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A

abortShutdown(String) - Method in class org.cytoscape.application.events.CyShutdownEvent
A callback to the firing class that allows a listener to abort the shutdown.
abortShutdownReason() - Method in class org.cytoscape.application.events.CyShutdownEvent
Returns the reason that the application should not be shut down.
AboutToRemoveColumnViewEvent - Class in org.cytoscape.view.model.events
When column Views are about to be removed from a CyTableView, this event will be fired.
AboutToRemoveColumnViewEvent(CyTableView, View<CyColumn>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveColumnViewEvent
 
AboutToRemoveColumnViewListener - Interface in org.cytoscape.view.model.events
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
AboutToRemoveRowViewsEvent - Class in org.cytoscape.view.model.events
When row Views are about to be removed from a CyTableView, this event will be fired.
AboutToRemoveRowViewsEvent(CyTableView, Collection<View<CyRow>>) - Constructor for class org.cytoscape.view.model.events.AboutToRemoveRowViewsEvent
 
AboutToRemoveRowViewsListener - Interface in org.cytoscape.view.model.events
AbstractBounded<N extends Comparable<N>> - Class in org.cytoscape.work.util
A bounded number object whose bounds values cannot be modified
AbstractBounded(N, N, N, boolean, boolean) - Constructor for class org.cytoscape.work.util.AbstractBounded
Creates a new Bounded object.
AbstractCellEditor - Class in org.cytoscape.util.swing
An abstract, convenience implementation of a Cell Editor that really only adds event listener support.
AbstractCellEditor() - Constructor for class org.cytoscape.util.swing.AbstractCellEditor
 
AbstractConfigDirPropsReader - Class in org.cytoscape.property
An abstract implementation of CyProperty<Properties> that attempts to read the specified properties file first from the jar file running this code and then appends any properties found in the local configuration directory to that properties object.
AbstractConfigDirPropsReader(String, String, CyProperty.SavePolicy) - Constructor for class org.cytoscape.property.AbstractConfigDirPropsReader
Creates a new AbstractConfigDirPropsReader object.
AbstractCyAction - Class in org.cytoscape.application.swing
An abstract implementation of the CyAction interface.
AbstractCyAction(String) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object that is always enabled.
AbstractCyAction(String, CyApplicationManager, String, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object that is enabled for the specific "enableFor" state.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, CyApplicationManager, CyNetworkViewManager, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyAction(Map<String, String>, TaskFactory) - Constructor for class org.cytoscape.application.swing.AbstractCyAction
Creates a new AbstractCyAction object.
AbstractCyActivator - Class in org.cytoscape.service.util
A simple BundleActivator with convenience methods for registering OSGi services and either getting references to single services or registering interest in all services of a specified type.
AbstractCyActivator() - Constructor for class org.cytoscape.service.util.AbstractCyActivator
Constructor.
AbstractCyApp - Class in org.cytoscape.app
Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCyApp(CyAppAdapter) - Constructor for class org.cytoscape.app.AbstractCyApp
Deprecated.
The constructor that all apps must call using "super(adapter);" where the "adapter" is a CyAppAdapter reference provided as an argument to the constructor.
AbstractCyEdit - Class in org.cytoscape.work.undo
A small class used to create new undoable edits.
AbstractCyEdit(String) - Constructor for class org.cytoscape.work.undo.AbstractCyEdit
Constructor.
AbstractCyEvent<T> - Class in org.cytoscape.event
A base implementation of CyEvent that can be used by events.
AbstractCyEvent(T, Class<?>) - Constructor for class org.cytoscape.event.AbstractCyEvent
Constructor.
AbstractCyJob - Class in org.cytoscape.jobs
This can be used as a base class for custom implementations of CyJob
AbstractCyJob(String, String, CyJobExecutionService, CyJobDataService, CyJobMonitor) - Constructor for class org.cytoscape.jobs.AbstractCyJob
 
AbstractCyNetworkReader - Class in org.cytoscape.io.read
 
AbstractCyNetworkReader(InputStream, CyApplicationManager, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
 
AbstractCyNetworkReader(InputStream, CyNetworkViewFactory, CyNetworkFactory, CyNetworkManager, CyRootNetworkManager) - Constructor for class org.cytoscape.io.read.AbstractCyNetworkReader
 
AbstractCyPayloadEvent<T,​P> - Class in org.cytoscape.event
A base implementation of CyPayloadEvent that can be used by events.
AbstractCyPayloadEvent(T, Class<?>, Collection<P>) - Constructor for class org.cytoscape.event.AbstractCyPayloadEvent
Constructor.
AbstractCySwingApp - Class in org.cytoscape.app.swing
Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
AbstractCySwingApp(CySwingAppAdapter) - Constructor for class org.cytoscape.app.swing.AbstractCySwingApp
Deprecated.
The constructor that all apps must call using "super(adapter);" where the "adapter" is a CySwingAppAdapter reference provided as an argument to the constructor.
AbstractEdgeViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on an edge view and possibly its associated network view.
AbstractEdgeViewTask(View<CyEdge>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractEdgeViewTask
Base constructor for all tasks that need an edge view to operate on.
AbstractEdgeViewTaskFactory - Class in org.cytoscape.task
An EdgeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractEdgeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractEdgeViewTaskFactory
 
AbstractFunction - Class in org.cytoscape.equations
Base class for all Function implementations.
AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction
Base class constructor for easy creation of Functions from function argument descriptors.
AbstractGUITunableHandler - Class in org.cytoscape.work.swing
Base class for the various Swing implementations of TunableHandler.
AbstractGUITunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that annotate a control.
AbstractGUITunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.swing.AbstractGUITunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractGUITunableHandler.TunableFieldPanel - Class in org.cytoscape.work.swing
The main goal of this panel is to store the handler's label and control, in order to make it possible to consistently align labels and controls created by different AbstractGUITunableHandler subclasses when creating the Tunable form.
AbstractInputStreamTaskFactory - Class in org.cytoscape.io.read
TODO: Missing documentation
AbstractInputStreamTaskFactory(CyFileFilter) - Constructor for class org.cytoscape.io.read.AbstractInputStreamTaskFactory
 
AbstractLayoutAlgorithm - Class in org.cytoscape.view.layout
The AbstractLayoutAlgorithm provides a basic implementation of a layout TaskFactory.
AbstractLayoutAlgorithm(String, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutAlgorithm
The Constructor.
AbstractLayoutTask - Class in org.cytoscape.view.layout
This is a basic implementation of a LayoutAlgorithm Task that does some bookkeeping, but primarily delegates to the doLayout() method.
AbstractLayoutTask(String, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractLayoutTask
Constructor.
AbstractNetworkCollectionTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a Collection of CyNetworks.
AbstractNetworkCollectionTask(Collection<CyNetwork>) - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTask
Base Constructor for a task that will operate on a collection of networks
AbstractNetworkCollectionTaskFactory - Class in org.cytoscape.task
An NetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkCollectionTaskFactory
 
AbstractNetworkSearchTaskFactory - Class in org.cytoscape.application.swing.search
This abstract implementation of NetworkSearchTaskFactory makes the method AbstractNetworkSearchTaskFactory.getQueryComponent() optional.
AbstractNetworkSearchTaskFactory(String, String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
AbstractNetworkSearchTaskFactory(String, String, String, Icon, URL) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
AbstractNetworkSearchTaskFactory(String, String, Icon) - Constructor for class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
AbstractNetworkTask - Class in org.cytoscape.task
Base class for all tasks that need to operate on a CyNetwork.
AbstractNetworkTask(CyNetwork) - Constructor for class org.cytoscape.task.AbstractNetworkTask
Base class for tasks that need to operate on a CyNetwork
AbstractNetworkTaskFactory - Class in org.cytoscape.task
A NetworkTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkTaskFactory
 
AbstractNetworkViewCollectionTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a Collection of CyNetworkViews.
AbstractNetworkViewCollectionTask(Collection<CyNetworkView>) - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTask
Base class for any tasks that need to operate on a collection of network views.
AbstractNetworkViewCollectionTaskFactory - Class in org.cytoscape.task
A NetworkViewCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewCollectionTaskFactory
 
AbstractNetworkViewLocationTaskFactory - Class in org.cytoscape.task
A base class for task factories that need to add a functionality to the network view considering a given location (for example adding a node where a mouse was clicked).
AbstractNetworkViewLocationTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewLocationTaskFactory
 
AbstractNetworkViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a network view.
AbstractNetworkViewTask(CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNetworkViewTask
A base class for tasks that need to operate on a network view.
AbstractNetworkViewTaskFactory - Class in org.cytoscape.task
A NetworkViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNetworkViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNetworkViewTaskFactory
 
AbstractNode - Class in org.cytoscape.equations
A node in the parse tree.
AbstractNode(int) - Constructor for class org.cytoscape.equations.AbstractNode
Base class constructor for any Node type.
AbstractNodeViewTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTask(View<CyNode>, CyNetworkView) - Constructor for class org.cytoscape.task.AbstractNodeViewTask
Base class constructor for all tasks that need to operate on a node view and possibly its associated network view.
AbstractNodeViewTaskFactory - Class in org.cytoscape.task
A NodeViewTaskFactory that is always ready to produce a TaskIterator.
AbstractNodeViewTaskFactory() - Constructor for class org.cytoscape.task.AbstractNodeViewTaskFactory
 
AbstractParallelPartitionLayoutTask - Class in org.cytoscape.view.layout
This is an even more helpful implementation of a LayoutAlgorithm Task that extends AbstractPartitionLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractParallelPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractParallelPartitionLayoutTask
Creates a new AbstractPartitionLayoutTask object.
AbstractPartitionLayoutTask - Class in org.cytoscape.view.layout
This is a more helpful implementation of a LayoutAlgorithm Task that extends AbstractBasicLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually.
AbstractPartitionLayoutTask(String, boolean, CyNetworkView, Set<View<CyNode>>, String, UndoSupport) - Constructor for class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Creates a new AbstractPartitionLayoutTask object.
AbstractRootNetworkCollectionTask - Class in org.cytoscape.task
The base class for all tasks that need to operate on a Collection of CyRootNetworks.
AbstractRootNetworkCollectionTask(Collection<CyRootNetwork>) - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTask
 
AbstractRootNetworkCollectionTaskFactory - Class in org.cytoscape.task
A RootNetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
AbstractRootNetworkCollectionTaskFactory() - Constructor for class org.cytoscape.task.AbstractRootNetworkCollectionTaskFactory
 
AbstractRowTask - Class in org.cytoscape.task
Base class for all tasks that need to operate on a CyRow.
AbstractRowTask(CyRow) - Constructor for class org.cytoscape.task.AbstractRowTask
Base class constructor for all tasks that need to be provisioned with a CyRow.
AbstractStringTunableHandler - Class in org.cytoscape.command
 
AbstractStringTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
 
AbstractStringTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.command.AbstractStringTunableHandler
 
AbstractTableCellTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on a single CyTable cell.
AbstractTableCellTask(CyColumn, Object) - Constructor for class org.cytoscape.task.AbstractTableCellTask
Initializes a Task that needs to operate on a CyTable cell entry.
AbstractTableCellTaskFactory - Class in org.cytoscape.task
A TableCellTaskFactory that is always ready to produce a TaskIterator.
AbstractTableCellTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableCellTaskFactory
 
AbstractTableColumnTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on an entire CyTable column.
AbstractTableColumnTask(CyColumn) - Constructor for class org.cytoscape.task.AbstractTableColumnTask
Initializes a Task that needs to operate on a CyTable column.
AbstractTableColumnTaskFactory - Class in org.cytoscape.task
A TableColumnTaskFactory that is always ready to produce a TaskIterator.
AbstractTableColumnTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableColumnTaskFactory
 
AbstractTableTask - Class in org.cytoscape.task
A base class for Tasks that need to operate on an entire CyTable.
AbstractTableTask(CyTable) - Constructor for class org.cytoscape.task.AbstractTableTask
Initializes a Task that needs to operate on a CyTable.
AbstractTableTaskFactory - Class in org.cytoscape.task
A TableTaskFactory that is always ready to produce a TaskIterator.
AbstractTableTaskFactory() - Constructor for class org.cytoscape.task.AbstractTableTaskFactory
 
AbstractTask - Class in org.cytoscape.work
A base class for tasks that need to be able to access the TaskIterator that contains them.
AbstractTask() - Constructor for class org.cytoscape.work.AbstractTask
 
AbstractTaskFactory - Class in org.cytoscape.work
A TaskFactory that is always ready to produce a TaskIterator.
AbstractTaskFactory() - Constructor for class org.cytoscape.work.AbstractTaskFactory
 
AbstractTaskManager<T,​C> - Class in org.cytoscape.work
Provides access to a TunableInterceptor to all derived classes and a utility method to determine if an object has been annotated with Tunables.
AbstractTaskManager(TunableMutator) - Constructor for class org.cytoscape.work.AbstractTaskManager
Initializes an AbstractTaskManager object by setting its TunableInterceptor.
AbstractToolBarComponent - Class in org.cytoscape.application.swing
An abstract, convenience implementation of ToolBarComponent.
AbstractToolBarComponent() - Constructor for class org.cytoscape.application.swing.AbstractToolBarComponent
 
AbstractTransformer<C,​E> - Class in org.cytoscape.filter.model
A convenience base class for Transformers.
AbstractTransformer() - Constructor for class org.cytoscape.filter.model.AbstractTransformer
Creates a new AbstractTransformer.
AbstractTreeTableModel - Class in org.cytoscape.util.swing
An abstract implementation of the TreeTableModel interface, handling the list of listeners.
AbstractTreeTableModel(Object) - Constructor for class org.cytoscape.util.swing.AbstractTreeTableModel
Creates a new AbstractTreeTableModel object.
AbstractTunableHandler - Class in org.cytoscape.work
Provides the standard implementation for most of the methods declared by the TunableHandler interface.
AbstractTunableHandler(Field, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that annotate a field.
AbstractTunableHandler(Method, Method, Object, Tunable) - Constructor for class org.cytoscape.work.AbstractTunableHandler
Standard base class constructor for TunableHandlers that deal with Tunables that use getter and setter methods.
AbstractTunableInterceptor<T extends TunableHandler> - Class in org.cytoscape.work
An abstract base class for TunableRecorder and TunableMutator implementations.
AbstractTunableInterceptor() - Constructor for class org.cytoscape.work.AbstractTunableInterceptor
Creates a new AbstractTunableInterceptor object.
AbstractValidatableTransformer<C,​E> - Class in org.cytoscape.filter.model
A convenience base class for ValidatableTransformers.
AbstractValidatableTransformer() - Constructor for class org.cytoscape.filter.model.AbstractValidatableTransformer
Creates a new AbstractValidatableTransformer.
AbstractViewUpdater<S> - Class in org.cytoscape.application.swing
A utility class that provides an implementation of RowsSetListener for a particular column and VisualProperty.
AbstractViewUpdater(VisualProperty<S>, String, Map<CyRow, View<?>>) - Constructor for class org.cytoscape.application.swing.AbstractViewUpdater
Constructor.
AbstractVisualLexicon - Class in org.cytoscape.view.presentation.property
Reusable template implementation of VisualLexicon.
AbstractVisualLexicon(VisualProperty<NullDataType>) - Constructor for class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
AbstractVisualMappingFunction<K,​V> - Class in org.cytoscape.view.vizmap.mappings
A base class for visual mapping functions where all fields are immutable.
AbstractVisualMappingFunction(String, Class<K>, VisualProperty<V>, CyEventHelper) - Constructor for class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Constructs this AbstractVisualMappingFunction.
AbstractVisualProperty<T> - Class in org.cytoscape.view.model
An abstract implementation of VisualProperty that omits the methods dealing with serializing data.
AbstractVisualProperty(T, Range<T>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.model.AbstractVisualProperty
Constructor to set all immutable fields.
AbstractVisualPropertyEditor<T> - Class in org.cytoscape.view.vizmap.gui.editor
Abstract implementation of Visual Property Editor.
AbstractVisualPropertyEditor(Class<T>, PropertyEditor, ContinuousEditorType, ContinuousMappingCellRendererFactory) - Constructor for class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
Creates a new AbstractVisualPropertyEditor object.
AbstractVisualPropertyValue - Class in org.cytoscape.view.presentation.property.values
Base class for all VisualPropertyValue.
AbstractVisualPropertyValue(String, String) - Constructor for class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
Constructs an AbstractVisualPropertyValue.
AbstractWebServiceClient - Class in org.cytoscape.io.webservice.client
Abstract class for all web service clients.
AbstractWebServiceClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.client.AbstractWebServiceClient
Constructs this AbstractWebServiceClient.
AbstractWebServiceGUIClient - Class in org.cytoscape.io.webservice.swing
Abstract base class for web service clients with Swing GUI.
AbstractWebServiceGUIClient(String, String, String) - Constructor for class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
Constructor.
ACCELERATOR - Static variable in interface org.cytoscape.work.ServiceProperties
Shortcut key combination for desktop app.
acceleratorKeyStroke - Variable in class org.cytoscape.application.swing.AbstractCyAction
The accelerator keystroke, if set.
acceleratorSet - Variable in class org.cytoscape.application.swing.AbstractCyAction
Indicates whether accelerator keys have been set for the action.
accept(File) - Method in class org.cytoscape.util.swing.FileChooserFilter
Accept or not the file from JFileChooser.
accepts(C, E) - Method in interface org.cytoscape.filter.model.Filter
Returns true if this filter accepts the given element from context.
accepts(InputStream, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
This method always returns false in this particular implementation.
accepts(InputStream, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter
A method that attempts to determine whether the specified InputStream can be read by the Reader using this filter.
accepts(URI, DataCategory) - Method in class org.cytoscape.io.BasicCyFileFilter
 
accepts(URI, DataCategory) - Method in interface org.cytoscape.io.CyFileFilter
A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor
Returns true if this ArgDescriptor accepts multiple arguments, otherwise false.
acceptsMultipleArgs() - Method in enum class org.cytoscape.equations.ArgType
Returns true if this type accepts multiple args.
ActionEnableSupport - Class in org.cytoscape.application.swing
A class that allows the enabled state of an Action of JMenuItem to managed in a consistent way.
ActionEnableSupport(Action, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
ActionEnableSupport(JMenuItem, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
ActionEnableSupport(DynamicSubmenuListener, String, CyApplicationManager, CyNetworkViewManager) - Constructor for class org.cytoscape.application.swing.ActionEnableSupport
Constructor.
actuallyShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent
Returns true if no reason is provided to abort the shutdown and false if anyone processing this event wants to prevent shutdown.
adapter - Variable in class org.cytoscape.app.AbstractCyApp
Deprecated.
Reference to access Cytoscape functionality -- various managers and factories that are normally available as OSGi services.
add(Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, Object) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(Component, Object, int) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(String, Component) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
Overridden to add any new components to the content panel, as might be expected.
add(URL) - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Adds "newURL" to the list of recently opened file names and trims the list if it has exceeded its maximum length.
addAction(CyAction) - Method in interface org.cytoscape.application.swing.CySwingApplication
Add a CyAction to application.
addAggregator(Aggregator<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Add a new aggregator to the available aggregators.
addAnnotation(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Add an annotation to the specified network view.
addAnnotations(Collection<? extends Annotation>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Adds annotations to the specified network view.
addAppFiles(String, List<File>) - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent
A method that allows apps to specify a list of files that should be stored in the session.
addArrow(ArrowAnnotation) - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Add an arrow annotation to this annotation.
addBasicVisualProperty(VisualProperty<?>) - Static method in class org.cytoscape.view.vizmap.gui.util.PropertySheetUtil
Deprecated.
addBendFactory(BendFactory, Map<?, ?>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
addCellEditorListener(CellEditorListener) - Method in class org.cytoscape.util.swing.AbstractCellEditor
addChangeListener(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Adds the argument as a new dependency to this GUITunableHandler.
addChangeListener(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler
Adds a GUITunableHandler that listens to THIS tunable handler.
addCollapseListener(BasicCollapsiblePanel.CollapseListener) - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
 
addData(CyJobData, String, Object) - Method in interface org.cytoscape.jobs.CyJobDataService
Add a single data item to a CyJobData object.
addData(CyJobData, String, Map<Object, Object>) - Method in interface org.cytoscape.jobs.CyJobDataService
Add generic key, value pairs to a CyJobData item.
addData(CyJobData, String, CyNetwork, List<? extends CyIdentifiable>, List<String>, List<String>) - Method in interface org.cytoscape.jobs.CyJobDataService
An optional method to add network data to a CyJobData item.
addData(CyJobData, String, CyTable, List<CyRow>, List<String>) - Method in interface org.cytoscape.jobs.CyJobDataService
An optional method to add table data to a CyJobData item.
addData(CyJobData, String, CyNetworkView, List<? extends CyIdentifiable>, List<VisualProperty<?>>) - Method in interface org.cytoscape.jobs.CyJobDataService
An optional method to add network view data to a CyJobData item.
addDependent(GUITunableHandler) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Adds the argument as a new dependency to this GUITunableHandler.
addDependent(GUITunableHandler) - Method in interface org.cytoscape.work.swing.GUITunableHandler
Adds a GUITunableHandler that depends on THIS tunable handler.
AddedColumnViewEvent - Class in org.cytoscape.view.model.events
When column View is added to a CyTableView, this event will be fired.
AddedColumnViewEvent(CyTableView, View<CyColumn>) - Constructor for class org.cytoscape.view.model.events.AddedColumnViewEvent
 
AddedColumnViewListener - Interface in org.cytoscape.view.model.events
Listener for AddedColumnViewEvent.
AddedEdgesEvent - Class in org.cytoscape.model.events
An event fired when an edge is added to a network.
AddedEdgesEvent(CyNetwork, Collection<CyEdge>) - Constructor for class org.cytoscape.model.events.AddedEdgesEvent
Constructs event.
AddedEdgesListener - Interface in org.cytoscape.model.events
Listener for AddedEdgesEvents.
AddedEdgeViewsEvent - Class in org.cytoscape.view.model.events
When edge View is added to a CyNetworkView, this event will be fired.
AddedEdgeViewsEvent(CyNetworkView, Collection<View<CyEdge>>) - Constructor for class org.cytoscape.view.model.events.AddedEdgeViewsEvent
Creates the event for new edge views.
AddedEdgeViewsListener - Interface in org.cytoscape.view.model.events
Listener for AddedEdgeViewsEvent.
addEdge(CyEdge) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Adds an edge to this CySubNetwork.
addEdge(CyEdge, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition
Add an edge to this partition assuming that the source and target nodes are not yet known.
addEdge(CyEdge, LayoutNode, LayoutNode, CyRow) - Method in class org.cytoscape.view.layout.LayoutPartition
Add an edge to this partition assuming that the source and target nodes are known.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.CyNetwork
This method is used to create and add an edge to this network.
addEdge(CyNode, CyNode, boolean) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
A shortcut method that Creates a new CyEdge in both this subnetwork AND in the CyRootNetwork.
addEdges(List<CyEdge>) - Method in interface org.cytoscape.group.CyGroup
Add a list of edges to a group.
AddedNodesEvent - Class in org.cytoscape.model.events
Event for upper layers.
AddedNodesEvent(CyNetwork, Collection<CyNode>) - Constructor for class org.cytoscape.model.events.AddedNodesEvent
Constructs event.
AddedNodesListener - Interface in org.cytoscape.model.events
Listener for AddedNodesEvents.
AddedNodeViewsEvent - Class in org.cytoscape.view.model.events
When node View is added to a CyNetworkView, this event will be fired.
AddedNodeViewsEvent(CyNetworkView, Collection<View<CyNode>>) - Constructor for class org.cytoscape.view.model.events.AddedNodeViewsEvent
Creates the event for a new node view.
AddedNodeViewsListener - Interface in org.cytoscape.view.model.events
Listener for AddedNodeViewsEvent.
AddedRowViewsEvent - Class in org.cytoscape.view.model.events
When row View is added to a CyTableView, this event will be fired.
AddedRowViewsEvent(CyTableView, Collection<View<CyRow>>) - Constructor for class org.cytoscape.view.model.events.AddedRowViewsEvent
 
