cytoscape.giny
Interface CytoscapeRootGraph

All Superinterfaces:

giny.model.RootGraph

All Known Implementing Classes:

CytoscapeFingRootGraph

public interface CytoscapeRootGraph
extends giny.model.RootGraph

Method Summary

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

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

Uses Code copied from ColtRootGraph to create a new CyNetwork.

createNetwork

CyNetwork createNetwork(Collection nodes,
                        Collection edges)

createNetwork

CyNetwork createNetwork(int[] node_indices,
                        int[] edge_indices)

Uses Code copied from ColtRootGraph to create a new Network.

getNode

CyNode getNode(String identifier)

getEdge

CyEdge getEdge(String identifier)

setNodeIdentifier

void setNodeIdentifier(String identifier,
                       int index)

setEdgeIdentifier

void setEdgeIdentifier(String identifier,
                       int index)