Uses of Interface
org.cytoscape.view.model.CyNetworkView

Packages that use CyNetworkView

Package	Description
org.cytoscape.application	This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.application.events	This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
org.cytoscape.application.swing	This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
org.cytoscape.command	Interface to support execution of tasks as commands, including the ability to get a list of namespaces, commands, and arguments, and then execute those commands with a set of arguments.
org.cytoscape.io.read	Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.write	This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
org.cytoscape.jobs	This package provides a mechanism for executing remote jobs from within Cytoscape.
org.cytoscape.session	This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
org.cytoscape.task	This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.create	This package provides a variety of task factory interfaces for creating new instances of network and other objects.
org.cytoscape.task.hide	This package includes a set of task factory interfaces showing and hiding nodes and edges within network views.
org.cytoscape.task.write	This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.view.layout	This package provides access to the available layout algorithms, as well as provides abstract layout classes and layout information containers for the convenience of implementing other layout algorithms.
org.cytoscape.view.model	Module for View Models and Visual Properties.
org.cytoscape.view.model.events	Definitions for View-Model related events and their listeners.
org.cytoscape.view.presentation.annotations	This package provides support for graphical annotations associated with a Cytoscape CyNetworkView.
org.cytoscape.view.presentation.customgraphics	This package provides an API for augmenting a RenderingEngines node rendering with custom graphics.
org.cytoscape.view.presentation.property.values	Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
org.cytoscape.view.vizmap	Visual Mapping basic API module.
org.cytoscape.view.vizmap.events	Events for Visual Mappings.

Uses of CyNetworkView in org.cytoscape.application

Methods in org.cytoscape.application that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	CyApplicationManager.getCurrentNetworkView()	Returns the current network view.

Methods in org.cytoscape.application that return types with arguments of type CyNetworkView

Modifier and Type	Method	Description
List<CyNetworkView>	CyApplicationManager.getSelectedNetworkViews()	Returns the list of selected network views.

Methods in org.cytoscape.application with parameters of type CyNetworkView

Modifier and Type	Method	Description
void	CyApplicationManager.setCurrentNetworkView(CyNetworkView netView)	Sets the current network view to the specified network view.

Method parameters in org.cytoscape.application with type arguments of type CyNetworkView

Modifier and Type	Method	Description
void	CyApplicationManager.setSelectedNetworkViews(List<CyNetworkView> views)	Sets the specified network views as selected.

Uses of CyNetworkView in org.cytoscape.application.events

Methods in org.cytoscape.application.events that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	SetCurrentNetworkViewEvent.getNetworkView()	Returns the network view associated with this event.

Methods in org.cytoscape.application.events that return types with arguments of type CyNetworkView

Modifier and Type	Method	Description
List<CyNetworkView>	SetSelectedNetworkViewsEvent.getNetworkViews()	Returns the list of network views that have been selected.

Constructors in org.cytoscape.application.events with parameters of type CyNetworkView

Constructor	Description
SetCurrentNetworkViewEvent(CyApplicationManager source, CyNetworkView view)	Constructor.

Constructor parameters in org.cytoscape.application.events with type arguments of type CyNetworkView

Constructor	Description
SetSelectedNetworkViewsEvent(CyApplicationManager source, List<CyNetworkView> views)	Constructor.

Uses of CyNetworkView in org.cytoscape.application.swing

Methods in org.cytoscape.application.swing with parameters of type CyNetworkView

Modifier and Type	Method	Description
CyMenuItem	CyEdgeViewContextMenuFactory.createMenuItem(CyNetworkView netView, View<CyEdge> edgeView)	This method should return a CyMenuItem to be added to the context menu of the specified edge view.
CyMenuItem	CyNetworkViewContextMenuFactory.createMenuItem(CyNetworkView netView)	This method should return a CyMenuItem to be added to the context menu of the specified network view.
CyMenuItem	CyNodeViewContextMenuFactory.createMenuItem(CyNetworkView netView, View<CyNode> nodeView)	This method should return a CyMenuItem to be added to the context menu of the specified node view.
Rectangle	CyNetworkViewDesktopMgr.getBounds(CyNetworkView view)	Deprecated. This method has been deprecated in version 3.4.
void	CyNetworkViewDesktopMgr.setBounds(CyNetworkView view, Rectangle bounds)	Deprecated. This method has been deprecated in version 3.4 and does not do anything anymore.