AddedRowViewsListener - Interface in org.cytoscape.view.model.events
Listener for AddedRowViewsEvent.
addEventPayload(S, P, Class<E>) - Method in interface org.cytoscape.event.CyEventHelper
Adds a payload object to be accumulated in a CyPayloadEvent.
addGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager
Registers a group with the group manager.
addGroups(List<CyGroup>) - Method in interface org.cytoscape.group.CyGroupManager
Registers a list of groups with the group manager.
addGroupToNetwork(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Add a group to an additional network.
addIcon(String, Icon) - Method in interface org.cytoscape.util.swing.IconManager
 
addIconFont(Font) - Method in interface org.cytoscape.util.swing.IconManager
 
addIdentifierMapping(Class<?>, String, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
addJob(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager
Add a job to be managed by the job manager.
addListener(TransformerListener) - Method in class org.cytoscape.filter.model.AbstractTransformer
 
addListener(TransformerListener) - Method in interface org.cytoscape.filter.model.Transformer
Subscribes the given listener to changes in this Transformer's parameters.
addListener(BoundedChangeListener<N>) - Method in class org.cytoscape.work.util.AbstractBounded
Adds a listener that will listen for changes to this object
addListener(ListChangeListener<T>) - Method in class org.cytoscape.work.util.ListSelection
Adds a listener that will listen for changes to this object
addMember(Annotation) - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation
Add a new annotation to the group.
addMenu(JMenu, double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a new submenu into a position based on "gravity" of the new item.
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenu(JMenu, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addMenuItem(JMenuItem, double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a new menu item into a position based on "gravity" of the new item.
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenuItem(JMenuItem, double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addMenuSeparator(double) - Method in interface org.cytoscape.util.swing.GravityTracker
Adds a separator into a position based on "gravity" of the new item.
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
addMenuSeparator(double) - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
addNamedTransformer(NamedTransformer<C, E>) - Method in interface org.cytoscape.filter.TransformerContainer
Add a NamedTransformer to this container.
addNeighbor(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
Convenience function to keep track of neighbors of this node.
addNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager
Registers a network with the network manager and sets the network as current.
addNetwork(CyNetwork, boolean) - Method in interface org.cytoscape.model.CyNetworkManager
Registers a network with the network manager.
addNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Registers a network view with the network view manager and sets the new view as current.
addNetworkView(CyNetworkView, boolean) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Registers a network view with the network view manager.
addNetworkViewListener(CyNetworkViewListener) - Method in interface org.cytoscape.view.model.CyNetworkView
Adds a CyNetworkViewListener (optional operation).
addNode() - Method in interface org.cytoscape.model.CyNetwork
This method is used to create and add a node to this network.
addNode() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
A shortcut method that Creates a new CyNode in both this subnetwork AND in the CyRootNetwork.
addNode(CyNetwork, View<CyNode>, boolean) - Method in class org.cytoscape.view.layout.LayoutPartition
Add a node to this partition.
addNode(CyNode) - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Adds a node to this CySubNetwork.
addNodes(List<CyNode>) - Method in interface org.cytoscape.group.CyGroup
Add a list of nodes and their edges
addNodes(LayoutNode, LayoutNode) - Method in class org.cytoscape.view.layout.LayoutEdge
Set the nodes associated with this edge.
addNonClearableVisualProperty(VisualProperty<?>) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig
Add a VisualProperty that will not have its value cleared when View.clearVisualProperties() is called.
addPaletteProvider(PaletteProvider) - Method in interface org.cytoscape.util.color.PaletteProviderManager
Add a palette provider to the manager.
addPoint(K, BoundaryRangeValues<V>) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Adds a New Data Point.
addRangeValue(T) - Method in class org.cytoscape.view.model.DiscreteRange
Add a value to this DiscreteRange.
addRenderingEngine(RenderingEngine<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Add new RenderingEngine to this manager.
addScalarArgumentTypes(List<Class>) - Static method in class org.cytoscape.equations.FunctionUtil
Adds the scalar types that equations use internally to the argument, i.e.
addSubNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create an empty CySubNetwork.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create a CySubNetwork containing the specified CyNodes and CyEdges.
addSubNetwork(Iterable<CyNode>, Iterable<CyEdge>, SavePolicy) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create a CySubNetwork containing the specified CyNodes and CyEdges.
addSubNetwork(SavePolicy) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Create an empty CySubNetwork which can have a different save policy from that of this root network, as long as the root network's policy is not SavePolicy.DO_NOT_SAVE.
addTable(CyTable) - Method in interface org.cytoscape.model.CyTableManager
Registers a new table with the manager and fires a TableAddedEvent event.
addTrackedVisualProperty(Object, VisualProperty<? extends T>, Predicate<V>) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig
Turns on tracking of the given VisualProperty such that nodes/edge that have the VisualProperty set to a value that satisfies the given Predicate are returned by the CyNetworkViewSnapshot.getTrackedNodes(Object) or CyNetworkViewSnapshot.getTrackedEdges(Object) method .
addTrackedVisualProperty(Object, VisualProperty<? extends T>, V) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryConfig
Turns on tracking of the given VisualProperty such that nodes/edge that have the VisualProperty set to a value that is equal to the given value are returned by the CyNetworkViewSnapshot.getTrackedNodes(Object) or CyNetworkViewSnapshot.getTrackedEdges(Object) method .
addTreeModelListener(TreeModelListener) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
 
addTunableHandlerFactory(TunableHandlerFactory<T>, Map) - Method in class org.cytoscape.work.AbstractTunableInterceptor
Allows TunableHandlerFactory services to be added to the list of factories used to process Tunables.
addTunableRecorder(TunableRecorder, Map) - Method in class org.cytoscape.work.AbstractTaskManager
Adds the specified TunableRecorder service to the task manager.
addValueEditor(ValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Add value editor OSGi services.
addVirtualColumn(String, String, CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable
Adds a "virtual" column to the the current table.
addVirtualColumns(CyTable, String, boolean) - Method in interface org.cytoscape.model.CyTable
Adds all columns in another table as "virtual" columns to the the current table.
addVisualMappingFunction(VisualMappingFunction<?, ?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Add a new VisualMappingFunction to this VisualStyle.
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
addVisualProperties(VisualProperty<NullDataType>) - Method in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
addVisualProperty(VisualProperty<?>, VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
Insert a VisualProperty to the tree.
addVisualPropertyDependency(VisualPropertyDependency<?>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
addVisualPropertyValueEditor(VisualPropertyValueEditor<?>, Map) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Add value editor--invoked by OSGi when a new bundle exports an instance.
addVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Add a new VisualStyle to this manager.
ADJACENCY_TRANSFORMER - Static variable in interface org.cytoscape.filter.transformers.Transformers
The id of the core Adjacency Transformer, which finds adjacent nodes and edges based on how they are connected to the input nodes.
adjustColumnPreferredWidth(JTable, int) - Static method in class org.cytoscape.util.swing.ColumnResizer
Adjust one table column to its preferred width.
adjustColumnPreferredWidth(JTable, int, boolean) - Static method in class org.cytoscape.util.swing.ColumnResizer
Adjust one table column to its preferred width.
adjustColumnPreferredWidths(JTable) - Static method in class org.cytoscape.util.swing.ColumnResizer
Adjust the columns in the table to their preferred widths.
adjustColumnPreferredWidths(JTable, boolean) - Static method in class org.cytoscape.util.swing.ColumnResizer
Adjust the columns in the table to their preferred widths.
aggregate(CyTable, CyGroup, CyColumn) - Method in interface org.cytoscape.group.data.Aggregator
Aggregate the column for the members of the specified group into the group.
Aggregator<T> - Interface in org.cytoscape.group.data
The Aggregator interface acts as a service interface for different methods of aggregating attribute data for the nodes in a CyGroup.
ALL - Enum constant in enum class org.cytoscape.filter.model.CompositeFilter.Type
Use set-intersection semantics (logical AND) to combine the results.
ALL - Static variable in class org.cytoscape.view.presentation.property.table.TableModeVisualProperty
 
ALL_NODE_VIEWS - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithm
A convenience declaration for an empty set signifying that all node views should be laid out when creating the task iterator.
allFinished(FinishStatus) - Method in interface org.cytoscape.work.TaskObserver
Called by a TaskManager to tell us that the task iterator has completed.
AMPERSAND - Enum constant in enum class org.cytoscape.equations.Token.Type
 
AnalyzeNetworkCollectionTaskFactory - Interface in org.cytoscape.task.analyze
Provides a TaskIterator to analyze a collection of networks.
ANCHOR - Enum constant in enum class org.cytoscape.view.presentation.annotations.ArrowAnnotation.AnchorType
 
AND - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType
Aggregated as a logical AND of all values.
ANGLE_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
Annotation - Interface in org.cytoscape.view.presentation.annotations
This is the base interface for all Annotations.
AnnotationFactory<T extends Annotation> - Interface in org.cytoscape.view.presentation.annotations
An interface describing a factory used to create Annotations.
AnnotationManager - Interface in org.cytoscape.view.presentation.annotations
The annotation manager is responsible for managing all of the annotations currently assigned to a particular org.cytoscape.view.model.NetworkView.
ANY - Enum constant in enum class org.cytoscape.equations.ArgType
Any scalar argument.
ANY - Enum constant in enum class org.cytoscape.filter.model.CompositeFilter.Type
Use set-union semantics (logical OR) to combine the results.
ANY - Enum constant in enum class org.cytoscape.model.CyEdge.Type
matches any edge
ANY - Enum constant in enum class org.cytoscape.util.color.BrewerType
Any (or all) palettes
ANY_LIST - Enum constant in enum class org.cytoscape.equations.ArgType
One or more lists with arbitrary member element types and/or one or more scalars.
append(Filter<C, E>) - Method in interface org.cytoscape.filter.model.CompositeFilter
Appends filter to the list of children.
append(Task) - Method in class org.cytoscape.work.TaskIterator
Adds the given task to the end of this iterator.
append(TaskIterator) - Method in class org.cytoscape.work.TaskIterator
Adds the tasks in the given TaskIterator to the end of this iterator.
appFileListMap(Map<String, List<File>>) - Method in class org.cytoscape.session.CySession.Builder
Returns an instance of Builder that has at least been configured with the specified app file list map.
The app name should follow the java class namespace convention (e.g.
apply(C, E, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.ElementTransformer
Transforms the given element.
apply(C, TransformerSource<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.model.HolisticTransformer
Transforms the elements in source from context.
apply(CyRow, View<? extends CyIdentifiable>) - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Apply mapping to the view model.
apply(CyRow, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Apply Visual Property values only to the given View Object (node or edge).
apply(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Apply Visual Style to the entire network view.
apply(View<CyColumn>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Apply Visual Style to the entire table view.
ApplyPreferredLayoutTaskFactory - Interface in org.cytoscape.task.visualize
This interface provides a task iterator for applying the preferred layout.
applyTunables(Object, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter
Applies each value from the key-value pairs in tunableValues to the tunable in the given object whose name matches the corresponding key.
ApplyVisualStyleTaskFactory - Interface in org.cytoscape.task.visualize
Marker interface which provides a task iterator for applying a visual style to views.
APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
Define standard context menus.
AppsFinishedStartingEvent - Class in org.cytoscape.app.event
An event that occurs when the Cytoscape core has started, and any installed apps have either finished starting or failed to start.
AppsFinishedStartingEvent(Object) - Constructor for class org.cytoscape.app.event.AppsFinishedStartingEvent
Create a new event with the given source.
AppsFinishedStartingListener - Interface in org.cytoscape.app.event
Listener for the AppsFinishedStartingEvent.
ARBITRARY_DOUBLE_RANGE - Static variable in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
ARBITRARY_STRING_RANGE - Static variable in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
ARCHIVE - Enum constant in enum class org.cytoscape.io.DataCategory
Data to be exported is an archive file
ArgDescriptor - Class in org.cytoscape.equations
A class describing a function argument.
ArgDescriptor(ArgType, String, String) - Constructor for class org.cytoscape.equations.ArgDescriptor
 
ArgType - Enum Class in org.cytoscape.equations
An enum specifying a function argument type.
argTypesAreValid(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
arrangeWindows(CyNetworkViewDesktopMgr.ArrangeType) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Request the desktop view manager to tile (or untile) the current network windows.
ARROW - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Pointy triangle shaped arrow
ARROW_SHORT - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Shorter pointy triangle shaped arrow
ArrowAnnotation - Interface in org.cytoscape.view.presentation.annotations
This is the interface for an arrow annotation.
ArrowAnnotation.AnchorType - Enum Class in org.cytoscape.view.presentation.annotations
This enum is used to indicate how the arrow is anchored to the source or target.
ArrowAnnotation.ArrowEnd - Enum Class in org.cytoscape.view.presentation.annotations
This enum is used to indicate which end of the arrow the operation is referring to.
ArrowShape - Interface in org.cytoscape.view.presentation.property.values
Marker interface representing edge end shape (arrow).
ArrowShapeVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for ArrowShape values.
ArrowShapeVisualProperty(ArrowShape, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Constructor.
associateMonitor(CyJob, String, int) - Method in interface org.cytoscape.jobs.CyJobManager
Associate a handler with a job.
associateMonitor(CyJob, CyJobMonitor, int) - Method in interface org.cytoscape.jobs.CyJobManager
Associate a monitor with a job.
attribNameAsReference(String) - Static method in class org.cytoscape.equations.EquationUtil
Converts a bare name to a variable reference.
AttributeHandlingType - Enum Class in org.cytoscape.group.data
The AttributeHandlingType enum contains the list of all of the different ways that attributes can be aggregated.
AUTO - Static variable in class org.cytoscape.view.presentation.property.table.TableModeVisualProperty
 
AUTO_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeStackingVisualProperty
 
AvailableCommands - Interface in org.cytoscape.command
TODO: Missing documentation
AVG - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType
Aggregated as the average of all values.

B

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

C

calcSampleVariance(double[]) - Static method in class org.cytoscape.equations.FunctionUtil
Calculates the sample variance of some numbers.
calculate_max_dimension(double, double, double, double, List<LayoutPartition>) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
 
calculateEdgeWeights() - Method in class org.cytoscape.view.layout.LayoutPartition
Calculate and set the edge weights.
calculateHandleLocation(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.view.presentation.property.values.Handle
Calculate absolute position of this handle for the given edge view.
cancel() - Method in class org.cytoscape.work.AbstractTask
Calling this attempts to abort the current Task.
cancel() - Method in interface org.cytoscape.work.Task
This method is called by the TaskManager when the user chooses to cancel the Task.
cancelCellEditing() - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
 
CANCELED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
 
cancelJob(CyJob) - Method in interface org.cytoscape.jobs.CyJobExecutionService
Cancel a running job.
cancelJob(CyJob) - Method in interface org.cytoscape.jobs.CyJobManager
Cancel the specified job
cancelled - Variable in class org.cytoscape.work.AbstractTask
If this is true, we should abort whatever the Task is currently doing in the run() method.
CANCELLED - Enum constant in enum class org.cytoscape.work.FinishStatus.Type
Indicates that the task iterator did not complete because one of its tasks was cancelled by the user.
CANVAS - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation
Arg map key to initialize the canvas to draw this annotation on
CARET - Enum constant in enum class org.cytoscape.equations.Token.Type
 
CASCADE - Enum constant in enum class org.cytoscape.application.swing.CyNetworkViewDesktopMgr.ArrangeType
 
category - Variable in class org.cytoscape.io.BasicCyFileFilter
Type of data that this filter applies to.
CELL - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CELL_BACKGROUND_PAINT - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CELL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CELL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CELL_TEXT_COLOR - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CELL_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
CellFormat - Class in org.cytoscape.view.presentation.property.table
 
CellFormat(String) - Constructor for class org.cytoscape.view.presentation.property.table.CellFormat
 
CellFormatVisualProperty - Class in org.cytoscape.view.presentation.property.table
Visual Property for CellFormat values.
CellFormatVisualProperty(CellFormat, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.table.CellFormatVisualProperty
 
CENTER - Enum constant in enum class org.cytoscape.view.presentation.annotations.ArrowAnnotation.AnchorType
 
CENTER - Enum constant in enum class org.cytoscape.view.presentation.property.values.Position
 
changeOccurred(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
 
changeOccurred(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler
This is called when a GUITunableHandler that this tunable handler listens to makes a change.
CheckBoxJList - Class in org.cytoscape.util.swing
This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 By Joshua Marinacci, Chris Adamson
CheckBoxJList() - Constructor for class org.cytoscape.util.swing.CheckBoxJList
Creates a new CheckBoxJList object.
checkDependency(String, String) - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
 
checkDependency(String, String) - Method in interface org.cytoscape.work.swing.GUITunableHandler
To check the dependencies of this GUITunableHandler with the others.
checkJobStatus(CyJob) - Method in interface org.cytoscape.jobs.CyJobExecutionService
Check on the status of a running job.
CIRCLE - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Circle shaped arrow
clamp(Double) - Method in class org.cytoscape.work.util.BoundedDouble
Clamp the value to be within the range.
clamp(Float) - Method in class org.cytoscape.work.util.BoundedFloat
Clamp the value to be within the range.
clamp(Integer) - Method in class org.cytoscape.work.util.BoundedInteger
Clamp the value to be within the range.
clamp(Long) - Method in class org.cytoscape.work.util.BoundedLong
Clamp the value to be within the range.
clamp(N) - Method in class org.cytoscape.work.util.AbstractBounded
Clamps the value of the Bounded object.
clear() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Clears the list of recently opened file names.
clear() - Method in interface org.cytoscape.jobs.CyJobData
Clear all of the data
clearValueLock(VisualProperty<?>) - Method in interface org.cytoscape.view.model.View
Clear value lock for given VisualProperty.
clearVisualProperties() - Method in interface org.cytoscape.view.model.View
Clear all VisualProperty values previously set to this view.
CloneNetworkTaskFactory - Interface in org.cytoscape.task.create
This interface provides a task iterator for network cloning.
CLOSE_BRACE - Enum constant in enum class org.cytoscape.equations.Token.Type
 
CLOSE_PAREN - Enum constant in enum class org.cytoscape.equations.Token.Type
 
CodeAndSourceLocation - Class in org.cytoscape.equations
Encapsulates compiled code with the location in the original source equation.
CodeAndSourceLocation(Object, int) - Constructor for class org.cytoscape.equations.CodeAndSourceLocation
 
collapse(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Collapse this group in the designated network.
collapsed() - Method in class org.cytoscape.group.events.GroupCollapsedEvent
Is the group collapsed or expanded?
collapsed() - Method in interface org.cytoscape.util.swing.BasicCollapsiblePanel.CollapseListener
 
CollapseGroupTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator collapsing selection of nodes from a node view.
collapsing() - Method in class org.cytoscape.group.events.GroupAboutToCollapseEvent
Is the group collapsed or expanded?
collect(T) - Method in interface org.cytoscape.filter.model.TransformerSink
Called for each element that is produced from a transformation.
COLON - Enum constant in enum class org.cytoscape.equations.Token.Type
 
COLOR - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
Used for mapping continuous attribute values to color visual property types such as Node Color.
COLOR - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Arg string to set the text color
ColorButton - Class in org.cytoscape.util.swing
JButton that opens a Color Chooser when clicked and shows the previously set color as an icon.
ColorButton(Color) - Constructor for class org.cytoscape.util.swing.ColorButton
The basic constructor for a color button without palettes.
ColorButton(CyServiceRegistrar, Palette, PaletteType, Color, boolean) - Constructor for class org.cytoscape.util.swing.ColorButton
The basic constructor for a color button with palettes.
ColorUtils - Class in org.cytoscape.util.color
 
ColorUtils() - Constructor for class org.cytoscape.util.color.ColorUtils
 
column - Variable in class org.cytoscape.task.AbstractTableCellTask
The CyColumn of the CyTable cell
column - Variable in class org.cytoscape.task.AbstractTableColumnTask
The CyColumn that descendants will operate on.
COLUMN - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_EDITABLE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_EXAMPLE - Static variable in interface org.cytoscape.command.StringToModel
 
COLUMN_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers
The id of the core Column Filter, which finds nodes and edges based on their column values.
COLUMN_FORMAT - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_GRAVITY - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
COLUMN_SELECTED - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_TEXT_WRAPPED - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
COLUMN_WIDTH - Static variable in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
ColumnCreatedEvent - Class in org.cytoscape.model.events
This event signals that a column has been created.
ColumnCreatedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnCreatedEvent
Deprecated.
ColumnCreatedEvent(CyTable, String, Long) - Constructor for class org.cytoscape.model.events.ColumnCreatedEvent
 
ColumnCreatedListener - Interface in org.cytoscape.model.events
Listener for ColumnCreatedEvents.
ColumnDeletedEvent - Class in org.cytoscape.model.events
This event signals that a column has been deleted.
ColumnDeletedEvent(CyTable, String) - Constructor for class org.cytoscape.model.events.ColumnDeletedEvent
Deprecated.
ColumnDeletedEvent(CyTable, String, Long) - Constructor for class org.cytoscape.model.events.ColumnDeletedEvent
 
ColumnDeletedListener - Interface in org.cytoscape.model.events
Listener for ColumnDeletedEvents.
columnName - Variable in class org.cytoscape.application.swing.AbstractViewUpdater
The name of the column that the RowsSetListener is provided for.
columnName - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Mapping attribute name.
ColumnNameChangedEvent - Class in org.cytoscape.model.events
This event signals that a columns name has been changed.
ColumnNameChangedEvent(CyTable, String, String) - Constructor for class org.cytoscape.model.events.ColumnNameChangedEvent
Constructs event.
ColumnNameChangedListener - Interface in org.cytoscape.model.events
Listener for ColumnNameChangedEvents.
ColumnResizer - Class in org.cytoscape.util.swing
Automatically resize column based on the objects in the cell.
columnType - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
Type of attribute.
ColumnVisualStyleSetEvent - Class in org.cytoscape.view.vizmap.events.table
Event fired when a VisualStyle is set to a column view through TableVisualMappingManager.setVisualStyle(View, VisualStyle).
ColumnVisualStyleSetEvent(TableVisualMappingManager, VisualStyle, View<CyColumn>) - Constructor for class org.cytoscape.view.vizmap.events.table.ColumnVisualStyleSetEvent
Creates the event.
ColumnVisualStyleSetListener - Interface in org.cytoscape.view.vizmap.events.table
COMMA - Enum constant in enum class org.cytoscape.equations.Token.Type
 
COMMAND - Static variable in interface org.cytoscape.work.ServiceProperties
Name of command used by Command Executor.
COMMAND_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties
Description for a command.
COMMAND_EXAMPLE_JSON - Static variable in interface org.cytoscape.work.ServiceProperties
A valid JSON string representative of the expected JSON output of a command.
COMMAND_LONG_DESCRIPTION - Static variable in interface org.cytoscape.work.ServiceProperties
Prose description for a command.
COMMAND_NAMESPACE - Static variable in interface org.cytoscape.work.ServiceProperties
Name space for a command.
COMMAND_SUPPORTS_JSON - Static variable in interface org.cytoscape.work.ServiceProperties
Indicates if the command supports JSON output.
CommandExecutorTaskFactory - Interface in org.cytoscape.command
TODO: Missing documentation
compare(TunableHandler, TunableHandler) - Method in class org.cytoscape.work.TunableGravityOrderer
 
compareTo(LayoutEdge) - Method in class org.cytoscape.view.layout.LayoutEdge
 
compareTo(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
 
compareTo(VisualLexiconNode) - Method in class org.cytoscape.view.model.VisualLexiconNode
Compare by display name of this Visual Property.
comparing(VisualProperty<V>) - Static method in interface org.cytoscape.view.model.VisualProperty
Utility method for sorting collections of Views according to the value of a VisualProperty.
compile(String, Map<String, Class<?>>) - Method in interface org.cytoscape.equations.EquationCompiler
Compiles a string to byte code plus some metadata as encapsulated by the Equation class
CompositeFilter<C,​E> - Interface in org.cytoscape.filter.model
A Filter that computes the set-union or set-intersection of the Filters it contains.
CompositeFilter.Type - Enum Class in org.cytoscape.filter.model
Determines how a CompositeFilter combines the results of its contained Filters.
COMPOUND - Enum constant in enum class org.cytoscape.group.CyGroupSettingsManager.GroupViewType
 
CONCAT - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType
Aggregated as a concatenation of all values.
CONFIG_DIR - Enum constant in enum class org.cytoscape.property.CyProperty.SavePolicy
These properties are loaded from and written to the default config directory and are user defaults.
configurationProperties - Variable in class org.cytoscape.application.swing.AbstractCyAction
The configuration properties.
ConnectSelectedNodesTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for connecting selected nodes.
CONTAINS - Enum constant in enum class org.cytoscape.filter.predicates.Predicate
A binary predicate that tests whether the first parameter is contained within the second parameter.
containsBookmarks(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Check if a bookmark is in the bookmarks.
containsColumn(String) - Method in class org.cytoscape.model.events.RowsSetEvent
Returns true if any of the changed records' column name is colName
containsDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Check if a DataSource already existed in the DataSourceManager
containsEdge(CyEdge) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains a particular edge.
containsEdge(CyNode, CyNode) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains an edge between two nodes.
containsKey(String) - Method in interface org.cytoscape.jobs.CyJobData
Test to see if a key exists in the current CyJobData.
containsNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns true if the network to be checked is a subnetwork of this root network and returns false otherwise.
containsNode(CyNode) - Method in interface org.cytoscape.model.CyNetwork
Determine if this CyNetwork contains a particular node.
ContainsTunables - Annotation Interface in org.cytoscape.work
An annotation designed to signal that the annotated field contains fields and methods that are annotated with the Tunable annotation.
contentTypes - Variable in class org.cytoscape.io.BasicCyFileFilter
 
context() - Element in annotation interface org.cytoscape.work.Tunable
Returns the context that this Tunable is meant for.
CONTEXT - Static variable in class org.cytoscape.work.AbstractTunableHandler
 
