Uses of Interface
giny.model.Node

Packages that use Node

cytoscape	Core Cytoscape Classes.
cytoscape.data	Basic data classes used by Cytoscape.
cytoscape.giny
cytoscape.view	Classes that provide a window to display a graph and UI components connected to that window, such as the menus.
cytoscape.visual	Framework for generalized mappings from graph attributes to visual attributes.
cytoscape.visual.calculators	Objects that calculate from the data attributes the value for one visual attribute, such as color, shape, or size.
ding.view
fing.model
giny.model
giny.view

Uses of Node in cytoscape

Classes in cytoscape that implement Node

class

CyNode

Methods in cytoscape that return Node

Node	CyEdge.getSource() DOCUMENT ME!
Node	CyEdge.getTarget() DOCUMENT ME!

Methods in cytoscape with parameters of type Node

CyNode	CyNetwork.addNode(Node cytoscape_node) Add a node to this Network that already exists in Cytoscape
static CyEdge	Cytoscape.getCyEdge(Node node_1, Node node_2, String attribute, Object attribute_value, boolean create) Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.
static CyEdge	Cytoscape.getCyEdge(Node source, Node target, String attribute, Object attribute_value, boolean create, boolean directed) Gets the first CyEdge found between the two nodes that has the given value for the given attribute.
boolean	CyNetwork.isSelected(Node node) Returns the selected state of the given node.
void	CyNetwork.setSelectedNodeState(Node node, boolean selected_state) Sets the selected state of a single node.

Uses of Node in cytoscape.data

Methods in cytoscape.data that return types with arguments of type Node

Set<Node>

SelectFilter.setSelectedNodes(Collection<Node> nodesToSet, boolean newState) Sets the selected state defined by the second argument for all Nodes contained in the first argument, which should be a Collection of Node objects contained in the referenced GraphPerspective.

Methods in cytoscape.data with parameters of type Node

static double	NetworkData.getNodeAttributeDoubleValue(Node node, String attribute) DOCUMENT ME!
static Object	NetworkData.getNodeAttributeObjectValue(Node node, String attribute) DOCUMENT ME!
static String	NetworkData.getNodeAttributeStringValue(Node node, String attribute) DOCUMENT ME!
static Object	NetworkData.getNodeAttributeValue(Node node, String attribute) DOCUMENT ME!
boolean	SelectFilter.isSelected(Node node) Returns true if the argument is a selected Node in the referenced GraphPerspective, false otherwise.
static int	NetworkData.setNodeAttributeDoubleValue(Node node, String attribute, double value) DOCUMENT ME!
static int	NetworkData.setNodeAttributeObjectValue(Node node, String attribute, Object value) DOCUMENT ME!
static int	NetworkData.setNodeAttributeStringValue(Node node, String attribute, String value) DOCUMENT ME!
static int	NetworkData.setNodeAttributeValue(Node node, String attribute, Object value) DOCUMENT ME!
static int	NetworkData.setNodeAttributeValue(Node node, String attribute, Object value, int attribute_type) Attempts to set the value for a node, for a given attribute.
boolean	SelectFilter.setSelected(Node node, boolean newState) If the first argument is a Node in the referenced GraphPerspective, sets its selected state to the value of the second argument.

Method parameters in cytoscape.data with type arguments of type Node

Set<Node>

SelectFilter.setSelectedNodes(Collection<Node> nodesToSet, boolean newState) Sets the selected state defined by the second argument for all Nodes contained in the first argument, which should be a Collection of Node objects contained in the referenced GraphPerspective.