Uses of CyNetworkView in org.cytoscape.command

Methods in org.cytoscape.command that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	StringToModel.getNetworkView(String strNetView)	Convert a string request for a network view into a CyNetworkView.

Uses of CyNetworkView in org.cytoscape.io.read

Methods in org.cytoscape.io.read that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	CyNetworkReader.buildCyNetworkView(CyNetwork network)	A method to build a CyNetworkView from one of the networks just read.

Uses of CyNetworkView in org.cytoscape.io.write

Methods in org.cytoscape.io.write with parameters of type CyNetworkView

Modifier and Type	Method	Description
CyWriter	CyNetworkViewWriterFactory.createWriter(OutputStream os, CyNetworkView view)	Creates a single Task that will write the specified network to the specified OutputStream.
CyWriter	CyNetworkViewWriterManager.getWriter(CyNetworkView view, CyFileFilter filter, File file)	Returns the CyWriter Task that will attempt to write the specified view to the specified file of the specified file type.
CyWriter	CyNetworkViewWriterManager.getWriter(CyNetworkView view, CyFileFilter filter, OutputStream os)	Returns the CyWriter Task that will attempt to write the specified view to the specified output steam of the specified file type.

Uses of CyNetworkView in org.cytoscape.jobs

Methods in org.cytoscape.jobs that return CyNetworkView

Modifier and Type	Method	Description
default CyNetworkView	CyJobDataService.getViewData(CyJobData data, String key)	Optional method to extract data for a CyNetworkView from a CyJobData object.

Methods in org.cytoscape.jobs with parameters of type CyNetworkView

Modifier and Type	Method	Description
default CyJobData	CyJobDataService.addData(CyJobData data, String key, CyNetworkView networkView, List<? extends CyIdentifiable> nodesAndEdges, List<VisualProperty<?>> properties)	An optional method to add network view data to a CyJobData item.

Uses of CyNetworkView in org.cytoscape.session

Methods in org.cytoscape.session that return types with arguments of type CyNetworkView

Modifier and Type	Method	Description
Set<CyNetworkView>	CySession.getNetworkViews()	Returns a set of all CyNetworkView objects contained in this Session.
Map<CyNetworkView,String>	CySession.getViewVisualStyleMap()	Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.

Method parameters in org.cytoscape.session with type arguments of type CyNetworkView

Modifier and Type	Method	Description
CySession.Builder	CySession.Builder.networkViews(Set<CyNetworkView> views)	Returns an instance of Builder that has at least been configured with the specified network views.
CySession.Builder	CySession.Builder.viewVisualStyleMap(Map<CyNetworkView,String> vs)	Returns an instance of Builder that has at least been configured with the specified network view visual style name map.

Uses of CyNetworkView in org.cytoscape.task

Fields in org.cytoscape.task declared as CyNetworkView

Modifier and Type	Field	Description
protected CyNetworkView	AbstractEdgeViewTask.netView	The network view associated with AbstractEdgeViewTask.edgeView.
protected CyNetworkView	AbstractNodeViewTask.netView	The network view that descendants of this class will operate on.
protected CyNetworkView	AbstractNetworkViewTask.view	The network view that descendants of this class will operate on.

Fields in org.cytoscape.task with type parameters of type CyNetworkView

Modifier and Type	Field	Description
protected Collection<CyNetworkView>	AbstractNetworkViewCollectionTask.networkViews	A collection of network views to operate on for any descendants of this class.