CONTINUOUS - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
Used for mapping continuous attribute values to continuous visual property types such as Node Size.
CONTINUOUS - Static variable in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
A label string for this mapping.
ContinuousEditorType - Enum Class in org.cytoscape.view.vizmap.gui.editor
An enum describing the possible types of continuous editors.
ContinuousMapping<K,​V> - Interface in org.cytoscape.view.vizmap.mappings
An interface describing a continuous mapping from attribute value to visual property.
ContinuousMappingCellRendererFactory - Interface in org.cytoscape.view.vizmap.gui.editor
A factory for creating TableCellRenderers for a particular ContinuousMappingEditor.
ContinuousMappingEditor<K extends Number,​V> - Interface in org.cytoscape.view.vizmap.gui.editor
A basic interface used to display continuous mapping editors.
ContinuousMappingPoint<K,​V> - Class in org.cytoscape.view.vizmap.mappings
Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(K, BoundaryRangeValues<V>, ContinuousMapping<K, V>, CyEventHelper) - Constructor for class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Constructor.
ContinuousRange<T> - Class in org.cytoscape.view.model
Defines a continuous range of values for VisualPropertys.
ContinuousRange(Class<T>, T, T, Boolean, Boolean) - Constructor for class org.cytoscape.view.model.ContinuousRange
Constructs this ContinuousRange.
CONTRAST - Static variable in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
This value allows the image contrast to be adjusted
controlsMutuallyExclusiveNestedChildren() - Method in class org.cytoscape.work.AbstractTunableHandler
 
controlsMutuallyExclusiveNestedChildren() - Method in interface org.cytoscape.work.TunableHandler
Returns true if the associated Tunable allows switching of mutually exclusive nested children, else false.
CORE_PROPRERTY_NAME - Static variable in class org.cytoscape.property.SimpleCyProperty
Core Cytoscape Property (Cytoscape System Property)
countMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable
Returns the number of rows with the in the specified column with the specified value in the user namespace.
countMatchingRows(String, String, Object) - Method in interface org.cytoscape.model.CyTable
Returns the number of rows with the in the specified column with the specified value.
createAnnotation(Class<? extends T>, CyNetworkView, Map<String, String>) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
Create an annotation.
createBend() - Method in interface org.cytoscape.view.presentation.property.values.BendFactory
Creates an instance of edge bend.
createColumn(String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type.
createColumn(String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type.
createColumn(String, String, Class<? extends T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type in the specified namespace.
createColumn(String, String, Class<? extends T>, boolean, T) - Method in interface org.cytoscape.model.CyTable
Create a column of the specified name and the specified type in the specified namespace.
createColumnIdentifier(String) - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifierFactory
Returns a CyColumnIdentifier that represents a CyColumn from a default network CyTable (a table associated with a CyNetwork, CyNode or CyEdge).
createCompositeFilter(Class<C>, Class<E>) - Method in interface org.cytoscape.filter.TransformerManager
Returns a new empty CompositeFilter that selects elements of type elementType from an object of type contextType.
createConfig(VisualLexicon) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider
Create a default configuration object for the given VisualLexicon.
createCyJob(String) - Method in interface org.cytoscape.jobs.CyJobExecutionService
Create an empty (unsubmitted) CyJob
createEditor(CyCustomGraphics2<T>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Creates a UI component that configures the given CyCustomGraphics2.
createElementTransformer() - Method in interface org.cytoscape.filter.model.ElementTransformerFactory
Returns a new ElementTransformer with the same id as this factory.
createFilter() - Method in interface org.cytoscape.filter.model.FilterFactory
Returns a new Filter with the same id as this factory.
createFor(NetworkCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkViewCollectionTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(NetworkViewTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(RowTaskFactory, CyRow) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(TableCellTaskFactory, CyColumn, Object) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(TableColumnTaskFactory, CyColumn) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createFor(TableTaskFactory) - Method in interface org.cytoscape.task.DynamicTaskFactoryProvisioner
 
createGroup(CyNetwork, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network.
createGroup(CyNetwork, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network initially populated with the supplied nodes.
createGroup(CyNetwork, CyNode, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network from an existing CyNode.
createGroup(CyNetwork, CyNode, List<CyNode>, List<CyEdge>, boolean) - Method in interface org.cytoscape.group.CyGroupFactory
Creates a CyGroup object in the referenced network from an existing CyNode.
createHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.HandleFactory
Creates a new instance of the Handle.
createHelpButton(String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
createHolisticTransformer() - Method in interface org.cytoscape.filter.model.HolisticTransformerFactory
 
createIcon(VisualProperty<V>, V, int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine
Create Icon object for the given VisualProperty value.
createImage(int, int) - Method in interface org.cytoscape.view.presentation.RenderingEngine
Render an Image object from current visualization.
createImage(CyNetworkView, int, int) - Method in interface org.cytoscape.view.presentation.NetworkImageFactory
Creates a network image thumbnail with the given width and height.
createImage(CyNetworkView, Collection<Annotation>, Map<String, Object>) - Method in interface org.cytoscape.view.presentation.NetworkImageFactory
Creates a network image thumbnail with the given properties.
createLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
createLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns a new layout context object.
createListColumn(String, Class<T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type.
createListColumn(String, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type.
createListColumn(String, String, Class<T>, boolean) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type in the specified namespace.
createListColumn(String, String, Class<T>, boolean, List<T>) - Method in interface org.cytoscape.model.CyTable
Create a column of Lists with the specified name and the specified element type in the specified namespace.
createMenuItem(CyNetworkView) - Method in interface org.cytoscape.application.swing.CyNetworkViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified network view.
createMenuItem(CyNetworkView, View<CyEdge>) - Method in interface org.cytoscape.application.swing.CyEdgeViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified edge view.
createMenuItem(CyNetworkView, View<CyNode>) - Method in interface org.cytoscape.application.swing.CyNodeViewContextMenuFactory
This method should return a CyMenuItem to be added to the context menu of the specified node view.
createNamedTransformer(String, List<Transformer<C, E>>) - Method in interface org.cytoscape.filter.TransformerManager
Returns a new NamedTransformer with the given name and list of transformers.
createNetwork() - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object.
createNetwork(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object.
createNetworkView(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewFactory
Create a CyNetworkView from a CyNetwork object.
createNetworkViewFactory(VisualLexicon, String) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider
Creates a CyNetworkViewFactory with a default CyNetworkViewConfig that supports standard 2D rendering.
createNetworkViewFactory(VisualLexicon, String, CyNetworkViewFactoryConfig) - Method in interface org.cytoscape.view.model.CyNetworkViewFactoryProvider
Creates a CyNetworkViewFactory.
CreateNetworkViewTaskFactory - Interface in org.cytoscape.task.create
This interface provides a task iterator for creating network views.
createNetworkWithPrivateTables() - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object where the associated default tables are private.
createNetworkWithPrivateTables(SavePolicy) - Method in interface org.cytoscape.model.CyNetworkFactory
Returns a new, empty CyNetwork object where the associated default tables are private.
createNewEmptyNetworkView() - Method in interface org.cytoscape.task.create.NewEmptyNetworkViewFactory
Returns a new, empty CyNetworkView.
createOkCancelPanel(JButton, JButton) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to create a standard Cytoscape panel (usually added to the bottom of a dialog) that contains an "OK" and/or a "Cancel" button.
createOkCancelPanel(JButton, JButton, String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to create OK, Cancel and Help
createOkCancelPanel(JButton, JButton, String, JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to include a help button in the bottom left corner.
createOkCancelPanel(JButton, JButton, JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to create a standard Cytoscape panel (usually added to the bottom of a dialog) that contains an "OK" and/or a "Cancel" button, as well as other extra components.
createPanelBorder() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to create a simple panel Border which looks native on the current Look and Feel.
createPrintable() - Method in interface org.cytoscape.view.presentation.RenderingEngine
For export image function.
createRenderingEngine(Object, View<T>) - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory
A view model can have multiple presentations.
createSerializer() - Method in interface org.cytoscape.work.properties.TunablePropertySerializerFactory
 
createSnapshot() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns an immutable snapshot of this network view (optional operation).
createTable(String, String, Class<?>, boolean, boolean) - Method in interface org.cytoscape.model.CyTableFactory
Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTable(String, String, Class<?>, boolean, boolean, CyTableFactory.InitialTableSize) - Method in interface org.cytoscape.model.CyTableFactory
Creates a CyTable object with the specified name, primary key, visibility, and mutability.
createTableCellRenderer(ContinuousMappingEditor<? extends Number, ?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingCellRendererFactory
 
createTableView(CyTable) - Method in interface org.cytoscape.view.model.table.CyTableViewFactory
Create a CyTableView from a CyTable object.
createTableViewFactory(VisualLexicon, String) - Method in interface org.cytoscape.view.model.table.CyTableViewFactoryProvider
Returns a CyTableViewFactory for the given lexicon and with the given ID.
createTaskIterator() - Method in interface org.cytoscape.work.TaskFactory
Returns an iterator containing a sequence of Tasks.
createTaskIterator(boolean) - Method in interface org.cytoscape.task.create.NewSessionTaskFactory
Creates a task iterator for creating a new session and destroying the current session based on the input.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory
Creates a task iterator for loading a network from a file.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadTableFileTaskFactory
Creates the task iterator for importing an attribute file to a table.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory
Creates a task iterator for loading files into visual styles.
createTaskIterator(File) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory
Creates a task iterator for loading a session from a file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportSelectedNetworkTaskFactory
Creates the task iterator for exporting the selected network.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.ExportVizmapTaskFactory
Creates a task iterator for exporting the vizmap file.
createTaskIterator(File) - Method in interface org.cytoscape.task.write.SaveSessionAsTaskFactory
Creates a task iterator for saving the session in a specified file.
createTaskIterator(File, boolean) - Method in interface org.cytoscape.task.read.OpenSessionTaskFactory
Creates a task iterator for loading a session from a file, with an option to let the user confirm it before disposing the current session if it is not empty.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkFileTaskFactory
Creates a task iterator for loading a network from a file.
createTaskIterator(File, TaskObserver) - Method in interface org.cytoscape.task.read.LoadVizmapFileTaskFactory
Creates a task iterator for loading files into visual styles.
createTaskIterator(InputStream, String) - Method in interface org.cytoscape.io.read.InputStreamTaskFactory
Sets the input stream that will be read by the Reader created from this factory.
createTaskIterator(Object) - Method in interface org.cytoscape.io.webservice.WebServiceClient
Set query for the tasks to be executed.
createTaskIterator(String, String, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified command.
createTaskIterator(URL) - Method in interface org.cytoscape.task.read.LoadTableURLTaskFactory
Creates the task iterator for importing an attribute file to a table.
createTaskIterator(URL, TaskObserver) - Method in interface org.cytoscape.task.read.LoadNetworkURLTaskFactory
Creates a task iterator for loading a URL into a network.
createTaskIterator(Collection<CyNetwork>) - Method in interface org.cytoscape.task.NetworkCollectionTaskFactory
Provisions this factory with the collection of networks that will be passed into any task created by it.
createTaskIterator(Collection<CyNetwork>, CyNetworkViewFactory) - Method in interface org.cytoscape.task.create.CreateNetworkViewTaskFactory
Use this method to create a network view for each of the passed networks.
createTaskIterator(Collection<CyRootNetwork>) - Method in interface org.cytoscape.task.RootNetworkCollectionTaskFactory
Provisions this factory with the collection of root-networks that will be passed into any task created by it.
createTaskIterator(Collection<CyNetworkView>) - Method in interface org.cytoscape.task.NetworkViewCollectionTaskFactory
Provisions this factory with the collection of network views that will be passed into any task created by it.
createTaskIterator(List<File>, CyRootNetwork) - Method in interface org.cytoscape.task.read.LoadMultipleNetworkFilesTaskFactory
Creates a task iterator for loading one or more networks from supported files (e.g.
createTaskIterator(List<String>, TaskObserver) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskIterator(CyTableReader) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory
Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyColumn) - Method in interface org.cytoscape.task.TableColumnTaskFactory
Used to provision this factory with a CyColumn that will be used to create tasks.
createTaskIterator(CyColumn, Object) - Method in interface org.cytoscape.task.TableCellTaskFactory
Used to provision this factory with a CyColumn and a primary key that will be used to create tasks.
createTaskIterator(CyColumn, String) - Method in interface org.cytoscape.task.edit.RenameColumnTaskFactory
Create a task iterator for renaming a selected column.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.CloneNetworkTaskFactory
Returns a TaskIterator that clones the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFactory
Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.create.NewNetworkSelectedNodesOnlyTaskFactory
Returns a TaskIterator that creates a new network from the selected nodes in the given network.
createTaskIterator(CyNetwork) - Method in interface org.cytoscape.task.NetworkTaskFactory
Provisions this factory with the CyNetwork that will be passed into any task created by it.
createTaskIterator(CyNetwork, File) - Method in interface org.cytoscape.task.select.SelectFromFileListTaskFactory
Creates a task iterator for selecting items of a network based on a file.
createTaskIterator(CyNetwork, File) - Method in interface org.cytoscape.task.write.ExportNetworkTaskFactory
Creates the task iterator for exporting networks.
createTaskIterator(CyNetwork, String) - Method in interface org.cytoscape.task.edit.EditNetworkTitleTaskFactory
Creates a task iterator for editing a network's title.
createTaskIterator(CyRow) - Method in interface org.cytoscape.task.RowTaskFactory
Provisions this factory with the CyRow that will be passed into any task created by it.
createTaskIterator(CyTable) - Method in interface org.cytoscape.task.TableTaskFactory
Used to provision this factory with a CyTable that will be used to create tasks.
createTaskIterator(CyTable, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.ImportDataTableTaskFactory
Creates a task iterator for importing a table data in a network data table.
createTaskIterator(CyTable, boolean, List<CyNetwork>, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MapTableToNetworkTablesTaskFactory
 
createTaskIterator(CyTable, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.JoinTablesTaskTaskFactory
 
createTaskIterator(CyTable, File) - Method in interface org.cytoscape.task.write.ExportTableTaskFactory
Returns a task factory that write the specified table to the specified file.
createTaskIterator(CyTable, Collection<CyTable>) - Method in interface org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory
Creates a task iterator for mapping a selected global table to a selected local table.
createTaskIterator(CyTable, CyTable, List<String>, String, boolean, boolean, boolean, List<CyNetwork>, CyRootNetwork, CyColumn, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.task.edit.MergeTablesTaskFactory
Creates a task iterator for merging two data tables.
createTaskIterator(CyNetworkView) - Method in interface org.cytoscape.task.NetworkViewTaskFactory
Creates a new TaskIterator using the given CyNetworkView
createTaskIterator(CyNetworkView, Point2D, Point2D) - Method in interface org.cytoscape.task.NetworkViewLocationTaskFactory
Creates a task iterator using the specified network view and points.
createTaskIterator(CyNetworkView, File) - Method in interface org.cytoscape.task.write.ExportNetworkViewTaskFactory
Creates the task iterator for exporting network views.
createTaskIterator(CyNetworkView, Object, Set<View<CyNode>>, String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Creates a task iterator containing the layout tasks.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.HideTaskFactory
Creates a task iterator that will hide the given nodes and edges.
createTaskIterator(CyNetworkView, Collection<CyNode>, Collection<CyEdge>) - Method in interface org.cytoscape.task.hide.UnHideTaskFactory
Creates a task iterator that will show the given nodes and edges.
createTaskIterator(View<CyEdge>, CyNetworkView) - Method in interface org.cytoscape.task.EdgeViewTaskFactory
Creates a new TaskIterator using the given edge view and network view.
createTaskIterator(View<CyNode>, CyNetworkView) - Method in interface org.cytoscape.task.NodeViewTaskFactory
Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.
createTaskIterator(TaskIterator, Map<String, Object>) - Method in interface org.cytoscape.work.TunableSetter
This method takes as input a TaskIterator and a map of tunable names to tunable values and applies those values to any tunables found in the Tasks found in the TaskIterator.
createTaskIterator(TaskIterator, Map<String, Object>, TaskObserver) - Method in interface org.cytoscape.work.TunableSetter
This version of createTaskIterator adds a TaskObserver argument.
createTaskIterator(TaskObserver, String...) - Method in interface org.cytoscape.command.CommandExecutorTaskFactory
Creates a task iterator that will execute the specified commands.
createTaskStatusPanel() - Method in interface org.cytoscape.work.swing.StatusBarPanelFactory
 
createTaskStatusPanel() - Method in interface org.cytoscape.work.swing.TaskStatusPanelFactory
Deprecated.
 
createTitledBorder(String) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Use this method to create a Titled Border which looks native on the current Look and Feel.
createTransformer(String) - Method in interface org.cytoscape.filter.TransformerManager
Returns a new Transformer with the given id.
createTunableHandler(Field, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
 
createTunableHandler(Field, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory
This method returns a TunableHandler for a field annotated as a Tunable if this factory can produce an appropriate handler for this type of field.
createTunableHandler(Method, Method, Object, Tunable) - Method in class org.cytoscape.work.BasicTunableHandlerFactory
 
createTunableHandler(Method, Method, Object, Tunable) - Method in interface org.cytoscape.work.TunableHandlerFactory
This method returns a TunableHandler for a method annotated as a Tunable if this factory can produce an appropriate handler for this type of method.
createView(Transformer<?, ?>) - Method in interface org.cytoscape.filter.view.TransformerViewFactory
Creates a UI panel that configures the given transformer.
createVisualMappingFunction(String, Class<K>, VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory
Create a new VisualMappingFunction.
createVisualPropertyDependency() - Method in interface org.cytoscape.view.vizmap.VisualPropertyDependencyFactory
 
createVisualStyle(String) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory
Create a new VisualStyle.
createVisualStyle(VisualStyle) - Method in interface org.cytoscape.view.vizmap.VisualStyleFactory
Create a copy of given VisualStyle.
createWriter(OutputStream, Object) - Method in interface org.cytoscape.io.write.CyPropertyWriterFactory
Creates a single Task that will write the specified property object to the specified OutputStream.
createWriter(OutputStream, Set<VisualStyle>) - Method in interface org.cytoscape.io.write.VizmapWriterFactory
Creates a single Task that will write the specified set of VisualStyle objects to the specified OutputStream.
createWriter(OutputStream, Set<VisualStyle>, Set<VisualStyle>) - Method in interface org.cytoscape.io.write.VizmapWriterFactory
Creates a single Task that will write the specified set of VisualStyle objects to the specified OutputStream.
createWriter(OutputStream, CyNetwork) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory
Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, CyTable) - Method in interface org.cytoscape.io.write.CyTableWriterFactory
Creates a single Task that will write the specified CyTable object to the specified OutputStream.
createWriter(OutputStream, CySession) - Method in interface org.cytoscape.io.write.CySessionWriterFactory
Creates a single Task that will write the specified CySession object to the specified OutputStream.
createWriter(OutputStream, CyNetworkView) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterFactory
Creates a single Task that will write the specified network to the specified OutputStream.
createWriter(OutputStream, RenderingEngine<?>) - Method in interface org.cytoscape.io.write.PresentationWriterFactory
Creates a single Task that will write the contents of the specified RenderingEngine object to the specified OutputStream.
CROSS_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Triangle shaped arrow with a cross hatch
CROSS_OPEN_DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Unfilled triangle shaped arrow with a cross hatch
CSV - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType
Aggregated as comma-separated values.
current_size - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Partition size used for taskMonitor.
current_start - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
Starting node number used for taskMonitor.
CUSTOM - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
 
CUSTOM - Static variable in interface org.cytoscape.util.swing.FileUtil
Equal to FileDialog.LOAD + FileDialog.SAVE.
CustomGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics
This interface defines the minimum interface to add a custom graphics to a CyNode.
CUSTOMSHAPE - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
A flag that this is a "custom" shape
CY_EDGE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
 
CY_EDGE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NETWORK_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NETWORK_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NETWORK_VIEW_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NETWORK_VIEW_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NODE_LIST_EXAMPLE_STRING - Static variable in interface org.cytoscape.command.StringToModel
 
CY_NODE_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
CY_ROW_LIST_LONG_DESCRIPTION - Static variable in interface org.cytoscape.command.StringToModel
 
Cy2DGraphicLayer - Interface in org.cytoscape.view.presentation.customgraphics
Custom graphic layer interface that allows a custom graphics implementation to draw directly onto the CyNetworkView's Graphics2D object.
CyAction - Interface in org.cytoscape.application.swing
An interface that describes how an action should be placed within the menus and/or toolbars of the Swing application.
CyActivator - Class in org.cytoscape.service.util.internal
 
CyActivator() - Constructor for class org.cytoscape.service.util.internal.CyActivator
 
CyAppAdapter - Interface in org.cytoscape.app
Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
CyApplicationConfiguration - Interface in org.cytoscape.application
Application-wide setting will be accessible through this interface.
cyApplicationManager - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
 
CyApplicationManager - Interface in org.cytoscape.application
Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.
CyColorChooser - Class in org.cytoscape.util.swing
This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColorPaletteChooser - Interface in org.cytoscape.util.swing
This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColorPaletteChooserFactory - Interface in org.cytoscape.util.swing
This defines a color chooser that allows users to choose colors from a palette and (optionally) change palettes.
CyColumn - Interface in org.cytoscape.model
This class describes a column in a CyTable.
CyColumnComboBox - Class in org.cytoscape.application.swing
An implementation of JComboBox that displays a list of CyColumns with their namespace icons.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox
Creates a CyColumnComboBox with all entries enabled.
CyColumnComboBox(CyColumnPresentationManager, Collection<CyColumn>, Predicate<CyColumn>) - Constructor for class org.cytoscape.application.swing.CyColumnComboBox
Creates a CyColumnComboBox.
CyColumnIdentifier - Interface in org.cytoscape.view.presentation.property.values
Interface used to carry and save information that represents a CyColumn (usually from a network CyTable).
CyColumnIdentifierFactory - Interface in org.cytoscape.view.presentation.property.values
A factory for creating CyColumnIdentifier objects.
CyColumnPresentation - Interface in org.cytoscape.application.swing
Service that allows UI presentation to be given for a column namespace.
CyColumnPresentationManager - Interface in org.cytoscape.application.swing
This class provides access to registered CyColumnPresentation service objects.
CyColumnSelector - Class in org.cytoscape.application.swing
An Swing control that allows the user to select a set of CyColumn objects.
CyColumnSelector(IconManager, CyColumnPresentationManager) - Constructor for class org.cytoscape.application.swing.CyColumnSelector
Creates a CyColumnSelector.
cyColumnsToJson(Collection<CyColumn>) - Method in interface org.cytoscape.util.json.CyJSONUtil
Returns a list of references (via column name) for a collection of CyColumn.
CyColumnView - Interface in org.cytoscape.view.model.table
This interface is meant for internal use, it should not be used by Apps.
CyColumnViewMetadata - Class in org.cytoscape.view.model.table
A snapshot of information about a CyColumn and its associated visual property values.
CyColumnViewMetadata(String, String, Map<String, String>) - Constructor for class org.cytoscape.view.model.table.CyColumnViewMetadata
 
CyCustomGraphics<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
Base interface for all Custom Graphics.
CyCustomGraphics2<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
Just an extension of CyCustomGraphics which provides a way for the custom graphics instance to define itself as a set of properties.
CyCustomGraphics2Factory<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
Factory to create CyCustomGraphics2 objects.
CyCustomGraphicsFactory<T extends CustomGraphicLayer> - Interface in org.cytoscape.view.presentation.customgraphics
This interface provides the factory to create CyCustomGraphics objects.
CyDisposable - Interface in org.cytoscape.model
An interface for objects that require an explicit clean up at the end of their lifecycle.
CyEdge - Interface in org.cytoscape.model
An object that represents an edge within a network of nodes (vertices) and edges.
CyEdge.Type - Enum Class in org.cytoscape.model
The Type enum is used by methods in CyNetwork to restrict the edges that match a query.
CyEdgeViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified edge view.
CyEvent<T> - Interface in org.cytoscape.event
All Cytoscape events should extend this interface.
CyEventHelper - Interface in org.cytoscape.event
The basic event handling interface for Cytoscape.
CyFileFilter - Interface in org.cytoscape.io
An interface that captures the metadata description of a file type so that files of the specified type can be handled correctly by the application and the user interface.
CyFileFilterProvider - Interface in org.cytoscape.io
An interface extended by various reader and writer factories.
CyGroup - Interface in org.cytoscape.group
An object that represents a group of nodes and edges.
CyGroupAggregationManager - Interface in org.cytoscape.group.data
The CyGroupAggregationManager provides a mechanism to add new Aggregators to the group aggregation mechanism.
CyGroupFactory - Interface in org.cytoscape.group
An interface describing a factory used for creating CyGroup objects.
CyGroupManager - Interface in org.cytoscape.group
The CyGroupManager maintains information about all of the groups an instance of Cytoscape.
CyGroupSettingsManager - Interface in org.cytoscape.group
The CyGroupSettingsManager is responsible for providing an interface to all of the possible settings controlling CyGroups, including the default settings and group specific settings.
CyGroupSettingsManager.DoubleClickAction - Enum Class in org.cytoscape.group
The DoubleClickAciton enum provides the options for what to do when the user double-clicks on either a group node or a node that's a member of a group.
CyGroupSettingsManager.GroupViewType - Enum Class in org.cytoscape.group
The CyGroupSettingsManager.GroupViewType enum provides the options for how to visualize a group.
CyHelpBroker - Interface in org.cytoscape.application.swing
Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. This interface provides access to the Cytoscape Help Broker and Help Set for managing the JavaHelp system.
CyIdentifiable - Interface in org.cytoscape.model
CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
cyIdentifiablesToJson(Collection<? extends CyIdentifiable>) - Method in interface org.cytoscape.util.json.CyJSONUtil
Returns a list of references (via SUID) for a collection of CyIdentifiable.
CyJob - Interface in org.cytoscape.jobs
A CyJob represents all of the state information necessary to marshal and unmarshal data, submit jobs, query job status, and fetch results.
CyJobData - Interface in org.cytoscape.jobs
CyJobData presents a general interface to sending data to and receiving data from a job.
CyJobDataService - Interface in org.cytoscape.jobs
The main interface for the marshalling and unmarshalling of data to be exchanged with remote services.
CyJobExecutionService - Interface in org.cytoscape.jobs
The CyJobExecutionService is a stateless service that can be used to provide remote job services, including the execution, cancellation, status checking, and retrieval of results.
CyJobManager - Interface in org.cytoscape.jobs
CyJobManager is responsible for managing all currently running CyJobs, including polling for changes in the Status of the job and notifying the CyJobMonitor provided by the App of the change in status.
CyJobMonitor - Interface in org.cytoscape.jobs
Apps are expected to implement this interface to receive notifications about job completions.
CyJobStatus - Class in org.cytoscape.jobs
This object stores information about the status of a CyJob, including the actual job status (CyJobStatus.Status) and any message returned from the remote execution.
CyJobStatus(CyJobStatus.Status, String) - Constructor for class org.cytoscape.jobs.CyJobStatus
 
CyJobStatus.Status - Enum Class in org.cytoscape.jobs
This enum contains the primary status returned from the remote execution.
CyJSONUtil - Interface in org.cytoscape.util.json
This interface provides some very basic JSON representations of Cytoscape objects.
CyLayoutAlgorithm - Interface in org.cytoscape.view.layout
A task factory specifically for layout algorithms.
CyLayoutAlgorithmManager - Interface in org.cytoscape.view.layout
This class provides access to the available layout algorithms.
CyListener - Interface in org.cytoscape.event
The basic interface that any class interested in a particular type of event should implement.
CyMenuItem - Class in org.cytoscape.application.swing
A simple wrapper class that allows a JMenuItem to be associated with a gravity value which defines where in a menu the item should fall.
CyMenuItem(JMenuItem, float) - Constructor for class org.cytoscape.application.swing.CyMenuItem
Constructor.
CyNetwork - Interface in org.cytoscape.model
CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
cyNetworkFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.
CyNetworkFactory - Interface in org.cytoscape.model
A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager - Interface in org.cytoscape.model
Basic access to networks and view in an instance of Cytoscape.
CyNetworkNaming - Interface in org.cytoscape.session
A utility that helps with the creation of unique network names.
CyNetworkReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns an array of CyNetwork objects that are read as part of the Task.
CyNetworkReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyNetworkReader for the input.
CyNetworkTableManager - Interface in org.cytoscape.model
Provides access to all network-table relationships.
CyNetworkView - Interface in org.cytoscape.view.model
Additional methods for CyNetworkView.
CyNetworkViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified network view.
CyNetworkViewDesktopMgr - Interface in org.cytoscape.application.swing
Interface for managing CyNetworkViews within the desktop where they reside.
CyNetworkViewDesktopMgr.ArrangeType - Enum Class in org.cytoscape.application.swing
 
cyNetworkViewFactory - Variable in class org.cytoscape.io.read.AbstractCyNetworkReader
Will be used for creating network views.
CyNetworkViewFactory - Interface in org.cytoscape.view.model
Factory for CyNetworkView objects.
CyNetworkViewFactoryConfig - Interface in org.cytoscape.view.model
Used to configure the behavior of CyNetworkView objects created using the CyNetworkViewFactoryFactory service.
CyNetworkViewFactoryProvider - Interface in org.cytoscape.view.model
A singleton factory that is used to create CyNetworkViewFactory objects.
CyNetworkViewListener - Interface in org.cytoscape.view.model
Callback interface for use with CyNetworkView instances that are created from CyNetworkViewFactoryProvider factories.
CyNetworkViewManager - Interface in org.cytoscape.view.model
Basic access to network views in an instance of Cytoscape.
CyNetworkViewSnapshot - Interface in org.cytoscape.view.model
An immutable snapshot of a CyNetworkView created using the CyNetworkView.createSnapshot() method.
CyNetworkViewWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CyNetworkView or CyNetwork to be specified and written to an OutputStream.
CyNetworkViewWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CyNetworkView objects.
CyNode - Interface in org.cytoscape.model
An object that represents a node (vertex) within a network of nodes and edges.
CyNodeViewContextMenuFactory - Interface in org.cytoscape.application.swing
A factory interface used to produce a CyMenuItem (JMenuItem) that will be added to the context menu for the specified node view.
CyPayloadEvent<S,​P> - Interface in org.cytoscape.event
An extension of CyEvent specifically for payload events.
CyProperty<P> - Interface in org.cytoscape.property
A general property service interface for providing access to different types of property objects as OSGi services.
CyProperty.SavePolicy - Enum Class in org.cytoscape.property
SavePolicy specifies how the CyProperty will be saved, or if it will not be saved.
CyPropertyReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns a property object.
CyPropertyReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyPropertyReader for the input.
CyPropertyWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a property Object to be specified and written.
CyPropertyWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing property objects.
CyRootNetwork - Interface in org.cytoscape.model.subnetwork
CyRootNetwork is an interface for managing Cytoscape's meta-network implementation.
CyRootNetworkManager - Interface in org.cytoscape.model.subnetwork
A manager that provides access to the CyRootNetwork objects associated with CyNetwork objects.
CyRow - Interface in org.cytoscape.model
This interface represents one row in a CyTable.
CyRowViewMetadata - Class in org.cytoscape.view.model.table
A snapshot of information about a CyRow and its associated visual property values.
CyRowViewMetadata(Object, Map<String, String>) - Constructor for class org.cytoscape.view.model.table.CyRowViewMetadata
 
