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

cytoscape.giny
Class CytoscapeFingRootGraph

java.lang.Object
  extended by fing.model.FingExtensibleRootGraph
      extended by cytoscape.giny.CytoscapeFingRootGraph
All Implemented Interfaces:
CytoscapeRootGraph, cytoscape.graph.dynamic.DynamicGraph, cytoscape.graph.fixed.FixedGraph, RootGraph

public class CytoscapeFingRootGraph
extends 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
 boolean addEdgeMetaChild(int parentNodeInx, int childEdgeInx)
          DOCUMENT ME!
 boolean addMetaChild(Node parent, Edge child)
          DOCUMENT ME!
 boolean addMetaChild(Node parent, Node child)
          DOCUMENT ME!
 boolean addNodeMetaChild(int parentNodeInx, int childNodeInx)
          DOCUMENT ME!
 boolean containsEdge(Edge edge)
          DOCUMENT ME!
 boolean containsNode(Node node)
          DOCUMENT ME!
 int createEdge(int sourceNodeIndex, int targetNodeIndex)
          DOCUMENT ME!
 int createEdge(int sourceNodeIndex, int targetNodeIndex, boolean directed)
          DOCUMENT ME!
 int createEdge(Node source, Node target)
          DOCUMENT ME!
 int createEdge(Node source, Node target, boolean directed)
          DOCUMENT ME!
 int[] createEdges(int[] sourceNodeIndices, int[] targetNodeIndices, boolean directed)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(int[] nodeInx, int[] edgeInx)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(Node[] nodes, Edge[] edges)
          DOCUMENT ME!
 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(Node[] nodes, Edge[] edges)
          Creates a new Network
 int createNode()
          DOCUMENT ME!
 int createNode(GraphPerspective perspective)
          DOCUMENT ME!
 int createNode(int[] nodeIndices, int[] edgeIndices)
          DOCUMENT ME!
 int createNode(Node[] nodes, Edge[] edges)
          DOCUMENT ME!
 int[] createNodes(int numNewNodes)
          DOCUMENT ME!
 int edgeCreate(int sourceNode, int targetNode, boolean directed)
          DOCUMENT ME!
 boolean edgeExists(int fromNodeInx, int toNodeInx)
          DOCUMENT ME!
 boolean edgeExists(Node from, Node to)
          DOCUMENT ME!
 List edgeMetaChildrenList(int parentNodeInx)
          DOCUMENT ME!
 List edgeMetaChildrenList(Node node)
          DOCUMENT ME!
 List edgeMetaParentsList(int edgeInx)
          DOCUMENT ME!
 boolean edgeRemove(int edge)
          DOCUMENT ME!
 IntEnumerator edges()
          DOCUMENT ME!
 IntEnumerator edgesAdjacent(int node, boolean outgoing, boolean incoming, boolean undirected)
          DOCUMENT ME!
 IntIterator edgesConnecting(int node0, int node1, boolean outgoing, boolean incoming, boolean undirected)
          DOCUMENT ME!
 Iterator edgesIterator()
          DOCUMENT ME!
 List edgesList()
          DOCUMENT ME!
 List edgesList(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges)
          DOCUMENT ME!
 List edgesList(Node from, Node to)
          DOCUMENT ME!
 int edgeSource(int edge)
          DOCUMENT ME!
 int edgeTarget(int edge)
          DOCUMENT ME!
 byte edgeType(int edge)
          DOCUMENT ME!
 void ensureCapacity(int nodes, int edges)
          DOCUMENT ME!
 int[] getAdjacentEdgeIndicesArray(int nodeInx, boolean undirected, boolean incomingDirected, boolean outgoingDirected)
          DOCUMENT ME!
 int[] getChildlessMetaDescendants(int nodeInx)
          DOCUMENT ME!
 int[] getConnectingEdgeIndicesArray(int[] nodeInx)
          DOCUMENT ME!
 int[] getConnectingNodeIndicesArray(int[] edgeInx)
          DOCUMENT ME!
 int getDegree(int nodeInx)
          DOCUMENT ME!
 int getDegree(Node node)
          DOCUMENT ME!
 Edge getEdge(int edgeInx)
          DOCUMENT ME!
 CyEdge getEdge(String identifier)
          DOCUMENT ME!
 int getEdgeCount()
          DOCUMENT ME!
 int getEdgeCount(int fromNodeInx, int toNodeInx, boolean countUndirectedEdges)
          DOCUMENT ME!
 int getEdgeCount(Node from, Node to, boolean countUndirectedEdges)
          DOCUMENT ME!