Uses of Node in cytoscape.giny

Methods in cytoscape.giny with parameters of type Node

CyNode	FingCyNetwork.addNode(Node cytoscape_node) Add a node to this Network that already exists in Cytoscape
CyNetwork	CytoscapeRootGraph.createNetwork(Node[] nodes, Edge[] edges) Uses Code copied from ColtRootGraph to create a new CyNetwork.
CyNetwork	CytoscapeFingRootGraph.createNetwork(Node[] nodes, Edge[] edges) Creates a new Network
String[]	FingCyNetwork.getNodeAttributesList(Node[] nodes) Return all available Attributes for the given Nodes
Object	FingCyNetwork.getNodeAttributeValue(Node node, String attribute) Return the requested Attribute for the given Node
boolean	FingCyNetwork.isSelected(Node node) Returns the selected state of the given node.
boolean	FingCyNetwork.setNodeAttributeValue(Node node, String attribute, Object value) Return the requested Attribute for the given Node
void	FingCyNetwork.setSelectedNodeState(Node node, boolean selected_state) Sets the selected state of a node.

Uses of Node in cytoscape.view

Methods in cytoscape.view that return Node

static Node[]	BasicGraphViewHandler.removeGraphViewNodes(GraphView graph_view, Node[] nodes) It removes the nodes in the array from the given giny.view.GraphView object, it also removes the connected edges to these nodes (an edge without a connecting node makes no mathematical sense).
static Node[]	BasicGraphViewHandler.restoreGraphViewNodes(GraphView graph_view, Node[] nodes, boolean restore_connected_edges) It restores the views of the nodes in the array in the given giny.view.GraphView object
static Node[]	BasicGraphViewHandler.selectGraphViewNodes(GraphView graph_view, Node[] nodes) It selects the nodes in the array in the given giny.view.GraphView object.
static Node[]	BasicGraphViewHandler.unselectGraphViewNodes(GraphView graph_view, Node[] nodes) It unselects the nodes in the array in the given giny.view.GraphView object

Methods in cytoscape.view with parameters of type Node

static Node[]	BasicGraphViewHandler.removeGraphViewNodes(GraphView graph_view, Node[] nodes) It removes the nodes in the array from the given giny.view.GraphView object, it also removes the connected edges to these nodes (an edge without a connecting node makes no mathematical sense).
static Node[]	BasicGraphViewHandler.restoreGraphViewNodes(GraphView graph_view, Node[] nodes, boolean restore_connected_edges) It restores the views of the nodes in the array in the given giny.view.GraphView object
static Node[]	BasicGraphViewHandler.selectGraphViewNodes(GraphView graph_view, Node[] nodes) It selects the nodes in the array in the given giny.view.GraphView object.
static Node[]	BasicGraphViewHandler.unselectGraphViewNodes(GraphView graph_view, Node[] nodes) It unselects the nodes in the array in the given giny.view.GraphView object

Uses of Node in cytoscape.visual

Methods in cytoscape.visual with parameters of type Node

void	NodeAppearanceCalculator.calculateNodeAppearance(NodeAppearance appr, Node node, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
NodeAppearance	NodeAppearanceCalculator.calculateNodeAppearance(Node node, CyNetwork network) Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.

Uses of Node in cytoscape.visual.calculators

Methods in cytoscape.visual.calculators with parameters of type Node

void	Calculator.apply(Appearance appr, Node n, CyNetwork net) DOCUMENT ME!
void	AbstractCalculator.apply(Appearance appr, Node n, CyNetwork net) DOCUMENT ME!

Uses of Node in ding.view

Methods in ding.view that return Node

Node	DNodeView.getNode() DOCUMENT ME!

Methods in ding.view with parameters of type Node

List	DGraphView.getEdgeViewsList(Node oneNode, Node otherNode) DOCUMENT ME!
NodeView	DGraphView.getNodeView(Node node) DOCUMENT ME!
NodeView	DGraphView.removeNodeView(Node node) Removes a NodeView based on specified Node.

Uses of Node in fing.model

Methods in fing.model that return Node

Node	FingNodeDepot.getNode(RootGraph root, int index, String id) This either instantiates a new node or gets one from the recyclery, initializing it with the parameters specified.

Methods in fing.model with parameters of type Node

void	FingNodeDepot.recycleNode(Node node) Recycles a node.