CyServiceRegistrar - Interface in org.cytoscape.service.util
An interface to hide the OSGi dependencies needed to register services dynamically at runtime.
CyServiceRegistrarFactory - Class in org.cytoscape.service.util.internal
 
CyServiceRegistrarFactory() - Constructor for class org.cytoscape.service.util.internal.CyServiceRegistrarFactory
 
CyServiceRegistrarImpl - Class in org.cytoscape.service.util.internal
Implementation of CyServiceRegistrar.
CyServiceRegistrarImpl(BundleContext) - Constructor for class org.cytoscape.service.util.internal.CyServiceRegistrarImpl
 
CySession - Class in org.cytoscape.session
A session is an immutable snapshot of the data contents of Cytoscape.
CySession.Builder - Class in org.cytoscape.session
A implementation of the builder pattern used to construct immutable instances of CySession objects.
CySessionManager - Interface in org.cytoscape.session
This class primarily acts as a listener and tracks the state of the Cytoscape application.
CySessionReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns a org.cytoscape.property.session.Cysession object.
CySessionReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CySessionReader for the input.
CySessionWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CySession to be specified and written.
CySessionWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CySession objects.
CyShutdown - Interface in org.cytoscape.application
A service that will shutdown Cytoscape cleanly.
CyShutdownEvent - Class in org.cytoscape.application.events
An event fired immediately before Cytoscape will be shutdown.
CyShutdownEvent(Object) - Constructor for class org.cytoscape.application.events.CyShutdownEvent
Constructor.
CyShutdownEvent(Object, boolean) - Constructor for class org.cytoscape.application.events.CyShutdownEvent
Constructor.
CyShutdownListener - Interface in org.cytoscape.application.events
The listener for the CyShutdownEvent.
CyStartEvent - Class in org.cytoscape.application.events
An event fired after Cytoscape startup mostly complete (but not necessarily 100 percent).
CyStartEvent(Object) - Constructor for class org.cytoscape.application.events.CyStartEvent
Constructor.
CyStartListener - Interface in org.cytoscape.application.events
The listener for the CyStartEvent.
CySubNetwork - Interface in org.cytoscape.model.subnetwork
A CySubNetwork is a CyNetwork that is contained within a parent CyNetwork.
CySwingAppAdapter - Interface in org.cytoscape.app.swing
Deprecated.
(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
CySwingApplication - Interface in org.cytoscape.application.swing
This interface provides basic access to the Swing objects that constitute this application.
CyTable - Interface in org.cytoscape.model
A simple representation of a table object consisting of rows and columns.
CyTable.Mutability - Enum Class in org.cytoscape.model
Mutability of the table specifies whether or not it is able to be deleted..
CyTableFactory - Interface in org.cytoscape.model
An interface describing a factory used for creating CyTable objects.
CyTableFactory.InitialTableSize - Enum Class in org.cytoscape.model
A description of the initial size of the table.
CyTableManager - Interface in org.cytoscape.model
A singleton object for managing registered CyTables.
CyTableMetadata - Interface in org.cytoscape.model
A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.
CyTableReader - Interface in org.cytoscape.io.read
An extension of the Task interface that returns an array of CyTable objects.
CyTableReaderManager - Interface in org.cytoscape.io.read
An object that registers all InputStreamReaderFactory singletons, processes specified input to determine the appropriate factory to use and then returns an instance of the correct CyTableReader for the input.
CyTableUtil - Class in org.cytoscape.model
A collection of state-less, static utility methods provided to simplify querying of table objects.
CyTableView - Interface in org.cytoscape.view.model.table
Additional methods for table views.
CyTableViewFactory - Interface in org.cytoscape.view.model.table
Factory for CyTableView objects.
CyTableViewFactoryProvider - Interface in org.cytoscape.view.model.table
A singleton factory that is used to create CyTableViewFactory objects.
CyTableViewManager - Interface in org.cytoscape.view.model.table
Basic access to table views in an instance of Cytoscape.
CyTableViewMetadata - Class in org.cytoscape.view.model.table
A snapshot of information about a CyTable and its associated visual property values.
CyTableViewMetadata(long, String, String, Map<String, String>, List<CyColumnViewMetadata>, List<CyRowViewMetadata>, Class<?>, Class<?>) - Constructor for class org.cytoscape.view.model.table.CyTableViewMetadata
 
CyTableWriterFactory - Interface in org.cytoscape.io.write
A specialization of CyWriterFactory that allows a CyTable to be specified and written.
CyTableWriterManager - Interface in org.cytoscape.io.write
A CyWriterManager specific to writing CyTable objects.
CyToolTip - Class in org.cytoscape.util.swing
 
CyToolTip(JComponent, String, String, Icon) - Constructor for class org.cytoscape.util.swing.CyToolTip
 
CytoPanel - Interface in org.cytoscape.application.swing
Interface to a CytoPanel.
CytoPanelComponent - Interface in org.cytoscape.application.swing
An interface that allows a component to be registered as a service that will then be added to the appropriate CytoPanel.
CytoPanelComponent2 - Interface in org.cytoscape.application.swing
Implement this interface rather than CytoPanelComponent, if you want to allow your component to be retrieved from the CytoPanel by its identifier.
CytoPanelComponentSelectedEvent - Class in org.cytoscape.application.swing.events
The event fired to indicate that a CytoPanelComponent has been selected.
CytoPanelComponentSelectedEvent(Object, CytoPanel, int) - Constructor for class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Constructor.
CytoPanelComponentSelectedListener - Interface in org.cytoscape.application.swing.events
The listener for handling CytoPanelComponentSelectedEvent.
CytoPanelName - Enum Class in org.cytoscape.application.swing
An enum that describes CytoPanels uses compass directions to describe their location within the application.
CytoPanelState - Enum Class in org.cytoscape.application.swing
The different display states available for a CytoPanel.
CytoPanelStateChangedEvent - Class in org.cytoscape.application.swing.events
An event to indicate that a CytoPanel has changed state.
CytoPanelStateChangedEvent(Object, CytoPanel, CytoPanelState) - Constructor for class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Constructor.
CytoPanelStateChangedListener - Interface in org.cytoscape.application.swing.events
A listener for handling CytoPanelStateChangedEvents.
CyTransformerReader - Interface in org.cytoscape.io.read
 
CyTransformerWriter - Interface in org.cytoscape.io.write
 
CyUserLog - Interface in org.cytoscape.application
This contains the name of the user log.
CyVersion - Interface in org.cytoscape.application
An interface providing access to version information about this version of the Cytoscape application.
CyWriter - Interface in org.cytoscape.io.write
A marker interface used to identify tasks involved in writing data.
CyWriterFactory - Interface in org.cytoscape.io.write
A marker interface used to identify factories that create CyWriter instances.
CyWriterManager<W extends CyWriterFactory> - Interface in org.cytoscape.io.write
A CyWriterManager aggregates CyWriterFactory services for specific DataCategories and provides a mechanism for choosing the CyWriterFactory given a particular file type.

D

DASH_DOT - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty
Dash space dot space dash, etc.
DataCategory - Enum Class in org.cytoscape.io
An enum that captures the types of data the IO package can read and write.
DataImportFinishedEvent<T> - Class in org.cytoscape.io.webservice.events
An event indicating that data has been successfully imported.
DataImportFinishedEvent(WebServiceClient, T) - Constructor for class org.cytoscape.io.webservice.events.DataImportFinishedEvent
Constructs the event.
DataImportFinishedListener - Interface in org.cytoscape.io.webservice.events
dataService - Variable in class org.cytoscape.jobs.AbstractCyJob
 
DataSource - Interface in org.cytoscape.io.datasource
Immutable data source object, which represents one data file associated with an URL.
DataSourceManager - Interface in org.cytoscape.io.datasource
Entry point to access all data sources implemented as OSGi services.
debounce(Object, Runnable) - Method in class org.cytoscape.event.DebounceTimer
Starts a timer that will run the runnable after a short delay (on a separate thread).
debounce(Runnable) - Method in class org.cytoscape.event.DebounceTimer
Starts a timer that will run the runnable after a short delay (on a separate thread).
DebounceTimer - Class in org.cytoscape.event
A timer that can be used to ensure that time-consuming tasks, usually triggered by events, do not run too often.
DebounceTimer() - Constructor for class org.cytoscape.event.DebounceTimer
Creates a new DebounceTimer with the default delay.
DebounceTimer(int) - Constructor for class org.cytoscape.event.DebounceTimer
Creates a new DebounceTimer with the given delay (in milliseconds).
decrement(double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Decrement the location of this node by (x,y).
decrement(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Decrement the location of this node by (x,y,z).
decrementDisp(double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Decrement the displacement recorded for this node by (x,y).
decrementDisp(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Decrement the displacement recorded for this node by (x,y,z).
DEF_WEB_BROWSER_PROP_NAME - Static variable in interface org.cytoscape.util.swing.OpenBrowser
The name of a property for a Properties object used to define an alternative web browser command.
DEFAULT - Enum constant in enum class org.cytoscape.group.data.AttributeHandlingType
Default, no aggregation.
DEFAULT_ATTRS - Static variable in interface org.cytoscape.model.CyNetwork
The name of the default public CyTable that is created by default for CyNetworks, CyNodes, and CyEdges.
DEFAULT_CONTEXT - Static variable in interface org.cytoscape.application.NetworkViewRenderer
 
DEFAULT_CONTEXT - Static variable in interface org.cytoscape.application.TableViewRenderer
 
DEFAULT_DELAY_MILLISECONDS - Static variable in class org.cytoscape.event.DebounceTimer
 
DEFAULT_EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.EdgeBendVisualProperty
The default edge bend.
DEFAULT_FONT_NAME - Static variable in interface org.cytoscape.util.swing.IconManager
 
DEFAULT_LAYOUT_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
The name of the default layout.
DEFAULT_LAYOUT_PROPERTY_NAME - Static variable in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
The name of the default layout property.
DEFAULT_PAYLOAD_INTERVAL_MILLIS - Static variable in interface org.cytoscape.event.CyEventHelper
The default number of milliseconds to wait before the next time that we will check for payload events to fire.
DEFAULT_POSITION - Static variable in class org.cytoscape.view.presentation.property.values.ObjectPosition
 
DEFAULT_PROPS_CONFIG_DIR - Static variable in interface org.cytoscape.property.CyProperty
The name of the default directory where we will look for properties files.
DefaultDataSource - Class in org.cytoscape.io.datasource
Basic implementation of DataSource.
DefaultDataSource(String, String, String, DataCategory, URL) - Constructor for class org.cytoscape.io.datasource.DefaultDataSource
Constructor for the default data source.
defaultEdgeWeight - Variable in class org.cytoscape.view.layout.EdgeWeighter
 
DefaultViewEditor - Interface in org.cytoscape.view.vizmap.gui
Deprecated.
DefaultViewPanel - Interface in org.cytoscape.view.vizmap.gui
Deprecated.
DefaultVisualizableVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property to represent abstract concept such as Node or Edge.
DefaultVisualizableVisualProperty(String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty
 
defineHandle(CyNetworkView, View<CyEdge>, double, double) - Method in interface org.cytoscape.view.presentation.property.values.Handle
Define this handle.
DEGREE_FILTER - Static variable in interface org.cytoscape.filter.transformers.Transformers
The id of the core Degree Filter, which finds nodes based on their degree.
delayedFireTableDataChanged() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Invokes fireTableDataChanged after all the pending events have been processed.
deleteBookmark(Bookmarks, String, DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Delete a bookmark (pDataSource) from the category (pCategoryName) in the bookmarks object (pBookmarks)
deleteColumn(String) - Method in interface org.cytoscape.model.CyTable
Will delete the column with the specified fully-qualified name.
deleteColumn(String, String) - Method in interface org.cytoscape.model.CyTable
Will delete the column of the specified name in the specified namespace.
DeleteColumnTaskFactory - Interface in org.cytoscape.task.destroy
This interface provides a task iterator for deleting a column.
deleteDataSource(DataSource) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Remove a DataSource from the DataSourceManager
deleteRows(Collection<?>) - Method in interface org.cytoscape.model.CyTable
Deletes the rows corresponding to the given primary keys and returns true if at least one row was deleted.
DeleteSelectedNodesAndEdgesTaskFactory - Interface in org.cytoscape.task.destroy
This interface provides a task iterator for deleting selected nodes and edges.
deleteTable(long) - Method in interface org.cytoscape.model.CyTableManager
Deletes a mutable table.
DeleteTableTaskFactory - Interface in org.cytoscape.task.destroy
This interface provides a task iterator for deleting a table.
DELTA - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Triangle shaped arrow
DELTA_SHORT_1 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Shorter triangle shaped arrow
DELTA_SHORT_2 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Even shorter triangle shaped arrow
dependsOn() - Method in class org.cytoscape.work.AbstractTunableHandler
 
dependsOn() - Element in annotation interface org.cytoscape.work.Tunable
To add a dependency between two or more Tunables, where the display of one Tunable depends on the the state of another.
dependsOn() - Method in interface org.cytoscape.work.TunableHandler
Returns the dependsOn property of the associated Tunable.
description - Variable in class org.cytoscape.io.BasicCyFileFilter
 
description() - Element in annotation interface org.cytoscape.work.Tunable
Mandatory, human-readable label identifying the Tunable as displayed to a user.
DeselectAllEdgesTaskFactory - Interface in org.cytoscape.task.select
This interface provides a task iterator for deselecting all of the edges.
DeselectAllNodesTaskFactory - Interface in org.cytoscape.task.select
This interface provides a task iterator for deselecting all of the nodes.
DeselectAllTaskFactory - Interface in org.cytoscape.task.select
This interface provides a task iterator for deselecting all of the items.
deserialize(InputStream) - Method in interface org.cytoscape.jobs.CyJobDataService
This method is used to create a new CyJobData object from a serialized data stream retrieved from a remote execution.
deserialize(Reader) - Method in interface org.cytoscape.jobs.CyJobDataService
This method is used to create a new CyJobData object from a serialized data stream retrieved from a remote execution.
deserialize(Object) - Method in interface org.cytoscape.jobs.CyJobDataService
This method is used to create a new CyJobData object from a serialized data object retrieved from a remote execution.
destroyGroup(CyGroup) - Method in interface org.cytoscape.group.CyGroupManager
Destroy a group.
destroyNetwork(CyNetwork) - Method in interface org.cytoscape.model.CyNetworkManager
Destroys a network.
DestroyNetworkTaskFactory - Interface in org.cytoscape.task.destroy
This interface provides a task iterator for destruction of networks.
destroyNetworkView(CyNetworkView) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Destroys a network view.
DestroyNetworkViewTaskFactory - Interface in org.cytoscape.task.destroy
This interface provides a task iterator that destroys a network view.
destroyTableView(CyTableView) - Method in interface org.cytoscape.view.model.table.CyTableViewManager
Destroys the given table view.
DialogTaskManager - Interface in org.cytoscape.work.swing
A specialization of TaskManager that creates a JDialog configuration object and expects the dialog parent to be a Window.
DIAMOND - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
 
DIAMOND - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Diamond shaped arrow
DIAMOND - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
Diamond shape.
DIAMOND_SHORT_1 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Sorter diamond shaped arrow
DIAMOND_SHORT_2 - Static variable in class org.cytoscape.view.presentation.property.ArrowShapeVisualProperty
Even shorter diamond shaped arrow
DIRECTED - Enum constant in enum class org.cytoscape.model.CyEdge.Type
matches directed edges regardless of whether this node is the source or the target
DirectlyPresentableTunableHandler - Interface in org.cytoscape.work.swing
TODO: Missing documentation
dirty(boolean) - Method in interface org.cytoscape.view.model.CyNetworkView
If this network view supports creating snapshots using the CyNetworkView.createSnapshot() method, then this method will return true if the state of the network has changed since last clearing the dirty flag.
DISCRETE - Enum constant in enum class org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
Used for mapping continuous attribute values to discrete visual property types such as Node Shape.
DISCRETE - Static variable in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping
A label string describing the mapping.
DiscreteMapping<K,​V> - Interface in org.cytoscape.view.vizmap.mappings
An interface describing a discrete mapping from attribute value to visual property.
DiscreteMappingGenerator<V> - Interface in org.cytoscape.view.vizmap.gui.util
Generates Discrete mapping for a set of attribute values and a Visual Property.
DiscreteRange<T> - Class in org.cytoscape.view.model
Defines a discrete range of values for VisualPropertys.
DiscreteRange(Class<T>, Set<T>) - Constructor for class org.cytoscape.view.model.DiscreteRange
Constructor for this DiscreteRange.
discreteTableCellRenderer - Variable in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
The cell renderer for discrete mappings.
dispose() - Method in interface org.cytoscape.model.CyDisposable
Free up any memory or resources used by this object.
disposeCurrentSession() - Method in interface org.cytoscape.session.CySessionManager
Disposes the current session.
distance(double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Return the Euclidean distance (in 2D) between this node and a location.
distance(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
Return the Euclidean distance (in 2D) between this node and another node.
DISTANCE - Enum constant in enum class org.cytoscape.view.layout.WeightTypes
Use 1 minus the normalized value.
distance3D(double, double, double) - Method in class org.cytoscape.view.layout.LayoutNode
Return the Euclidean distance (in 3D) between this node and a location.
distance3D(LayoutNode) - Method in class org.cytoscape.view.layout.LayoutNode
Return the Euclidean distance (in 3D) between this node and another node.
DIV - Enum constant in enum class org.cytoscape.equations.Token.Type
 
DIVERGING - Enum constant in enum class org.cytoscape.util.color.BrewerType
Diverging palettes -- typically used to represent centered data with extremes in either direction.
DO_NOT_SAVE - Enum constant in enum class org.cytoscape.model.SavePolicy
The object should not be saved.
DO_NOT_SAVE - Enum constant in enum class org.cytoscape.property.CyProperty.SavePolicy
These properties are preset by Cytoscape to some default value and are never written out.
DOCK - Enum constant in enum class org.cytoscape.application.swing.CytoPanelState
The CytoPanel will be open and appear as a nested frame within the application.
DOES_NOT_CONTAIN - Enum constant in enum class org.cytoscape.filter.predicates.Predicate
A binary predicate that tests whether the first parameter does not contain the second parameter.
doLayout(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractLayoutTask
This method is designed to actually encapsulate the layout algorithm.
doLayout(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractParallelPartitionLayoutTask
AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.
doLayout(TaskMonitor) - Method in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.
DOLLAR - Enum constant in enum class org.cytoscape.equations.Token.Type
 
dontMove(boolean) - Method in class org.cytoscape.view.layout.LayoutPartition
 
DOT - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty
Dot space dot, etc.
doubleToLong(double) - Static method in class org.cytoscape.equations.EquationUtil
Checked conversion of a double to a long following the Excelâ„¢ rules.
DoubleVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for Double values.
DoubleVisualProperty(Double, Range<Double>, String, String, boolean, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DoubleVisualProperty
Constructor.
DoubleVisualProperty(Double, Range<Double>, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.DoubleVisualProperty
Constructor.
draw(Graphics2D, Shape, CyNetworkView, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.presentation.customgraphics.Cy2DGraphicLayer
This method is called by Cytoscape when a CyNetworkView is being updated in order to let the custom graphics draw onto its Graphics2D object.
draw(Graphics2D, CyTableView, CyColumn, CyRow) - Method in interface org.cytoscape.view.presentation.customgraphics.Cy2DGraphicLayer
This method is called by Cytoscape when a CyTableView is being updated in order to let the custom graphics draw onto its cells.
drawIcon(int, int, boolean) - Method in interface org.cytoscape.view.vizmap.gui.editor.ContinuousMappingEditor
Returns an icon representing this editor for use in a user interface.
DropDownMenuButton - Class in org.cytoscape.util.swing
Button with drop down menu.
DropDownMenuButton() - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
 
DropDownMenuButton(AbstractAction) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
Creates a new DropDownMenuButton object.
DropDownMenuButton(JPopupMenu) - Constructor for class org.cytoscape.util.swing.DropDownMenuButton
 
DynamicSubmenuListener - Interface in org.cytoscape.work.swing
An extension of MenuListener that is used to describe dynamic submenus.
DynamicTaskFactoryProvisioner - Interface in org.cytoscape.task
TODO: Missing documentation

E

EAST - Enum constant in enum class org.cytoscape.application.swing.CytoPanelName
The east or right-hand panel.
EAST - Enum constant in enum class org.cytoscape.view.presentation.property.values.Position
 
EDGE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
EDGE_APPS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_BEND - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
If Edge Bend is defined, edges will be rendered as straight or curved lines.
EDGE_DYNAMIC_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_EDIT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_LABEL - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The text used for the edge label.
EDGE_LABEL_COLOR - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
TODO Documentation
EDGE_LABEL_FONT_FACE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The font used for the edge label.
EDGE_LABEL_FONT_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The size of the font used for the edge label.
EDGE_LABEL_ROTATION - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
A value used to rotate the edge label about its center, in degrees.
EDGE_LABEL_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The opacity of the color of the edge label.
EDGE_LABEL_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
TODO Documentation
EDGE_LINE_TYPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The type of stoke used to render the line (solid, dashed, etc.)
EDGE_LINKOUTS_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the whole edge (including the stroke and arrows) when it is selected or unselected.
EDGE_PREFERENCES_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_SELECT_MENU - Static variable in interface org.cytoscape.work.ServiceProperties
 
EDGE_SELECTED - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
TODO Documentation
EDGE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the whole edge (stroke and arrows) when selected.
EDGE_SOURCE_ARROW_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge source arrow when selected.
EDGE_SOURCE_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The shape of the arrow on the source node end of the edge.
EDGE_SOURCE_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
TODO Documentation
EDGE_SOURCE_ARROW_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge source arrow when unselected.
EDGE_STACKING - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The strategy to use to render edges when there are more than one edge between a pair of nodes.
EDGE_STACKING_DENSITY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
Controls how tightly packed edges are when there are more than one edge between a pair of nodes.
EDGE_STROKE_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge line when selected.
EDGE_STROKE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge line.
EDGE_TARGET_ARROW_SELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge target arrow when selected.
EDGE_TARGET_ARROW_SHAPE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The shape of the arrow on the target node end of the edge.
EDGE_TARGET_ARROW_SIZE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
TODO Documentation
EDGE_TARGET_ARROW_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the edge target arrow when unselected.
EDGE_TOOLTIP - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The text of the tooltip that appears when a mouse hovers over the edge.
EDGE_TRANSPARENCY - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The opacity of the of the edge.
EDGE_UNSELECTED_PAINT - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The color of the whole edge (stroke and arrows) when it is not selected.
EDGE_VISIBLE - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
Hides the edge if set to false.
EDGE_WIDTH - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
The width of the edge line.
EDGE_Z_ORDER - Static variable in class org.cytoscape.view.presentation.property.BasicVisualLexicon
When rendering edges in 2D, edges with a higher Z-order will be rendered on top of edges with lower Z-order.
EdgeBendVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for Edge Bend values.
EdgeBendVisualProperty(Bend, String, String) - Constructor for class org.cytoscape.view.presentation.property.EdgeBendVisualProperty
Constructor.
EDGECOLOR - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
The color of the border
edgeCount() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the number of edges in this partition
edgeIterator() - Method in class org.cytoscape.view.layout.LayoutPartition
Return an iterator over all of the LayoutEdges in this partition
EdgeList - Class in org.cytoscape.command.util
This class implements a wrapper for a List of CyEdges that can be used by the Tunables mechanism.
EdgeList() - Constructor for class org.cytoscape.command.util.EdgeList
Empty constructor for an EdgeList.
EdgeList(CyNetwork) - Constructor for class org.cytoscape.command.util.EdgeList
Constructor for EdgeList when the network is known at time of creation.
EDGEOPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
The opacity of the border
edgesChanged() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns true if the selection stated of edges has changed.
EdgeSpacialIndex2DEnumerator - Interface in org.cytoscape.view.model.spacial
Enumerator returned when querying a NetworkSpacialIndex2D, used to iterate over the results of the query.
EdgeStacking - Interface in org.cytoscape.view.presentation.property.values
Marker interface for edge stacking.
EdgeStackingVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for EdgeStacking values.
EdgeStackingVisualProperty(EdgeStacking, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.EdgeStackingVisualProperty
 
EDGETHICKNESS - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
The thickness of the border
edgeView - Variable in class org.cytoscape.task.AbstractEdgeViewTask
The edge view that descendant tasks will operate on.
EdgeViewTaskFactory - Interface in org.cytoscape.task
A task factory that creates one or more tasks that operate on the specified View<CyEdge> within the specified CyNetworkView.
edgeWeighter - Variable in class org.cytoscape.view.layout.AbstractPartitionLayoutTask
The EdgeWeighter used for edge weight calculations.
EdgeWeighter - Class in org.cytoscape.view.layout
The EdgeWeighter class.
EdgeWeighter() - Constructor for class org.cytoscape.view.layout.EdgeWeighter
 
EditNetworkTitleTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator for editing a network's title.
EDITOR_WINDOW_CLOSED - Static variable in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Tell vizMapper main which editor is disabled/enabled.
EDITOR_WINDOW_OPENED - Static variable in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Editor window state
EditorManager - Interface in org.cytoscape.view.vizmap.gui.editor
Manages all editor objects for the VizMap GUI.
ElementTransformer<C,​E> - Interface in org.cytoscape.filter.model
A transformer that transforms its input one element at a time and pushes the results into the given sink.
ElementTransformerFactory<C,​E> - Interface in org.cytoscape.filter.model
A factory for creating ElementTransformers.
ELLIPSE - Enum constant in enum class org.cytoscape.view.presentation.annotations.ShapeAnnotation.ShapeType
 
