Class HiddenMarkovModel

java.lang.Object
  HiddenMarkovModel

public class HiddenMarkovModel
extends java.lang.Object

Calculates and stores states according to the exon data

Author:

arthiramachandran

Field Summary

(package private) static java.util.HashMap<java.lang.String,State>	States
static double	UNDERFLOW
static double	UNDERFLOW_factor

Constructor Summary

HiddenMarkovModel()

Method Summary

private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>>	computeBackwardProbabilities(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Computes the backward probabilities for the observation
private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>>	computeForwardProbabilities(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Computes the forward probabilities for the observation
private static State	getStateFromIndex(int stateIndex) From state number, figures out the state
static void	getStates(java.util.ArrayList<Exon> exons, java.util.ArrayList<Exon> expectedValues, java.util.ArrayList<Exon> stdDeviations, java.lang.String parameterFileName, double threshold, int nSamples, cern.jet.random.Gamma gamma, double gammaK, double gammaTheta, double gammaSNPsK, double gammaSNPsTheta) Gets the most likely states given the observations using forward-backward algorithm
static void	initialize(java.lang.String parameterFileName) Initializes the states with the values from the parameter file

Methods inherited from class java.lang.Object

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

Field Detail

States

static java.util.HashMap<java.lang.String,State> States

UNDERFLOW

public static final double UNDERFLOW

See Also:

Constant Field Values

UNDERFLOW_factor

public static final double UNDERFLOW_factor

See Also:

Constant Field Values

Constructor Detail

HiddenMarkovModel

public HiddenMarkovModel()

Method Detail

initialize

public static void initialize(java.lang.String parameterFileName)

Initializes the states with the values from the parameter file

Parameters:

parameterFileName - name of parameter file

getStates

public static void getStates(java.util.ArrayList<Exon> exons,
                             java.util.ArrayList<Exon> expectedValues,
                             java.util.ArrayList<Exon> stdDeviations,
                             java.lang.String parameterFileName,
                             double threshold,
                             int nSamples,
                             cern.jet.random.Gamma gamma,
                             double gammaK,
                             double gammaTheta,
                             double gammaSNPsK,
                             double gammaSNPsTheta)

Gets the most likely states given the observations using forward-backward algorithm

Parameters:

exons - observed values of each exon (in sample to call)

expectedValues - expected values for observations of each exon

stdDeviations - std deviations for observations of each exon

parameterFileName - name of parameter file

threshold - threshold for when an exon is called as not normal

nSamples - number of samples

gamma - (to remove)

gammaK - Gamma parameter k of coverage

gammaTheta - Gamma parameter Theta of coverage

gammaSNPsK - Gamma parameter k of heterozygosity

gammaSNPsTheta - Gamma parameter Theta of heterozygosity

getStateFromIndex

private static State getStateFromIndex(int stateIndex)

From state number, figures out the state

Parameters:

stateIndex -

Returns:

state associated with that index

computeBackwardProbabilities

private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>> computeBackwardProbabilities(java.util.ArrayList<Exon> exons,
                                                                                                           java.util.ArrayList<Exon> expectedValues,
                                                                                                           java.util.ArrayList<Exon> stdDeviations,
                                                                                                           int nSamples,
                                                                                                           cern.jet.random.Gamma gamma,
                                                                                                           double gammaK,
                                                                                                           double gammaTheta,
                                                                                                           double gammaSNPsK,
                                                                                                           double gammaSNPsTheta)

Computes the backward probabilities for the observation

Parameters:

exons - observed values of each exon (in sample to call)

expectedValues - expected values for observations of each exon

stdDeviations - std deviations for observations of each exon

nSamples - number of samples

gamma - (to remove)

gammaK - Gamma parameter k of coverage

gammaTheta - Gamma parameter Theta of coverage

gammaSNPsK - Gamma parameter k of heterozygosity

gammaSNPsTheta - Gamma parameter Theta of heterozygosity

Returns:

Array of backward probabilities for each state for each exon

computeForwardProbabilities

private static java.util.ArrayList<java.util.HashMap<State,java.lang.Double>> computeForwardProbabilities(java.util.ArrayList<Exon> exons,
                                                                                                          java.util.ArrayList<Exon> expectedValues,
                                                                                                          java.util.ArrayList<Exon> stdDeviations,
                                                                                                          int nSamples,
                                                                                                          cern.jet.random.Gamma gamma,
                                                                                                          double gammaK,
                                                                                                          double gammaTheta,
                                                                                                          double gammaSNPsK,
                                                                                                          double gammaSNPsTheta)

Computes the forward probabilities for the observation

Parameters:

exons - observed values of each exon (in sample to call)

expectedValues - expected values for observations of each exon

stdDeviations - std deviations for observations of each exon

nSamples - number of samples

gamma - (to remove)

gammaK - Gamma parameter k of coverage

gammaTheta - Gamma parameter Theta of coverage

gammaSNPsK - Gamma parameter k of heterozygosity

gammaSNPsTheta - Gamma parameter Theta of heterozygosity

Returns:

Array of forward probabilities for each state for each exon