 int[] getEdgeIndicesArray()
          DOCUMENT ME!
 int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges)
          DOCUMENT ME!
 int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean undirectedEdges, boolean bothDirections)
          DOCUMENT ME!
 int[] getEdgeMetaChildIndicesArray(int parentNodeInx)
          DOCUMENT ME!
 int[] getEdgeMetaParentIndicesArray(int edgeInx)
          DOCUMENT ME!
 int getEdgeSourceIndex(int edgeInx)
          DOCUMENT ME!
 int getEdgeTargetIndex(int edgeInx)
          DOCUMENT ME!
 int getInDegree(int nodeInx)
          DOCUMENT ME!
 int getInDegree(int nodeInx, boolean countUndirectedEdges)
          DOCUMENT ME!
 int getInDegree(Node node)
          DOCUMENT ME!
 int getInDegree(Node node, boolean countUndirectedEdges)
          DOCUMENT ME!
 int getIndex(Edge edge)
          DOCUMENT ME!
 int getIndex(Node node)
          DOCUMENT ME!
 Node getNode(int nodeInx)
          DOCUMENT ME!
 CyNode getNode(String identifier)
          DOCUMENT ME!
 int getNodeCount()
          DOCUMENT ME!
 int[] getNodeIndicesArray()
          DOCUMENT ME!
 int[] getNodeMetaChildIndicesArray(int parentNodeInx)
          DOCUMENT ME!
 int[] getNodeMetaChildIndicesArray(int parentNodeInx, boolean recursive)
          DOCUMENT ME!
 int[] getNodeMetaParentIndicesArray(int nodeInx)
          DOCUMENT ME!
 int getOutDegree(int nodeInx)
          DOCUMENT ME!
 int getOutDegree(int nodeInx, boolean countUndirectedEdges)
          DOCUMENT ME!
 int getOutDegree(Node node)
          DOCUMENT ME!
 int getOutDegree(Node node, boolean countUndirectedEdges)
          DOCUMENT ME!
 boolean isEdgeDirected(int edgeInx)
          DOCUMENT ME!
 boolean isEdgeMetaChild(int parentNodeInx, int childEdgeInx)
          DOCUMENT ME!
 boolean isEdgeMetaParent(int childEdgeInx, int parentNodeInx)
          DOCUMENT ME!
 boolean isMetaChild(Node parent, Edge child)
          DOCUMENT ME!
 boolean isMetaChild(Node parent, Node child)
          DOCUMENT ME!
 boolean isMetaParent(Edge child, Node parent)
          DOCUMENT ME!
 boolean isMetaParent(Node child, Node parent)
          DOCUMENT ME!
 boolean isNeighbor(int nodeInxA, int nodeInxB)
          DOCUMENT ME!
 boolean isNeighbor(Node a, Node b)
          DOCUMENT ME!
 boolean isNodeMetaChild(int parentNodeInx, int childNodeInx)
          DOCUMENT ME!
 boolean isNodeMetaChild(int parentNodeInx, int childNodeInx, boolean recursive)
          DOCUMENT ME!
 boolean isNodeMetaParent(int childNodeInx, int parentNodeInx)
          DOCUMENT ME!
 List metaParentsList(Edge edge)
          DOCUMENT ME!
 List metaParentsList(Node node)
          DOCUMENT ME!
 List neighborsList(Node node)
          DOCUMENT ME!
 int nodeCreate()
          DOCUMENT ME!
 boolean nodeExists(int node)
          DOCUMENT ME!
 List nodeMetaChildrenList(int parentNodeInx)
          DOCUMENT ME!
 List nodeMetaChildrenList(Node node)
          DOCUMENT ME!
 List nodeMetaParentsList(int nodeInx)
          DOCUMENT ME!
 boolean nodeRemove(int node)
          DOCUMENT ME!
 IntEnumerator nodes()
          DOCUMENT ME!
 Iterator nodesIterator()
          DOCUMENT ME!
 List nodesList()
          DOCUMENT ME!
 Edge removeEdge(Edge edge)
          DOCUMENT ME!
 int removeEdge(int edgeInx)
          DOCUMENT ME!
 boolean removeEdgeMetaChild(int parentNodeInx, int childEdgeInx)
          DOCUMENT ME!
 int[] removeEdges(int[] edgeIndices)
          DOCUMENT ME!
 List removeEdges(List edges)
          DOCUMENT ME!
 int removeNode(int nodeInx)
          DOCUMENT ME!
 Node removeNode(Node node)
          DOCUMENT ME!
 boolean removeNodeMetaChild(int parentNodeInx, int childNodeInx)
          DOCUMENT ME!
 int[] removeNodes(int[] nodeIndices)
          DOCUMENT ME!
 List removeNodes(List nodes)
          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(Node[] nodes,
                               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!

