fr.curie.BiNoM.pathways.analysis.structure
Class StructureAnalysisUtils

java.lang.Object
  fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils

public class StructureAnalysisUtils
extends java.lang.Object

Connector class between GraphAlgorithms and BiographUtils and Cytoscape interface

Nested Class Summary

static class

StructureAnalysisUtils.Option Options container

Constructor Summary

StructureAnalysisUtils()

Method Summary

static java.util.Set<java.lang.String>	findPaths(edu.rpi.cs.xgmml.GraphDocument network, java.util.Vector<java.lang.String> sources, java.util.Vector<java.lang.String> targets, StructureAnalysisUtils.Option options)
static java.util.Set<java.lang.String>	findPaths(Graph network, java.util.Vector<java.lang.String> sources, java.util.Vector<java.lang.String> targets, StructureAnalysisUtils.Option options)
static java.util.Vector<edu.rpi.cs.xgmml.GraphDocument>	getClusteredNetworks(java.util.Vector<edu.rpi.cs.xgmml.GraphDocument> networks, float intersectionThreshold)
static java.util.Vector	getConnectedComponents(edu.rpi.cs.xgmml.GraphDocument graph)
static java.util.Vector	getCyclicComponents(edu.rpi.cs.xgmml.GraphDocument graph, StructureAnalysisUtils.Option options)
static java.util.Vector	getMaterialComponents(edu.rpi.cs.xgmml.GraphDocument graph)
static edu.rpi.cs.xgmml.GraphDocument	getModularView(edu.rpi.cs.xgmml.GraphDocument graph, java.util.Vector<edu.rpi.cs.xgmml.GraphDocument> modules, boolean showIntersections, boolean nodeIntersectionView)
static java.util.Vector	getPrunedGraph(edu.rpi.cs.xgmml.GraphDocument graph, boolean includeInterface)
static java.util.Vector	getStronglyConnectedComponents(edu.rpi.cs.xgmml.GraphDocument graph)

Methods inherited from class java.lang.Object

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

Constructor Detail

StructureAnalysisUtils

public StructureAnalysisUtils()

Method Detail

getPrunedGraph

public static java.util.Vector getPrunedGraph(edu.rpi.cs.xgmml.GraphDocument graph,
                                              boolean includeInterface)

getStronglyConnectedComponents

public static java.util.Vector getStronglyConnectedComponents(edu.rpi.cs.xgmml.GraphDocument graph)

getConnectedComponents

public static java.util.Vector getConnectedComponents(edu.rpi.cs.xgmml.GraphDocument graph)

getMaterialComponents

public static java.util.Vector getMaterialComponents(edu.rpi.cs.xgmml.GraphDocument graph)

getCyclicComponents

public static java.util.Vector getCyclicComponents(edu.rpi.cs.xgmml.GraphDocument graph,
                                                   StructureAnalysisUtils.Option options)

getModularView

public static edu.rpi.cs.xgmml.GraphDocument getModularView(edu.rpi.cs.xgmml.GraphDocument graph,
                                                            java.util.Vector<edu.rpi.cs.xgmml.GraphDocument> modules,
                                                            boolean showIntersections,
                                                            boolean nodeIntersectionView)

getClusteredNetworks

public static java.util.Vector<edu.rpi.cs.xgmml.GraphDocument> getClusteredNetworks(java.util.Vector<edu.rpi.cs.xgmml.GraphDocument> networks,
                                                                                    float intersectionThreshold)

findPaths

public static java.util.Set<java.lang.String> findPaths(edu.rpi.cs.xgmml.GraphDocument network,
                                                        java.util.Vector<java.lang.String> sources,
                                                        java.util.Vector<java.lang.String> targets,
                                                        StructureAnalysisUtils.Option options)

findPaths

public static java.util.Set<java.lang.String> findPaths(Graph network,
                                                        java.util.Vector<java.lang.String> sources,
                                                        java.util.Vector<java.lang.String> targets,
                                                        StructureAnalysisUtils.Option options)