Methods in org.cytoscape.task with parameters of type CyNetworkView

Modifier and Type	Method	Description
TaskIterator	EdgeViewTaskFactory.createTaskIterator(View<CyEdge> edgeView, CyNetworkView networkView)	Creates a new TaskIterator using the given edge view and network view.
TaskIterator	NetworkViewLocationTaskFactory.createTaskIterator(CyNetworkView networkView, Point2D javaPt, Point2D xformPt)	Creates a task iterator using the specified network view and points.
TaskIterator	NetworkViewTaskFactory.createTaskIterator(CyNetworkView networkView)	Creates a new TaskIterator using the given CyNetworkView
TaskIterator	NodeViewTaskFactory.createTaskIterator(View<CyNode> nodeView, CyNetworkView networkView)	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.
boolean	AbstractEdgeViewTaskFactory.isReady(View<CyEdge> edgeView, CyNetworkView networkView)	Returns true if the supplied edge and network views are not null.
boolean	AbstractNetworkViewLocationTaskFactory.isReady(CyNetworkView networkView, Point2D javaPt, Point2D xformPt)	Returns true if the supplied view and coordinates are not null.
boolean	AbstractNetworkViewTaskFactory.isReady(CyNetworkView networkView)	Returns true if the supplied network view is not null.
boolean	AbstractNodeViewTaskFactory.isReady(View<CyNode> nodeView, CyNetworkView networkView)	Returns true of the supplied network and node views are not null.
boolean	EdgeViewTaskFactory.isReady(View<CyEdge> edgeView, CyNetworkView networkView)	Returns true if this task factory is ready to produce a TaskIterator.
boolean	NetworkViewLocationTaskFactory.isReady(CyNetworkView networkView, Point2D javaPt, Point2D xformPt)	Returns true if this task factory is ready to produce a TaskIterator.
boolean	NetworkViewTaskFactory.isReady(CyNetworkView networkView)	Returns true if this task factory is ready to produce a TaskIterator.
boolean	NodeViewTaskFactory.isReady(View<CyNode> nodeView, CyNetworkView networkView)	Returns true if the node view and network view are in a state that is ready to be processed by the generated tasks and false otherwise.

Method parameters in org.cytoscape.task with type arguments of type CyNetworkView

Modifier and Type	Method	Description
TaskIterator	NetworkViewCollectionTaskFactory.createTaskIterator(Collection<CyNetworkView> networkViews)	Provisions this factory with the collection of network views that will be passed into any task created by it.
boolean	AbstractNetworkViewCollectionTaskFactory.isReady(Collection<CyNetworkView> networkViews)	Returns true if the supplied collection is not null.
boolean	NetworkViewCollectionTaskFactory.isReady(Collection<CyNetworkView> networkViews)	Returns true if this task factory is ready to produce a TaskIterator.

Constructors in org.cytoscape.task with parameters of type CyNetworkView

Constructor	Description
AbstractEdgeViewTask(View<CyEdge> edgeView, CyNetworkView netView)	Base constructor for all tasks that need an edge view to operate on.
AbstractNetworkViewTask(CyNetworkView view)	A base class for tasks that need to operate on a network view.
AbstractNodeViewTask(View<CyNode> nodeView, CyNetworkView netView)	Base class constructor for all tasks that need to operate on a node view and possibly its associated network view.

Constructor parameters in org.cytoscape.task with type arguments of type CyNetworkView

Constructor	Description
AbstractNetworkViewCollectionTask(Collection<CyNetworkView> networkViews)	Base class for any tasks that need to operate on a collection of network views.

Uses of CyNetworkView in org.cytoscape.task.create

Methods in org.cytoscape.task.create that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	NewEmptyNetworkViewFactory.createNewEmptyNetworkView()	Returns a new, empty CyNetworkView.

Uses of CyNetworkView in org.cytoscape.task.hide

Methods in org.cytoscape.task.hide with parameters of type CyNetworkView

Modifier and Type	Method	Description
TaskIterator	HideTaskFactory.createTaskIterator(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges)	Creates a task iterator that will hide the given nodes and edges.
TaskIterator	UnHideTaskFactory.createTaskIterator(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges)	Creates a task iterator that will show the given nodes and edges.

Uses of CyNetworkView in org.cytoscape.task.write

Methods in org.cytoscape.task.write with parameters of type CyNetworkView

Modifier and Type	Method	Description
TaskIterator	ExportNetworkViewTaskFactory.createTaskIterator(CyNetworkView view, File file)	Creates the task iterator for exporting network views.