nodes

public IntEnumerator nodes()
DOCUMENT ME!

Specified by:
nodes in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
nodes in interface cytoscape.graph.fixed.FixedGraph
Returns:
DOCUMENT ME!

edges

public IntEnumerator edges()
DOCUMENT ME!

Specified by:
edges in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edges in interface cytoscape.graph.fixed.FixedGraph
Returns:
DOCUMENT ME!

nodeCreate

public int nodeCreate()
DOCUMENT ME!

Specified by:
nodeCreate in interface cytoscape.graph.dynamic.DynamicGraph
Returns:
DOCUMENT ME!

nodeRemove

public boolean nodeRemove(int node)
DOCUMENT ME!

Specified by:
nodeRemove in interface cytoscape.graph.dynamic.DynamicGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeCreate

public int edgeCreate(int sourceNode,
                      int targetNode,
                      boolean directed)
DOCUMENT ME!

Specified by:
edgeCreate in interface cytoscape.graph.dynamic.DynamicGraph
Parameters:
sourceNode - DOCUMENT ME!
targetNode - DOCUMENT ME!
directed - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeRemove

public boolean edgeRemove(int edge)
DOCUMENT ME!

Specified by:
edgeRemove in interface cytoscape.graph.dynamic.DynamicGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

nodeExists

public boolean nodeExists(int node)
DOCUMENT ME!

Specified by:
nodeExists in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
nodeExists in interface cytoscape.graph.fixed.FixedGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeType

public byte edgeType(int edge)
DOCUMENT ME!

Specified by:
edgeType in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edgeType in interface cytoscape.graph.fixed.FixedGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeSource

public int edgeSource(int edge)
DOCUMENT ME!

Specified by:
edgeSource in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edgeSource in interface cytoscape.graph.fixed.FixedGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeTarget

public int edgeTarget(int edge)
DOCUMENT ME!

Specified by:
edgeTarget in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edgeTarget in interface cytoscape.graph.fixed.FixedGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgesAdjacent

public IntEnumerator edgesAdjacent(int node,
                                   boolean outgoing,
                                   boolean incoming,
                                   boolean undirected)
DOCUMENT ME!

Specified by:
edgesAdjacent in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edgesAdjacent in interface cytoscape.graph.fixed.FixedGraph
Parameters:
node - DOCUMENT ME!
outgoing - DOCUMENT ME!
incoming - DOCUMENT ME!
undirected - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgesConnecting

public IntIterator edgesConnecting(int node0,
                                   int node1,
                                   boolean outgoing,
                                   boolean incoming,
                                   boolean undirected)
DOCUMENT ME!

Specified by:
edgesConnecting in interface cytoscape.graph.dynamic.DynamicGraph
Specified by:
edgesConnecting in interface cytoscape.graph.fixed.FixedGraph
Parameters:
node0 - DOCUMENT ME!
node1 - DOCUMENT ME!
outgoing - DOCUMENT ME!
incoming - DOCUMENT ME!
undirected - DOCUMENT ME!
Returns:
DOCUMENT ME!

createGraphPerspective

public GraphPerspective createGraphPerspective(Node[] nodes,
                                               Edge[] edges)
DOCUMENT ME!

Specified by:
createGraphPerspective in interface RootGraph
Parameters:
nodes - DOCUMENT ME!
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] nodeInx,
                                               int[] edgeInx)
DOCUMENT ME!

Specified by:
createGraphPerspective in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

ensureCapacity

public void ensureCapacity(int nodes,
                           int edges)
DOCUMENT ME!

