fing.model
Class FingExtensibleGraphPerspective

java.lang.Object
  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()

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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()

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Specified by:

nodesIterator in interface GraphPerspective

Returns:

DOCUMENT ME!

nodesList

public List nodesList()

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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()

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Specified by:

edgesList in interface GraphPerspective

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.edgesIterator()

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

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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)

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Specified by:

restoreEdges in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

containsNode

public boolean containsNode(Node node)

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Specified by:

containsNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

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See Also:

GraphPerspective.containsNode(Node, boolean)

containsNode

public boolean containsNode(Node node,
                            boolean recurse)

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Specified by:

containsNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

recurse - DOCUMENT ME!

Returns:

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containsEdge

public boolean containsEdge(Edge edge)

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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:

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join

public GraphPerspective join(GraphPerspective persp)

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Specified by:

join in interface GraphPerspective

Parameters:

persp - DOCUMENT ME!

Returns:

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createGraphPerspective

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

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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)

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Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

rootGraphEdgeInx - DOCUMENT ME!

Returns:

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See Also:

RootGraph.createGraphPerspective(int[], int[])

createGraphPerspective

public GraphPerspective createGraphPerspective(Filter filter)

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Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

filter - DOCUMENT ME!

Returns:

DOCUMENT ME!

neighborsList

public List neighborsList(Node node)

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Specified by:

neighborsList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.neighborsArray(int)

neighborsArray

public int[] neighborsArray(int nodeIndex)

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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)

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Specified by:

getRootGraphNodeIndex in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNode

public Node getNode(int rootGraphNodeInx)

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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)

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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)

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Specified by:

getEdgeSourceIndex in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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getEdgeTargetIndex

public int getEdgeTargetIndex(int edgeInx)

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Specified by:

getEdgeTargetIndex in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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isEdgeDirected

public boolean isEdgeDirected(int edgeInx)

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Specified by:

isEdgeDirected in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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isMetaParent

public boolean isMetaParent(Node child,
                            Node parent)

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Specified by:

isMetaParent in interface GraphPerspective

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

DOCUMENT ME!

isNodeMetaParent

public boolean isNodeMetaParent(int childNodeInx,
                                int parentNodeInx)

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Specified by:

isNodeMetaParent in interface GraphPerspective

Parameters:

childNodeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

metaParentsList

public List metaParentsList(Node node)

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Specified by:

metaParentsList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

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nodeMetaParentsList

public List nodeMetaParentsList(int nodeInx)

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Specified by:

nodeMetaParentsList in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int nodeInx)

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Specified by:

getNodeMetaParentIndicesArray in interface GraphPerspective

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 GraphPerspective

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 GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(Node node)

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Specified by:

nodeMetaChildrenList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

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nodeMetaChildrenList

public List nodeMetaChildrenList(int parentInx)

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Specified by:

nodeMetaChildrenList in interface GraphPerspective

Parameters:

parentInx - DOCUMENT ME!

Returns:

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getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentInx)

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Specified by:

getNodeMetaChildIndicesArray in interface GraphPerspective

Parameters:

parentInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaParent

public boolean isMetaParent(Edge child,
                            Node parent)

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Specified by:

isMetaParent in interface GraphPerspective

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

DOCUMENT ME!

isEdgeMetaParent

public boolean isEdgeMetaParent(int childEdgeInx,
                                int parentNodeInx)

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Specified by:

isEdgeMetaParent in interface GraphPerspective

Parameters:

childEdgeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

metaParentsList

public List metaParentsList(Edge edge)

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Specified by:

metaParentsList in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

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edgeMetaParentsList

public List edgeMetaParentsList(int edgeInx)

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Specified by:

edgeMetaParentsList in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int edgeInx)

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Specified by:

getEdgeMetaParentIndicesArray in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaChild

public boolean isMetaChild(Node parent,
                           Edge child)

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Specified by:

isMetaChild in interface GraphPerspective

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

DOCUMENT ME!

isEdgeMetaChild

public boolean isEdgeMetaChild(int parentNodeInx,
                               int childEdgeInx)

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Specified by:

isEdgeMetaChild in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

childEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(Node node)

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Specified by:

edgeMetaChildrenList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(int parentNodeInx)

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Specified by:

edgeMetaChildrenList in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int parentNodeInx)

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Specified by:

getEdgeMetaChildIndicesArray in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

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getAdjacentEdgesList

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

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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)

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Specified by:

getAdjacentEdgeIndicesArray in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

undirected - DOCUMENT ME!

incomingDirected - DOCUMENT ME!

outgoingDirected - DOCUMENT ME!

Returns:

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getConnectingEdges

public List getConnectingEdges(List nodes)

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Specified by:

getConnectingEdges in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

Returns:

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getConnectingEdgeIndicesArray

public int[] getConnectingEdgeIndicesArray(int[] nodeInx)

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Specified by:

getConnectingEdgeIndicesArray in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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getConnectingNodeIndicesArray

public int[] getConnectingNodeIndicesArray(int[] edgeInx)

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Specified by:

getConnectingNodeIndicesArray in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

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See Also:

GraphPerspective.getEdgeSourceIndex(int), GraphPerspective.getEdgeTargetIndex(int)

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] nodeInx)

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Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

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finalize

public void finalize()

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Overrides:

finalize in class Object