Uses of Interface
org.cytoscape.model.CyNode

Packages that use CyNode

Package	Description
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.command.util	Tunable classes useful for command applications
org.cytoscape.group	This package provides an API for creating and managing groups in Cytoscape.
org.cytoscape.group.events	This package contains the various events and listeners related to group management, creation, and destruction.
org.cytoscape.io.read	Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.model	This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
org.cytoscape.model.events	This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
org.cytoscape.model.subnetwork	This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.task	This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
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.

Uses of CyNode in org.cytoscape.application.swing

Method parameters in org.cytoscape.application.swing with type arguments of type CyNode

Modifier and Type	Method and Description
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.

Uses of CyNode in org.cytoscape.command

Methods in org.cytoscape.command that return types with arguments of type CyNode

Modifier and Type	Method and Description
List<CyNode>	StringToModel.getNodeList(CyNetwork net, String nodelist) Convert a string request for a nodelist into a list of CyNodes.

Uses of CyNode in org.cytoscape.command.util

Methods in org.cytoscape.command.util that return types with arguments of type CyNode

Modifier and Type	Method and Description
List<CyNode>	NodeList.getValue() Get the list of nodes

Method parameters in org.cytoscape.command.util with type arguments of type CyNode

Modifier and Type	Method and Description
void	NodeList.setValue(List<CyNode> nodeList) Set the list of nodes

Uses of CyNode in org.cytoscape.group

Methods in org.cytoscape.group that return CyNode

Modifier and Type	Method and Description
CyNode	CyGroup.getGroupNode() Return the CyNode that represents this group in the network.

Methods in org.cytoscape.group that return types with arguments of type CyNode

Modifier and Type	Method and Description
List<CyNode>	CyGroup.getNodeList() Returns the list of nodes contained within this group.

Methods in org.cytoscape.group with parameters of type CyNode

Modifier and Type	Method and Description
CyGroup	CyGroupFactory.createGroup(CyNetwork network, CyNode node, boolean register) Creates a CyGroup object in the referenced network from an existing CyNode.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, CyNode node, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network from an existing CyNode.
CyGroup	CyGroupManager.getGroup(CyNode node, CyNetwork network) Return the group the corresponds to a particular node in a CyNetwork.
List<CyGroup>	CyGroupManager.getGroupsForNode(CyNode node) Return the list of CyGroups this node is in.
List<CyGroup>	CyGroupManager.getGroupsForNode(CyNode node, CyNetwork network) Return the list of CyGroups this node is in for a particular network.
boolean	CyGroupManager.isGroup(CyNode node, CyNetwork network) Test to see if this node represents a CyGroup in a particular CyNetwork.

Method parameters in org.cytoscape.group with type arguments of type CyNode

Modifier and Type	Method and Description
void	CyGroup.addNodes(List<CyNode> nodes) Add a list of nodes and their edges
CyGroup	CyGroupFactory.createGroup(CyNetwork network, CyNode node, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network from an existing CyNode.
CyGroup	CyGroupFactory.createGroup(CyNetwork network, List<CyNode> nodes, List<CyEdge> edges, boolean register) Creates a CyGroup object in the referenced network initially populated with the supplied nodes.
void	CyGroup.removeNodes(List<CyNode> nodes) Remove a set of nodes and their edges from a group

Uses of CyNode in org.cytoscape.group.events

Constructors in org.cytoscape.group.events with parameters of type CyNode

Constructor and Description
GroupNodesAddedEvent(CyGroup source, CyNode node) Constructs event.
GroupNodesRemovedEvent(CyGroup source, CyNode node) Constructs event.

Constructor parameters in org.cytoscape.group.events with type arguments of type CyNode

Constructor and Description
GroupNodesAddedEvent(CyGroup source, List<CyNode> nodes) Constructs event.
GroupNodesRemovedEvent(CyGroup source, List<CyNode> nodes) Constructs event.

Uses of CyNode in org.cytoscape.io.read

Methods in org.cytoscape.io.read that return types with arguments of type CyNode

Modifier and Type	Method and Description
protected Map<Object,CyNode>	AbstractCyNetworkReader.getNodeMap() Returns map from key value to existing CyNode.