ELLIPSE - Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
Ellipse shape.
ENABLE_FOR - Static variable in interface org.cytoscape.work.ServiceProperties
Action should be enabled or disabled by states if this property is set
ENABLE_FOR_ALWAYS - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable always.
ENABLE_FOR_NETWORK - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when at least one network exists.
ENABLE_FOR_NETWORK_AND_VIEW - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when at least one network WITH view exists.
ENABLE_FOR_NETWORK_WITHOUT_VIEW - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when at least one network with NO view exists.
ENABLE_FOR_SELECTED_EDGES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when edges have been selected in a network.
ENABLE_FOR_SELECTED_NODES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when nodes have been selected in a network.
ENABLE_FOR_SELECTED_NODES_OR_EDGES - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when either nodes or edges have been selected in a network.
ENABLE_FOR_SINGLE_NETWORK - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when only one network is selected.
ENABLE_FOR_TABLE - Static variable in class org.cytoscape.application.swing.ActionEnableSupport
Enable when at least one network exists.
EOS - Enum constant in enum class org.cytoscape.equations.Token.Type
 
eqnTypeIsCompatible(Class<?>, Class<?>, Class<?>) - Static method in class org.cytoscape.equations.EquationUtil
Returns whether the given column type is compatible with an equation type
EQUAL - Enum constant in enum class org.cytoscape.equations.Token.Type
 
EQUAL_DASH - Static variable in class org.cytoscape.view.presentation.property.LineTypeVisualProperty
Equal dash and space
equalizeSize(JComponent...) - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
Resizes the given components making them equal in size.
equals(Object) - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
equals(Object) - Method in class org.cytoscape.equations.Equation
Compares one Equation to another.
equals(Object) - Method in class org.cytoscape.equations.Token
 
equals(Object) - Method in class org.cytoscape.util.swing.FileChooserFilter
 
equals(Object) - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Compare two ObjectPositions
equals(Object) - Method in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
 
equals(Object) - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
 
equalValue - Variable in class org.cytoscape.view.vizmap.mappings.BoundaryRangeValues
Will be used when the domain value is exactly equal to the associated boundary domain value
Equation - Class in org.cytoscape.equations
The class representing an equation.
Equation(String, Set<String>, Map<String, Object>, Object[], int[], Class<?>) - Constructor for class org.cytoscape.equations.Equation
Constructs an Equation.
EquationCompiler - Interface in org.cytoscape.equations
Compiler that compiles equations to byte (non-Java) code.
EquationFunctionAddedEvent - Class in org.cytoscape.equations.event
 
EquationFunctionAddedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionAddedEvent
 
EquationFunctionAddedListener - Interface in org.cytoscape.equations.event
 
EquationFunctionRemovedEvent - Class in org.cytoscape.equations.event
 
EquationFunctionRemovedEvent(EquationParser, Collection<Function>) - Constructor for class org.cytoscape.equations.event.EquationFunctionRemovedEvent
 
EquationFunctionRemovedListener - Interface in org.cytoscape.equations.event
 
EquationParser - Interface in org.cytoscape.equations
Parser for a string representing an equation.
EquationTokeniser - Interface in org.cytoscape.equations
Tokeniser for a string representing an equation.
EquationUtil - Class in org.cytoscape.equations
Various static utility methods relating to equations.
ERROR - Enum constant in enum class org.cytoscape.equations.Token.Type
 
ERROR - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
 
ERROR - Enum constant in enum class org.cytoscape.work.TaskMonitor.Level
A message that informs the user that a non-recoverable error has occured.
evaluateFunction(Object[]) - Method in interface org.cytoscape.equations.Function
Used to invoke this function.
eventHelper - Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
exampleStringValue() - Element in annotation interface org.cytoscape.work.Tunable
Optional example string for use in scripting environments.
execService - Variable in class org.cytoscape.jobs.AbstractCyJob
 
execute(C, List<Transformer<C, E>>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager
Applies the given chain of transformers to the context.
execute(C, Transformer<C, E>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager
Applies transformer to the context.
execute(C, TransformerSource<C, E>, List<Transformer<C, E>>, TransformerSink<E>) - Method in interface org.cytoscape.filter.TransformerManager
Applies the given chain of transformers to the context, via source.
execute(Equation, Map<String, IdentDescriptor>) - Method in interface org.cytoscape.equations.Interpreter
Executes the code represented by "equation".
execute(TaskIterator) - Method in interface org.cytoscape.work.TaskManager
This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
execute(TaskIterator, TaskObserver) - Method in interface org.cytoscape.work.TaskManager
This method is called to execute the Tasks in a TaskIterator provided by a TaskFactory.
executeJob(CyJob, String, Map<String, Object>, CyJobData) - Method in interface org.cytoscape.jobs.CyJobExecutionService
Submit a CyJob for remote execution.
executionContext - Variable in class org.cytoscape.work.AbstractTaskManager
The execution context of the task manager.
exists(K) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D
Returns true if an object with the given key is stored in this SpacialIndex2D.
exit(int) - Method in interface org.cytoscape.application.CyShutdown
Calling this method indicates that the application should shutdown.
exit(int, boolean) - Method in interface org.cytoscape.application.CyShutdown
Calling this method indicates that the application should shutdown.
expand(CyNetwork) - Method in interface org.cytoscape.group.CyGroup
Expand this group in the designated network.
EXPANDCONTRACT - Enum constant in enum class org.cytoscape.group.CyGroupSettingsManager.DoubleClickAction
 
expanded() - Method in interface org.cytoscape.util.swing.BasicCollapsiblePanel.CollapseListener
 
ExpandGroupTaskFactory - Interface in org.cytoscape.task.edit
This interface provides a task iterator expanding a group from a node view.
ExportNetworkImageTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for exporting networks as image.
ExportNetworkTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for exporting network views.
ExportNetworkViewTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for exporting network views.
ExportSelectedNetworkTaskFactory - Interface in org.cytoscape.task.write
 
ExportSelectedTableTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for exporting the current table.
ExportTableTaskFactory - Interface in org.cytoscape.task.write
This task factory provides a task iterator for writing a specified table to a specified file.
ExportVizmapTaskFactory - Interface in org.cytoscape.task.write
This interface provides a task iterator for exporting the vizmap visual style.
extensions - Variable in class org.cytoscape.io.BasicCyFileFilter
 

F

FAILED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
 
FAILED - Enum constant in enum class org.cytoscape.work.FinishStatus.Type
Indicates that the task iterator did not complete because one of its tasks failed by throwing an exception.
fetchResults(CyJob, CyJobData) - Method in interface org.cytoscape.jobs.CyJobExecutionService
After a CyJob status returns CyJobStatus.Status.FINISHED, this method is used to fetch the results from the job execution.
FileChooserFilter - Class in org.cytoscape.util.swing
Used to hold extension(s) of acceptable file types and a short description of them.
FileChooserFilter(String, String) - Constructor for class org.cytoscape.util.swing.FileChooserFilter
Construct this FileChooserFilter using one acceptable file type extension.
FileChooserFilter(String, String[]) - Constructor for class org.cytoscape.util.swing.FileChooserFilter
Construct this FileChooserFilter using multiple acceptable file type extensions.
FileUtil - Interface in org.cytoscape.util.swing
Provides a platform-dependent way to open files.
FILLCOLOR - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
The fill color of the shape
FILLOPACITY - Static variable in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
The opacity of the shape fill
Filter<C,​E> - Interface in org.cytoscape.filter.model
A transformer that decides whether to accept or reject elements.
FilterFactory<C,​E> - Interface in org.cytoscape.filter.model
A factory for creating Filters.
FINISHED - Enum constant in enum class org.cytoscape.jobs.CyJobStatus.Status
 
FinishStatus - Class in org.cytoscape.work
Indicates the status of a task iterator when it has finished for TaskObservers.
FinishStatus(FinishStatus.Type, Task, Exception) - Constructor for class org.cytoscape.work.FinishStatus
 
FinishStatus.Type - Enum Class in org.cytoscape.work
 
fireEditingCanceled() - Method in class org.cytoscape.util.swing.AbstractCellEditor
Notify all listeners that have registered interest for notification on this event type.
fireEditingStopped() - Method in class org.cytoscape.util.swing.AbstractCellEditor
Notify all listeners that have registered interest for notification on this event type.
fireEvent(E) - Method in interface org.cytoscape.event.CyEventHelper
Calls each listener found in the Service Registry identified by the listenerClass interface by the supplied CyEvent.
fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Notify all listeners that have registered interest for notification on this event type.
FIT_CONTENT - Static variable in interface org.cytoscape.view.presentation.NetworkImageFactory
If true the network will be automatically centered and scaled to fit inside the image bounds.
fitContent() - Method in interface org.cytoscape.view.model.CyNetworkView
Utility method to fit content to the presentation container (usually a Swing Window).
FitContentEvent - Class in org.cytoscape.view.model.events
Fit network visualization to the given container.
FitContentEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitContentEvent
Fit the size of network view to the current container.
FitContentListener - Interface in org.cytoscape.view.model.events
Listener for FitContentEvent.
fitSelected() - Method in interface org.cytoscape.view.model.CyNetworkView
Utility method to fit selected graph objects to the presentation container.
FitSelectedEvent - Class in org.cytoscape.view.model.events
Fit only selected graph object views to the container.
FitSelectedEvent(CyNetworkView) - Constructor for class org.cytoscape.view.model.events.FitSelectedEvent
Fit the selected part of network view to the container.
FitSelectedListener - Interface in org.cytoscape.view.model.events
Listener for FitSelectedEvent.
fitShapeToText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
This method causes the shape to be resized to fit the provided text.
fixEdges() - Method in class org.cytoscape.view.layout.LayoutPartition
Convenience routine to update the source and target for all of the edges in a partition.
FLOAT - Enum constant in enum class org.cytoscape.application.swing.CytoPanelState
The CytoPanel will be open and appear as a separate frame independent of the application.
FLOAT - Enum constant in enum class org.cytoscape.equations.ArgType
An argument that can be converted to a floating point value.
FLOAT_CONSTANT - Enum constant in enum class org.cytoscape.equations.Token.Type
 
FLOATS - Enum constant in enum class org.cytoscape.equations.ArgType
An non-empty sequence of arguments that consist of lists of floating point numbers and scalars that can be converted to a floating point number.
flushPayloadEvents() - Method in interface org.cytoscape.event.CyEventHelper
Forces accumulated payload events to be fired.
flushPayloadEvents(Object) - Method in interface org.cytoscape.event.CyEventHelper
Forces accumulated payload events to be fired.
FONTFAMILY - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Arg string to set the font family
FONTSIZE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Arg string to set the font size
FONTSTYLE - Static variable in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Arg string to set the font style
FontVisualProperty - Class in org.cytoscape.view.presentation.property
Visual Property for Font values.
FontVisualProperty(Font, String, String, Class<? extends CyIdentifiable>) - Constructor for class org.cytoscape.view.presentation.property.FontVisualProperty
Constructor.
forceShutdown() - Method in class org.cytoscape.application.events.CyShutdownEvent
Returns true if we want to force the shutdown without any user prompt
FOREGROUND - Static variable in interface org.cytoscape.view.presentation.annotations.Annotation
The foreground canvas
format() - Element in annotation interface org.cytoscape.work.Tunable
Provides a decimal format string suitable for DecimalFormat.
FORMAT - Static variable in class org.cytoscape.work.AbstractTunableHandler
 
FORMAT_RANGE - Static variable in class org.cytoscape.view.presentation.property.table.CellFormatVisualProperty
 
Function - Interface in org.cytoscape.equations
The basic description of a Function.
FunctionError - Exception in org.cytoscape.equations
A class describing an error in a function.
FunctionError(String, int) - Constructor for exception org.cytoscape.equations.FunctionError
Constructor.
FunctionUtil - Class in org.cytoscape.equations
A collection of static methods that may be useful for the implementation of built-in functions.

G

genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.AbstractNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in interface org.cytoscape.equations.TreeNode
Generated code for this node and pushes it onto the execution stack.
generateMap(Set<T>) - Method in interface org.cytoscape.view.vizmap.gui.util.DiscreteMappingGenerator
For a given set of attribute values, create discrete mapping.
get(int) - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the Filter at the given index.
get(String) - Method in interface org.cytoscape.jobs.CyJobData
Returns the Object that contains the value for the specified key, or null if that key doesn't exist.
get(String, Class<? extends T>) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get(String, Class<? extends T>, T) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get(String, String, Class<? extends T>) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get(String, String, Class<? extends T>, T) - Method in interface org.cytoscape.model.CyRow
Returns the value found for this row in the specified column with the specified type.
get(K, double[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D
Retrieves the extents of the rectangle with the given key.
get(K, float[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D
Retrieves the extents of the rectangle with the given key.
get_ApplyPreferredLayoutTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ApplyPreferredLayoutTaskFactory.
get_ApplyVisualStyleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ApplyVisualStyleTaskFactory.
get_CloneNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CloneNetworkTaskFactory.
get_CollapseGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CollapseGroupTaskFactory.
get_ConnectSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ConnectSelectedNodesTaskFactory.
get_CreateNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CreateNetworkViewTaskFactory.
get_DeleteColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DeleteColumnTaskFactory.
get_DeleteSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
get_DeleteTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DeleteTableTaskFactory.
get_DeselectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DeselectAllEdgesTaskFactory.
get_DeselectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DeselectAllNodesTaskFactory.
get_DeselectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DeselectAllTaskFactory.
get_DestroyNetworkTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DestroyNetworkTaskFactory.
get_DestroyNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DestroyNetworkViewTaskFactory.
get_EditNetworkTitleTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of EditNetworkTitleTaskFactory.
get_ExpandGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExpandGroupTaskFactory.
get_ExportNetworkImageTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExportNetworkImageTaskFactory.
get_ExportNetworkViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExportNetworkViewTaskFactory.
get_ExportSelectedTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExportSelectedTableTaskFactory.
get_ExportTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExportTableTaskFactory.
get_ExportVizmapTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of ExportVizmapTaskFactory.
get_GroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of GroupNodesTaskFactory.
get_HideSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of HideSelectedEdgesTaskFactory.
get_HideSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of HideSelectedNodesTaskFactory.
get_HideSelectedTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of HideSelectedTaskFactory.
get_InvertSelectedEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of InvertSelectedEdgesTaskFactory.
get_InvertSelectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of InvertSelectedNodesTaskFactory.
get_LoadNetworkFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of LoadNetworkFileTaskFactory.
get_LoadNetworkURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of LoadNetworkURLTaskFactory.
get_LoadTableFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of LoadTableFileTaskFactory.
get_LoadTableURLTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of LoadTableURLTaskFactory.
get_LoadVizmapFileTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of LoadVizmapFileTaskFactory.
get_MapGlobalToLocalTableTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of MapGlobalToLocalTableTaskFactory.
get_MapTableToNetworkTablesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of MapTableToNetworkTablesTaskFactory.
get_NewEmptyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of NewEmptyNetworkViewFactory.
get_NewNetworkSelectedNodesAndEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
get_NewNetworkSelectedNodesOnlyTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
get_NewSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of NewSessionTaskFactory.
get_OpenSessionTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of OpenSessionTaskFactory.
get_RenameColumnTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of RenameColumnTaskFactory.
get_SaveSessionAsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SaveSessionAsTaskFactory.
get_SelectAdjacentEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectAdjacentEdgesTaskFactory.
get_SelectAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectAllEdgesTaskFactory.
get_SelectAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectAllNodesTaskFactory.
get_SelectAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectAllTaskFactory.
get_SelectConnectedNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectConnectedNodesTaskFactory.
get_SelectFirstNeighborsNodeViewTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
get_SelectFirstNeighborsTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryInEdge() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFirstNeighborsTaskFactoryOutEdge() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectFirstNeighborsTaskFactory.
get_SelectFromFileListTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of SelectFromFileListTaskFactory.
get_UnGroupNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UnGroupNodesTaskFactory.
get_UnGroupTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UnGroupTaskFactory.
get_UnHideAllEdgesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UnHideAllEdgesTaskFactory.
get_UnHideAllNodesTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UnHideAllNodesTaskFactory.
get_UnHideAllTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UnHideAllTaskFactory.
getAcceleratorKeyStroke() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getAcceleratorKeyStroke() - Method in interface org.cytoscape.application.swing.CyAction
Returns the accelerator KeyStroke defined for this action.
getActionListener() - Method in class org.cytoscape.work.swing.util.UserAction
 
getAdjacentEdgeIterable(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns an Iterable that contains the edges that are adjacent (connected) to the given node.
getAdjacentEdgeIterable(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Gets an Iteable of edges that connect to this node.
getAdjacentEdgeIterable(View<CyNode>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns an Iterable that contains the edges that are adjacent (connected) to the given node.
getAdjacentEdgeList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of edges that connect to this node.
getAggregator(CyGroup, CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the Aggregator that will be used to aggregate the values in a specific CyColumn for all of the nodes in a group onto the corresponding column in the group node.
getAggregators() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of aggregators.
getAggregators(Class<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of aggregators for a particular Class.
getAll() - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping
Gets all map values.
getAllCategories() - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data categories
getAllDataSources() - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources registered as OSGi services
getAllDescendants(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon
Get collection of visual properties for a given object type (node/edge/network).
getAllDescendants(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getAllHandles() - Method in interface org.cytoscape.view.presentation.property.values.Bend
Get List of all handles on this edge
getAllLayouts() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns a collection of all available layouts.
getAllPoints() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets all Data Points.
getAllRenderingEngines() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Get all RenderingEngines registered in this manager.
getAllRows() - Method in interface org.cytoscape.model.CyTable
Return a list of all the rows stored in this data table.
getAllTables(boolean) - Method in interface org.cytoscape.model.CyTableManager
Returns a Set of all tables with the specified visibility.
getAllValues() - Method in interface org.cytoscape.jobs.CyJobData
Return all of the values in this CyJobData
getAllValues() - Method in interface org.cytoscape.model.CyRow
Returns a map of fully-qualified column names to Objects that contain the values contained in this Row.
getAllViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of all View including those for Nodes, Edges, and Network.
getAllVisualLexicon() - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager
Returns a Set of all VisualLexicons.
getAllVisualLexicon() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns a Set of all VisualLexicons.
getAllVisualMappingFunctions() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns all VisualMappingFunctions in this style.
getAllVisualProperties() - Method in interface org.cytoscape.view.model.VisualLexicon
Returns the Set of VisualPropertys supported by this Renderer.
getAllVisualProperties() - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getAllVisualPropertyDependencies() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Get all dependencies for this style.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager
Returns all available VisualStyles managed by this object.
getAllVisualStyles() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns all available VisualStyles managed by this object.
getAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Return the anchor of the label (or other object).
getAnchorType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the anchor type for one end of the arrow
getAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Retrieve the list of annotations for a specific network view.
getAppConfigurationDirectoryLocation(Class<?>) - Method in interface org.cytoscape.application.CyApplicationConfiguration
Returns the absolute path to the configuration directory of a particular app.
getAppFileListMap() - Method in class org.cytoscape.session.CySession
Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.
getAppFileListMap() - Method in class org.cytoscape.session.events.SessionAboutToBeSavedEvent
This method is not meant to be used by listeners for this event, although you can and no harm should come to you.
getArea() - Method in class org.cytoscape.view.layout.LayoutPartition
 
getArgAsBoolean(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
getArgAsDouble(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgAsLong(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
getArgAsString(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "String".
getArgDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the value of the description field for this argument.
getArgExampleStringValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the value of the defaultStringValue field for this argument.
getArgLongDescription(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the value of the longDescription field for this argument.
getArgMap() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the argument map that is used to serialize this annotation.
getArgName() - Method in class org.cytoscape.equations.ArgDescriptor
Returns the name of the argument.
getArgNumber() - Method in exception org.cytoscape.equations.FunctionError
Returns the argument number the error is associated with.
getArgRequired(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the value of the required field for this argument.
getArgTooltip(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the value of the tooltip field for this argument.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
 
getArgType(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the type of the argument.
getArgTypeString(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a human-readable string for this argument of the form: argument=<type>
getArgumentDescriptors() - Method in class org.cytoscape.equations.AbstractFunction
Returns the usage descriptions for the function's arguments.
getArgumentDescriptors() - Method in interface org.cytoscape.equations.Function
Returns the usage descriptions for the function's arguments.
getArguments(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of arguments for the specified namespace and command in alphabetical order.
getArgValue(String, String, String) - Method in interface org.cytoscape.command.AvailableCommands
Deprecated.
getArrowColor(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the color of one end of the arrow
getArrows() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get all arrows that are currently linked to this annotation.
getArrowSize(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the size of one end of the arrow
getArrowType(ArrowAnnotation.ArrowEnd) - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the type of one end of the arrow
getAttribute(DataSource, String) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Given the attribute name, return the value in a bookmark
getAttributeSelectors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns set of selector for available attributes (table columns).
getAvailableCommands() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of AvailableCommands.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyFileFilters known to this CyWriter manager.
getAvailableWriterFilters() - Method in interface org.cytoscape.io.write.CyWriterManager
Returns a list of the available CyFileFilters that define the available output types.
getAverageLocation() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the average location of the nodes in this partition
getBaseNetwork() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
The initial network of CyNodes and CyEdges.
getBooleans(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of booleans.
getBorderColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the border (stroke) color.
getBorderOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the border (stroke) opacity.
getBorderWidth() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the border (stroke) width.
getBounds() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Returns the bounds of the annotation.
getBounds(CyNetworkView) - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Deprecated.
This method has been deprecated in version 3.4.
getBounds2D() - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer
Return the bounds of the area covered by this CustomGraphicLayer as a java.awt.Rectangle2D
getBugFixVersion() - Method in interface org.cytoscape.application.CyVersion
The third of the three numbers defining the version of the software, meaning "5" if the version is "3.2.5".
getBypassValues() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
 
getBypassValues() - Method in class org.cytoscape.view.model.table.CyRowViewMetadata
 
getBypassValues() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getCanvasName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Return the canvas that this Annotation is on
getCategory(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Select specific category from a list of categories.
getCategoryName() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getCellEditors() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns editors for individual cells in discrete mapping editor.
getCellEditorValue() - Method in class org.cytoscape.util.swing.AbstractCellEditor
getCellVisualProperty(VisualProperty<? extends T>) - Method in interface org.cytoscape.view.model.table.CyColumnView
 
getChangeSources() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
 
getChangeSources() - Method in interface org.cytoscape.work.swing.GUITunableHandler
Returns the name of different GUITunableHandlers that this tunable handler listens to.
getChildKey() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getChildKey() - Method in interface org.cytoscape.work.TunableHandler
Returns the name of the key that determines the selection of which controlled nested child is currently presented, or the empty string if controlsMutuallyExclusiveNestedChildren() returns false.
getChildren() - Method in class org.cytoscape.view.model.VisualLexiconNode
Returns collection of all children of this node.
getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation
 
getCode() - Method in class org.cytoscape.equations.Equation
Returns the compiled code (not Java byte code!) for the VM representing this Equation.
getColor() - Method in class org.cytoscape.util.swing.ColorButton
 
getColorPaletteChooser(PaletteType, boolean) - Method in interface org.cytoscape.util.swing.CyColorPaletteChooserFactory
 
getColors() - Method in interface org.cytoscape.util.color.Palette
Return the palette as an array of colors
getColors(int) - Method in interface org.cytoscape.util.color.Palette
Return the palette as an array of colors of the requested length.
getColumn() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the name of the column of the data that was set.
getColumn(String) - Method in interface org.cytoscape.model.CyTable
Returns the column with the specified fully-qualified name.
getColumn(String, String) - Method in interface org.cytoscape.model.CyTable
Returns the column for the specified name in the specified namespace.
getColumnClass(int) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the class of the column specified in the argument.
getColumnClass(int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the type for column number column.
getColumnClass(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the class of the column at the given column number.
getColumnCount() - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the number of available columns.
getColumnCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the number of columns in the TreeTabelModel.
getColumnName() - Method in class org.cytoscape.model.events.ColumnDeletedEvent
Returns the fully-qualified name of the column for this event.
getColumnName() - Method in interface org.cytoscape.view.presentation.property.values.CyColumnIdentifier
 
getColumnName(int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the name for column number column.
getColumnName(int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the column name at the given column number.
getColumnNames(CyTable) - Static method in class org.cytoscape.model.CyTableUtil
Returns all the column names of a given table.
getColumnPresentation(String) - Method in interface org.cytoscape.application.swing.CyColumnPresentationManager
Returns a CyColumnPresentation for the given namespace.
getColumnRecords(String) - Method in class org.cytoscape.model.events.RowsSetEvent
Returns all of the RowSetRecords whose specified column value is set.
getColumns() - Method in interface org.cytoscape.model.CyTable
Returns the column types for all columns in this table.
getColumns() - Method in class org.cytoscape.model.events.RowsSetEvent
Returns a unmodifiable Set of the names of the columns that are contained in this event.
getColumns(String) - Method in interface org.cytoscape.model.CyTable
Returns the column types for all columns in this table in the given namespace.
getColumnView() - Method in class org.cytoscape.view.model.events.AboutToRemoveColumnViewEvent
 
getColumnView() - Method in class org.cytoscape.view.model.events.AddedColumnViewEvent
 
getColumnView() - Method in class org.cytoscape.view.vizmap.events.table.ColumnVisualStyleSetEvent
Get the The target column view model.
getColumnView(long) - Method in interface org.cytoscape.view.model.table.CyTableView
Returns the View for the specified column using its view SUID as key.
getColumnView(String) - Method in interface org.cytoscape.view.model.table.CyTableView
Returns the View for a specified column.
getColumnView(CyColumn) - Method in interface org.cytoscape.view.model.table.CyTableView
Returns the View for a specified column.
getColumnViews() - Method in interface org.cytoscape.view.model.table.CyTableView
Returns all column views in this table view, in the same order as CyTable.getColumns().
getColumnViews() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getCommandExecutorTaskFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CommandExecutorTaskFactory which can be used to execute commands.
getCommands(String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of available commands in alphabetical order for the specified namespace.
getCompatibleTypes() - Method in class org.cytoscape.equations.ArgDescriptor
Returns the types that are compatible with this argument.
getCompatibleTypes() - Method in enum class org.cytoscape.equations.ArgType
Returns an array of compatible Class types.
getComponent() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the Component to be added to the CytoPanel.
getComponent() - Method in interface org.cytoscape.application.swing.ToolBarComponent
Returns the Component to be added to the ToolBar.
getComponentAt(int) - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the component at the passed index.
getCompositeFilter() - Method in interface org.cytoscape.filter.model.SubFilterTransformer
 
getConfiguration(TaskFactory, Object) - Method in interface org.cytoscape.work.TaskManager
Returns a configuration object generated from the Tunables read from the TaskFactory.
getConfigurationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration
Returns absolute path to CytoscapeConfiguration location.
getConnectingEdgeList(CyNode, CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of edges that connect two nodes.
getContentPane() - Method in class org.cytoscape.util.swing.BasicCollapsiblePanel
This class requires that all content be placed within a designated panel, this method returns that panel.
getContentTypes() - Method in class org.cytoscape.io.BasicCyFileFilter
 