Uses of Node in giny.model

Methods in giny.model that return Node

abstract Node[]	RootGraphChangeEvent.getCreatedNodes()
abstract Node[]	GraphPerspectiveChangeEvent.getHiddenNodes() Deprecated. Use getHiddenNodeIndices() instead; the nodes returned by this method may have undefined state.
abstract Node[][]	RootGraphChangeEvent.getMetaRelationshipCreatedNodes()
abstract Node[][]	RootGraphChangeEvent.getMetaRelationshipRemovedNodes()
Node	NestedNetworkChangeEvent.getNestedNode()
Node	RootGraph.getNode(int node_index) Return the Node with the given index in this RootGraph.
Node	GraphPerspective.getNode(int index) Return a Node which is in this GraphPerspective.
abstract Node[]	RootGraphChangeEvent.getRemovedNodes() Deprecated. Use getRemovedNodeIndices() instead; the nodes returned by this method may have undefined state.
abstract Node[]	GraphPerspectiveChangeEvent.getRestoredNodes()
abstract Node[]	GraphPerspectiveChangeEvent.getSelectedNodes() Deprecated. Nowhere in GraphPerspective is there functionality that specifies node selection logic.
Node	Edge.getSource()
Node	Edge.getTarget()
abstract Node[]	GraphPerspectiveChangeEvent.getUnselectedNodes() Deprecated. Nowhere in GraphPerspective is there functionality that specifies node un-selection logic.
Node	GraphPerspective.hideNode(Node node) If this GraphPerspective does not hide the given Node, change it so that it does hide the node and all of its incident edges.
Node	RootGraph.removeNode(Node node) Remove the given Node and all Edges incident on it from this RootGraph and all of its GraphPerspectives.
Node	GraphPerspective.restoreNode(Node node) If this GraphPerspective hides the given Node, change it so that it does not hide the node.

