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

fing.model
Class FingExtensibleGraphPerspective

java.lang.Object
  extended by fing.model.FingExtensibleGraphPerspective
All Implemented Interfaces:
cytoscape.graph.fixed.FixedGraph, GraphPerspective
Direct Known Subclasses:
FingCyNetwork

public class FingExtensibleGraphPerspective
extends Object

Please try to restrain from using this class. This class was created so that certain legacy applications would have an easier time using this giny.model implementation. Please use FingRootGraphFactory instead of this class.

See Also:
FingRootGraphFactory

Field Summary
 
Fields inherited from interface cytoscape.graph.fixed.FixedGraph
DIRECTED_EDGE, UNDIRECTED_EDGE
 
Constructor Summary
FingExtensibleGraphPerspective(FingExtensibleRootGraph root, IntIterator rootGraphNodeInx, IntIterator rootGraphEdgeInx)
          rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor.
 
Method Summary
 void addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
          DOCUMENT ME!
 Object clone()
          DOCUMENT ME!
 boolean containsEdge(Edge edge)
          DOCUMENT ME!
 boolean containsEdge(Edge edge, boolean recurse)
          DOCUMENT ME!
 boolean containsNode(Node node)
          DOCUMENT ME!
 boolean containsNode(Node node, boolean recurse)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(Filter filter)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(int[] nodeInx)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(int[] rootGraphNodeInx, int[] rootGraphEdgeInx)
          DOCUMENT ME!
 GraphPerspective createGraphPerspective(Node[] nodes, Edge[] edges)
          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!
 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 finalize()
          DOCUMENT ME!
 int[] getAdjacentEdgeIndicesArray(int nodeInx, boolean undirected, boolean incomingDirected, boolean outgoingDirected)
          DOCUMENT ME!
 List getAdjacentEdgesList(Node node, boolean undirected, boolean incoming, boolean outgoing)
          DOCUMENT ME!
 int[] getConnectingEdgeIndicesArray(int[] nodeInx)
          DOCUMENT ME!
 List getConnectingEdges(List nodes)
          DOCUMENT ME!
 int[] getConnectingNodeIndicesArray(int[] edgeInx)
          DOCUMENT ME!
 int getDegree(int nodeInx)
          DOCUMENT ME!
 int getDegree(Node node)
          DOCUMENT ME!
 Edge getEdge(int rootGraphEdgeInx)
          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 getEdgeIndex(int rootGraphEdgeInx)
          DOCUMENT ME!
 int[] getEdgeIndicesArray()
          DOCUMENT ME!
 int[] getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges)
          DOCUMENT ME!
 int[] getEdgeIndicesArray(int rootGraphFromNodeInx, int rootGraphToNodeInx, 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 rootGraphNodeInx)
          DOCUMENT ME!
 int getNodeCount()
          DOCUMENT ME!
 int getNodeIndex(int rootGraphNodeInx)
          DOCUMENT ME!
 int[] getNodeIndicesArray()
          DOCUMENT ME!
 int[] getNodeMetaChildIndicesArray(int parentInx)
          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!
 RootGraph getRootGraph()
          DOCUMENT ME!
 int getRootGraphEdgeIndex(int rootGraphEdgeInx)
          DOCUMENT ME!
 int getRootGraphNodeIndex(int rootGraphNodeInx)
          DOCUMENT ME!
 Edge hideEdge(Edge edge)
          DOCUMENT ME!
 int hideEdge(int rootGraphEdgeInx)
          DOCUMENT ME!
 int[] hideEdges(int[] rootGraphEdgeInx)
          DOCUMENT ME!
 List hideEdges(List edges)
          DOCUMENT ME!
 int hideNode(int rootGraphNodeInx)
          DOCUMENT ME!
 Node hideNode(Node node)
          DOCUMENT ME!
 int[] hideNodes(int[] rootGraphNodeInx)
          DOCUMENT ME!
 List hideNodes(List nodes)
          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 isNodeMetaParent(int childNodeInx, int parentNodeInx)
          DOCUMENT ME!
 GraphPerspective join(GraphPerspective persp)
          DOCUMENT ME!
 List metaParentsList(Edge edge)
          DOCUMENT ME!
 List metaParentsList(Node node)
          DOCUMENT ME!
 int[] neighborsArray(int nodeIndex)
          DOCUMENT ME!
 List neighborsList(Node node)
          DOCUMENT ME!
 boolean nodeExists(int node)
          DOCUMENT ME!
 List nodeMetaChildrenList(int parentInx)
          DOCUMENT ME!
 List nodeMetaChildrenList(Node node)
          DOCUMENT ME!
 List nodeMetaParentsList(int nodeInx)
          DOCUMENT ME!
 IntEnumerator nodes()
          DOCUMENT ME!
 Iterator nodesIterator()
          DOCUMENT ME!
 List nodesList()
          DOCUMENT ME!
 void removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
          DOCUMENT ME!
 Edge restoreEdge(Edge edge)
          DOCUMENT ME!
 int restoreEdge(int rootGraphEdgeInx)
          DOCUMENT ME!
 int[] restoreEdges(int[] rootGraphEdgeInx)
          DOCUMENT ME!
 List restoreEdges(List edges)
          DOCUMENT ME!
 int restoreNode(int rootGraphNodeInx)
          DOCUMENT ME!
 Node restoreNode(Node node)
          DOCUMENT ME!
 int[] restoreNodes(int[] rootGraphNodeInx)
          DOCUMENT ME!
 int[] restoreNodes(int[] rootGraphNodeInx, boolean restoreIncidentEdges)
          DOCUMENT ME!
 List restoreNodes(List nodes)
          DOCUMENT ME!
 List restoreNodes(List nodes, boolean restoreIncidentEdges)
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FingExtensibleGraphPerspective

