cytoscape.giny
Class CytoscapeFingRootGraph

java.lang.Object
  fing.model.FingExtensibleRootGraph
      cytoscape.giny.CytoscapeFingRootGraph

All Implemented Interfaces:

CytoscapeRootGraph, cytoscape.graph.dynamic.DynamicGraph, cytoscape.graph.fixed.FixedGraph, giny.model.RootGraph

public class CytoscapeFingRootGraph
extends fing.model.FingExtensibleRootGraph
implements CytoscapeRootGraph

Field Summary

Fields inherited from interface cytoscape.graph.dynamic.DynamicGraph

DIRECTED_EDGE, UNDIRECTED_EDGE

Constructor Summary

CytoscapeFingRootGraph()
Creates a new CytoscapeFingRootGraph object.

Method Summary

CyNetwork	createNetwork(Collection nodes, Collection edges) DOCUMENT ME!
CyNetwork	createNetwork(int[] nodeInx, int[] edgeInx) Uses Code copied from ColtRootGraph to create a new Network.
CyNetwork	createNetwork(giny.model.Node[] nodes, giny.model.Edge[] edges) Creates a new Network
CyEdge	getEdge(String identifier) DOCUMENT ME!
CyNode	getNode(String identifier) DOCUMENT ME!
void	setEdgeIdentifier(String identifier, int index) DOCUMENT ME!
void	setNodeIdentifier(String identifier, int index) DOCUMENT ME!

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface giny.model.RootGraph

addEdgeMetaChild, addMetaChild, addMetaChild, addNodeMetaChild, containsEdge, containsNode, createEdge, createEdge, createEdge, createEdge, createEdges, createGraphPerspective, createGraphPerspective, createNode, createNode, createNode, createNode, createNodes, edgeExists, edgeExists, edgeMetaChildrenList, edgeMetaChildrenList, edgeMetaParentsList, edgesIterator, edgesList, edgesList, edgesList, ensureCapacity, getAdjacentEdgeIndicesArray, getChildlessMetaDescendants, getConnectingEdgeIndicesArray, getConnectingNodeIndicesArray, getDegree, getDegree, getEdge, getEdgeCount, getEdgeCount, getEdgeCount, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeMetaChildIndicesArray, getEdgeMetaParentIndicesArray, getEdgeSourceIndex, getEdgeTargetIndex, getInDegree, getInDegree, getInDegree, getInDegree, getIndex, getIndex, getNode, getNodeCount, getNodeIndicesArray, getNodeMetaChildIndicesArray, getNodeMetaChildIndicesArray, getNodeMetaParentIndicesArray, getOutDegree, getOutDegree, getOutDegree, getOutDegree, isEdgeDirected, isEdgeMetaChild, isEdgeMetaParent, isMetaChild, isMetaChild, isMetaParent, isMetaParent, isNeighbor, isNeighbor, isNodeMetaChild, isNodeMetaChild, isNodeMetaParent, metaParentsList, metaParentsList, neighborsList, nodeMetaChildrenList, nodeMetaChildrenList, nodeMetaParentsList, nodesIterator, nodesList, removeEdge, removeEdge, removeEdgeMetaChild, removeEdges, removeEdges, removeNode, removeNode, removeNodeMetaChild, removeNodes, removeNodes

Constructor Detail

CytoscapeFingRootGraph

public CytoscapeFingRootGraph()

Creates a new CytoscapeFingRootGraph object.

Method Detail

createNetwork

public CyNetwork createNetwork(Collection nodes,
                               Collection edges)

DOCUMENT ME!

Specified by:

createNetwork in interface CytoscapeRootGraph

Parameters:

nodes - DOCUMENT ME!

edges - DOCUMENT ME!

Returns:

DOCUMENT ME!

createNetwork

public CyNetwork createNetwork(giny.model.Node[] nodes,
                               giny.model.Edge[] edges)

Creates a new Network

Specified by:

createNetwork in interface CytoscapeRootGraph

createNetwork

public CyNetwork createNetwork(int[] nodeInx,
                               int[] edgeInx)

Uses Code copied from ColtRootGraph to create a new Network.

Specified by:

createNetwork in interface CytoscapeRootGraph

getNode

public CyNode getNode(String identifier)

DOCUMENT ME!

Specified by:

getNode in interface CytoscapeRootGraph

Parameters:

identifier - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdge

public CyEdge getEdge(String identifier)

DOCUMENT ME!

Specified by:

getEdge in interface CytoscapeRootGraph

Parameters:

identifier - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeIdentifier

public void setNodeIdentifier(String identifier,
                              int index)

DOCUMENT ME!

Specified by:

setNodeIdentifier in interface CytoscapeRootGraph

Parameters:

identifier - DOCUMENT ME!

index - DOCUMENT ME!

setEdgeIdentifier

public void setEdgeIdentifier(String identifier,
                              int index)

DOCUMENT ME!

Specified by:

setEdgeIdentifier in interface CytoscapeRootGraph

Parameters:

identifier - DOCUMENT ME!

index - DOCUMENT ME!