org.gersteinlab.tyna.core.graph
Class UndirectedSimpleGraph

java.lang.Object
  org.gersteinlab.tyna.core.graph.AbstractGraph
      org.gersteinlab.tyna.core.graph.AbstractSimpleGraph
          org.gersteinlab.tyna.core.graph.UndirectedSimpleGraph

All Implemented Interfaces:

AdvancedGraph, AdvancedUndirectedGraph, Graph, java.io.Serializable, SimpleGraph, UndirectedGraph

public class UndirectedSimpleGraph

extends AbstractSimpleGraph

implements AdvancedUndirectedGraph

	This class represents an undirected simple graph. See UndirectedGraph
	and SimpleGraph for definitions.
	

Version:

1.0 (September 20, 2005) Change History: 1.0 - Initial version

Author:

Kevin Yuk-Lap Yip

See Also:

Serialized Form

Nested Class Summary

protected class

UndirectedSimpleGraph.UndirectedSimpleGraphEdgeIterator

Nested classes inherited from class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph

AbstractSimpleGraph.AbstractSimpleGraphEdgeIterator

Nested classes inherited from class org.gersteinlab.tyna.core.graph.AbstractGraph

AbstractGraph.AbstractGraphEdgeIterator, AbstractGraph.AbstractGraphNodeIterator, AbstractGraph.BetweennessNode, AbstractGraph.DuplicateTree, AbstractGraph.HeadTailTree, AbstractGraph.HeadTree, AbstractGraph.TailTree

Field Summary

Fields inherited from class org.gersteinlab.tyna.core.graph.AbstractGraph

attrs, edgeCount, edges, lastModified, nodes, revEdges

Constructor Summary

UndirectedSimpleGraph()
Default constructor: creates an empty graph.

UndirectedSimpleGraph(Graph graph)

Method Summary

java.util.List	getDefectiveCliquesMissingEdges(int k, int l) Get the missing edges in defective cliques formed by two cliques with .
int	getDegree(Node node) Get the degree of a node.
java.util.Map	getDegrees() Get the degrees of all nodes in the graph.
double[][]	getDiffusionSimilarityMatrix(double beta, int[][] negLaplacianMatrix) Get the diffusion similarity matrix of a subgraph according to a given Laplacian matrix.
double[][]	getDiffusionSimilarityMatrix(double beta, java.util.List nodeList) Get the diffusion similarity matrix of a subgraph according to a given node order.
EdgeIterator	getEdgeIterator() Return an iterator of the edges in the graph.
java.util.List	getEdges(Node node) Get the edges incident on a node.
java.util.List	getMaximalCliques() Get all maximal cliques
java.util.List	getMaximalIndependentSets() Get all maximal independent sets
int[][]	getNegativeLaplacianMatrix(int[][] adjacencyMatrix) Get the Laplacian matrix of a subgraph according to a given adjacency matrix.
int[][]	getNegativeLaplacianMatrix(java.util.List nodeList) Get the negation of the Laplacian matrix of a subgraph according to a given node order.
java.util.Set	getNeighbors(Node node) Get the neighbors of a node.

Methods inherited from class org.gersteinlab.tyna.core.graph.AbstractSimpleGraph

addEdge, getInDegree, getInEdges, getOutDegree, getOutEdges

Methods inherited from class org.gersteinlab.tyna.core.graph.AbstractGraph

accumulateLocalBetweenness, addNode, checkEdge, checkNode, computeLocalBetweenness, containsEdge, containsNode, eigSym, getAdjacencyMatrix, getAllUnweightedShortestPaths, getAllUnweightedShortestPaths, getAllUnweightedShortestPaths, getAttr, getAttrs, getBetweenness, getBetweennesses, getClusCoef, getClusCoefs, getConnectedComponentCount, getConnectedComponents, getCycles, getCycles, getEccentricities, getEccentricity, getEdgeBetweennesses, getEdgeCount, getEdgeNodePairs, getFeedforwardLoops, getFeedforwardLoops, getInDegrees, getInNeighbors, getMaximalChains, getMaximalCompleteTwoLayerSubgraphs, getMinimalChains, getNode, getNodeCount, getNodeIterator, getOutDegrees, getOutNeighbors, getUnweightedShortestPath, getUnweightedShortestPathLength, getUnweightedShortestPathLengths, getUnweightedShortestPathLengths, getUnweightedShortestPaths, getUnweightedShortestPaths, getUnweightedShortestPaths, getUnweightedShortestPaths, markModified, saveGraph, setAttr

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.gersteinlab.tyna.core.graph.Graph

addEdge, addNode, containsEdge, containsNode, getAttr, getAttrs, getEdgeCount, getEdgeNodePairs, getNode, getNodeCount, getNodeIterator, setAttr

Constructor Detail

UndirectedSimpleGraph

public UndirectedSimpleGraph()

Default constructor: creates an empty graph.

UndirectedSimpleGraph

public UndirectedSimpleGraph(Graph graph)
                      throws GraphTypeException

See Also:

AbstractGraph.AbstractGraph(Graph)

Method Detail

getEdgeIterator

public EdgeIterator getEdgeIterator()

Description copied from interface: Graph

Return an iterator of the edges in the graph. Unless otherwise specified by the implemented class, the edge order in the returned iterator needs not be predictable from the order in which the edges are added and/or removed.

Specified by:

getEdgeIterator in interface Graph

Returns:

The iterator

getDegree

public int getDegree(Node node)
              throws java.lang.IllegalArgumentException,
                     java.lang.NullPointerException

Description copied from interface: UndirectedGraph

Get the degree of a node.