Specified by:
ensureCapacity in interface RootGraph
Parameters:
nodes - DOCUMENT ME!
edges - DOCUMENT ME!

getNodeCount

public int getNodeCount()
DOCUMENT ME!

Specified by:
getNodeCount in interface RootGraph
Returns:
DOCUMENT ME!

getEdgeCount

public int getEdgeCount()
DOCUMENT ME!

Specified by:
getEdgeCount in interface RootGraph
Returns:
DOCUMENT ME!

nodesIterator

public Iterator nodesIterator()
DOCUMENT ME!

Specified by:
nodesIterator in interface RootGraph
Returns:
DOCUMENT ME!

nodesList

public List nodesList()
DOCUMENT ME!

Specified by:
nodesList in interface RootGraph
Returns:
DOCUMENT ME!
See Also:
RootGraph.nodesIterator()

getNodeIndicesArray

public int[] getNodeIndicesArray()
DOCUMENT ME!

Specified by:
getNodeIndicesArray in interface RootGraph
Returns:
DOCUMENT ME!
See Also:
RootGraph.nodesIterator(), GraphObject.getRootGraphIndex()

edgesIterator

public Iterator edgesIterator()
DOCUMENT ME!

Specified by:
edgesIterator in interface RootGraph
Returns:
DOCUMENT ME!

edgesList

public List edgesList()
DOCUMENT ME!

Specified by:
edgesList in interface RootGraph
Returns:
DOCUMENT ME!
See Also:
RootGraph.edgesIterator()

getEdgeIndicesArray

public int[] getEdgeIndicesArray()
DOCUMENT ME!

Specified by:
getEdgeIndicesArray in interface RootGraph
Returns:
DOCUMENT ME!
See Also:
RootGraph.edgesIterator(), GraphObject.getRootGraphIndex()

removeNode

public Node removeNode(Node node)
DOCUMENT ME!

Specified by:
removeNode in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeNode

public int removeNode(int nodeInx)
DOCUMENT ME!

Specified by:
removeNode in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeNodes

public List removeNodes(List nodes)
DOCUMENT ME!

Specified by:
removeNodes in interface RootGraph
Parameters:
nodes - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.removeNode(Node), RootGraph.removeNodes(int[])

removeNodes

public int[] removeNodes(int[] nodeIndices)
DOCUMENT ME!

Specified by:
removeNodes in interface RootGraph
Parameters:
nodeIndices - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.removeNode(int)

createNode

public int createNode()
DOCUMENT ME!

Specified by:
createNode in interface RootGraph
Returns:
DOCUMENT ME!

createNode

public int createNode(Node[] nodes,
                      Edge[] edges)
DOCUMENT ME!

Specified by:
createNode in interface RootGraph
Parameters:
nodes - DOCUMENT ME!
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!

createNode

public int createNode(GraphPerspective perspective)
DOCUMENT ME!

Specified by:
createNode in interface RootGraph
Parameters:
perspective - DOCUMENT ME!
Returns:
DOCUMENT ME!

createNode

public int createNode(int[] nodeIndices,
                      int[] edgeIndices)
DOCUMENT ME!

Specified by:
createNode in interface RootGraph
Parameters:
nodeIndices - DOCUMENT ME!
edgeIndices - DOCUMENT ME!
Returns:
DOCUMENT ME!

createNodes

public int[] createNodes(int numNewNodes)
DOCUMENT ME!

Specified by:
createNodes in interface RootGraph
Parameters:
numNewNodes - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.createNode()

removeEdge

public Edge removeEdge(Edge edge)
DOCUMENT ME!

Specified by:
removeEdge in interface RootGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeEdge

public int removeEdge(int edgeInx)
DOCUMENT ME!

Specified by:
removeEdge in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeEdges

public List removeEdges(List edges)
DOCUMENT ME!

Specified by:
removeEdges in interface RootGraph
Parameters:
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.removeEdge(Edge), RootGraph.removeEdges(int[])

removeEdges

public int[] removeEdges(int[] edgeIndices)
DOCUMENT ME!

Specified by:
removeEdges in interface RootGraph
Parameters:
edgeIndices - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.removeEdge(int)

createEdge

public int createEdge(Node source,
                      Node target)
DOCUMENT ME!

