Uses of Class
cytoscape.CyNode

Packages that use CyNode

cytoscape	Core Cytoscape Classes.
cytoscape.data	Basic data classes used by Cytoscape.
cytoscape.ding
cytoscape.giny
cytoscape.groups
cytoscape.view	Classes that provide a window to display a graph and UI components connected to that window, such as the menus.

Uses of CyNode in cytoscape

Methods in cytoscape that return CyNode

CyNode	CyNetwork.addNode(Node cytoscape_node) Add a node to this Network that already exists in Cytoscape
static CyNode	Cytoscape.getCyNode(String alias)
static CyNode	Cytoscape.getCyNode(String nodeID, boolean create)

Uses of CyNode in cytoscape.data

Methods in cytoscape.data with parameters of type CyNode

static void

Semantics.assignNodeAliases(CyNode node, String species, BioDataServer bds) Deprecated.

Uses of CyNode in cytoscape.ding

Methods in cytoscape.ding with parameters of type CyNode

void	DingNetworkView.applyLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) DOCUMENT ME!
void	DingNetworkView.applyLockedLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) DOCUMENT ME!
boolean	DingNetworkView.applyVizMap(CyNode node) DOCUMENT ME!
boolean	DingNetworkView.applyVizMap(CyNode node, VisualStyle style) DOCUMENT ME!
boolean	DingNetworkView.setSelected(CyNode[] nodes) DOCUMENT ME!

Uses of CyNode in cytoscape.giny

Methods in cytoscape.giny that return CyNode

CyNode	FingCyNetwork.addNode(Node cytoscape_node) Add a node to this Network that already exists in Cytoscape
CyNode	CytoscapeRootGraph.getNode(String identifier) DOCUMENT ME!
CyNode	CytoscapeFingRootGraph.getNode(String identifier) DOCUMENT ME!

Uses of CyNode in cytoscape.groups

Methods in cytoscape.groups that return CyNode

CyNode	CyGroupImpl.getGroupNode() Get the CyNode that represents this group
CyNode	CyGroup.getGroupNode() Get the CyNode that represents this group

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

Iterator<CyNode>	CyGroupImpl.getNodeIterator() Get an iterator over all of the nodes in this group
Iterator<CyNode>	CyGroup.getNodeIterator() Get an iterator over all of the nodes in this group
List<CyNode>	CyGroupImpl.getNodes() Get all of the nodes in this group
List<CyNode>	CyGroup.getNodes() Get all of the nodes in this group

Methods in cytoscape.groups with parameters of type CyNode

void	CyGroupImpl.addNode(CyNode node) Add a new node to this group
void	CyGroup.addNode(CyNode node) Add a new node to this group
void	CyGroupImpl.addNode(CyNode node, boolean addEdges) Add a new node to this group
boolean	CyGroupImpl.contains(CyNode node) Determine if a node is a member of this group
boolean	CyGroup.contains(CyNode node) Determine if a node is a member of this group
static CyGroup	CyGroupManager.createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer) Create a new group with a list of nodes as initial members, and a precreated group node.
static CyGroup	CyGroupManager.createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer, CyNetwork network) Create a new group with a list of nodes as initial members, and a precreated group node.
static CyGroup	CyGroupManager.getCyGroup(CyNode groupNode) getCyGroup is a static method that returns a CyGroup structure when given the CyNode that represents this group.
static List<CyGroup>	CyGroupManager.getGroup(CyNode memberNode) getGroup is a static method that returns a CyGroup structure when given a CyNode that is a member of a group.
static boolean	CyGroupManager.isaGroup(CyNode groupNode) See if this CyNode represents a group
static void	CyGroupManager.removeGroup(CyNode groupNode) Remove (delete) a group
void	CyGroupImpl.removeNode(CyNode node) Remove a node from a group
void	CyGroup.removeNode(CyNode node) Remove a node from a group

Method parameters in cytoscape.groups with type arguments of type CyNode

static CyGroup	CyGroupManager.createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer) Create a new group with a list of nodes as initial members, and a precreated group node.
static CyGroup	CyGroupManager.createGroup(CyNode groupNode, List<CyNode> nodeList, String viewer, CyNetwork network) Create a new group with a list of nodes as initial members, and a precreated group node.
static CyGroup	CyGroupManager.createGroup(String groupName, List<CyNode> nodeList, List<CyEdge> innerEdgeList, List<CyEdge> outerEdgeList, String viewer, CyNetwork network) Create a new group by specifying all components.
static CyGroup	CyGroupManager.createGroup(String groupName, List<CyNode> nodeList, String viewer) Create a new, empty group.
static CyGroup	CyGroupManager.createGroup(String groupName, List<CyNode> nodeList, String viewer, CyNetwork network) Create a new group with a list of nodes as initial members.

Constructors in cytoscape.groups with parameters of type CyNode

CyGroupImpl(CyNode groupNode)
Constructor to create an empty group when the group node is specified.

CyGroupImpl(CyNode groupNode, List<CyNode> nodeList)
Constructor to create a group with the listed nodes as initial members, and a predetermined CyNode to act as the group Node.

CyGroupImpl(CyNode groupNode, List<CyNode> nodeList, List<CyEdge> internalEdges, List<CyEdge> externalEdges, CyNetwork network)
Constructor to create an empty group.

Constructor parameters in cytoscape.groups with type arguments of type CyNode

CyGroupImpl(CyNode groupNode, List<CyNode> nodeList)
Constructor to create a group with the listed nodes as initial members, and a predetermined CyNode to act as the group Node.

CyGroupImpl(CyNode groupNode, List<CyNode> nodeList, List<CyEdge> internalEdges, List<CyEdge> externalEdges, CyNetwork network)
Constructor to create an empty group.

CyGroupImpl(String groupName, List<CyNode> nodeList)
Constructor to create a group with the listed nodes as initial members.

Uses of CyNode in cytoscape.view

Methods in cytoscape.view with parameters of type CyNode

void	CyNetworkView.applyLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) Applies the given layout to only the given Nodes and Edges.
void	CyNetworkView.applyLockedLayout(CyLayoutAlgorithm layout, CyNode[] nodes, CyEdge[] edges) Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place.
boolean	CyNetworkView.applyVizMap(CyNode node) Applies the given node to the given vizmapper
boolean	CyNetworkView.applyVizMap(CyNode node, VisualStyle style) Applies the given node to the given vizmapper
boolean	CyNetworkView.setSelected(CyNode[] nodes) Deprecated. this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)