public FingExtensibleGraphPerspective(FingExtensibleRootGraph root,
                                      IntIterator rootGraphNodeInx,
                                      IntIterator rootGraphEdgeInx)
rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor. If any index does not correspond to an existing node or edge, an IllegalArgumentException is thrown. The indices lists need not be non-repeating - the logic in this constructor handles duplicate filtering.

Method Detail

nodes

public IntEnumerator nodes()
DOCUMENT ME!

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.fixed.FixedGraph
Returns:
DOCUMENT ME!

nodeExists

public boolean nodeExists(int node)
DOCUMENT ME!

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.fixed.FixedGraph
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeSource

public int edgeSource(int edge)
DOCUMENT ME!

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.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.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.fixed.FixedGraph
Parameters:
node0 - DOCUMENT ME!
node1 - DOCUMENT ME!
outgoing - DOCUMENT ME!
incoming - DOCUMENT ME!
undirected - DOCUMENT ME!
Returns:
DOCUMENT ME!

addGraphPerspectiveChangeListener

public void addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
DOCUMENT ME!

Specified by:
addGraphPerspectiveChangeListener in interface GraphPerspective
Parameters:
listener - DOCUMENT ME!

removeGraphPerspectiveChangeListener

public void removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
DOCUMENT ME!

Specified by:
removeGraphPerspectiveChangeListener in interface GraphPerspective
Parameters:
listener - DOCUMENT ME!

clone

public Object clone()
DOCUMENT ME!

Specified by:
clone in interface GraphPerspective
Overrides:
clone in class Object
Returns:
DOCUMENT ME!

getRootGraph

public RootGraph getRootGraph()
DOCUMENT ME!

Specified by:
getRootGraph in interface GraphPerspective
Returns:
DOCUMENT ME!

getNodeCount

public int getNodeCount()
DOCUMENT ME!

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

getEdgeCount

public int getEdgeCount()
DOCUMENT ME!

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

nodesIterator

public Iterator nodesIterator()
DOCUMENT ME!