Specified by:
createEdge in interface RootGraph
Parameters:
source - DOCUMENT ME!
target - DOCUMENT ME!
Returns:
DOCUMENT ME!

createEdge

public int createEdge(Node source,
                      Node target,
                      boolean directed)
DOCUMENT ME!

Specified by:
createEdge in interface RootGraph
Parameters:
source - DOCUMENT ME!
target - DOCUMENT ME!
directed - DOCUMENT ME!
Returns:
DOCUMENT ME!

createEdge

public int createEdge(int sourceNodeIndex,
                      int targetNodeIndex)
DOCUMENT ME!

Specified by:
createEdge in interface RootGraph
Parameters:
sourceNodeIndex - DOCUMENT ME!
targetNodeIndex - DOCUMENT ME!
Returns:
DOCUMENT ME!

createEdge

public int createEdge(int sourceNodeIndex,
                      int targetNodeIndex,
                      boolean directed)
DOCUMENT ME!

Specified by:
createEdge in interface RootGraph
Parameters:
sourceNodeIndex - DOCUMENT ME!
targetNodeIndex - DOCUMENT ME!
directed - DOCUMENT ME!
Returns:
DOCUMENT ME!

createEdges

public int[] createEdges(int[] sourceNodeIndices,
                         int[] targetNodeIndices,
                         boolean directed)
DOCUMENT ME!

Specified by:
createEdges in interface RootGraph
Parameters:
sourceNodeIndices - DOCUMENT ME!
targetNodeIndices - DOCUMENT ME!
directed - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.createEdge(int, int, boolean)

containsNode

public boolean containsNode(Node node)
DOCUMENT ME!

Specified by:
containsNode in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

containsEdge

public boolean containsEdge(Edge edge)
DOCUMENT ME!

Specified by:
containsEdge in interface RootGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

neighborsList

public List neighborsList(Node node)
DOCUMENT ME!

Specified by:
neighborsList in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

isNeighbor

public boolean isNeighbor(Node a,
                          Node b)
DOCUMENT ME!

Specified by:
isNeighbor in interface RootGraph
Parameters:
a - DOCUMENT ME!
b - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

isNeighbor

public boolean isNeighbor(int nodeInxA,
                          int nodeInxB)
DOCUMENT ME!

Specified by:
isNeighbor in interface RootGraph
Parameters:
nodeInxA - DOCUMENT ME!
nodeInxB - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

edgeExists

public boolean edgeExists(Node from,
                          Node to)
DOCUMENT ME!

Specified by:
edgeExists in interface RootGraph
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

edgeExists

public boolean edgeExists(int fromNodeInx,
                          int toNodeInx)
DOCUMENT ME!

Specified by:
edgeExists in interface RootGraph
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getEdgeCount

public int getEdgeCount(Node from,
                        Node to,
                        boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getEdgeCount in interface RootGraph
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getEdgeCount

public int getEdgeCount(int fromNodeInx,
                        int toNodeInx,
                        boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getEdgeCount in interface RootGraph
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getAdjacentEdgeIndicesArray

public int[] getAdjacentEdgeIndicesArray(int nodeInx,
                                         boolean undirected,
                                         boolean incomingDirected,
                                         boolean outgoingDirected)
DOCUMENT ME!

Specified by:
getAdjacentEdgeIndicesArray in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
undirected - DOCUMENT ME!
incomingDirected - DOCUMENT ME!
outgoingDirected - DOCUMENT ME!
Returns:
DOCUMENT ME!

getConnectingEdgeIndicesArray

public int[] getConnectingEdgeIndicesArray(int[] nodeInx)
DOCUMENT ME!

Specified by:
getConnectingEdgeIndicesArray in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getConnectingNodeIndicesArray

public int[] getConnectingNodeIndicesArray(int[] edgeInx)
DOCUMENT ME!

Specified by:
getConnectingNodeIndicesArray in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getEdgeSourceIndex(int), RootGraph.getEdgeTargetIndex(int), RootGraph.createGraphPerspective(int[], int[])

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int fromNodeInx,
                                 int toNodeInx,
                                 boolean undirectedEdges,
                                 boolean bothDirections)
DOCUMENT ME!

Specified by:
getEdgeIndicesArray in interface RootGraph
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
undirectedEdges - DOCUMENT ME!
bothDirections - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

edgesList

public List edgesList(Node from,
                      Node to)
DOCUMENT ME!