Uses of CyNode in org.cytoscape.model

Methods in org.cytoscape.model that return CyNode

Modifier and Type	Method and Description
CyNode	CyNetwork.addNode() This method is used to create and add a node to this network.
CyNode	CyNetwork.getNode(long suid) Return the CyNode that has the SUID.
CyNode	CyEdge.getSource() Returns the source node determining this edge.
CyNode	CyEdge.getTarget() Returns the target node determining this edge.

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

Modifier and Type	Method and Description
List<CyNode>	CyNetwork.getNeighborList(CyNode node, CyEdge.Type edgeType) 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.
List<CyNode>	CyNetwork.getNodeList() Return a list of the nodes in this network.
static List<CyNode>	CyTableUtil.getNodesInState(CyNetwork net, String columnName, boolean state) 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.

Methods in org.cytoscape.model with parameters of type CyNode

Modifier and Type	Method and Description
CyEdge	CyNetwork.addEdge(CyNode source, CyNode target, boolean isDirected) This method is used to create and add an edge to this network.
boolean	CyNetwork.containsEdge(CyNode from, CyNode to) Determine if this CyNetwork contains an edge between two nodes.
boolean	CyNetwork.containsNode(CyNode node) Determine if this CyNetwork contains a particular node.
Iterable<CyEdge>	CyNetwork.getAdjacentEdgeIterable(CyNode node, CyEdge.Type edgeType) Gets an Iteable of edges that connect to this node.
List<CyEdge>	CyNetwork.getAdjacentEdgeList(CyNode node, CyEdge.Type edgeType) Get the list of edges that connect to this node.
List<CyEdge>	CyNetwork.getConnectingEdgeList(CyNode source, CyNode target, CyEdge.Type edgeType) Get the list of edges that connect two nodes.
List<CyNode>	CyNetwork.getNeighborList(CyNode node, CyEdge.Type edgeType) 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.

Method parameters in org.cytoscape.model with type arguments of type CyNode

Modifier and Type	Method and Description
boolean	CyNetwork.removeNodes(Collection<CyNode> node) Remove a node from the network and delete the node (if it only exists in this network).

Uses of CyNode in org.cytoscape.model.events

Methods in org.cytoscape.model.events that return types with arguments of type CyNode

Modifier and Type	Method and Description
Collection<CyNode>	AboutToRemoveNodesEvent.getNodes() Returns the collection of nodes about to be removed.

Constructors in org.cytoscape.model.events with parameters of type CyNode

Constructor and Description
SetNetworkPointerEvent(CyNode node, CyNetwork network) Constructs event.
UnsetNetworkPointerEvent(CyNode node, CyNetwork network) Constructs event.

Constructor parameters in org.cytoscape.model.events with type arguments of type CyNode

Constructor and Description
AboutToRemoveNodesEvent(CyNetwork source, Collection<CyNode> nodes) Constructs event.
AddedNodesEvent(CyNetwork source, Collection<CyNode> nodes) Constructs event.

Uses of CyNode in org.cytoscape.model.subnetwork

Methods in org.cytoscape.model.subnetwork that return CyNode

Modifier and Type	Method and Description
CyNode	CySubNetwork.addNode() A shortcut method that Creates a new CyNode in both this subnetwork AND in the CyRootNetwork.

Methods in org.cytoscape.model.subnetwork with parameters of type CyNode

Modifier and Type	Method and Description
CyEdge	CySubNetwork.addEdge(CyNode source, CyNode target, boolean directed) A shortcut method that Creates a new CyEdge in both this subnetwork AND in the CyRootNetwork.
boolean	CySubNetwork.addNode(CyNode node) Adds a node to this CySubNetwork.
void	CyRootNetwork.restoreNode(CyNode node) Causes the given node to (temporarily) remain in the root network even if it has already been removed from all subnetworks.