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

nodesList

public List nodesList()
DOCUMENT ME!

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

getNodeIndicesArray

public int[] getNodeIndicesArray()
DOCUMENT ME!

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

edgesIterator

public Iterator edgesIterator()
DOCUMENT ME!

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

edgesList

public List edgesList()
DOCUMENT ME!

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

getEdgeIndicesArray

public int[] getEdgeIndicesArray()
DOCUMENT ME!

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

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int rootGraphFromNodeInx,
                                 int rootGraphToNodeInx,
                                 boolean undirectedEdges,
                                 boolean bothDirections)
DOCUMENT ME!

Specified by:
getEdgeIndicesArray in interface GraphPerspective
Parameters:
rootGraphFromNodeInx - DOCUMENT ME!
rootGraphToNodeInx - DOCUMENT ME!
undirectedEdges - DOCUMENT ME!
bothDirections - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

hideNode

public Node hideNode(Node node)
DOCUMENT ME!

Specified by:
hideNode in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

hideNode

public int hideNode(int rootGraphNodeInx)
DOCUMENT ME!

Specified by:
hideNode in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

hideNodes

public List hideNodes(List nodes)
DOCUMENT ME!

Specified by:
hideNodes in interface GraphPerspective
Parameters:
nodes - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.hideNode(Node), GraphPerspective.hideNodes(int[])

hideNodes

public int[] hideNodes(int[] rootGraphNodeInx)
DOCUMENT ME!

Specified by:
hideNodes in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreNode

public Node restoreNode(Node node)
DOCUMENT ME!

Specified by:
restoreNode in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreNode

public int restoreNode(int rootGraphNodeInx)
DOCUMENT ME!

Specified by:
restoreNode in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreNodes

public List restoreNodes(List nodes)
DOCUMENT ME!

Specified by:
restoreNodes in interface GraphPerspective
Parameters:
nodes - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.restoreNode(Node), GraphPerspective.restoreNodes(int[])

restoreNodes

public List restoreNodes(List nodes,
                         boolean restoreIncidentEdges)
DOCUMENT ME!

Specified by:
restoreNodes in interface GraphPerspective
Parameters:
nodes - DOCUMENT ME!
restoreIncidentEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.restoreNodes(int[]), GraphPerspective.restoreEdges(int[]), RootGraph.getConnectingEdgeIndicesArray(int[])

restoreNodes

public int[] restoreNodes(int[] rootGraphNodeInx,
                          boolean restoreIncidentEdges)
DOCUMENT ME!

Specified by:
restoreNodes in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
restoreIncidentEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.restoreNodes(int[]), GraphPerspective.restoreEdges(int[]), RootGraph.getConnectingEdgeIndicesArray(int[])

restoreNodes

public int[] restoreNodes(int[] rootGraphNodeInx)
DOCUMENT ME!

Specified by:
restoreNodes in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

hideEdge

public Edge hideEdge(Edge edge)
DOCUMENT ME!

Specified by:
hideEdge in interface GraphPerspective
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

hideEdge

public int hideEdge(int rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
hideEdge in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

hideEdges

public List hideEdges(List edges)
DOCUMENT ME!

Specified by:
hideEdges in interface GraphPerspective
Parameters:
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.hideEdge(Edge), GraphPerspective.hideEdges(int[])

hideEdges

public int[] hideEdges(int[] rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
hideEdges in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreEdge

public Edge restoreEdge(Edge edge)
DOCUMENT ME!

Specified by:
restoreEdge in interface GraphPerspective
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreEdge

public int restoreEdge(int rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
restoreEdge in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

restoreEdges

public List restoreEdges(List edges)
DOCUMENT ME!

Specified by:
restoreEdges in interface GraphPerspective
Parameters:
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.restoreEdges(int[])

restoreEdges

public int[] restoreEdges(int[] rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
restoreEdges in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

containsNode

public boolean containsNode(Node node)
DOCUMENT ME!