Specified by:
edgesList in interface RootGraph
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

edgesList

public List edgesList(int fromNodeInx,
                      int toNodeInx,
                      boolean includeUndirectedEdges)
DOCUMENT ME!

Specified by:
edgesList in interface RootGraph
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
includeUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int fromNodeInx,
                                 int toNodeInx,
                                 boolean includeUndirectedEdges)
DOCUMENT ME!

Specified by:
getEdgeIndicesArray in interface RootGraph
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
includeUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getInDegree

public int getInDegree(Node node)
DOCUMENT ME!

Specified by:
getInDegree in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

getInDegree

public int getInDegree(int nodeInx)
DOCUMENT ME!

Specified by:
getInDegree in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getInDegree

public int getInDegree(Node node,
                       boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getInDegree in interface RootGraph
Parameters:
node - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

getInDegree

public int getInDegree(int nodeInx,
                       boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getInDegree in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

getOutDegree

public int getOutDegree(Node node)
DOCUMENT ME!

Specified by:
getOutDegree in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

getOutDegree

public int getOutDegree(int nodeInx)
DOCUMENT ME!

Specified by:
getOutDegree in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getOutDegree

public int getOutDegree(Node node,
                        boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getOutDegree in interface RootGraph
Parameters:
node - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

getOutDegree

public int getOutDegree(int nodeInx,
                        boolean countUndirectedEdges)
DOCUMENT ME!

Specified by:
getOutDegree in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

getDegree

public int getDegree(Node node)
DOCUMENT ME!

Specified by:
getDegree in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

getDegree

public int getDegree(int nodeInx)
DOCUMENT ME!

Specified by:
getDegree in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getIndex

public int getIndex(Node node)
DOCUMENT ME!

Specified by:
getIndex in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNode

public Node getNode(int nodeInx)
DOCUMENT ME!

Specified by:
getNode in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getIndex

public int getIndex(Edge edge)
DOCUMENT ME!

Specified by:
getIndex in interface RootGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdge

public Edge getEdge(int edgeInx)
DOCUMENT ME!

Specified by:
getEdge in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeSourceIndex

public int getEdgeSourceIndex(int edgeInx)
DOCUMENT ME!

Specified by:
getEdgeSourceIndex in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeTargetIndex

public int getEdgeTargetIndex(int edgeInx)
DOCUMENT ME!

Specified by:
getEdgeTargetIndex in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isEdgeDirected

public boolean isEdgeDirected(int edgeInx)
DOCUMENT ME!

Specified by:
isEdgeDirected in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

addMetaChild

public boolean addMetaChild(Node parent,
                            Node child)
DOCUMENT ME!

Specified by:
addMetaChild in interface RootGraph
Parameters:
parent - DOCUMENT ME!
child - DOCUMENT ME!
Returns:
DOCUMENT ME!

addNodeMetaChild

public boolean addNodeMetaChild(int parentNodeInx,
                                int childNodeInx)
DOCUMENT ME!

Specified by:
addNodeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeNodeMetaChild

public boolean removeNodeMetaChild(int parentNodeInx,
                                   int childNodeInx)
DOCUMENT ME!

Specified by:
removeNodeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isMetaParent

public boolean isMetaParent(Node child,
                            Node parent)
DOCUMENT ME!

Specified by:
isMetaParent in interface RootGraph
Parameters:
child - DOCUMENT ME!
parent - DOCUMENT ME!
Returns:
DOCUMENT ME!

isNodeMetaParent

public boolean isNodeMetaParent(int childNodeInx,
                                int parentNodeInx)
DOCUMENT ME!

Specified by:
isNodeMetaParent in interface RootGraph
Parameters:
childNodeInx - DOCUMENT ME!
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

metaParentsList

public List metaParentsList(Node node)
DOCUMENT ME!

Specified by:
metaParentsList in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getNodeMetaParentIndicesArray(int)

nodeMetaParentsList

public List nodeMetaParentsList(int nodeInx)
DOCUMENT ME!

Specified by:
nodeMetaParentsList in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getNodeMetaParentIndicesArray(int)

getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int nodeInx)
DOCUMENT ME!

Specified by:
getNodeMetaParentIndicesArray in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isMetaChild

public boolean isMetaChild(Node parent,
                           Node child)
DOCUMENT ME!