Uses of CyNetworkView in org.cytoscape.view.layout

Fields in org.cytoscape.view.layout declared as CyNetworkView

Modifier and Type	Field	Description
protected CyNetworkView	AbstractLayoutTask.networkView	The network view that the layout will be applied to.

Methods in org.cytoscape.view.layout with parameters of type CyNetworkView

Modifier and Type	Method	Description
TaskIterator	CyLayoutAlgorithm.createTaskIterator(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute)	Creates a task iterator containing the layout tasks.
String	CyLayoutAlgorithmManager.getLayoutAttribute(CyLayoutAlgorithm layout, CyNetworkView view)	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.
boolean	AbstractLayoutAlgorithm.isReady(CyNetworkView view, Object tunableContext, Set<View<CyNode>> nodesToLayout, String attributeName)
boolean	CyLayoutAlgorithm.isReady(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute)	Returns true if the task factory is ready to produce a task iterator.
static List<LayoutPartition>	PartitionUtil.partition(CyNetworkView networkView, boolean selectedOnly, EdgeWeighter edgeWeighter)	Partition the graph -- this builds the LayoutEdge and LayoutNode arrays as a byproduct.
static List<LayoutPartition>	PartitionUtil.partition(CyNetworkView networkView, Collection<CyNode> nodeSet, EdgeWeighter edgeWeighter)	Partition the graph -- this builds the LayoutEdge and LayoutNode arrays as a byproduct.

Constructors in org.cytoscape.view.layout with parameters of type CyNetworkView

Constructor	Description
AbstractLayoutTask(String displayName, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo)	Constructor.
AbstractParallelPartitionLayoutTask(String displayName, boolean singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo)	Creates a new AbstractPartitionLayoutTask object.
AbstractPartitionLayoutTask(String displayName, boolean singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo)	Creates a new AbstractPartitionLayoutTask object.
LayoutEdit(String name, CyNetworkView view)	Constructor.
LayoutPartition(CyNetworkView networkView, Collection<View<CyNode>> nodeSet, EdgeWeighter edgeWeighter)	LayoutPartition: use this constructor to create a LayoutPartition that includes the entire network.

Uses of CyNetworkView in org.cytoscape.view.model

Subinterfaces of CyNetworkView in org.cytoscape.view.model

Modifier and Type	Interface	Description
interface	CyNetworkViewSnapshot	An immutable snapshot of a CyNetworkView created using the createSnapshot() method.
interface	NullCyNetworkView	A CyNetwork with no corresponding view.

Methods in org.cytoscape.view.model that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	CyNetworkViewFactory.createNetworkView(CyNetwork network)	Create a CyNetworkView from a CyNetwork object.
CyNetworkView	CyNetworkViewSnapshot.getMutableNetworkView()	Returns the mutable CyNetworkView that was used to create this snapshot.

Methods in org.cytoscape.view.model that return types with arguments of type CyNetworkView

Modifier and Type	Method	Description
Collection<CyNetworkView>	CyNetworkViewManager.getNetworkViews(CyNetwork network)	Returns a collection of network views corresponding to the specified network, if found.
Set<CyNetworkView>	CyNetworkViewManager.getNetworkViewSet()	Provides the set of network views that are currently known to the network manager.

Methods in org.cytoscape.view.model with parameters of type CyNetworkView

Modifier and Type	Method	Description
void	CyNetworkViewManager.addNetworkView(CyNetworkView view)	Registers a network view with the network view manager and sets the new view as current.
void	CyNetworkViewManager.addNetworkView(CyNetworkView view, boolean setCurrent)	Registers a network view with the network view manager.
void	CyNetworkViewManager.destroyNetworkView(CyNetworkView view)	Destroys a network view.