getContentTypes() - Method in interface org.cytoscape.io.CyFileFilter
The MIME content types supported by this filter.
getContext() - Method in class org.cytoscape.work.AbstractTunableHandler
This returns the context of the Tunable.
getContextType() - Method in interface org.cytoscape.filter.model.Transformer
Returns the type of the context object this Transformer is compatible with.
getContextType() - Method in interface org.cytoscape.filter.model.TransformerSource
Returns the type of the context object this TransformerSource is compatible with.
getContinuousEditor(VisualProperty<?>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns the continuous editor for the specified visual property.
getContinuousEditorType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getContinuousEditorType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
Returns type of Continuous Editor.
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getContinuousTableCellRenderer(ContinuousMappingEditor<? extends Number, T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
A custom cell renderer for Continuous table cells.
getControl() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
 
getCoreProperties() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyProperty of type Properties.
getCurrentDirectory() - Method in interface org.cytoscape.application.CyApplicationManager
Get the current working directory.
getCurrentNetwork() - Method in interface org.cytoscape.application.CyApplicationManager
Provides access to the current network.
getCurrentNetworkView() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the current network view.
getCurrentNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the NetworkViewRenderer associated with the current RenderingEngine.
getCurrentRenderingEngine() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the rendering engine associated with the current network view.
getCurrentSession() - Method in interface org.cytoscape.session.CySessionManager
This method returns a CySession object describing the current state of Cytoscape.
getCurrentSessionFileName() - Method in interface org.cytoscape.session.CySessionManager
Returns the name of the current session file.
getCurrentTable() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the currently active table.
getCurrentVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns currently selected Visual Style.
getCyApplicationConfiguration() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
 
getCyApplicationManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyApplicationManager.
getCyEventHelper() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyEventHelper.
getCyGroupAggregationManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyGroupAggregationManager.
getCyGroupFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyGroupFactory.
getCyGroupManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyGroupManager.
getCyLayoutAlgorithmManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyLayoutAlgorithmManager.
getCyNetworkFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkFactory.
getCyNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkManager.
getCyNetworkViewFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkViewFactory.
getCyNetworkViewManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkViewManager.
getCyNetworkViewReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkReaderManager.
getCyNetworkViewWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyNetworkViewWriterManager.
getCyPropertyReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyPropertyReaderManager.
getCyPropertyWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyPropertyWriterManager.
getCyRootNetworkManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyRootNetworkManager.
getCyServiceRegistrar() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyServiceRegistrar.
getCySessionManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CySessionManager.
getCySessionReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CySessionReaderManager.
getCySessionWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CySessionWriterManager.
getCySwingApplication() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Deprecated.
Returns an instance of CySwingApplication.
getCyTableFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyTableFactory.
getCyTableManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyTableManager.
getCyTableReaderManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyTableReaderManager.
getCyTableWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyTableWriterManager.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Returns the CytoPanel on which a component was selected.
getCytoPanel() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Returns the CytoPanel whose state has changed.
getCytoPanel(CytoPanelName) - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the appropriate CytoPanel for the specified compass direction.
getCytoPanelComponentCount() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the number of components in the CytoPanel.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the position in the layout.
getCytoPanelName() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the name of the CytoPanel that this component should be added to.
getCyVersion() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of CyVersion.
getData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService
Extract data from a CyJobData object.
getDataCategory() - Method in class org.cytoscape.io.BasicCyFileFilter
 
getDataCategory() - Method in interface org.cytoscape.io.CyFileFilter
The DataCategory supported by this filter.
getDataCategory() - Method in interface org.cytoscape.io.datasource.DataSource
DataCategory of this data.
getDataCategory() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getDataInstance() - Method in interface org.cytoscape.jobs.CyJobDataService
Returns an empty instance of CyJobData that may be used with this service.
getDataService() - Method in interface org.cytoscape.jobs.CyJobExecutionService
Return the CyJobDataService that is used by service to marshall and unmarshall data for the remote service.
getDataSourceList(String, List<Category>) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Traverse bookmark tree and get a list of data sources from the specified category.
getDataSourceManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of DataSourceManager.
getDataSources(String) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources from a data provider
getDataSources(DataCategory) - Method in interface org.cytoscape.io.datasource.DataSourceManager
Returns all data sources under the given category.
getDataTableComboBoxEditor(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Attribute selector for the given table entry type.
getDataType() - Method in interface org.cytoscape.view.vizmap.gui.util.DiscreteMappingGenerator
Returns the type of the visual property.
getDefault() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getDefault() - Method in interface org.cytoscape.view.model.VisualProperty
The default value of this property.
getDefaultAggregation(Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the default Aggregator for a specific column type as expressed as a java Class.
getDefaultAggregation(CyGroup, Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the Aggregator for a specific column type as expressed as a java Class that will be used in the specified CyGroup.
getDefaultComboBoxEditor(String) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Get JComboBox type editor
getDefaultEdgeTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for the edges of this network.
getDefaultIcon(int, int) - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getDefaultIcon(int, int) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
This is for default view editor.
getDefaultLayout() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns Cytoscape's default layout.
getDefaultLayoutContext() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getDefaultLayoutContext() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the default instance of the layout context.
getDefaultListAggregation(Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the default Aggregator for a specific List column type as expressed as a java Class.
getDefaultListAggregation(CyGroup, Class<?>) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the Aggregator for a specific List column type as expressed as a java Class that will be used in the specified CyGroup.
getDefaultNetworkTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for this network.
getDefaultNetworkViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the NetworkViewRenderer that should be used to create CyNetworkViews.
getDefaultNodeTable() - Method in interface org.cytoscape.model.CyNetwork
A convenience method returns the default attribute table for the nodes of this network.
getDefaultTableViewRenderer() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the TableViewRenderer that should be used to create CyTableViews.
getDefaultTableVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Provide default table VisualLexicon from a default engine factory.
getDefaultValue() - Method in interface org.cytoscape.model.CyColumn
Returns the default value for the column, possibly null.
getDefaultValue(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns default value for the VisualProperty.
getDefaultVariableValues() - Method in class org.cytoscape.equations.Equation
Returns default values for variable references, if any.
getDefaultVariableValues() - Method in interface org.cytoscape.equations.EquationParser
Returns a map of variable names to their default values, if any.
getDefaultView(VisualStyle) - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewEditor
Deprecated.
getDefaultViewEditor() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI
Deprecated.
getDefaultViewPanel() - Method in interface org.cytoscape.view.vizmap.gui.VizMapGUI
Deprecated.
getDefaultVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Provide default network VisualLexicon from a default engine factory.
getDefaultVisualStyle() - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Return default VisualStyle.
getDegree() - Method in class org.cytoscape.view.layout.LayoutNode
Return the node's degree (i.e.
getDependency() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
 
getDependency() - Method in interface org.cytoscape.work.swing.GUITunableHandler
Returns the name of a different GUITunableHandler that this tunable handler depends on.
getDepth() - Method in class org.cytoscape.view.layout.LayoutNode
Return the height of this node
getDepth() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the total depth of all of the LayoutNodes
getDescription() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getDescription() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
An optional short text describing what this search provider does.
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor
Returns the description of the argument.
getDescription() - Method in class org.cytoscape.io.BasicCyFileFilter
 
getDescription() - Method in interface org.cytoscape.io.CyFileFilter
A short, human readable description of the file extensions suitable for display in FileChoosers.
getDescription() - Method in interface org.cytoscape.io.datasource.DataSource
Description for this data.
getDescription() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getDescription() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getDescription() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Get human-readable description of this client.
getDescription() - Method in class org.cytoscape.util.swing.FileChooserFilter
Returns the short description of the acceptable file type.
getDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getDescription() - Method in interface org.cytoscape.work.TunableHandler
Returns the associated Tunable's description.
getDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the description of the specified command in the specified namespace.
getDesktopViewAreaSize() - Method in interface org.cytoscape.application.swing.CyNetworkViewDesktopMgr
Deprecated.
This method has been deprecated in version 3.4.
getDialogTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Deprecated.
Returns an instance of DialogTaskManager.
getDisabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent
Get set of Visual Properties to be disabled in the lexicon.
getDiscreteTableCellRenderer() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getDiscreteTableCellRenderer() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
A custom cell renderer for Discrete table cells.
getDisplayName() - Method in enum class org.cytoscape.io.DataCategory
 
getDisplayName() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getDisplayName() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Returns display name of this client.
getDisplayName() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getDisplayName() - Method in interface org.cytoscape.view.model.VisualProperty
Returns a short string suitable for presentation to humans.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Display name is a simple description of this image object.
getDisplayName() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Return the CyCustomGraphics2 name which is will be displayed to the user.
getDisplayName() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
 
getDisplayName() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue
Name of this value type.
getDisplayName() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Provides human-readable name of this dependency.
getDisplayNames() - Static method in enum class org.cytoscape.view.presentation.property.values.Position
Return a sorted list containing all of the display names for all of the Position anchors.
getDoubleClickAction() - Method in interface org.cytoscape.group.CyGroupSettingsManager
getDoubleClickAction(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the current CyGroupSettingsManager.DoubleClickAction for the specified group.
getDoubles(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of doubles.
getEdge() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the Edge this LayoutEdge represents
getEdge(long) - Method in interface org.cytoscape.model.CyNetwork
Return the CyEdge that has the SUID.
getEdgeCount() - Method in interface org.cytoscape.model.CyNetwork
Return the number of edges in this network.
getEdgeCount() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the number of edges in the network view.
getEdgeInfo(View<CyEdge>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns an object that provides more information about the given edge.
getEdgeList() - Method in interface org.cytoscape.model.CyNetwork
Return a list of the edges in this network.
getEdgeList() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the list of LayoutEdges within this partition.
getEdgeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a edgelist into a list of CyEdges.
getEdges() - Method in class org.cytoscape.group.events.GroupEdgesRemovedEvent
Returns the list of edges associated with this event.
getEdges() - Method in class org.cytoscape.model.events.AboutToRemoveEdgesEvent
Returns the collection of edges about to be removed.
getEdgesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil
A utility method that returns a list of edges that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getEdgeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the immutable edge View for the given view SUID.
getEdgeView(CyEdge) - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a View for a specified Edge.
getEdgeViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of Views for all CyEdges in the network.
getEdgeViews() - Method in class org.cytoscape.view.model.events.AddedEdgeViewsEvent
Returns new edge view added to the source network view object.
getEdgeViewsIterable() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns an Iterable for all edge views in the network.
getEditingRow() - Method in class org.cytoscape.util.swing.JTreeTable
Returns the row being edited.
getElementCount(C) - Method in interface org.cytoscape.filter.model.TransformerSource
Returns the number of elements that could be produced from the given context.
getElementList(C) - Method in interface org.cytoscape.filter.model.TransformerSource
Returns a List of elements from the given context.
getElementType() - Method in interface org.cytoscape.filter.model.Transformer
Returns the type of the elements this Transformer is compatible with.
getElementType() - Method in interface org.cytoscape.filter.model.TransformerSource
Returns the type of the elements this TransformerSource is compatible with.
getEnableAttributeAggregation() - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the setting for whether or not we're enabling aggregation.
getEnableAttributeAggregation(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the setting for whether or not we're enabling aggregation for a specific group.
getEnabled() - Method in class org.cytoscape.view.vizmap.gui.event.LexiconStateChangedEvent
Get set of Visual Properties to be enabled in the lexicon.
getEnabled() - Method in class org.cytoscape.work.swing.util.UserAction
 
getEnd() - Method in class org.cytoscape.equations.Token
 
getEquation() - Method in interface org.cytoscape.equations.EquationCompiler
If compile() returns true, this returns the result of the compilation.
getErrorColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
getErrorEquation(String, Class<?>, String) - Method in interface org.cytoscape.equations.EquationCompiler
A factory method that returns an Equation that always fails at runtime.
getErrorLocation() - Method in interface org.cytoscape.equations.EquationCompiler
If compile() failed, this will return the index in the equation where the error was encountered.
getErrorLocation() - Method in interface org.cytoscape.equations.EquationParser
If parse() failed, this will return the index in the equation where the error was encountered.
getErrorMsg() - Method in interface org.cytoscape.equations.EquationParser
If parse() failed, this will return the last error messages.
getExampleJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns a valid JSON string representative of the expected JSON output of the command.
getExampleStringValue() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getExampleStringValue() - Method in interface org.cytoscape.work.TunableHandler
Returns the exampleStringValue property of the associated Tunable.
getException() - Method in class org.cytoscape.session.events.SessionLoadCancelledEvent
Deprecated.
 
getException() - Method in class org.cytoscape.session.events.SessionSaveCancelledEvent
 
getException() - Method in class org.cytoscape.work.FinishStatus
Returns the exception thrown by the task that failed, or null if the task iterator succeeded or was cancelled.
getExtension(String) - Method in class org.cytoscape.io.BasicCyFileFilter
Returns a string of the characters following the last '.' in the input string, which is to say the file extension assuming that the input string represents a file name.
getExtensions() - Method in class org.cytoscape.io.BasicCyFileFilter
 
getExtensions() - Method in interface org.cytoscape.io.CyFileFilter
Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
getExtensions() - Method in class org.cytoscape.util.swing.FileChooserFilter
Returns an array of the extensions associated with this FileChooserFilter.
getExternalEdgeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of exterior edges connected to the nodes within this group.
getFactories() - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager
Returns all available factories.
getFactory(Class<?>) - Method in interface org.cytoscape.view.vizmap.gui.MappingFunctionFactoryManager
Factory for the specific mapping type.
getFile(Component, String, int, String, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileFilter() - Method in interface org.cytoscape.io.CyFileFilterProvider
Return the file filter associated with the IOFactory.
getFileFilter() - Method in class org.cytoscape.io.read.AbstractInputStreamTaskFactory
Return the file filter associated with the IOFactory.
getFiles(Component, String, int, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, String, boolean, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, String, String, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, Collection<FileChooserFilter>) - Method in interface org.cytoscape.util.swing.FileUtil
Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFillColor() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the fill color.
getFillOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Return the fill opacity, a value between 0.0 (fully transparent) and 100.0 (fully opaque).
getFitRatio() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Get the fit ratio for this custom graphic.
getFolder(Component, String, String) - Method in interface org.cytoscape.util.swing.FileUtil
Returns a File object representing a folder, this method should be used instead of rolling your own JFileChooser.
getFont() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font being used
getFont() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font being used
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font family to be used for the text display
getFontFamily() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font family to be used for the text display
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the size of the font used to display the text
getFontSize() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the size of the font used to display the text
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the font style
getFontStyle() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the font style
getFormat() - Method in class org.cytoscape.view.presentation.property.table.CellFormat
 
getFormat() - Method in class org.cytoscape.work.AbstractTunableHandler
Provides a format string suitable for passing to String.format.
getFunction(String) - Method in interface org.cytoscape.equations.EquationParser
Returns the function associated with the name "functionName" or null if no such function exists.
getFunctionSummary() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getGlobalTables() - Method in interface org.cytoscape.model.CyTableManager
Returns a set of all global tables.
getGravity() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the gravity value for the annotation.
getGravityTracker(String) - Method in class org.cytoscape.util.swing.JMenuTracker
This method will fetch an existing menu or create a new one if a menu with the specified name does not exist.
getGroup() - Method in class org.cytoscape.group.events.GroupAddedEvent
 
getGroup(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Return the group the corresponds to a particular node in a CyNetwork.
getGroupNetwork() - Method in interface org.cytoscape.group.CyGroup
Returns the network referenced by this group.
getGroupNode() - Method in interface org.cytoscape.group.CyGroup
Return the CyNode that represents this group in the network.
getGroups() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getGroups() - Method in interface org.cytoscape.work.TunableHandler
Returns the associated Tunable's groups or nesting hierarchy.
getGroupSet(CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Provides the set of all the groups known to the groups manager in a particular network.
getGroupsForNode(CyNode) - Method in interface org.cytoscape.group.CyGroupManager
Return the list of CyGroups this node is in.
getGroupsForNode(CyNode, CyNetwork) - Method in interface org.cytoscape.group.CyGroupManager
Return the list of CyGroups this node is in for a particular network.
getGroupViewType() - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the current default CyGroupSettingsManager.GroupViewType.
getGroupViewType(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the current CyGroupSettingsManager.GroupViewType for the specified group.
getHandler(String) - Method in interface org.cytoscape.view.vizmap.gui.event.VizMapEventHandlerManager
Returns handler for the event.
getHandlers(Object) - Method in class org.cytoscape.work.AbstractTunableInterceptor
Returns a list of TunableHandler objects that have been found to process the fields and methods annotated with Tunable.
getHeader(InputStream, int) - Method in class org.cytoscape.io.BasicCyFileFilter
Returns a string containing the specified number of lines from the beginning of the file.
getHeight() - Method in class org.cytoscape.view.layout.LayoutNode
Return the height of this node
getHeight() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the total height of all of the LayoutNodes
getHeight() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Returns height of current object.
getHelpBroker() - Method in interface org.cytoscape.application.swing.CyHelpBroker
Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpBroker.
getHelpSet() - Method in interface org.cytoscape.application.swing.CyHelpBroker
Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpSet.
getIcon() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the Icon to be used along with the title in the tab for this this component.
getIcon() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getIcon() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
An icon that represents this search provider.
getIcon() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
An icon that represents this AnnotationFactory.
getIcon(int, int) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
 
getIcon(String) - Method in interface org.cytoscape.util.swing.IconManager
 
getIconFont(float) - Method in interface org.cytoscape.util.swing.IconManager
Returns the font that renders the text as an icon.
getIconFont(String, float) - Method in interface org.cytoscape.util.swing.IconManager
 
getIconHeight() - Method in class org.cytoscape.util.swing.TextIcon
 
getIconWidth() - Method in class org.cytoscape.util.swing.TextIcon
 
getId() - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getId() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getId() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
Returns the unique id of this network search provider.
getId() - Method in interface org.cytoscape.application.TableViewRenderer
 
getId() - Method in interface org.cytoscape.filter.model.Transformer
Returns the unique id of this type of Transformer.
getId() - Method in interface org.cytoscape.filter.model.TransformerFactory
Returns the unique id of the Transformer produced by this factory.
getId() - Method in interface org.cytoscape.filter.view.TransformerViewFactory
Returns the unique id of the Transformer this factory produces views for.
getId() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
Returns the unique id of the AnnotationFactory implementation.
getId() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Return the prefix to identify this Custom Graphics factory.
getIdentifier() - Method in interface org.cytoscape.application.swing.CytoPanelComponent2
Returns this component's identifier, which should be unique.
getIdentifier() - Method in interface org.cytoscape.util.color.Palette
Return the internal identifier of this palette.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the edge's identifier.
getIdentifier() - Method in class org.cytoscape.view.layout.LayoutNode
Return the node's identifier.
getIdentifier() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Immutable session-unique identifier of this custom graphic generated by the custom graphics manager.
getIdString() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getIdString() - Method in interface org.cytoscape.view.model.VisualProperty
Returns a short string used to identify this visual property and suitable for serializing to XML and other text formats.
getIdString() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Provides serializable string of this dependency.
getImage() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the image currently assigned to this annotation.
getImageBrightness() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the brightness adjustment for this image.
getImageContrast() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the contrast adjustment for this image.
getImageOpacity() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the current opacity of the image.
getImageURL() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Get the URL for the image to be displayed.
getImportedObject() - Method in class org.cytoscape.io.webservice.events.DataImportFinishedEvent
Returns the object that was imported.
getIndex() - Method in class org.cytoscape.view.layout.LayoutNode
Returns the index of this LayoutNode.
getIndex(Handle) - Method in interface org.cytoscape.view.presentation.property.values.Bend
Get index of a Handle
getIndexOfChild(Object, Object) - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the index of a child given a parent.
getInfoColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
getInputStream(String) - Method in interface org.cytoscape.io.util.StreamUtil
Gets the input stream from given a string.
getInputStream(URL) - Method in interface org.cytoscape.io.util.StreamUtil
Gets the input stream from given URL.
getInstallationDirectoryLocation() - Method in interface org.cytoscape.application.CyApplicationConfiguration
Returns absolute path to Cytoscape installation directory location.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Get a new instance of a CyCustomGraphics2.
getInstance(String) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Get a new instance of the CyCustomGraphics.
getInstance(URL) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Get a new instance of the CyCustomGraphics based on pulling the data from a URL.
getInstance(Map<String, Object>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Get a new instance of a CyCustomGraphics2 with the passed properties.
getInstance(CyCustomGraphics2<T>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Get a new instance of a CyCustomGraphics2 that is a clone of the passed argument.
getInternalEdgeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of edges contained within this group.
getJFrame() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JFrame that contains the application.
getJMenu(String) - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JMenu for the specified name and null if no menu exists for the name.
getJMenuBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JMenuBar object for the application.
getJobDataService() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getJobDataService() - Method in interface org.cytoscape.jobs.CyJob
Return the CyJobDataService that was used to create this job.
getJobExecutionService() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getJobExecutionService() - Method in interface org.cytoscape.jobs.CyJob
Return the CyJobExecutionService that created this job.
getJobId() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getJobId() - Method in interface org.cytoscape.jobs.CyJob
Return the ID for this job.
getJobMonitor() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getJobMonitor() - Method in interface org.cytoscape.jobs.CyJob
Return the service that handles status changes for this job.
getJobName() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getJobName() - Method in interface org.cytoscape.jobs.CyJob
Return the name for this job
getJobs() - Method in interface org.cytoscape.jobs.CyJobManager
Return the list of CyJobs currently managed by the CyJobManager.
getJPanel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns the panel associated with this GUITunableHandler.
getJPanel() - Method in interface org.cytoscape.work.swing.GUITunableHandler
To get the panel that contains the GUI representation (JTextField, JFileChooser, JLabel, JList ...)
getJSON() - Method in interface org.cytoscape.work.json.JSONResult
 
getJToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the JToolBar object for the application.
getJustify() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Return the justification of the label (or other object).
getKeys() - Method in class org.cytoscape.model.events.RowsDeletedEvent
Returns the primary keys of the rows for this event.
getKeyValue() - Method in class org.cytoscape.view.model.table.CyRowViewMetadata
 
getLabel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
 
getLastErrorMsg() - Method in interface org.cytoscape.equations.EquationCompiler
Returns an error message for an error encountered during a call to compile, if any.
getLastInternalError() - Method in interface org.cytoscape.model.CyTable
Returns a descriptive message for certain internal errors.
getLayers(CyNetworkView, View<? extends CyIdentifiable>) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Get layers that belong to this object.
getLayers(CyTableView, CyColumnView, CyRow) - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
 
getLayout(String) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns a layout algorithm of the specified name and null if no algorithm exists with that name.
getLayoutAttribute(CyLayoutAlgorithm, CyNetworkView) - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithmManager
Returns the attribute name that has been associated with the layout, or the empty string if there is no valid attribute associated to the layout for the given view.
getLeftChild() - Method in class org.cytoscape.equations.AbstractNode
 
getLeftChild() - Method in interface org.cytoscape.equations.TreeNode
Returns the left child if it exists or null if it doesn't.
getLength() - Method in class org.cytoscape.equations.Token
 
getLength() - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the number of direct children Filters contained by this CompositeFilter.
getLineColor() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Set the line color for this arrow
getLineWidth() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the line width for this arrow
getList(String, Class<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getList(String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getList(String, String, Class<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getList(String, String, Class<T>, List<T>) - Method in interface org.cytoscape.model.CyRow
Returns a list which is a view on the underlying column value for this row.
getListAggregators() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of aggregators for List columns.
getListAggregators(Class<?>) - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of List aggregators for a particular Class.
getListElementType() - Method in interface org.cytoscape.model.CyColumn
Returns the data type of the list elements if the column type is List.class otherwise null.
getListenerClass() - Method in class org.cytoscape.event.AbstractCyEvent
The Class of the listener that is expected to handle this event.
getListenerClass() - Method in interface org.cytoscape.event.CyEvent
The Class of the listener that is expected to handle this event.
getListeners() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the list of listeners that will listen for changes to this object
getListeners() - Method in class org.cytoscape.work.util.ListSelection
Returns the list of listeners that will listen for changes to this object
getLoadedFileName() - Method in class org.cytoscape.session.events.SessionLoadedEvent
Returns the file name of the session just loaded.
getLoadedSession() - Method in class org.cytoscape.session.events.SessionLoadedEvent
Returns the session that was just loaded.
getLocalTables(Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyTableManager
Returns set of all local tables for the given data type.
getLocation() - Method in interface org.cytoscape.io.datasource.DataSource
Location of this data file.
getLocation() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getLogWeight() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the current value for this edge's logWeight (-log(weight)).
getLongDescription() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getLongDescription() - Method in interface org.cytoscape.work.TunableHandler
Returns the associated Tunable's longDescription
getLongDescription(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns the longDescription of the specified command in the specified namespace.
getLongs(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of longs.
getLowerBound() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the lower limit of the object.
getMajorVersion() - Method in interface org.cytoscape.application.CyVersion
The first of the three numbers defining the version of the software, meaning "3" if the version is "3.2.5".
getMapData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService
Extract a map from a CyJobData object.
getMappedColumns() - Method in interface org.cytoscape.view.presentation.property.values.MappableVisualPropertyValue
 
getMappedValue(CyRow) - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns the mapped value for a CyRow.
getMappingColumnName() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getMappingColumnName() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns attribute name used in this mapping.
getMappingColumnType() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getMappingColumnType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Returns data type of mapping attribute.
getMappingFunctionSelector() - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns selector for Mapping Type.
getMappingFunctionType() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunctionFactory
Returns the type of this VisualMappingFunctionFactory.
getMapValue(K) - Method in interface org.cytoscape.view.vizmap.mappings.DiscreteMapping
Gets Value for Specified Key.
getMatchingFactory(CyFileFilter) - Method in interface org.cytoscape.io.write.CyWriterManager
Returns a CyWriterFactory for the appropriate filter.
getMatchingKeys(String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable
Returns all the keys of a specified column that match the given value.
getMatchingKeys(String, String, Object, Class<T>) - Method in interface org.cytoscape.model.CyTable
Returns all the keys of a specified column that match the given value.
getMatchingRows(String, Object) - Method in interface org.cytoscape.model.CyTable
Returns all the rows of a specified column that contain a certain value for that column.
getMatchingRows(String, String, Object) - Method in interface org.cytoscape.model.CyTable
Returns all the rows of a specified column that contain a certain value for that column.
getMax() - Method in class org.cytoscape.view.model.ContinuousRange
Returns the maximum value of this range.
getMaxX() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the maximum X location of all of the LayoutNodes
getMaxY() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the maximum Y location of all of the LayoutNodes
getMaxZ() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the maximum Z location of all of the LayoutNodes
getMBR(double[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D
Returns the "Minimum Bounding Rectangle", the smallest rectangle that contains all the objects stored in this SpacialIndex2D.
getMBR(float[]) - Method in interface org.cytoscape.view.model.spacial.SpacialIndex2D
Returns the "Minimum Bounding Rectangle", the smallest rectangle that contains all the objects stored in this SpacialIndex2D.
getMembers() - Method in interface org.cytoscape.view.presentation.annotations.GroupAnnotation
Return the list of members for this group
getMenu() - Method in interface org.cytoscape.util.swing.GravityTracker
Returns the JPopupMenu or JMenu that this gravity tracker tracks.
getMenu() - Method in class org.cytoscape.util.swing.MenuGravityTracker
 
