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, 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)

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Specified by:

getInDegree in interface RootGraph

Parameters:

node - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

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getInDegree

public int getInDegree(int nodeInx,
                       boolean countUndirectedEdges)

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Specified by:

getInDegree in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

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getOutDegree

public int getOutDegree(Node node)

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Specified by:

getOutDegree in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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getOutDegree

public int getOutDegree(int nodeInx)

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Specified by:

getOutDegree in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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getOutDegree

public int getOutDegree(Node node,
                        boolean countUndirectedEdges)

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Specified by:

getOutDegree in interface RootGraph

Parameters:

node - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

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getOutDegree

public int getOutDegree(int nodeInx,
                        boolean countUndirectedEdges)

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Specified by:

getOutDegree in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

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getDegree

public int getDegree(Node node)

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Specified by:

getDegree in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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getDegree

public int getDegree(int nodeInx)

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Specified by:

getDegree in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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getIndex

public int getIndex(Node node)

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Specified by:

getIndex in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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getNode

public Node getNode(int nodeInx)

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Specified by:

getNode in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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getIndex

public int getIndex(Edge edge)

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Specified by:

getIndex in interface RootGraph

Parameters:

edge - DOCUMENT ME!

Returns:

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getEdge

public Edge getEdge(int edgeInx)

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Specified by:

getEdge in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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getEdgeSourceIndex

public int getEdgeSourceIndex(int edgeInx)

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Specified by:

getEdgeSourceIndex in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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getEdgeTargetIndex

public int getEdgeTargetIndex(int edgeInx)

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Specified by:

getEdgeTargetIndex in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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isEdgeDirected

public boolean isEdgeDirected(int edgeInx)

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Specified by:

isEdgeDirected in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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addMetaChild

public boolean addMetaChild(Node parent,
                            Node child)

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Specified by:

addMetaChild in interface RootGraph

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

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addNodeMetaChild

public boolean addNodeMetaChild(int parentNodeInx,
                                int childNodeInx)

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Specified by:

addNodeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

Returns:

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removeNodeMetaChild

public boolean removeNodeMetaChild(int parentNodeInx,
                                   int childNodeInx)

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Specified by:

removeNodeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

Returns:

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isMetaParent

public boolean isMetaParent(Node child,
                            Node parent)

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Specified by:

isMetaParent in interface RootGraph

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

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isNodeMetaParent

public boolean isNodeMetaParent(int childNodeInx,
                                int parentNodeInx)

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Specified by:

isNodeMetaParent in interface RootGraph

Parameters:

childNodeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

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metaParentsList

public List metaParentsList(Node node)

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Specified by:

metaParentsList in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getNodeMetaParentIndicesArray(int)

nodeMetaParentsList

public List nodeMetaParentsList(int nodeInx)

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Specified by:

nodeMetaParentsList in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getNodeMetaParentIndicesArray(int)

getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int nodeInx)

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Specified by:

getNodeMetaParentIndicesArray in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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isMetaChild

public boolean isMetaChild(Node parent,
                           Node child)

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Specified by:

isMetaChild in interface RootGraph

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

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isNodeMetaChild

public boolean isNodeMetaChild(int parentNodeInx,
                               int childNodeInx)

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Specified by:

isNodeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

Returns:

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isNodeMetaChild

public boolean isNodeMetaChild(int parentNodeInx,
                               int childNodeInx,
                               boolean recursive)

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Specified by:

isNodeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

recursive - DOCUMENT ME!

Returns:

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nodeMetaChildrenList

public List nodeMetaChildrenList(Node node)

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Specified by:

nodeMetaChildrenList in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getNodeMetaChildIndicesArray(int)

nodeMetaChildrenList

public List nodeMetaChildrenList(int parentNodeInx)

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Specified by:

nodeMetaChildrenList in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

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getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentNodeInx)

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Specified by:

getNodeMetaChildIndicesArray in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

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getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentNodeInx,
                                          boolean recursive)

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Specified by:

getNodeMetaChildIndicesArray in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

recursive - DOCUMENT ME!

Returns:

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getChildlessMetaDescendants

public int[] getChildlessMetaDescendants(int nodeInx)

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Specified by:

getChildlessMetaDescendants in interface RootGraph

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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addMetaChild

public boolean addMetaChild(Node parent,
                            Edge child)

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Specified by:

addMetaChild in interface RootGraph

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

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addEdgeMetaChild

public boolean addEdgeMetaChild(int parentNodeInx,
                                int childEdgeInx)

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Specified by:

addEdgeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childEdgeInx - DOCUMENT ME!

Returns:

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removeEdgeMetaChild

public boolean removeEdgeMetaChild(int parentNodeInx,
                                   int childEdgeInx)

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Specified by:

removeEdgeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childEdgeInx - DOCUMENT ME!

Returns:

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isMetaParent

public boolean isMetaParent(Edge child,
                            Node parent)

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Specified by:

isMetaParent in interface RootGraph

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

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isEdgeMetaParent

public boolean isEdgeMetaParent(int childEdgeInx,
                                int parentNodeInx)

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Specified by:

isEdgeMetaParent in interface RootGraph

Parameters:

childEdgeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

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metaParentsList

public List metaParentsList(Edge edge)

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Specified by:

metaParentsList in interface RootGraph

Parameters:

edge - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getEdgeMetaParentIndicesArray(int)

edgeMetaParentsList

public List edgeMetaParentsList(int edgeInx)

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Specified by:

edgeMetaParentsList in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getEdgeMetaParentIndicesArray(int)

getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int edgeInx)

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Specified by:

getEdgeMetaParentIndicesArray in interface RootGraph

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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isMetaChild

public boolean isMetaChild(Node parent,
                           Edge child)

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Specified by:

isMetaChild in interface RootGraph

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

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isEdgeMetaChild

public boolean isEdgeMetaChild(int parentNodeInx,
                               int childEdgeInx)

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Specified by:

isEdgeMetaChild in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

childEdgeInx - DOCUMENT ME!

Returns:

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edgeMetaChildrenList

public List edgeMetaChildrenList(Node node)

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Specified by:

edgeMetaChildrenList in interface RootGraph

Parameters:

node - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getEdgeMetaChildIndicesArray(int)

edgeMetaChildrenList

public List edgeMetaChildrenList(int parentNodeInx)

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Specified by:

edgeMetaChildrenList in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

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See Also:

RootGraph.getEdgeMetaChildIndicesArray(int)

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int parentNodeInx)

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Specified by:

getEdgeMetaChildIndicesArray in interface RootGraph

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

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