Methods in giny.model with parameters of type Node

boolean	RootGraph.addMetaChild(Node parent, Edge child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.addMetaChild(Node parent, Node child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.containsNode(Node node) Return true if the given Node is in this RootGraph.
boolean	GraphPerspective.containsNode(Node node) Return true if the given Node is in this GraphPerspective.
boolean	GraphPerspective.containsNode(Node node, boolean recurse) Return true if the given Node is in this GraphPerspective.
int	RootGraph.createEdge(Node source, Node target) Create a directed Edge from the given source Node to the given target Node, and return its index.
int	RootGraph.createEdge(Node source, Node target, boolean directed) Create an Edge from the given source Node to the given target Node, and return its index.
GraphPerspective	RootGraph.createGraphPerspective(Node[] nodes, Edge[] edges) Create a new GraphPerspective with just the given Nodes and Edges (and all Nodes incident on the given Edges).
GraphPerspective	GraphPerspective.createGraphPerspective(Node[] nodes, Edge[] edges) Deprecated. Use RootGraph.createGraphPerspective(int[], int[]) instead.
int	RootGraph.createNode(Node[] nodes, Edge[] edges) Create a new Node in this RootGraph, and return its index.
boolean	RootGraph.edgeExists(Node from, Node to) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways: this method returns true if and only if either 1) there exists a directed edge E in this RootGraph such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this RootGraph such that E's endpoints are the from and to nodes specified.
boolean	GraphPerspective.edgeExists(Node from, Node to) This method returns true if and only if either 1) there exists a directed edge E in this GraphPerspective such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this GraphPerspective such that E's endpoints are the from and to nodes specified.
List	RootGraph.edgeMetaChildrenList(Node node) Deprecated. Use getEdgeMetaChildIndicesArray(int) instead.
List	GraphPerspective.edgeMetaChildrenList(Node node) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
List	RootGraph.edgesList(Node from, Node to) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
List	GraphPerspective.edgesList(Node from, Node to) Return a new List of the Edges in this GraphPerspective from the first given Node to the second given Node.
List	GraphPerspective.getAdjacentEdgesList(Node node, boolean include_undirected_edges, boolean incoming_edges, boolean outgoing_edges) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
int	RootGraph.getDegree(Node node) Return the number of distinct Edges incident on the given Node.
int	GraphPerspective.getDegree(Node node) Return the number of distinct Edges in this GraphPerspective incident on the given Node.
int	RootGraph.getEdgeCount(Node from, Node to, boolean count_undirected_edges) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
int	GraphPerspective.getEdgeCount(Node from, Node to, boolean count_undirected_edges) Count the number of edges from the first Node to the second.
int	RootGraph.getInDegree(Node node) Return the number of Edges e such that e.getTarget().equals( node ).
int	GraphPerspective.getInDegree(Node node) Return the number of Edges e in this GraphPerspective such that e.getTarget().equals( node ).
int	RootGraph.getInDegree(Node node, boolean count_undirected_edges) Return the number of Edges e such that e.getSource().equals( node ).
int	GraphPerspective.getInDegree(Node node, boolean count_undirected_edges) Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ).
int	RootGraph.getIndex(Node node) Return the index of the given Node.
int	GraphPerspective.getIndex(Node node) Return the index of the given Node in the underlying RootGraph.
int	RootGraph.getOutDegree(Node node) Return the number of Edges e such that e.getSource().equals( node ).
int	GraphPerspective.getOutDegree(Node node) Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ).
int	RootGraph.getOutDegree(Node node, boolean count_undirected_edges) Return the number of Edges e such that e.getSource().equals( node ).
int	GraphPerspective.getOutDegree(Node node, boolean count_undirected_edges) Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ).
Node	GraphPerspective.hideNode(Node node) If this GraphPerspective does not hide the given Node, change it so that it does hide the node and all of its incident edges.
boolean	RootGraph.isMetaChild(Node parent, Edge child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	GraphPerspective.isMetaChild(Node parent, Edge child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.isMetaChild(Node parent, Node child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	GraphPerspective.isMetaChild(Node parent, Node child) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.isMetaParent(Edge child, Node parent) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	GraphPerspective.isMetaParent(Edge child, Node parent) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.isMetaParent(Node child, Node parent) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	GraphPerspective.isMetaParent(Node child, Node parent) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
boolean	RootGraph.isNeighbor(Node a_node, Node another_node) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways, please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if a_node is a "node neighbor" of another_node in this RootGraph.
boolean	GraphPerspective.isNeighbor(Node a_node, Node another_node) Please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if a_node is a "node neighbor" of another_node in this GraphPerspective.
List	RootGraph.metaParentsList(Node node) Deprecated. Use getNodeMetaParentIndicesArray(int) instead.
List	GraphPerspective.metaParentsList(Node node) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
List	RootGraph.neighborsList(Node node) Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways, please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns a non-repeating list of all nodes N in this RootGraph such that N is a "node neighbor" of node, the input parameter.
List	GraphPerspective.neighborsList(Node node) Please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns a non-repeating list of indices of all nodes N in this GraphPerspective such that N is a "node neighbor" of the node at specified index, or null if no node at specified index exists in this GraphPerspective.
List	RootGraph.nodeMetaChildrenList(Node node) Deprecated. Use getNodeMetaChildIndicesArray(int) instead.
List	GraphPerspective.nodeMetaChildrenList(Node node) Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
Node	RootGraph.removeNode(Node node) Remove the given Node and all Edges incident on it from this RootGraph and all of its GraphPerspectives.
Node	GraphPerspective.restoreNode(Node node) If this GraphPerspective hides the given Node, change it so that it does not hide the node.

Constructors in giny.model with parameters of type Node

NestedNetworkChangeEvent(Object source, Node parentNode, GraphView nestedGraphView)

Uses of Node in giny.view

Methods in giny.view that return Node

abstract Node[]	GraphViewChangeEvent.getHiddenNodes()
Node	NodeView.getNode()
abstract Node[]	GraphViewChangeEvent.getRestoredNodes()
abstract Node[]	GraphViewChangeEvent.getSelectedNodes()
abstract Node[]	GraphViewChangeEvent.getUnselectedNodes()

Methods in giny.view with parameters of type Node

List	GraphView.getEdgeViewsList(Node oneNode, Node otherNode) Note that this will return a list of Edge objects, the other one will return indices
NodeView	GraphView.getNodeView(Node node)
NodeView	GraphView.removeNodeView(Node node) This will entirely remove a NodeView/EdgeView from the GraphView.