getMenu() - Method in class org.cytoscape.util.swing.PopupMenuGravityTracker
 
getMenuGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getMenuGravity() - Method in interface org.cytoscape.application.swing.CyAction
Returns the gravity used to place the menu item for this action.
getMenuGravity() - Method in class org.cytoscape.application.swing.CyMenuItem
Returns the gravity used to place the menu item in a menu.
getMenuItem() - Method in class org.cytoscape.application.swing.CyMenuItem
Returns the menu item to be placed in a menu according to the specified menu gravity.
getMessage() - Method in class org.cytoscape.jobs.CyJobStatus
Return any message associated with the job status.
getMin() - Method in class org.cytoscape.view.model.ContinuousRange
Returns the minimum value of this range.
getMinorVersion() - Method in interface org.cytoscape.application.CyVersion
The second of the three numbers defining the version of the software, meaning "2" if the version is "3.2.5".
getMinX() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the minimum X location of all of the LayoutNodes
getMinY() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the minimum Y location of all of the LayoutNodes
getMinZ() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the minimum Z location of all of the LayoutNodes
getModel() - Method in interface org.cytoscape.view.model.View
Get source data structure, such as CyNode, CyEdge, etc.
getModelSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the SUID of the underlying model object.
getModelSUID() - Method in interface org.cytoscape.view.model.SnapshotNodeInfo
Returns the SUID of the underlying model object.
getMostRecentlyOpenedURL() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Returns the last addition or null if there are no URLs.
getMultiLineLabel() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
 
getMutability() - Method in interface org.cytoscape.model.CyTable
The table can be deleted if this returns Mutability.MUTABLE, otherwise it cannot be deleted!
getMutableEdgeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the mutable edge View for the given view SUID, or null if the edge view no longer exists in the mutable network view.
getMutableNetworkView() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the mutable CyNetworkView that was used to create this snapshot.
getMutableNodeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the mutable node View for the given view SUID, or null if the node view no longer exists in the mutable network view.
getName() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getName() - Method in interface org.cytoscape.application.swing.CyAction
Returns the name of the action.
getName() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getName() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
A short name to be displayed to the user.
getName() - Method in interface org.cytoscape.equations.Function
Used to parse the function string.
getName() - Method in interface org.cytoscape.filter.model.NamedTransformer
Returns the name of this NamedTransformer.
getName() - Method in interface org.cytoscape.filter.model.Transformer
Returns the user-friendly display name of this type of Transformer.
getName() - Method in interface org.cytoscape.io.datasource.DataSource
Name of this data source
getName() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getName() - Method in enum class org.cytoscape.jobs.CyJobStatus.Status
 
getName() - Method in interface org.cytoscape.model.CyColumn
Returns the fully-qualified name of the column.
getName() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the name of the CyProperty.
getName() - Method in interface org.cytoscape.property.CyProperty
Returns the name of the CyProperty.
getName() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the name of the CyProperty.
getName() - Method in interface org.cytoscape.util.color.Palette
Return the name of this palette.
getName() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getName() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the computer-readable name of the layout.
getName() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
 
getName() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the name for this annotation.
getName() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
A short name to be displayed to the user.
getName() - Method in enum class org.cytoscape.view.presentation.property.values.Justification
Return the display name of this justification type.
getName() - Method in enum class org.cytoscape.view.presentation.property.values.Position
Return the display name of this anchor position.
getName() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getName() - Method in interface org.cytoscape.work.TunableHandler
Returns a name representing a tunable property.
getNamedTransformer(String) - Method in interface org.cytoscape.filter.TransformerContainer
Returns the transformer with the given name, or null if a transformer with the given name does not exist in this container.
getNamedTransformers() - Method in interface org.cytoscape.filter.TransformerContainer
Returns the list of transformers contained in this container.
getNameOnly() - Method in interface org.cytoscape.model.CyColumn
Returns the name portion without the namespace.
getNameOnly() - Method in class org.cytoscape.model.events.ColumnDeletedEvent
Returns the name portion without the namespace.
getNameOnly() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the name portion without the namespace.
getNames() - Static method in enum class org.cytoscape.view.presentation.property.values.Justification
Return the display names for all of the Justifcation values
getNamespace() - Method in interface org.cytoscape.model.CyColumn
Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in interface org.cytoscape.model.CyTableMetadata
getNamespace() - Method in class org.cytoscape.model.events.ColumnDeletedEvent
Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the namespace of the column, or null if the column does not have a namespace.
getNamespace() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getNamespaceDescription() - Method in interface org.cytoscape.application.swing.CyColumnPresentation
Returns a String description of the namespace.
getNamespaceIcon() - Method in interface org.cytoscape.application.swing.CyColumnPresentation
Returns an icon associated with the namespace.
getNamespaces() - Method in interface org.cytoscape.command.AvailableCommands
Returns a list of available command namespaces in alphabetical order.
getNamespaces() - Method in interface org.cytoscape.model.CyTable
Returns all the namespaces used in the table.
getNeighborList(CyNode, CyEdge.Type) - Method in interface org.cytoscape.model.CyNetwork
Get the list of nodes that neighbor this node where the definition of "neighbor" is a node that is connected to this node by the passed edgeType.
getNeighbors() - Method in class org.cytoscape.view.layout.LayoutNode
Convenience function to return the list of neighbors (connected nodes) of this node.
getNetwork() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
Returns the network associated with this event.
getNetwork() - Method in class org.cytoscape.command.util.EdgeList
Return the network used by this EdgeList
getNetwork() - Method in class org.cytoscape.command.util.NodeList
Get the network for this nodelist
getNetwork() - Method in class org.cytoscape.group.events.GroupCollapsedEvent
 
getNetwork() - Method in interface org.cytoscape.model.CyTableMetadata
Returns all the networks associated with this object's table.
getNetwork() - Method in class org.cytoscape.model.events.UnsetNetworkPointerEvent
Returns the CyNetwork for this event.
getNetwork() - Method in class org.cytoscape.model.events.NetworkAddedEvent
 
getNetwork() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns the CyNetwork event source.
getNetwork(long) - Method in interface org.cytoscape.model.CyNetworkManager
Returns the network corresponding to the provided ID
getNetwork(String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a network into a CyNetwork.
getNetworkData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService
Optional method to extract network data from a CyJobData object.
getNetworkForTable(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the network this table is registered with.
getNetworkPointer() - Method in interface org.cytoscape.model.CyNode
Returns the network referenced by this node.
getNetworks() - Method in class org.cytoscape.application.events.SetSelectedNetworksEvent
Returns the list of networks selected.
getNetworks() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getNetworks() - Method in interface org.cytoscape.io.read.CyNetworkReader
Returns an array of networks read after executing the run() method of Task.
getNetworks() - Method in class org.cytoscape.session.CySession
Returns a set of all CyNetwork objects contained in this Session.
getNetworkSet() - Method in interface org.cytoscape.group.CyGroup
Return the list of CyNetworks this group is in.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkManager
Provides the set of all the networks known to the network manager.
getNetworkSet() - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns a read-only set of all networks managed by this instance.
getNetworkView() - Method in class org.cytoscape.application.events.SetCurrentNetworkViewEvent
Returns the network view associated with this event.
getNetworkView() - Method in class org.cytoscape.view.model.events.NetworkViewAddedEvent
 
getNetworkView() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Return the view that this Annotation is for
getNetworkView() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
Get the The target network view model.
getNetworkView(String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a network view into a CyNetworkView.
getNetworkViewFactory() - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getNetworkViewFactory() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getNetworkViewRenderer(String) - Method in interface org.cytoscape.application.CyApplicationManager
Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.
getNetworkViewRendererList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getNetworkViewRendererSet() - Method in interface org.cytoscape.application.CyApplicationManager
Returns a set with all the NetworkViewRenderer objects that have been registered.
getNetworkViews() - Method in class org.cytoscape.application.events.SetSelectedNetworkViewsEvent
Returns the list of network views that have been selected.
getNetworkViews() - Method in class org.cytoscape.session.CySession
Returns a set of all CyNetworkView objects contained in this Session.
getNetworkViews(CyNetwork) - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Returns a collection of network views corresponding to the specified network, if found.
getNetworkViewSet() - Method in interface org.cytoscape.view.model.CyNetworkViewManager
Provides the set of network views that are currently known to the network manager.
getNewColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the new name of the column.
getNewNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the name name portion without the namespace.
getNewNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the new namespace of the column, or null if the column does not have a namespace.
getNewProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent
The new properties after being modified.
getNewState() - Method in class org.cytoscape.application.swing.events.CytoPanelStateChangedEvent
Returns the new state of the CytoPanel.
getNextSUID() - Static method in class org.cytoscape.model.SUIDFactory
Returns the next available SUID.
getNode() - Method in class org.cytoscape.model.events.UnsetNetworkPointerEvent
Returns the CyNode for this event.
getNode() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the Node associated with this LayoutNode.
getNode(long) - Method in interface org.cytoscape.model.CyNetwork
Return the CyNode that has the SUID.
getNodeCount() - Method in interface org.cytoscape.model.CyNetwork
Return the number of nodes in this network.
getNodeCount() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the number of nodes in the network view.
getNodeInfo(View<CyNode>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns an object that provides more information about the given node.
getNodeList() - Method in interface org.cytoscape.group.CyGroup
Returns the list of nodes contained within this group.
getNodeList() - Method in interface org.cytoscape.model.CyNetwork
Return a list of the nodes in this network.
getNodeList() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the list of LayoutNodes within this partition.
getNodeList(CyNetwork, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a nodelist into a list of CyNodes.
getNodeMap() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
Returns map from key value to existing CyNode.
getNodes() - Method in class org.cytoscape.group.events.GroupNodesRemovedEvent
Returns the list of nodes associated with this event.
getNodes() - Method in class org.cytoscape.model.events.AboutToRemoveNodesEvent
Returns the collection of nodes about to be removed.
getNodesInState(CyNetwork, String, boolean) - Static method in class org.cytoscape.model.CyTableUtil
A utility method that returns a list of nodes that have a boolean attribute in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in the specified state.
getNodeView() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the View associated with this LayoutNode.
getNodeView(long) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the immutable node View for the given view SUID.
getNodeView(CyNode) - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a View for a specified Node.
getNodeViews() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns a list of Views for all CyNodes in the network.
getNodeViews() - Method in class org.cytoscape.view.model.events.AddedNodeViewsEvent
Returns new node view object.
getNodeViewsIterable() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns an Iterable for all node views in the network.
getNumTasks() - Method in class org.cytoscape.work.TaskIterator
Returns the current total number of tasks in the iterator.
getObject(Long, Class<T>) - Method in class org.cytoscape.session.CySession
When a session is restored, Cytoscape automatically generates new SUIDs.
getObject(String, Class<T>) - Method in class org.cytoscape.session.CySession
When a session is restored, Cytoscape automatically generates new SUIDs.
getOffsetX() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Return the X offset of the object
getOffsetY() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Return the Y offset of the object
getOldColumnName() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the old name of the column.
getOldNameOnly() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the old name portion without the namespace.
getOldNamespace() - Method in class org.cytoscape.model.events.ColumnNameChangedEvent
Returns the old namespace of the column, or null if the column did not have a namespace.
getOldProperties() - Method in class org.cytoscape.application.swing.events.PreferencesUpdatedEvent
The old properties before they were modified.
getOldTitle() - Method in class org.cytoscape.model.events.TableTitleChangedEvent
 
getOptionsComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
This implementation simply returns null, which means that no options component will be displayed, unless the subclass overwrites this method to return a custom component.
getOptionsComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
You can use this method to return a component that contains extra search parameters.
getOrdinal(int) - Static method in class org.cytoscape.equations.FunctionUtil
Converts an integer to an ordinal string.
getOverrideAggregation(CyGroup, CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the override aggregation setting for a column (if any) in a specific group.
getOverrideAggregation(CyColumn) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the override aggregation setting for a column (if any).
getPaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Paint to fill the shape with.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.CustomGraphicLayer
Return the Paint to be used to fill the Shape.
getPaint(Rectangle2D) - Method in interface org.cytoscape.view.presentation.customgraphics.ImageCustomGraphicLayer
Return the TexturePaint to be used as an image to fill a node
getPalette() - Method in class org.cytoscape.util.swing.ColorButton
 
getPalette(Object) - Method in interface org.cytoscape.util.color.PaletteProvider
Get a palette by its internal identifier
getPalette(Object, int) - Method in interface org.cytoscape.util.color.PaletteProvider
Get a palette by its internal identifier
getPalette(String) - Method in interface org.cytoscape.util.color.PaletteProvider
Get a palette by its name
getPalette(String, int) - Method in interface org.cytoscape.util.color.PaletteProvider
Get a palette of the specified size by its name
getPaletteProvider() - Method in interface org.cytoscape.util.color.Palette
Return the PaletteProvider for this palette.
getPaletteProvider(String) - Method in interface org.cytoscape.util.color.PaletteProviderManager
Return the palette provider that matches the name in the argument.
getPaletteProviders() - Method in interface org.cytoscape.util.color.PaletteProviderManager
Return the list of currently registered palette providers
getPaletteProviders(PaletteType, boolean) - Method in interface org.cytoscape.util.color.PaletteProviderManager
Return the list of currently registered palette providers that provide palettes of the requested type.
getPaletteTypes() - Method in interface org.cytoscape.util.color.PaletteProvider
Return the list of org.cytoscape.util.color.Palette.PaletteTypes supported by this provider
getPanelTaskManager() - Method in interface org.cytoscape.app.swing.CySwingAppAdapter
Deprecated.
Returns an instance of PanelTaskManager.
getParams() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getParams() - Method in interface org.cytoscape.work.TunableHandler
Returns the parsed result from Tunable.getParams().
getParent() - Method in class org.cytoscape.view.model.VisualLexiconNode
Get the parent of this VP node.
getParent() - Method in interface org.cytoscape.work.swing.TunableUIHelper
Get the parent of the current Tunable dialog.
getParentVisualProperty() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
Returns the parent visual property for this dependency.
getParser() - Method in interface org.cytoscape.equations.EquationCompiler
Returns the parser which can be used for checking the syntax of equations.
getParseTree() - Method in interface org.cytoscape.equations.EquationParser
Returns the parse tree.
getPartitionNumber() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the partition number of this partition
getPath() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getPath() - Method in interface org.cytoscape.jobs.CyJob
Return the base path for communicating with the remote service for this job
getPayloadCollection() - Method in class org.cytoscape.event.AbstractCyPayloadEvent
Returns an unmodifiable collection of payload objects.
getPayloadCollection() - Method in interface org.cytoscape.event.CyPayloadEvent
Returns a collection of payload objects.
getPoint(int) - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets Specified Point.
getPointCount() - Method in interface org.cytoscape.view.vizmap.mappings.ContinuousMapping
Gets Total Point Count.
getPollInterval() - Method in class org.cytoscape.jobs.AbstractCyJob
 
getPollInterval() - Method in interface org.cytoscape.jobs.CyJob
Return the time in seconds between calls to checkJobStatus.
getPossibleArgTypes(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
Used with the equation builder.
getPossibleArgTypes(Class<?>[]) - Method in interface org.cytoscape.equations.Function
Used with the equation builder.
getPossibleValues() - Method in class org.cytoscape.work.util.ListSelection
To get all the items of the List values.
getPreferredMenu() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getPreferredMenu() - Method in interface org.cytoscape.application.swing.CyAction
This method returns a Menu specification string.
getPreferredSize() - Method in class org.cytoscape.util.swing.DropDownMenuButton
 
getPrefix() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Return the prefix to identify this custom graphics factory.
getPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in logs and other descriptions of the edit.
getPresentationWriterManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of PresentationWriterManager.
getPrimaryKey() - Method in interface org.cytoscape.model.CyTable
Returns the column type of the primary key for this table.
getPrimaryKeyListElementType() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getPrimaryKeyType() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getProperties() - Method in class org.cytoscape.application.swing.AbstractCyAction
Return the config props.
getProperties() - Method in interface org.cytoscape.application.swing.CyAction
Returns the configuration properties that were passed to the CyAction when it was created.
getProperties() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Return a property object.
getProperties() - Method in interface org.cytoscape.property.CyProperty
Return a property object.
getProperties() - Method in class org.cytoscape.property.SimpleCyProperty
Return a property object.
getProperties() - Method in class org.cytoscape.session.CySession
Note: This is NOT the correct way for Apps to access CyProperty settings.
getProperties() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2
Provides an optional map of key/value properties which define the custom graphics instance.
getProperties() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Get property values for the rendering engine, like LOD.
getProperty() - Method in interface org.cytoscape.io.read.CyPropertyReader
Return a property object.
getPropertyEditor() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getPropertyEditor() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
Returns PropertyEditor object for this data type.
getPropertyEditor(VisualProperty<T>) - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor2
Returns PropertyEditor object for this data type.
getPropertyType() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the type of the property object.
getPropertyType() - Method in interface org.cytoscape.property.CyProperty
Returns the type of the property object.
getPropertyType() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the type of the property object.
getProvider() - Method in interface org.cytoscape.io.datasource.DataSource
Name of this data provider for this source.
getProvider() - Method in class org.cytoscape.io.datasource.DefaultDataSource
 
getProvider(DataSource) - Method in interface org.cytoscape.property.bookmark.BookmarksUtil
Get the provider name from DataSource object
getProviderName() - Method in interface org.cytoscape.util.color.PaletteProvider
Return the human-readable string identifier for this PaletteProvider.
getQualifiedName() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getQualifiedName() - Method in interface org.cytoscape.work.TunableHandler
Returns the name of the underlying class of the tunable followed by a dot and the name of the tunable field or getter/setter root name.
getQualifier() - Method in interface org.cytoscape.application.CyVersion
Any text following the last digit of the bug fix version.
getQuery() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getQueryBuilderGUI() - Method in class org.cytoscape.io.webservice.swing.AbstractWebServiceGUIClient
Returns query builder UI.
getQueryBuilderGUI() - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUIClient
Returns query builder UI.
getQueryComponent() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
This implementation simply returns null, which means Cytoscape will provide a default query component, unless the subclass overwrites this method to return a custom component.
getQueryComponent() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
Use this method to return a component that contains the main or mandatory search fields.
If this task factory provides its own query component, make sure the returned JComponent fires a PropertyChangeEvent for the property NetworkSearchTaskFactory.QUERY_PROPERTY whenever its fields change in a way that affects the return of the TaskFactory.isReady() method.
getRange() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getRange() - Method in interface org.cytoscape.view.model.VisualProperty
Returns the Range of this VisualProperty.
getRange() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Gets BoundaryRangeValues.
getRaw(String) - Method in interface org.cytoscape.model.CyRow
Returns the Object that contains the value for the specified column.
getRaw(String, String) - Method in interface org.cytoscape.model.CyRow
Returns the Object that contains the value for the specified column.
getRawValue() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the raw value that the data was set as.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader task.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(InputStream, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager
Given an InputStream this method will attempt to find a InputStreamReaderFactory that can read the stream, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyNetworkReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader task.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyPropertyReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CySessionReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.CyTableReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getReader(URI, String) - Method in interface org.cytoscape.io.read.VizmapReaderManager
Given a URI this method will attempt to find a InputStreamReaderFactory that can read the URI, will set the InputStream for the factory and will return the reader.
getRecentlyOpenedURLs() - Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
Returns the current list of recently opened file names.
getRedoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in redo menu items.
getRegisteredFunctions() - Method in interface org.cytoscape.equations.EquationParser
Returns the set of currently registered functions.
getRenderedImage() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
From layers of graphics objects, render a composite scaled Image object.
getRendererId() - Method in interface org.cytoscape.view.model.CyNetworkView
Returns the ID of the renderer that must be used to render this view.
getRendererId() - Method in interface org.cytoscape.view.model.table.CyTableView
Returns the ID of the renderer that must be used to render this view.
getRendererId() - Method in interface org.cytoscape.view.presentation.RenderingEngine
This method must return the same ID which is returned by the associated implementation of NetworkViewRenderer.
getRendererID() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getRenderingEngine() - Method in class org.cytoscape.application.events.SetCurrentRenderingEngineEvent
Return the rendering engine (presentation) that has been set as current.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAboutToBeRemovedEvent
Returns the RenderingEngine associated with the deleted presentation.
getRenderingEngine() - Method in class org.cytoscape.view.presentation.events.RenderingEngineAddedEvent
Get new rendering engine.
getRenderingEngine() - Method in interface org.cytoscape.view.vizmap.gui.DefaultViewPanel
Deprecated.
getRenderingEngineFactory(String) - Method in interface org.cytoscape.application.NetworkViewRenderer
 
getRenderingEngineFactory(String) - Method in interface org.cytoscape.application.TableViewRenderer
 
getRenderingEngineManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of RenderingEngineManager.
getRenderingEngines(View<?>) - Method in interface org.cytoscape.view.presentation.RenderingEngineManager
Get rendering engines for the given view model.
getRequired() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns true if this Tunable must be set (i.e.
getResultClasses() - Method in interface org.cytoscape.work.ObservableTask
Return the classes that can be used to query ObservableTask.getResults(Class)
getResults(Class<? extends R>) - Method in interface org.cytoscape.work.ObservableTask
Return the results from this task (if any)
getReturnType() - Method in interface org.cytoscape.equations.Function
 
getRightChild() - Method in class org.cytoscape.equations.AbstractNode
 
getRightChild() - Method in interface org.cytoscape.equations.TreeNode
Returns the right child if it exists or null if it doesn't.
getRoot() - Method in class org.cytoscape.util.swing.AbstractTreeTableModel
Returns the root of this AbstractTreeTableModel.
getRootNetwork() - Method in interface org.cytoscape.group.CyGroup
Return the root network for this group.
getRootNetwork() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
Get target network collection, i.e., parent root network for all networks to be loaded.
getRootNetwork() - Method in interface org.cytoscape.model.subnetwork.CySubNetwork
Return the CyRootNetwork that contains this CySubNetwork.
getRootNetwork(CyNetwork) - Method in interface org.cytoscape.model.subnetwork.CyRootNetworkManager
Converts a CyNetwork to a CyRootNetwork
getRootNetworkList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getRootVisualProperty() - Method in interface org.cytoscape.view.model.VisualLexicon
Get root of this tree.
getRootVisualProperty() - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getRotatedBounds() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Returns the bounds of the annotation, adjusted for rotation.
getRotation() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the rotation (in degrees) for this annotation
getRow() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the CyRow of the data that was set.
getRow() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the CyRow for this LayoutEdge
getRow() - Method in class org.cytoscape.view.layout.LayoutNode
Accessor function to return the CyRow associated with this LayoutNode.
getRow(Object) - Method in interface org.cytoscape.model.CyTable
Returns the row specified by the primary key object and if a row for the specified key does not yet exist in the table, a new row will be created and the new row will be returned.
getRow(CyIdentifiable) - Method in interface org.cytoscape.model.CyNetwork
A convenience method that returns the row in the default table for this object.
getRow(CyIdentifiable, String) - Method in interface org.cytoscape.model.CyNetwork
Returns the row for the specified table name for this object.
getRowCount() - Method in interface org.cytoscape.model.CyTable
Returns the number of rows in this table.
getRowCount() - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the number of rows in the JTree.
getRowList(CyTable, String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a rowlist into a list of CyRows.
getRowView(CyRow) - Method in interface org.cytoscape.view.model.table.CyTableView
Returns the View for the specified row.
getRowViews() - Method in interface org.cytoscape.view.model.table.CyTableView
Returns all row views in the table view.
getRowViews() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getSavedFileName() - Method in class org.cytoscape.session.events.SessionSavedEvent
Returns the file name of the session just loaded.
getSavedSession() - Method in class org.cytoscape.session.events.SessionSavedEvent
Returns the session that was just loaded.
getSavedTableSUID() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getSavePolicy() - Method in interface org.cytoscape.model.CyNetwork
Returns how (or if) this CyNetwork should be saved.
getSavePolicy() - Method in interface org.cytoscape.model.CyTable
Returns how (or if) this CyTable should be saved.
getSavePolicy() - Method in class org.cytoscape.property.AbstractConfigDirPropsReader
Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in interface org.cytoscape.property.CyProperty
Returns the CyProperty.SavePolicy of the CyProperty.
getSavePolicy() - Method in class org.cytoscape.property.SimpleCyProperty
Returns the CyProperty.SavePolicy of the CyProperty.
getSearchResult() - Method in class org.cytoscape.io.webservice.events.SearchFinishedEvent
Returns The search result.
getSelectedAnnotations(CyNetworkView) - Method in interface org.cytoscape.view.presentation.annotations.AnnotationManager
Retrieve the list of selected annotations for a specific network view.
getSelectedColor() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
Return the Color the user selected
getSelectedColumnNames() - Method in class org.cytoscape.application.swing.CyColumnSelector
Returns the names of the CyColumns that have been selected.
getSelectedComponent() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the currently selected component.
getSelectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
 
getSelectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns all the edges in the network that are currently selected.
getSelectedEdges(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil
Equivalent to
getSelectedIndex() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the currently selected index.
getSelectedIndex() - Method in class org.cytoscape.application.swing.events.CytoPanelComponentSelectedEvent
Returns the index of the CytoPanelComponent selected.
getSelectedItem() - Method in class org.cytoscape.application.swing.CyColumnComboBox
Override getSelectedItem() and use covariant return type to change return type to CyColumn.
getSelectedNetworks() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the list of selected networks.
getSelectedNetworkViews() - Method in interface org.cytoscape.application.CyApplicationManager
Returns the list of selected network views.
getSelectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
 
getSelectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns all the nodes in the network that are currently selected.
getSelectedNodes(CyNetwork) - Static method in class org.cytoscape.model.CyTableUtil
Equivalent to
getSelectedPalette() - Method in interface org.cytoscape.util.swing.CyColorPaletteChooser
Return the palette the user selected
getSelectedValue() - Method in class org.cytoscape.work.util.ListSingleSelection
Get the item that is currently selected.
getSelectedValues() - Method in class org.cytoscape.work.util.ListMultipleSelection
Get the items that are currently selected.
getSerializableString() - Method in class org.cytoscape.view.presentation.property.values.AbstractVisualPropertyValue
 
