EM_LLR_Utils
Class SeedGenerator<T extends edu.tau.compbio.interaction.AnnotatedInteractorSet>

java.lang.Object
  EM_LLR_Utils.SeedGenerator<T>

public class SeedGenerator<T extends edu.tau.compbio.interaction.AnnotatedInteractorSet>
extends java.lang.Object

Author:

ulitskyi

Nested Class Summary

static class	SeedGenerator.BestNeiSelection
static class	SeedGenerator.SeedConfinement
static class	SeedGenerator.SeedScore

Constructor Summary

SeedGenerator(edu.tau.compbio.interaction.InteractionMap im, edu.tau.compbio.ds.SimilarityMatrix wMat, int[] index2index, SeedGenerator.SeedScore scoreMethod, SeedGenerator.SeedConfinement seedMethod)

Method Summary

java.util.AbstractList<edu.tau.compbio.interaction.AnnotatedInteractorSet>	generateAllPairsSeeds(int size, float minSimilarity, float minSeedScore, int maxSize)
java.util.AbstractList<T>	generateAllPairsSeedsWithConfinedCut(int size, float minSimilarity, float minSeedScore, int maxSize, double maxCutWeight, java.util.Map<edu.tau.compbio.interaction.Interaction,java.lang.Double> weights)
protected java.util.AbstractList<edu.tau.compbio.interaction.Interactor>	orderNodes()
void	setBestNeiSelectionMethod(SeedGenerator.BestNeiSelection method)

Methods inherited from class java.lang.Object

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

Constructor Detail

SeedGenerator

public SeedGenerator(edu.tau.compbio.interaction.InteractionMap im,
                     edu.tau.compbio.ds.SimilarityMatrix wMat,
                     int[] index2index,
                     SeedGenerator.SeedScore scoreMethod,
                     SeedGenerator.SeedConfinement seedMethod)

Method Detail

setBestNeiSelectionMethod

public void setBestNeiSelectionMethod(SeedGenerator.BestNeiSelection method)

orderNodes

protected java.util.AbstractList<edu.tau.compbio.interaction.Interactor> orderNodes()

generateAllPairsSeeds

public java.util.AbstractList<edu.tau.compbio.interaction.AnnotatedInteractorSet> generateAllPairsSeeds(int size,
                                                                                                        float minSimilarity,
                                                                                                        float minSeedScore,
                                                                                                        int maxSize)

generateAllPairsSeedsWithConfinedCut

public java.util.AbstractList<T> generateAllPairsSeedsWithConfinedCut(int size,
                                                                      float minSimilarity,
                                                                      float minSeedScore,
                                                                      int maxSize,
                                                                      double maxCutWeight,
                                                                      java.util.Map<edu.tau.compbio.interaction.Interaction,java.lang.Double> weights)