Uses of CyNetworkView in org.cytoscape.view.model.events

Constructors in org.cytoscape.view.model.events with parameters of type CyNetworkView

Constructor	Description
AboutToRemoveEdgeViewsEvent(CyNetworkView source, Collection<View<CyEdge>> payload)	Creates the event for about to be removed edge views.
AboutToRemoveNodeViewsEvent(CyNetworkView source, Collection<View<CyNode>> payload)	Creates the event for about to be removed node views.
AddedEdgeViewsEvent(CyNetworkView source, Collection<View<CyEdge>> edgeViews)	Creates the event for new edge views.
AddedNodeViewsEvent(CyNetworkView source, Collection<View<CyNode>> nodeViews)	Creates the event for a new node view.
FitContentEvent(CyNetworkView source)	Fit the size of network view to the current container.
FitSelectedEvent(CyNetworkView source)	Fit the selected part of network view to the container.
NetworkViewAboutToBeDestroyedEvent(CyNetworkViewManager source, CyNetworkView view)	Creates the event for network views that are about to be destroyed.
NetworkViewAddedEvent(CyNetworkViewManager source, CyNetworkView view)	Creates the event for network views that are added.
UpdateNetworkPresentationEvent(CyNetworkView source)	Event for updating (redrawing) presentation.
ViewChangedEvent(CyNetworkView source, Collection<ViewChangeRecord<T>> payload)

Uses of CyNetworkView in org.cytoscape.view.presentation.annotations

Methods in org.cytoscape.view.presentation.annotations that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	Annotation.getNetworkView()	Return the view that this Annotation is for

Methods in org.cytoscape.view.presentation.annotations with parameters of type CyNetworkView

Modifier and Type	Method	Description
T	AnnotationFactory.createAnnotation(Class<? extends T> type, CyNetworkView view, Map<String,String> argMap)	Create an annotation.
List<Annotation>	AnnotationManager.getAnnotations(CyNetworkView networkView)	Retrieve the list of annotations for a specific network view.

Uses of CyNetworkView in org.cytoscape.view.presentation.customgraphics

Methods in org.cytoscape.view.presentation.customgraphics with parameters of type CyNetworkView

Modifier and Type	Method	Description
void	Cy2DGraphicLayer.draw(Graphics2D g, Shape shape, CyNetworkView networkView, View<? extends CyIdentifiable> view)	This method is called by Cytoscape when a CyNetworkView is being updated in order to let the custom graphics draw onto its Graphics2D object.
List<T>	CyCustomGraphics.getLayers(CyNetworkView networkView, View<? extends CyIdentifiable> grView)	Get layers that belong to this object.

Uses of CyNetworkView in org.cytoscape.view.presentation.property.values

Methods in org.cytoscape.view.presentation.property.values with parameters of type CyNetworkView

Modifier and Type	Method	Description
Point2D	Handle.calculateHandleLocation(CyNetworkView netView, View<CyEdge> edgeView)	Calculate absolute position of this handle for the given edge view.
Handle	HandleFactory.createHandle(CyNetworkView graphView, View<CyEdge> view, double x, double y)	Creates a new instance of the Handle.
void	Handle.defineHandle(CyNetworkView netView, View<CyEdge> edgeView, double x, double y)	Define this handle.

Uses of CyNetworkView in org.cytoscape.view.vizmap

Methods in org.cytoscape.view.vizmap with parameters of type CyNetworkView

Modifier and Type	Method	Description
void	VisualStyle.apply(CyNetworkView networkView)	Apply Visual Style to the entire network view.
VisualStyle	VisualMappingManager.getVisualStyle(CyNetworkView networkViewModel)	Returns the VisualStyle associated with the target network view model.
void	VisualMappingManager.setVisualStyle(VisualStyle visualStyle, CyNetworkView networkViewModel)	Set a VisualStyle to the target network view model.

Uses of CyNetworkView in org.cytoscape.view.vizmap.events

Methods in org.cytoscape.view.vizmap.events that return CyNetworkView

Modifier and Type	Method	Description
CyNetworkView	VisualStyleSetEvent.getNetworkView()	Get the The target network view model.

Constructors in org.cytoscape.view.vizmap.events with parameters of type CyNetworkView

Constructor	Description
VisualStyleSetEvent(VisualMappingManager source, VisualStyle style, CyNetworkView view)	Creates the event.