Specified by:
isMetaChild in interface RootGraph
Parameters:
parent - DOCUMENT ME!
child - DOCUMENT ME!
Returns:
DOCUMENT ME!

isNodeMetaChild

public boolean isNodeMetaChild(int parentNodeInx,
                               int childNodeInx)
DOCUMENT ME!

Specified by:
isNodeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isNodeMetaChild

public boolean isNodeMetaChild(int parentNodeInx,
                               int childNodeInx,
                               boolean recursive)
DOCUMENT ME!

Specified by:
isNodeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childNodeInx - DOCUMENT ME!
recursive - DOCUMENT ME!
Returns:
DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(Node node)
DOCUMENT ME!

Specified by:
nodeMetaChildrenList in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getNodeMetaChildIndicesArray(int)

nodeMetaChildrenList

public List nodeMetaChildrenList(int parentNodeInx)
DOCUMENT ME!

Specified by:
nodeMetaChildrenList in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentNodeInx)
DOCUMENT ME!

Specified by:
getNodeMetaChildIndicesArray in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentNodeInx,
                                          boolean recursive)
DOCUMENT ME!

Specified by:
getNodeMetaChildIndicesArray in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
recursive - DOCUMENT ME!
Returns:
DOCUMENT ME!

getChildlessMetaDescendants

public int[] getChildlessMetaDescendants(int nodeInx)
DOCUMENT ME!

Specified by:
getChildlessMetaDescendants in interface RootGraph
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

addMetaChild

public boolean addMetaChild(Node parent,
                            Edge child)
DOCUMENT ME!

Specified by:
addMetaChild in interface RootGraph
Parameters:
parent - DOCUMENT ME!
child - DOCUMENT ME!
Returns:
DOCUMENT ME!

addEdgeMetaChild

public boolean addEdgeMetaChild(int parentNodeInx,
                                int childEdgeInx)
DOCUMENT ME!

Specified by:
addEdgeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

removeEdgeMetaChild

public boolean removeEdgeMetaChild(int parentNodeInx,
                                   int childEdgeInx)
DOCUMENT ME!

Specified by:
removeEdgeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isMetaParent

public boolean isMetaParent(Edge child,
                            Node parent)
DOCUMENT ME!

Specified by:
isMetaParent in interface RootGraph
Parameters:
child - DOCUMENT ME!
parent - DOCUMENT ME!
Returns:
DOCUMENT ME!

isEdgeMetaParent

public boolean isEdgeMetaParent(int childEdgeInx,
                                int parentNodeInx)
DOCUMENT ME!

Specified by:
isEdgeMetaParent in interface RootGraph
Parameters:
childEdgeInx - DOCUMENT ME!
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

metaParentsList

public List metaParentsList(Edge edge)
DOCUMENT ME!

Specified by:
metaParentsList in interface RootGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getEdgeMetaParentIndicesArray(int)

edgeMetaParentsList

public List edgeMetaParentsList(int edgeInx)
DOCUMENT ME!

Specified by:
edgeMetaParentsList in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getEdgeMetaParentIndicesArray(int)

getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int edgeInx)
DOCUMENT ME!

Specified by:
getEdgeMetaParentIndicesArray in interface RootGraph
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isMetaChild

public boolean isMetaChild(Node parent,
                           Edge child)
DOCUMENT ME!

Specified by:
isMetaChild in interface RootGraph
Parameters:
parent - DOCUMENT ME!
child - DOCUMENT ME!
Returns:
DOCUMENT ME!

isEdgeMetaChild

public boolean isEdgeMetaChild(int parentNodeInx,
                               int childEdgeInx)
DOCUMENT ME!

Specified by:
isEdgeMetaChild in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
childEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(Node node)
DOCUMENT ME!

Specified by:
edgeMetaChildrenList in interface RootGraph
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getEdgeMetaChildIndicesArray(int)

edgeMetaChildrenList

public List edgeMetaChildrenList(int parentNodeInx)
DOCUMENT ME!

Specified by:
edgeMetaChildrenList in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.getEdgeMetaChildIndicesArray(int)

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int parentNodeInx)
DOCUMENT ME!

Specified by:
getEdgeMetaChildIndicesArray in interface RootGraph
Parameters:
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

www.cytoscape.org