EM_LLR_Utils
Class AbstractParamsEM

java.lang.Object
  EM_LLR_Utils.AbstractParamsEM

Direct Known Subclasses:

RegParamsEM

public abstract class AbstractParamsEM
extends java.lang.Object

Field Summary

protected int[]	_inds
protected int	_inpSize
protected double	_likelihood
protected edu.tau.compbio.stat.NormalDistribution	_matesDist
protected double	_matesP
protected edu.tau.compbio.stat.NormalDistribution	_nonDist
protected int	_nonNaNCount
protected int	_plotIterCount
protected double[]	_regPs
protected double	_regsSum
protected boolean	_sameStd
protected boolean	_selfInit
protected edu.tau.compbio.ds.SimilarityMatrix<java.lang.String>	_simMat
protected boolean	_updateExp
protected boolean	_updateP
protected boolean	_updateStd
protected double	EPS_IMPROVE
protected double	INIT_MATES_PROB
protected static int	MIN_VALS_NUM

Constructor Summary

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

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

Method Summary

protected double	calcExp(double[] g_i, double sumG_i)
protected double	calcStd(double[] g_i, double sumG_i, double exp)
double	getLikelihood()
edu.tau.compbio.stat.NormalDistribution	getMatesDistribution()
double	getMatesP()
edu.tau.compbio.stat.NormalDistribution	getNonMatesDistribution()
void	init(edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> simMat, double[] regPs)
protected void	initNonNaNCount()
void	setSameStd(boolean flag)
void	setUpdateMode(boolean updateExp, boolean updateStd, boolean updateP)

Methods inherited from class java.lang.Object

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

Field Detail

_matesDist

protected edu.tau.compbio.stat.NormalDistribution _matesDist

_nonDist

protected edu.tau.compbio.stat.NormalDistribution _nonDist

_matesP

protected double _matesP

_likelihood

protected double _likelihood

_regPs

protected double[] _regPs

_simMat

protected edu.tau.compbio.ds.SimilarityMatrix<java.lang.String> _simMat

_inpSize

protected int _inpSize

_updateExp

protected boolean _updateExp

_updateStd

protected boolean _updateStd

_updateP

protected boolean _updateP

_inds

protected int[] _inds

_nonNaNCount

protected int _nonNaNCount

_regsSum

protected double _regsSum

_selfInit

protected boolean _selfInit

_sameStd

protected boolean _sameStd

MIN_VALS_NUM

protected static final int MIN_VALS_NUM

See Also:

Constant Field Values

EPS_IMPROVE

protected final double EPS_IMPROVE

See Also:

Constant Field Values

INIT_MATES_PROB

protected final double INIT_MATES_PROB

See Also:

Constant Field Values

_plotIterCount

protected int _plotIterCount

Constructor Detail

AbstractParamsEM

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

AbstractParamsEM

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

Method Detail

setUpdateMode

public void setUpdateMode(boolean updateExp,
                          boolean updateStd,
                          boolean updateP)

init

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

getMatesDistribution

public edu.tau.compbio.stat.NormalDistribution getMatesDistribution()

getNonMatesDistribution

public edu.tau.compbio.stat.NormalDistribution getNonMatesDistribution()

getMatesP

public double getMatesP()

getLikelihood

public double getLikelihood()

setSameStd

public void setSameStd(boolean flag)

initNonNaNCount

protected void initNonNaNCount()

calcExp

protected double calcExp(double[] g_i,
                         double sumG_i)

calcStd

protected double calcStd(double[] g_i,
                         double sumG_i,
                         double exp)