component is enabled or not.
isForcedToSetDirectly() - Method in interface org.cytoscape.work.swing.DirectlyPresentableTunableHandler
If this method returns true, the boolean will be presented to set directly from GUI without being a part of a parent panel.
isGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Test to see if this node represents a CyGroup in a particular CyNetwork.
isImmutable() - Method in interface org.cytoscape.model.CyColumn
Returns true if the column is immutable i.e.
isImmutable() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns true if this virtual column was originally created immutable.
isInMenuBar() - Method in class org.cytoscape.application.swing.AbstractCyAction
By default all CytoscapeActions wish to be included in the menu bar at the 'preferredMenuName' location is specified and the 'Tools' menu not.
isInMenuBar() - Method in interface org.cytoscape.application.swing.CyAction
Returns whether the action should be in the menu bar.
isInNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Check to see if this group is defined in a particular network.
isInToolBar() - Method in class org.cytoscape.application.swing.AbstractCyAction
By default no CytoscapeActions will be included in the toolbar.
isInToolBar() - Method in interface org.cytoscape.application.swing.CyAction
Returns whether the action should be in the tool bar.
isLeaf(Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns true if the specified node is a leaf, false otherwise.
isLocked() - Method in class org.cytoscape.view.layout.LayoutNode
Returns "true" if this node is locked, false otherwise.
isLowerBoundStrict() - Method in class org.cytoscape.work.util.AbstractBounded
Does the value have to be strictly greater than the lower bound?
isOptional() - Method in class org.cytoscape.equations.ArgDescriptor
Returns whether the ArgType is optional.
isOptional() - Method in enum org.cytoscape.equations.ArgType
Returns true if this type is optional.
isPrimaryKey() - Method in interface org.cytoscape.model.CyColumn
Returns true if the column is the primary key, otherwise false.
isPublic() - Method in interface org.cytoscape.model.CyTable
A public CyTable is a table that is accessible to the user through the user interface.
isReady(InputStream, String) - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory
Returns true if the factory is ready to be produce a TaskIterator and false otherwise.
isReady(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory
Returns true if the factory is ready to be produce a TaskIterator and false otherwise.
isReady(View<CyEdge>, CyNetworkView) - Method in class org.cytoscape.task.AbstractEdgeViewTaskFactory
Returns true if the supplied edge and network views are not null.
isReady(Collection<CyNetwork>) - Method in class org.cytoscape.task.AbstractNetworkCollectionTaskFactory
Returns true if the supplied collection is not null.
isReady(CyNetwork) - Method in class org.cytoscape.task.AbstractNetworkTaskFactory
Returns true if the supplied network is not null.
isReady(Collection<CyNetworkView>) - Method in class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory
Returns true if the supplied collection is not null.
isReady(CyNetworkView, Point2D, Point2D) - Method in class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory
Returns true if the supplied view and coordinates are not null.
isReady(CyNetworkView) - Method in class org.cytoscape.task.AbstractNetworkViewTaskFactory
Returns true if the supplied network view is not null.
isReady(View<CyNode>, CyNetworkView) - Method in class org.cytoscape.task.AbstractNodeViewTaskFactory
Returns true of the supplied network and node views are not null.
isReady(CyColumn, Object) - Method in class org.cytoscape.task.AbstractTableCellTaskFactory
Returns true if the supplied column and value are not null.
isReady(CyColumn) - Method in class org.cytoscape.task.AbstractTableColumnTaskFactory
Returns true if the supplied column is not null.
isReady(CyTable) - Method in class org.cytoscape.task.AbstractTableTaskFactory
Returns true if the supplied table is not null.
isReady(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory
Returns true if this task factory is ready to produce a task iterator.
isReady(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory
Returns true if the node view and network view are in a state that is ready to be processed by the generated tasks and false otherwise.
isReady(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory
Returns true if this task factory is ready to produce a TaskIterator.
isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
isReady(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns true if the task factory is ready to produce a task iterator.
isReady() - Method in class org.cytoscape.work.AbstractTaskFactory
 
isReady() - Method in interface org.cytoscape.work.TaskFactory
Returns true if the TaskFactory has all necessary preconditions needed to generate a task that will execute properly, false otherwise.
isScalarArgType(Class) - Static method in class org.cytoscape.equations.FunctionUtil
Tests whether the argument is one of the scalar types used by equations.
isSelected() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Return true if this annotation is currently selected
isSet(String) - Method in interface org.cytoscape.model.CyRow
Indicates whether the column of the specified type contains a non-null value.
isSet(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View
Indicates whether or not the passed visual property is set with a non-null value.
isSupported(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon
Test the given Visual Property is supported in this Lexicon.
isSupported(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
isTypeOfList(Class) - Static method in class org.cytoscape.equations.FunctionUtil
Tests whether the argument is some kind of List.
isUpperBoundStrict() - Method in class org.cytoscape.work.util.AbstractBounded
Does the value have to be strictly lower than the upper bound?
isValueLocked(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View
Returns true if the value of the given VisualProperty or one of its ancestors is locked.
isVirtual() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns true if the column is virtual, otherwise false.

J

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

L

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

M

MapGlobalToLocalTableTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for mapping a global to a local table.
MappingFunctionFactoryManager - Interface in org.cytoscape.view.vizmap.gui
Manages factories to create actual mappings (discrete/passthrough/continuous).
MapTableToNetworkTablesTaskFactory - Interface in org.cytoscape.task.edit
TODO: Missing documentation
MAX_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
maxWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
 
MENU_GRAVITY - Static variable in interface org.cytoscape.work.ServiceProperties
Specify relative location of the action in the menu
menuCanceled(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction
This method can be used at your discretion, but otherwise does nothing.
menuDeselected(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction
This method can be used at your discretion, but otherwise does nothing.
menuGravity - Variable in class org.cytoscape.application.swing.AbstractCyAction
The float value placing the action within the menu.
MenuGravityTracker - Class in org.cytoscape.util.swing
This class inserts menu items and separators in a menu based on their "gravity".
MenuGravityTracker(JMenu) - Constructor for class org.cytoscape.util.swing.MenuGravityTracker
Constructor.
menuSelected(MenuEvent) - Method in class org.cytoscape.application.swing.AbstractCyAction
This method can be overridden by individual actions to set the state of menu items based on whatever unique circumstances that menu option cares about.
MergeTablesTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for merging two data tables.
MIN_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
minWeightCutoff - Variable in class org.cytoscape.view.layout.EdgeWeighter
 
moveAnnotation(Point2D) - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Move an annotation to the specified location
moveNodeToLocation(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutPartition
Move the node to its current X and Y values.
moveToLocation() - Method in class org.cytoscape.view.layout.LayoutNode
Move the node to its current x,y coordinate.

N

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

O

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

P

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

R

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

S

SAVE - Static variable in interface org.cytoscape.util.swing.FileUtil
Equal to FileDialog.SAVE.
saveBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Store a bookmark object in bookmarks object
saveBookmark(Bookmarks, String, DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Store a bookmark object in bookmarks object
saveDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Save a DataSource to the DataSourceManager
SavePolicy - Enum in org.cytoscape.model
The SavePolicy of an object specifies whether or not it will be saved.
savePolicy - Variable in class org.cytoscape.property.AbstractConfigDirPropsReader
The SavePolicy of this CyProperty.
SaveSessionAsTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for saving a session in a specified file.