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Bend
Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.Handle
Create string representation of this object for parsing.
getSerializableString() - Method in interface org.cytoscape.view.presentation.property.values.VisualPropertyValue
Returns serializable representation of this value.
getSerializedData(CyJobData) - Method in interface org.cytoscape.jobs.CyJobDataService
This method is used to extract the data from the CyJobData object in a form that is appropriate for use by the job execution service.
getService(Class<S>) - Method in interface org.cytoscape.service.util.CyServiceRegistrar
A method that attempts to get a service of the specified type.
getService(Class<S>) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarImpl
A method that attempts to get a service of the specified type.
getService(Class<S>, String) - Method in interface org.cytoscape.service.util.CyServiceRegistrar
A method that attempts to get a service of the specified type and that passes the specified filter.
getService(Class<S>, String) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarImpl
A method that attempts to get a service of the specified type and that passes the specified filter.
getService(BundleContext, Class<S>) - Method in class org.cytoscape.service.util.AbstractCyActivator
A method that attempts to get a service of the specified type.
getService(BundleContext, Class<S>, String) - Method in class org.cytoscape.service.util.AbstractCyActivator
A method that attempts to get a service of the specified type and that passes the specified filter.
getService(Bundle, ServiceRegistration) - Method in class org.cytoscape.service.util.internal.CyServiceRegistrarFactory
 
getServiceLocation() - Method in class org.cytoscape.io.webservice.client.AbstractWebServiceClient
 
getServiceLocation() - Method in interface org.cytoscape.io.webservice.WebServiceClient
Returns resource location of this service, i.e., service URL.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobDataService
The name of the service.
getServiceName() - Method in interface org.cytoscape.jobs.CyJobExecutionService
The name of the service.
getSession() - Method in interface org.cytoscape.io.read.CySessionReader
Returns a CySession object
getShape() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the current shape as a Shape object
getShape() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Shape
getShapeType() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the current shape type as a String
getSharedEdgeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the edge table shared by all subnetworks.
getSharedNetworkTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the network table shared by all subnetworks.
getSharedNodeTable() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Returns the node table shared by all subnetworks.
getShortName() - Method in enum class org.cytoscape.view.presentation.property.values.Justification
Return the short name of this justification type
getShortName() - Method in enum class org.cytoscape.view.presentation.property.values.Position
Return the short name of this anchor position.
getSize() - Method in enum class org.cytoscape.model.CyTableFactory.InitialTableSize
Returns the actual size value for the given enum.
getSmallFontSize() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
getSource() - Method in class org.cytoscape.event.AbstractCyEvent
The object that fired the event.
getSource() - Method in interface org.cytoscape.event.CyEvent
The object that fired the event.
getSource() - Method in interface org.cytoscape.model.CyEdge
Returns the source node determining this edge.
getSource() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the source of this edge
getSource() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Return the source Annotation for this arrow.
getSourceColumn() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the name of the column from the source table which contains the values this column provides.
getSourceJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the name of the column from the source table used for the join.
getSourceLocation() - Method in class org.cytoscape.equations.AbstractNode
 
getSourceLocation() - Method in class org.cytoscape.equations.CodeAndSourceLocation
 
getSourceLocation() - Method in interface org.cytoscape.equations.TreeNode
Returns the start of the location in the equation where the code was found that was turned into a node in the parse tree.
getSourceLocations() - Method in class org.cytoscape.equations.Equation
Returns the starting points in the original equation for each node in the parse tree that resulted from the original equation.
getSourceNodeView() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the source node view;
getSourceTable() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the originating table for this column if this column is virtual.
getSourceViewSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the SUID of the source node view.
getSpacialIndex2D() - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns an immutable NetworkSpacialIndex2D object that can be used to query the bounds of nodes in the network view, or null if the SpacialIndex has been turned off.
getSpecificZoom() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Deprecated.
getStart() - Method in class org.cytoscape.equations.Token
 
getState() - Method in interface org.cytoscape.application.swing.CytoPanel
Gets the state of the CytoPanel.
getState() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
Returns a string representation of the value of the Tunable associated with this GUITunableHandler.
getState() - Method in interface org.cytoscape.work.swing.GUITunableHandler
To get the current value of a Handler (or path for a FileHandler, or selected item(s) for ListMultipleSelection ListSingleSelection, ...)
getStatus() - Method in class org.cytoscape.jobs.CyJobStatus
Return the CyJobStatus.Status of the remote job
getStatusToolBar() - Method in interface org.cytoscape.application.swing.CySwingApplication
Returns the status JToolBar of the application.
getStreamUtil() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of StreamUtil.
getStrings(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Converts all arguments, including Lists to a uniform array of strings.
getStroke() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Stroke to use to outline the Shape provided by the PaintedShape.getShape() method above.
getStrokePaint() - Method in interface org.cytoscape.view.presentation.customgraphics.PaintedShape
Return the Paint to use to color the Stroke returned by PaintedShape.getStroke().
getStyleName() - Method in class org.cytoscape.view.model.table.CyColumnViewMetadata
 
getSubNetworkList() - Method in interface org.cytoscape.model.subnetwork.CyRootNetwork
Will return A list of all CySubNetworks contained in this root network.
getSucceeded() - Static method in class org.cytoscape.work.FinishStatus
Get a FinishStatus instance that indicates success.
getSuccessColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
getSuggestedNetworkTitle(String) - Method in interface org.cytoscape.session.CyNetworkNaming
Generates a unique network title based on a provided suggestion.
getSuggestedSubnetworkTitle(CyNetwork) - Method in interface org.cytoscape.session.CyNetworkNaming
Generates a unique title for a subnetwork based on a parent network.
getSUID() - Method in interface org.cytoscape.model.CyIdentifiable
Returns the SUID of the implementing object.
getSUID() - Method in class org.cytoscape.model.events.ColumnDeletedEvent
 
getSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the view SUID of the edge view.
getSUID() - Method in interface org.cytoscape.view.model.SnapshotNodeInfo
Returns the view SUID of the node view.
getSupportedArrows() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Get the list of supported arrow shapes
getSupportedClass() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
 
getSupportedClass() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Returns the class that this factory creates.
getSupportedClasses() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of classes for which have aggregators.
getSupportedEdgeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportedEdgeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedListClasses() - Method in interface org.cytoscape.group.data.CyGroupAggregationManager
Get the list of classes of List for which have aggregators.
getSupportedListType() - Method in interface org.cytoscape.group.data.Aggregator
Return the base Class of the List, if this is a list type.
getSupportedNodeAttributeTypes() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportedNodeAttributeTypes() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns the set of node attribute types potentially used by this layout algorithm.
getSupportedShapes() - Method in interface org.cytoscape.view.presentation.annotations.ShapeAnnotation
Get the list of supported shapes.
getSupportedTargetTypes() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory
Returns all the target types supported by this factory, usually CyNode and CyColumn.
getSupportedTargetTypes() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphicsFactory
Returns all the target types supported by this factory, usually CyNode and CyColumn.
getSupportedType() - Method in interface org.cytoscape.group.data.Aggregator
Return the Class this aggregator supports
getSupportedValueRange(VisualProperty<T>) - Method in interface org.cytoscape.view.model.VisualLexicon
Returns a filtered value range for a VisualProperty that uses a DiscreteRange.
getSupportedValueRange(VisualProperty<T>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getSupportsJSON(String, String) - Method in interface org.cytoscape.command.AvailableCommands
Returns true if the command is expected to provide JSON output.
getSupportsSelectedOnly() - Method in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
 
getSupportsSelectedOnly() - Method in interface org.cytoscape.view.layout.CyLayoutAlgorithm
Returns true if this algorithm supports being applied to only the currently selected nodes.
getSVG() - Method in interface org.cytoscape.view.presentation.annotations.ImageAnnotation
Return the SVG text currently assigned to this annotation.
getTable() - Method in class org.cytoscape.application.events.SetCurrentTableEvent
 
getTable() - Method in class org.cytoscape.command.util.RowList
Get the table for this rowlist
getTable() - Method in interface org.cytoscape.model.CyColumn
Returns the table for this column.
getTable() - Method in interface org.cytoscape.model.CyRow
Returns the CyTable that this row belongs to.
getTable() - Method in interface org.cytoscape.model.CyTableMetadata
Returns the table whose metadata is described by this instance.
getTable() - Method in class org.cytoscape.model.events.TableAboutToBeDeletedEvent
Returns the table that is about to be deleted from the table manager.
getTable() - Method in class org.cytoscape.model.events.TableAddedEvent
Returns the table added to the table manager.
getTable(long) - Method in interface org.cytoscape.model.CyTableManager
Returns the table with the specified SUID.
getTable(Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetwork
Returns the table with the specified namespace and type from this network.
getTable(String) - Method in interface org.cytoscape.command.StringToModel
Convert a string request for a table into a CyTable.
getTable(CyNetwork, Class<? extends CyIdentifiable>, String) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the table with the specified namespace and type from the network.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.cytoscape.util.swing.JTreeTable.TreeTableCellEditor
 
getTableData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService
Optional method to extract table data (usually not model associated tables) from a CyJobData object.
getTableNamespace(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the namespace of this table.
getTables() - Method in interface org.cytoscape.io.read.CyTableReader
Return an array of CyTable objects.
getTables() - Method in class org.cytoscape.session.CySession
Returns a set of all CyTable objects contained in this Session.
getTables(CyNetwork, Class<? extends CyIdentifiable>) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns a read-only map of all of the tables for the specified type from the network.
getTableStyles() - Method in class org.cytoscape.session.CySession
Returns a set containing all table VisualStyles defined for this session.
getTableType() - Method in interface org.cytoscape.application.swing.TableToolBarComponent
 
getTableType(CyTable) - Method in interface org.cytoscape.model.CyNetworkTableManager
Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.
getTableView() - Method in class org.cytoscape.view.model.events.TableViewAboutToBeDestroyedEvent
 
getTableView() - Method in class org.cytoscape.view.model.events.TableViewAddedEvent
 
getTableView(CyTable) - Method in interface org.cytoscape.view.model.table.CyTableViewManager
Returns the table view for the given table.
getTableViewFactory() - Method in interface org.cytoscape.application.TableViewRenderer
 
getTableViewRenderer(String) - Method in interface org.cytoscape.application.CyApplicationManager
Returns the TableViewRenderer that has the passed id or null if it doesn't exist.
getTableViewRendererSet() - Method in interface org.cytoscape.application.CyApplicationManager
Returns a set with all the TableViewRenderer objects that have been registered.
getTableViews() - Method in class org.cytoscape.session.CySession
Returns a set of all CyTableView objects contained in this Session.
getTableViewSet() - Method in interface org.cytoscape.view.model.table.CyTableViewManager
Returns all table views known to this manager.
getTableVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader
Returns a list of table VisualStyle objects.
getTarget() - Method in interface org.cytoscape.model.CyEdge
Returns the target node determining this edge.
getTarget() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the target of this edge
getTarget() - Method in interface org.cytoscape.view.presentation.annotations.ArrowAnnotation
Return the target object for this arrow.
getTargetAnchor() - Method in class org.cytoscape.view.presentation.property.values.ObjectPosition
Return the anchor of the target (e.g.
getTargetColumnList() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getTargetDataType() - Method in class org.cytoscape.view.model.AbstractVisualProperty
 
getTargetDataType() - Method in interface org.cytoscape.view.model.VisualProperty
VisualProperty is always associated with a data type.
getTargetJoinKey() - Method in interface org.cytoscape.model.VirtualColumnInfo
Returns the name of the column from the target table used for the join.
getTargetNodeView() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the target node view;
getTargetObjectType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ListEditor
Type of object managed by this editor.
getTargetViewSUID() - Method in interface org.cytoscape.view.model.SnapshotEdgeInfo
Returns the SUID of the target node view.
getTask() - Method in class org.cytoscape.work.FinishStatus
Returns the task that was cancelled or that had failed, or returns null if the task iterator succeeded.
getTaskIterator() - Method in class org.cytoscape.work.AbstractTask
 
getTaskManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of TaskManager.
getTaskObserver() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getTaskObserver() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
If you want to be notified when the search task is finished, you should return a TaskObserver here.
getText() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the text to be displayed as part of the annotation
getText() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the text to be displayed as part of the annotation
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.BoundedTextAnnotation
Get the color of the text to be displayed
getTextColor() - Method in interface org.cytoscape.view.presentation.annotations.TextAnnotation
Get the color of the text to be displayed
getThisComponent() - Method in interface org.cytoscape.application.swing.CytoPanel
Returns the Component that is this CytoPanel.
getTitle() - Method in interface org.cytoscape.application.swing.CytoPanelComponent
Returns the title of the tab within the CytoPanel for this component.
getTitle() - Method in enum class org.cytoscape.application.swing.CytoPanelName
Returns the human readable title used for labeling this CytoPanel.
getTitle() - Method in class org.cytoscape.io.read.AbstractCyNetworkReader
 
getTitle() - Method in interface org.cytoscape.model.CyTable
Returns a human readable name for the CyTable.
getTitle() - Method in interface org.cytoscape.view.vizmap.VisualStyle
Returns name of this visual style.
getTokenIterator(String) - Method in interface org.cytoscape.equations.EquationTokeniser
Returns an iterator of Token objects.
getTokenList(String) - Method in interface org.cytoscape.equations.EquationTokeniser
Returns a list of Token objects.
getToolbarGravity() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getToolbarGravity() - Method in interface org.cytoscape.application.swing.CyAction
Returns the gravity used to place this action in the toolbar.
getToolBarGravity() - Method in class org.cytoscape.application.swing.AbstractToolBarComponent
Returns the gravity value for this toolbar component.
getToolBarGravity() - Method in interface org.cytoscape.application.swing.ToolBarComponent
Returns the gravity used to place this component in the toolbar.
getTooltip() - Method in class org.cytoscape.work.AbstractTunableHandler
Returns the tooltip annotation for this Tunable if there is one.
getToolTipImage() - Method in class org.cytoscape.application.swing.AbstractCyAction
 
getToolTipImage() - Method in interface org.cytoscape.application.swing.CyAction
Optional image to be displayed in the target component's tool tip.
getToolTipText(MouseEvent) - Method in class org.cytoscape.util.swing.JTreeTable
The code in this method is copy and pasted from source code to the same method in javax.swing.JTable, except for one value change on one line.
getTrackedEdgeCount(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the number of edges that are being tracked using the given key.
getTrackedEdges(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns edges that were configured to have their VisualProperties tracked using CyNetworkViewFactoryConfig.addTrackedVisualProperty(Object, VisualProperty, java.util.function.Predicate) and pass the predicate.
getTrackedNodeCount(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the number of nodes that are being tracked using the given key.
getTrackedNodes(Object) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns nodes that were configured to have their VisualProperties tracked using CyNetworkViewFactoryConfig.addTrackedVisualProperty(Object, VisualProperty, java.util.function.Predicate) and pass the predicate.
getTransformers() - Method in interface org.cytoscape.filter.model.NamedTransformer
Returns the List of Transformers contained within this NamedTransformer.
getTransformerSource(Class<C>) - Method in interface org.cytoscape.filter.TransformerManager
Returns a TransformerSource for the given contextType.
getTranslatedValueType() - Method in interface org.cytoscape.view.vizmap.mappings.ValueTranslator
Returns compatible input data type.
getTree() - Method in class org.cytoscape.util.swing.JTreeTable
Returns the tree that is being shared between the model.
getTunableHandler() - Method in class org.cytoscape.work.swing.AbstractGUITunableHandler.TunableFieldPanel
 
getTunableMutator() - Method in class org.cytoscape.work.AbstractTaskManager
Returns the TunableMutator for this TaskManager or null if there is none.
getTunableMutator() - Method in interface org.cytoscape.work.TaskManager
This method returns the TunableMutator that is being used by this TaskManager.
getTunablePropertySerializerFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of TunablePropertySerializerFactory.
getType() - Method in class org.cytoscape.equations.AbstractNode
 
getType() - Method in class org.cytoscape.equations.Equation
The overall type of the Equation, e.g.
getType() - Method in interface org.cytoscape.equations.EquationParser
Returns the result type of the parsed equation if the parse succeeded, otherwise null.
getType() - Method in class org.cytoscape.equations.IdentDescriptor
Returns the, possibly adjusted, type of the descriptor as one of the types internally supported by equations.
getType() - Method in class org.cytoscape.equations.Token
 
getType() - Method in interface org.cytoscape.equations.TreeNode
Returns the type of this node.
getType() - Method in interface org.cytoscape.filter.model.CompositeFilter
Returns the type of combining semantics used by this filter.
getType() - Method in interface org.cytoscape.model.CyColumn
Returns the data type of the column.
getType() - Method in interface org.cytoscape.model.CyTableMetadata
Returns the type of the data associated with this object's table.
getType() - Method in interface org.cytoscape.util.color.Palette
This is the type of the palette, using the Cynthia Brewer's classification.
getType() - Method in class org.cytoscape.view.layout.EdgeWeighter
 
getType() - Method in class org.cytoscape.view.model.ContinuousRange
 
getType() - Method in class org.cytoscape.view.model.DiscreteRange
 
getType() - Method in interface org.cytoscape.view.model.Range
Type of object used in this range.
getType() - Method in interface org.cytoscape.view.presentation.annotations.AnnotationFactory
 
getType() - Method in class org.cytoscape.view.vizmap.gui.editor.AbstractVisualPropertyEditor
 
getType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyEditor
Returns the type of object managed in the Visual property.
getType() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getType() - Method in class org.cytoscape.work.FinishStatus
Specifies how the task iterator completed.
getType() - Method in interface org.cytoscape.work.TunableHandler
Returns the class type of the field or method annotated by Tunable.
getTypes() - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getTypes() - Method in class org.cytoscape.view.presentation.property.BasicVisualLexicon
 
getTypes() - Method in class org.cytoscape.view.presentation.property.table.BasicTableVisualLexicon
 
getUnderlyingTable() - Method in class org.cytoscape.view.model.table.CyTableViewMetadata
 
getUndoableEditSupport() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport
Returns the UndoableEditSupport associated with this UndoSupport instance.
getUndoManager() - Method in interface org.cytoscape.work.swing.undo.SwingUndoSupport
Returns the UndoManager associated with this UndoSupport instance.
getUndoPresentationName() - Method in class org.cytoscape.work.undo.AbstractCyEdit
Returns a human-readable description of this edit that will be used in undo menu items.
getUndoSupport() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of UndoSupport.
getUnqualifiedName(Class<?>) - Static method in class org.cytoscape.equations.EquationUtil
Returns the unqualified name of the given class
getUnselectedEdges() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
 
getUnselectedEdges() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns all the edges in the network that are currently unselected.
getUnselectedNodes() - Method in class org.cytoscape.application.events.SetCurrentNetworkEvent
 
getUnselectedNodes() - Method in class org.cytoscape.model.events.SelectedNodesAndEdgesEvent
Returns all the nodes in the network that are currently unselected.
getUpperBound() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the upper limit of the object.
getURLConnection(URL) - Method in interface org.cytoscape.io.util.StreamUtil
Obtain a URLConnection for a given URL.
getUsageDescription() - Method in class org.cytoscape.equations.AbstractFunction
Used to provide help for users.
getUsageDescription() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getUseNestedNetworks() - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the default setting for whether or not to create a nested network view on collapsed nodes.
getUseNestedNetworks(CyGroup) - Method in interface org.cytoscape.group.CyGroupSettingsManager
Get the setting for whether or not to create a nested network view on collapsed nodes for the specified CyGroup.
getUUID() - Method in interface org.cytoscape.view.presentation.annotations.Annotation
Get the UUID of this annotation
getValidationState(Appendable) - Method in interface org.cytoscape.work.TunableValidator
Executes the validation test on the annotated Tunables.
getValue() - Method in class org.cytoscape.command.util.EdgeList
Return the edgeList for this tunable
getValue() - Method in class org.cytoscape.command.util.NodeList
Get the list of nodes
getValue() - Method in class org.cytoscape.command.util.RowList
Get the list of rows
getValue() - Method in class org.cytoscape.equations.IdentDescriptor
Returns the value of the descriptor.
getValue() - Method in class org.cytoscape.model.events.RowSetRecord
Returns the value that the data was set as.
getValue() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the value that the visual property has been changed to.
getValue() - Method in class org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint
Gets Point Value.
getValue() - Method in class org.cytoscape.work.AbstractTunableHandler
 
getValue() - Method in interface org.cytoscape.work.TunableHandler
Returns an object describing a field / get method annotated with Tunable or null if no field / get method has been associated with this handler.
getValue() - Method in class org.cytoscape.work.util.AbstractBounded
Returns the value.
getValueAt(int, int) - Method in class org.cytoscape.util.swing.TreeTableModelAdapter
Returns the value at the given row and column.
getValueAt(Object, int) - Method in interface org.cytoscape.util.swing.TreeTableModel
Returns the value to be displayed for node node, at column number column.
getValueEditor(Class<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns value editor for the given data type.
getValues(Class<? extends T>) - Method in interface org.cytoscape.model.CyColumn
Returns all the values, some of which may be null, for this given column.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.ValueEditor
Get type of the value to be edited.
getValueType() - Method in interface org.cytoscape.view.vizmap.gui.editor.VisualPropertyValueEditor
Get type of the value to be edited.
getVariableReferences() - Method in class org.cytoscape.equations.Equation
Returns all the variable references that occur as part if this Equation.
getVariableReferences() - Method in interface org.cytoscape.equations.EquationParser
Returns all the variable names that have been detected in the most recently parsed equation.
getVersion() - Method in interface org.cytoscape.application.CyVersion
The full version as a string, for example "3.2.5-alpha".
getView() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the view that has been changed.
getViewData(CyJobData, String) - Method in interface org.cytoscape.jobs.CyJobDataService
Optional method to extract data for a CyNetworkView from a CyJobData object.
getViewDefault(VisualProperty<T>) - Method in interface org.cytoscape.view.model.CyNetworkViewSnapshot
Returns the default value of the VisualProperty that was set using CyNetworkView.setViewDefault(VisualProperty, Object).
getViewModel() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Returns View being rendered.
getViewVisualStyleMap() - Method in class org.cytoscape.session.CySession
Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.
getVirtualColumnInfo() - Method in interface org.cytoscape.model.CyColumn
Returns information about the virtual column definition of this column.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngine
Provide all compatible Visual Properties as a VisualLexicon.
getVisualLexicon() - Method in interface org.cytoscape.view.presentation.RenderingEngineFactory
Returns supported VisualLexicon supported by this rendering engine implementation.
getVisualLexiconNode(VisualProperty<?>) - Method in interface org.cytoscape.view.model.VisualLexicon
Get a tree node in for the given VisualProperty.
getVisualLexiconNode(VisualProperty<?>) - Method in class org.cytoscape.view.presentation.property.AbstractVisualLexicon
 
getVisualMappingFunction(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.VisualStyle
Get current VisualMappingFunction for the VisualProperty.
getVisualMappingFunctionContinuousFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionDiscreteFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingFunctionPassthroughFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of VisualMappingFunctionFactory.
getVisualMappingManager() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of VisualMappingManager.
getVisualProperties() - Method in class org.cytoscape.view.vizmap.VisualPropertyDependency
A set of Visual Properties to be set by the parent if locked.
getVisualProperty() - Method in class org.cytoscape.view.model.events.ViewChangeRecord
Returns the visual property that has been changed.
getVisualProperty() - Method in class org.cytoscape.view.model.VisualLexiconNode
Returns wrapped VisualProperty object.
getVisualProperty() - Method in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
 
getVisualProperty() - Method in interface org.cytoscape.view.vizmap.VisualMappingFunction
Visual Property associated with this function.
getVisualProperty(VisualProperty<T>) - Method in interface org.cytoscape.view.model.View
Get the actual value for the given visual property.
getVisualPropertyEditor(VisualProperty<V>) - Method in interface org.cytoscape.view.vizmap.gui.editor.EditorManager
Returns the VisualPropertyEditor for the given VisualProperty.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.SetCurrentVisualStyleEvent
Get the newly selected current Visual Style.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.table.ColumnVisualStyleSetEvent
Get the VisualStyle that was set to the column view.
getVisualStyle() - Method in class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
Get the VisualStyle that was set to the network view.
getVisualStyle(CyNetworkView) - Method in interface org.cytoscape.view.vizmap.VisualMappingManager
Returns the VisualStyle associated with the target network view model.
getVisualStyle(View<CyColumn>) - Method in interface org.cytoscape.view.vizmap.TableVisualMappingManager
Returns the VisualStyle associated with the target column view model.
getVisualStyleAdded() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent
Get the newly created VisualStyle.
getVisualStyleFactory() - Method in interface org.cytoscape.app.CyAppAdapter
Deprecated.
Returns an instance of VisualStyleFactory.
getVisualStyles() - Method in interface org.cytoscape.io.read.VizmapReader
Returns a list of network VisualStyle objects.
getVisualStyles() - Method in class org.cytoscape.session.CySession
Returns a set containing all network VisualStyles defined for this session.
getVisualStyleToBeRemoved() - Method in class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent
Returns target VisualStyle to be removed from manager.
getWarnColor() - Static method in class org.cytoscape.util.swing.LookAndFeelUtil
 
getWarning() - Method in class org.cytoscape.filter.model.ValidationWarning
 
getWebsite() - Method in class org.cytoscape.application.swing.search.AbstractNetworkSearchTaskFactory
 
getWebsite() - Method in interface org.cytoscape.application.swing.search.NetworkSearchTaskFactory
An optional URL the user can use to find more information about this search provider.
getWeight() - Method in class org.cytoscape.view.layout.LayoutEdge
Return the current value for this edge's weight.
getWidth() - Method in class org.cytoscape.view.layout.LayoutNode
Return the width of this node
getWidth() - Method in class org.cytoscape.view.layout.LayoutPartition
Return the total width of all of the LayoutNodes
getWidth() - Method in interface org.cytoscape.view.presentation.customgraphics.CyCustomGraphics
Returns width of current object.
getWindow(Class<?>) - Method in interface org.cytoscape.io.webservice.swing.WebServiceGUI
Returns the Window that contains the unified web service UI.
getWriter(Object, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyWriter Task that will attempt to write the specified property object to the specified file of the specified file type.
getWriter(Object, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyPropertyWriterManager
Returns the CyWriter Task that will attempt to write the specified property object to the specified output stream of the specified file type.
getWriter(Set<VisualStyle>, Set<VisualStyle>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified file of the specified file type.
getWriter(Set<VisualStyle>, Set<VisualStyle>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified output stream of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, File) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified file of the specified file type.
getWriter(Set<VisualStyle>, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.VizmapWriterManager
Returns the CyWriter Task that will attempt to write the specified vizmap to the specified output stream of the specified file type.
getWriter(CyNetwork, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified network to the specified file of the specified file type.
getWriter(CyNetwork, CyFileFilter, OutputStream) - Method in interface org.cytoscape.io.write.CyNetworkViewWriterManager
Returns the CyWriter Task that will attempt to write the specified network to the specified output steam of the specified file type.
getWriter(CyTable, CyFileFilter, File) - Method in interface org.cytoscape.io.write.CyTableWriterManager
Returns the CyWriter Task that will attempt to write the specified table to the specified file of the specified file type.
getWriter(CyTable, CyFileFilter, OutputStream) - Method in interf