Specified by:
containsNode in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.containsNode(Node, boolean)

containsNode

public boolean containsNode(Node node,
                            boolean recurse)
DOCUMENT ME!

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

containsEdge

public boolean containsEdge(Edge edge)
DOCUMENT ME!

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

containsEdge

public boolean containsEdge(Edge edge,
                            boolean recurse)
DOCUMENT ME!

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

join

public GraphPerspective join(GraphPerspective persp)
DOCUMENT ME!

Specified by:
join in interface GraphPerspective
Parameters:
persp - DOCUMENT ME!
Returns:
DOCUMENT ME!

createGraphPerspective

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

Specified by:
createGraphPerspective in interface GraphPerspective
Parameters:
nodes - DOCUMENT ME!
edges - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.createGraphPerspective(int[], int[])

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] rootGraphNodeInx,
                                               int[] rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
createGraphPerspective in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
RootGraph.createGraphPerspective(int[], int[])

createGraphPerspective

public GraphPerspective createGraphPerspective(Filter filter)
DOCUMENT ME!

Specified by:
createGraphPerspective in interface GraphPerspective
Parameters:
filter - DOCUMENT ME!
Returns:
DOCUMENT ME!

neighborsList

public List neighborsList(Node node)
DOCUMENT ME!

Specified by:
neighborsList in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.neighborsArray(int)

neighborsArray

public int[] neighborsArray(int nodeIndex)
DOCUMENT ME!

Specified by:
neighborsArray in interface GraphPerspective
Parameters:
nodeIndex - DOCUMENT ME!
Returns:
DOCUMENT ME!

isNeighbor

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

Specified by:
isNeighbor in interface GraphPerspective
Parameters:
a - DOCUMENT ME!
b - DOCUMENT ME!
Returns:
DOCUMENT ME!

isNeighbor

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

Specified by:
isNeighbor in interface GraphPerspective
Parameters:
nodeInxA - DOCUMENT ME!
nodeInxB - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeExists

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

Specified by:
edgeExists in interface GraphPerspective
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeExists

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

Specified by:
edgeExists in interface GraphPerspective
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeCount

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

Specified by:
getEdgeCount in interface GraphPerspective
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeCount

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

Specified by:
getEdgeCount in interface GraphPerspective
Parameters:
fromNodeInx - DOCUMENT ME!
toNodeInx - DOCUMENT ME!
countUndirectedEdges - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgesList

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

Specified by:
edgesList in interface GraphPerspective
Parameters:
from - DOCUMENT ME!
to - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgesList

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

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

getEdgeIndicesArray

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

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

getInDegree

public int getInDegree(Node node)
DOCUMENT ME!

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

getInDegree

public int getInDegree(int nodeInx)
DOCUMENT ME!

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

getInDegree

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

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

getOutDegree

public int getOutDegree(Node node)
DOCUMENT ME!

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

getOutDegree

public int getOutDegree(int nodeInx)
DOCUMENT ME!

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

getOutDegree

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

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

getDegree

public int getDegree(Node node)
DOCUMENT ME!

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

getDegree

public int getDegree(int nodeInx)
DOCUMENT ME!

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

getIndex

public int getIndex(Node node)
DOCUMENT ME!

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

getNodeIndex

public int getNodeIndex(int rootGraphNodeInx)
DOCUMENT ME!

Specified by:
getNodeIndex in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.getRootGraphNodeIndex(int)

getRootGraphNodeIndex

public int getRootGraphNodeIndex(int rootGraphNodeInx)
DOCUMENT ME!

Specified by:
getRootGraphNodeIndex in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNode

public Node getNode(int rootGraphNodeInx)
DOCUMENT ME!

Specified by:
getNode in interface GraphPerspective
Parameters:
rootGraphNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getIndex

public int getIndex(Edge edge)
DOCUMENT ME!

