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!