Method parameters in org.cytoscape.model.subnetwork with type arguments of type CyNode

Modifier and Type	Method and Description
CySubNetwork	CyRootNetwork.addSubNetwork(Iterable<CyNode> nodes, Iterable<CyEdge> edges) Create a CySubNetwork containing the specified CyNodes and CyEdges.
CySubNetwork	CyRootNetwork.addSubNetwork(Iterable<CyNode> nodes, Iterable<CyEdge> edges, SavePolicy policy) Create a CySubNetwork containing the specified CyNodes and CyEdges.
boolean	CySubNetwork.removeNodes(Collection<CyNode> node) Removes a node from this CySubNetwork but not from the CyRootNetwork.

Uses of CyNode in org.cytoscape.task

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

Modifier and Type	Field and Description
protected View<CyNode>	AbstractNodeViewTask.nodeView The node view that descendants of this class will operate on.

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

Modifier and Type	Method and Description
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	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.
boolean	AbstractNodeViewTaskFactory.isReady(View<CyNode> nodeView, CyNetworkView networkView) Returns true of the supplied network and node views are not null.

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

Constructor and Description
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.

Uses of CyNode in org.cytoscape.view.layout

Fields in org.cytoscape.view.layout with type parameters of type CyNode

Modifier and Type	Field and Description
static Set<View<CyNode>>	CyLayoutAlgorithm.ALL_NODE_VIEWS A convenience declaration for an empty set signifying that all node views should be laid out when creating the task iterator.
protected Set<View<CyNode>>	AbstractLayoutTask.nodesToLayOut The node views that will be laid out by the algorithm.

Methods in org.cytoscape.view.layout that return CyNode

Modifier and Type	Method and Description
CyNode	LayoutNode.getNode() Accessor function to return the Node associated with this LayoutNode.

Methods in org.cytoscape.view.layout that return types with arguments of type CyNode

Modifier and Type	Method and Description
View<CyNode>	LayoutNode.getNodeView() Accessor function to return the View associated with this LayoutNode.

Method parameters in org.cytoscape.view.layout with type arguments of type CyNode

Modifier and Type	Method and Description
protected void	LayoutPartition.addNode(CyNetwork network, View<CyNode> nv, boolean locked) Add a node to this partition.
TaskIterator	CyLayoutAlgorithm.createTaskIterator(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute) Creates a task iterator containing the layout tasks.
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.
boolean	AbstractLayoutAlgorithm.isReady(CyNetworkView view, Object tunableContext, Set<View<CyNode>> nodesToLayout, String attributeName)
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.

Constructor parameters in org.cytoscape.view.layout with type arguments of type CyNode

Constructor and 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.
LayoutNode(View<CyNode> nodeView, int index, CyRow row) The main constructor for a LayoutNode.
LayoutPartition(CyNetworkView networkView, Collection<View<CyNode>> nodeSet, EdgeWeighter edgeWeighter) LayoutPartition: use this constructor to create a LayoutPartition that includes the entire network.

Uses of CyNode in org.cytoscape.view.model

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

Modifier and Type	Method and Description
View<CyNode>	CyNetworkView.getNodeView(CyNode node) Returns a View for a specified Node.
Collection<View<CyNode>>	CyNetworkView.getNodeViews() Returns a list of Views for all CyNodes in the network.

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

Modifier and Type	Method and Description
View<CyNode>	CyNetworkView.getNodeView(CyNode node) Returns a View for a specified Node.

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

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

Modifier and Type	Method and Description
Collection<View<CyNode>>	AddedNodeViewsEvent.getNodeViews() Returns new node view object.

Constructor parameters in org.cytoscape.view.model.events with type arguments of type CyNode

Constructor and Description
AboutToRemoveNodeViewsEvent(CyNetworkView source, Collection<View<CyNode>> payload) Creates the event for about to be removed node views.
AddedNodeViewsEvent(CyNetworkView source, Collection<View<CyNode>> nodeViews) Creates the event for a new node view.

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

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

Modifier and Type	Method and Description
void	ArrowAnnotation.setTarget(CyNode target) Set the target for this arrow assuming the target is a CyNode