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

getEdgeIndex

public int getEdgeIndex(int rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
getEdgeIndex in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.getRootGraphEdgeIndex(int)

getRootGraphEdgeIndex

public int getRootGraphEdgeIndex(int rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
getRootGraphEdgeIndex in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdge

public Edge getEdge(int rootGraphEdgeInx)
DOCUMENT ME!

Specified by:
getEdge in interface GraphPerspective
Parameters:
rootGraphEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeSourceIndex

public int getEdgeSourceIndex(int edgeInx)
DOCUMENT ME!

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

getEdgeTargetIndex

public int getEdgeTargetIndex(int edgeInx)
DOCUMENT ME!

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

isEdgeDirected

public boolean isEdgeDirected(int edgeInx)
DOCUMENT ME!

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

isMetaParent

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

Specified by:
isMetaParent in interface GraphPerspective
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 GraphPerspective
Parameters:
childNodeInx - DOCUMENT ME!
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

metaParentsList

public List metaParentsList(Node node)
DOCUMENT ME!

Specified by:
metaParentsList in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

nodeMetaParentsList

public List nodeMetaParentsList(int nodeInx)
DOCUMENT ME!

Specified by:
nodeMetaParentsList in interface GraphPerspective
Parameters:
nodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNodeMetaParentIndicesArray

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

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

isMetaChild

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

Specified by:
isMetaChild in interface GraphPerspective
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 GraphPerspective
Parameters:
parentNodeInx - DOCUMENT ME!
childNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(Node node)
DOCUMENT ME!

Specified by:
nodeMetaChildrenList in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(int parentInx)
DOCUMENT ME!

Specified by:
nodeMetaChildrenList in interface GraphPerspective
Parameters:
parentInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getNodeMetaChildIndicesArray

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

Specified by:
getNodeMetaChildIndicesArray in interface GraphPerspective
Parameters:
parentInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

isMetaParent

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

Specified by:
isMetaParent in interface GraphPerspective
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 GraphPerspective
Parameters:
childEdgeInx - DOCUMENT ME!
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

metaParentsList

public List metaParentsList(Edge edge)
DOCUMENT ME!

Specified by:
metaParentsList in interface GraphPerspective
Parameters:
edge - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeMetaParentsList

public List edgeMetaParentsList(int edgeInx)
DOCUMENT ME!

Specified by:
edgeMetaParentsList in interface GraphPerspective
Parameters:
edgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeMetaParentIndicesArray

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

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

isMetaChild

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

Specified by:
isMetaChild in interface GraphPerspective
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 GraphPerspective
Parameters:
parentNodeInx - DOCUMENT ME!
childEdgeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(Node node)
DOCUMENT ME!

Specified by:
edgeMetaChildrenList in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
Returns:
DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(int parentNodeInx)
DOCUMENT ME!

Specified by:
edgeMetaChildrenList in interface GraphPerspective
Parameters:
parentNodeInx - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEdgeMetaChildIndicesArray

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

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

getAdjacentEdgesList

public List getAdjacentEdgesList(Node node,
                                 boolean undirected,
                                 boolean incoming,
                                 boolean outgoing)
DOCUMENT ME!

Specified by:
getAdjacentEdgesList in interface GraphPerspective
Parameters:
node - DOCUMENT ME!
undirected - DOCUMENT ME!
incoming - DOCUMENT ME!
outgoing - DOCUMENT ME!
Returns:
DOCUMENT ME!
See Also:
GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getAdjacentEdgeIndicesArray

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

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

getConnectingEdges

public List getConnectingEdges(List nodes)
DOCUMENT ME!

Specified by:
getConnectingEdges in interface GraphPerspective
Parameters:
nodes - DOCUMENT ME!
Returns:
DOCUMENT ME!

getConnectingEdgeIndicesArray

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

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

getConnectingNodeIndicesArray

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

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

createGraphPerspective

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

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

finalize

public void finalize()
DOCUMENT ME!

Overrides:
finalize in class Object

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