Uses of Interface
org.cytoscape.view.model.CyNetworkView
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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 CytoscapeCyNetworkView
.org.cytoscape.view.presentation.customgraphics This package provides an API for augmenting aRenderingEngine
s node rendering with custom graphics.org.cytoscape.view.presentation.property.values Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShapeorg.cytoscape.view.vizmap Visual Mapping basic API module.org.cytoscape.view.vizmap.events Events for Visual Mappings. -
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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 aCyNetworkView
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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 aCyNetworkView
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 theCyWriter
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 theCyWriter
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 aCyNetworkView
from aCyJobData
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 aCyJobData
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 withAbstractEdgeViewTask.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 givenCyNetworkView
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 aCyNetworkView
created using thecreateSnapshot()
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 aCyNetworkView
from aCyNetwork
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)
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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 forMethods 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 aCyNetworkView
is being updated in order to let the custom graphics draw onto itsGraphics2D
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.
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