graph_algorithms
Class MetaModuleFinder

java.lang.Object
  graph_algorithms.MetaModuleFinder

public class MetaModuleFinder
extends java.lang.Object

Field Summary

boolean[][]	areModulesFriends
double[][]	DC_graph
java.util.ArrayList<java.lang.String>	geneNames
java.util.LinkedList<MetaModule>	meta_modules
java.util.LinkedList<java.util.HashSet<java.lang.Integer>>	modules

Constructor Summary

MetaModuleFinder(double[][] c, double[][] dc, java.util.ArrayList<java.lang.String> ids)
Constructor

Method Summary

java.util.LinkedList<java.util.LinkedList<java.lang.Integer>>	addSingletonsToModules()
void	calculateMetaGraph()
java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>>	createNeighborsListsInGraph()
void	findSeedPairs()
java.util.LinkedList<ComparableEdge>	getEdgesForAlgo(double likelihoodThresholdForDCA)
void	getFinalSolution(int maxNumClusters, int minSize)
java.util.Hashtable<java.lang.Integer,java.lang.Double>	getWithinSetScores(java.util.Collection<java.lang.Integer> T)
boolean	greedyRemoveNodesFromTwoSides(java.util.Collection<java.lang.Integer> T, java.util.Collection<java.lang.Integer> S) This methods receives as input two distinct sets.
static void	removeCurrentListFromGraph(java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>> neighborsListsInDCAGraph, java.util.HashSet<java.lang.Integer> set)
static void	removeIntersection(java.util.HashSet<java.lang.Integer> neighborsOfU, java.util.HashSet<java.lang.Integer> neighborsOfV)
void	removeZeroDegreesMetaNodes()
void	setLikelihoodThresholdForDC(float likelihoodThresholdForDCA)
static void	sortEdgesByScores(java.util.LinkedList<ComparableEdge> edges, java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>> neighborsListsInDCAGraph) Static auxiliary methods

Methods inherited from class java.lang.Object

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

Field Detail

DC_graph

public double[][] DC_graph

geneNames

public java.util.ArrayList<java.lang.String> geneNames

modules

public java.util.LinkedList<java.util.HashSet<java.lang.Integer>> modules

areModulesFriends

public boolean[][] areModulesFriends

meta_modules

public java.util.LinkedList<MetaModule> meta_modules

Constructor Detail

MetaModuleFinder

public MetaModuleFinder(double[][] c,
                        double[][] dc,
                        java.util.ArrayList<java.lang.String> ids)

Constructor

Parameters:

c - - the consistent correlations graph

dc - - the DC analysis results

ids - - the gene names

Method Detail

greedyRemoveNodesFromTwoSides

public boolean greedyRemoveNodesFromTwoSides(java.util.Collection<java.lang.Integer> T,
                                             java.util.Collection<java.lang.Integer> S)

This methods receives as input two distinct sets. The set elements represent the index of a gene in the matrices. The algorithm greedily tries to remove a gene from T or S until the remaining sets satisfy the meta-module definition.

Parameters:

T -

S -

Returns:

getWithinSetScores

public java.util.Hashtable<java.lang.Integer,java.lang.Double> getWithinSetScores(java.util.Collection<java.lang.Integer> T)

findSeedPairs

public void findSeedPairs()

createNeighborsListsInGraph

public java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>> createNeighborsListsInGraph()

getEdgesForAlgo

public java.util.LinkedList<ComparableEdge> getEdgesForAlgo(double likelihoodThresholdForDCA)

calculateMetaGraph

public void calculateMetaGraph()

addSingletonsToModules

public java.util.LinkedList<java.util.LinkedList<java.lang.Integer>> addSingletonsToModules()

getFinalSolution

public void getFinalSolution(int maxNumClusters,
                             int minSize)

removeZeroDegreesMetaNodes

public void removeZeroDegreesMetaNodes()

setLikelihoodThresholdForDC

public void setLikelihoodThresholdForDC(float likelihoodThresholdForDCA)

sortEdgesByScores

public static void sortEdgesByScores(java.util.LinkedList<ComparableEdge> edges,
                                     java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>> neighborsListsInDCAGraph)

Static auxiliary methods

removeCurrentListFromGraph

public static void removeCurrentListFromGraph(java.util.Hashtable<java.lang.Integer,java.util.HashSet<java.lang.Integer>> neighborsListsInDCAGraph,
                                              java.util.HashSet<java.lang.Integer> set)

removeIntersection

public static void removeIntersection(java.util.HashSet<java.lang.Integer> neighborsOfU,
                                      java.util.HashSet<java.lang.Integer> neighborsOfV)