EM_LLR_Utils
Class RegParamsEM

java.lang.Object
  EM_LLR_Utils.AbstractParamsEM
      EM_LLR_Utils.RegParamsEM

public class RegParamsEM
extends AbstractParamsEM

Field Summary

Fields inherited from class EM_LLR_Utils.AbstractParamsEM

_inds, _inpSize, _likelihood, _matesDist, _matesP, _nonDist, _nonNaNCount, _plotIterCount, _regPs, _regsSum, _sameStd, _selfInit, _simMat, _updateExp, _updateP, _updateStd, EPS_IMPROVE, INIT_MATES_PROB, MIN_VALS_NUM

Constructor Summary

RegParamsEM(edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> simMat, double[] regPs)

RegParamsEM(edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> simMat, double[] regPs, int randCount)

Method Summary

protected double	calcCombinedStd(double[] g1_i, double[] g2_i, double sumG1_i, double sumG2_i, double exp1, double exp2)
protected double	calcGi(double[] g_i, double[] pfMult_i, double[] pfMult_other)
protected double	calcLikelihood(double[] pfMult_mates, double[] pfMult_nonMates)
protected void	calcPFMultFalse(double[] pfMult_i, double prob_i, edu.tau.compbio.stat.StatDistribution distrib_i)
protected void	calcPFMultTrue(double[] pfMult_i, double prob_i, edu.tau.compbio.stat.StatDistribution distrib_i)
void	run(edu.tau.compbio.util.ProgressManager progMan)
void	setInit(boolean i)
void	setInitial(edu.tau.compbio.stat.NormalDistribution matesDist, edu.tau.compbio.stat.NormalDistribution nonDist, double matesP)
void	setPMatesRange(float min, float max)

Methods inherited from class EM_LLR_Utils.AbstractParamsEM

calcExp, calcStd, getLikelihood, getMatesDistribution, getMatesP, getNonMatesDistribution, init, initNonNaNCount, setSameStd, setUpdateMode

Methods inherited from class java.lang.Object

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

Constructor Detail

RegParamsEM

public RegParamsEM(edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> simMat,
                   double[] regPs)

RegParamsEM

public RegParamsEM(edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> simMat,
                   double[] regPs,
                   int randCount)

Method Detail

setPMatesRange

public void setPMatesRange(float min,
                           float max)

setInitial

public void setInitial(edu.tau.compbio.stat.NormalDistribution matesDist,
                       edu.tau.compbio.stat.NormalDistribution nonDist,
                       double matesP)

calcPFMultTrue

protected void calcPFMultTrue(double[] pfMult_i,
                              double prob_i,
                              edu.tau.compbio.stat.StatDistribution distrib_i)

calcPFMultFalse

protected void calcPFMultFalse(double[] pfMult_i,
                               double prob_i,
                               edu.tau.compbio.stat.StatDistribution distrib_i)

calcGi

protected double calcGi(double[] g_i,
                        double[] pfMult_i,
                        double[] pfMult_other)

calcCombinedStd

protected double calcCombinedStd(double[] g1_i,
                                 double[] g2_i,
                                 double sumG1_i,
                                 double sumG2_i,
                                 double exp1,
                                 double exp2)

calcLikelihood

protected double calcLikelihood(double[] pfMult_mates,
                                double[] pfMult_nonMates)

run

public void run(edu.tau.compbio.util.ProgressManager progMan)

setInit

public void setInit(boolean i)