Specified by:

getDegree in interface UndirectedGraph

Overrides:

getDegree in class AbstractGraph

Throws:

java.lang.IllegalArgumentException

java.lang.NullPointerException

See Also:

UndirectedGraph.getDegree(Node)

getDegrees

public java.util.Map getDegrees()

Description copied from interface: UndirectedGraph

Get the degrees of all nodes in the graph.

Specified by:

getDegrees in interface UndirectedGraph

Overrides:

getDegrees in class AbstractGraph

See Also:

UndirectedGraph.getDegrees()

getEdges

public java.util.List getEdges(Node node)
                        throws java.lang.IllegalArgumentException,
                               java.lang.NullPointerException

Description copied from interface: UndirectedGraph

Get the edges incident on a node.

Specified by:

getEdges in interface UndirectedGraph

Overrides:

getEdges in class AbstractGraph

Throws:

java.lang.IllegalArgumentException

java.lang.NullPointerException

See Also:

UndirectedGraph.getDegree(Node)

getNeighbors

public java.util.Set getNeighbors(Node node)
                           throws java.lang.IllegalArgumentException,
                                  java.lang.NullPointerException

Description copied from interface: UndirectedGraph

Get the neighbors of a node.

Specified by:

getNeighbors in interface UndirectedGraph

Overrides:

getNeighbors in class AbstractGraph

Throws:

java.lang.IllegalArgumentException

java.lang.NullPointerException

See Also:

UndirectedGraph.getDegree(Node)

getNegativeLaplacianMatrix

public int[][] getNegativeLaplacianMatrix(java.util.List nodeList)

Description copied from interface: AdvancedUndirectedGraph

Get the negation of the Laplacian matrix of a subgraph according to a given node order.

Specified by:

getNegativeLaplacianMatrix in interface AdvancedUndirectedGraph

Overrides:

getNegativeLaplacianMatrix in class AbstractGraph

See Also:

AdvancedUndirectedGraph.getNegativeLaplacianMatrix(List)

getNegativeLaplacianMatrix

public int[][] getNegativeLaplacianMatrix(int[][] adjacencyMatrix)

Description copied from interface: AdvancedUndirectedGraph

Get the Laplacian matrix of a subgraph according to a given adjacency matrix.

Specified by:

getNegativeLaplacianMatrix in interface AdvancedUndirectedGraph

Overrides:

getNegativeLaplacianMatrix in class AbstractGraph

See Also:

AdvancedUndirectedGraph.getNegativeLaplacianMatrix(int[][])

getDiffusionSimilarityMatrix

public double[][] getDiffusionSimilarityMatrix(double beta,
                                               java.util.List nodeList)
                                        throws JSci.maths.MaximumIterationsExceededException

Description copied from interface: AdvancedUndirectedGraph

Get the diffusion similarity matrix of a subgraph according to a given node order.

Specified by:

getDiffusionSimilarityMatrix in interface AdvancedUndirectedGraph

Overrides:

getDiffusionSimilarityMatrix in class AbstractGraph

Throws:

JSci.maths.MaximumIterationsExceededException - If the eigen problem cannot be solved in a predefined number of iterations

See Also:

AdvancedUndirectedGraph.getDiffusionSimilarityMatrix(double, List)

getDiffusionSimilarityMatrix

public double[][] getDiffusionSimilarityMatrix(double beta,
                                               int[][] negLaplacianMatrix)
                                        throws JSci.maths.MaximumIterationsExceededException

Description copied from interface: AdvancedUndirectedGraph

Get the diffusion similarity matrix of a subgraph according to a given Laplacian matrix.

Specified by:

getDiffusionSimilarityMatrix in interface AdvancedUndirectedGraph

Overrides:

getDiffusionSimilarityMatrix in class AbstractGraph

Throws:

JSci.maths.MaximumIterationsExceededException - If the eigen problem cannot be solved in a predefined number of iterations

See Also:

AdvancedUndirectedGraph.getDiffusionSimilarityMatrix(double, int[][])

getMaximalIndependentSets

public java.util.List getMaximalIndependentSets()

Description copied from interface: AdvancedUndirectedGraph

Get all maximal independent sets

Specified by:

getMaximalIndependentSets in interface AdvancedUndirectedGraph

Overrides:

getMaximalIndependentSets in class AbstractGraph

See Also:

AdvancedUndirectedGraph.getMaximalIndependentSets()

getMaximalCliques

public java.util.List getMaximalCliques()

Description copied from interface: AdvancedUndirectedGraph

Get all maximal cliques

Specified by:

getMaximalCliques in interface AdvancedUndirectedGraph

Overrides:

getMaximalCliques in class AbstractGraph

See Also:

AdvancedUndirectedGraph.getMaximalCliques()

getDefectiveCliquesMissingEdges

public java.util.List getDefectiveCliquesMissingEdges(int k,
                                                      int l)
                                               throws java.lang.IllegalArgumentException

Description copied from interface: AdvancedUndirectedGraph

Get the missing edges in defective cliques formed by two cliques with . At least k vertices in common . At most l vertices not in common

Specified by:

getDefectiveCliquesMissingEdges in interface AdvancedUndirectedGraph

Overrides:

getDefectiveCliquesMissingEdges in class AbstractGraph

Throws:

java.lang.IllegalArgumentException

See Also:

AdvancedUndirectedGraph.getDefectiveCliquesMissingEdges(int, int)