Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.giny
Interface CytoscapeRootGraph

All Superinterfaces:
RootGraph
All Known Implementing Classes:
CytoscapeFingRootGraph

public interface CytoscapeRootGraph
extends RootGraph


Method Summary
 CyNetwork createNetwork(Collection nodes, Collection edges)
          DOCUMENT ME!
 CyNetwork createNetwork(int[] node_indices, int[] edge_indices)
          Uses Code copied from ColtRootGraph to create a new Network.
 CyNetwork createNetwork(Node[] nodes, Edge[] edges)
          Uses Code copied from ColtRootGraph to create a new CyNetwork.
 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 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
 

Method Detail

createNetwork

CyNetwork createNetwork(Node[] nodes,
                        Edge[] edges)
Uses Code copied from ColtRootGraph to create a new CyNetwork.


createNetwork

CyNetwork createNetwork(Collection nodes,
                        Collection edges)
DOCUMENT ME!

Parameters:
nodes - DOCUMENT ME!
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!

createNetwork

CyNetwork createNetwork(int[] node_indices,
                        int[] edge_indices)
Uses Code copied from ColtRootGraph to create a new Network.


getNode

CyNode getNode(String identifier)
DOCUMENT ME!

Parameters:
identifier - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdge

CyEdge getEdge(String identifier)
DOCUMENT ME!

Parameters:
identifier - DOCUMENT ME!
Returns:
DOCUMENT ME!

setNodeIdentifier

void setNodeIdentifier(String identifier,
                       int index)
DOCUMENT ME!

Parameters:
identifier - DOCUMENT ME!
index - DOCUMENT ME!

setEdgeIdentifier

void setEdgeIdentifier(String identifier,
                       int index)
DOCUMENT ME!

Parameters:
identifier - DOCUMENT ME!
index - DOCUMENT ME!

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