Package phase

Class HmmUpdater

java.lang.Object

phase.HmmUpdater

public class HmmUpdater
extends java.lang.Object

Instances of class HmmUpdater have methods for one-step updates of forward or backward HMM values.

Constructor Summary

Constructors

Constructor	Description
HmmUpdater(float pErr)	Constructs a new HmmUpdater instance from the specified data.

Method Summary

Modifier and Type	Method	Description
void	bwdUpdate(double[] bwd, double pSwitch, byte[] mismatch, int nStates)	Updates the backward values.
void	bwdUpdate(float[] bwd, float pSwitch, byte[] mismatch, int nStates)	Updates the backward values.
double	fwdUpdate(double[] fwd, double sum, double pSwitch, byte[] mismatch, int nStates)	Updates the forward values and returns the sum of the updated forward values.
float	fwdUpdate(float[] fwd, float sum, float pSwitch, byte[] mismatch, int nStates)	Updates the forward values and returns the sum of the updated forward values.

Methods inherited from class java.lang.Object

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

Constructor Detail

HmmUpdater

public HmmUpdater(float pErr)

Constructs a new HmmUpdater instance from the specified data.

Parameters:

pErr - the probability that the observed allele does not match the state allele

Method Detail

fwdUpdate

public float fwdUpdate(float[] fwd,
                       float sum,
                       float pSwitch,
                       byte[] mismatch,
                       int nStates)

Updates the forward values and returns the sum of the updated forward values.

Parameters:

fwd - the array of forward values that will be updated

pSwitch - the probability of jumping to a random state

sum - the sum of forward values in the specified array

mismatch - the number of allele mismatches (0 or 1) for each HMM state

nStates - the number of states

Returns:

the sum of the updated forward values

Throws:

java.lang.IndexOutOfBoundsException - if fwd.length < nStates || mismatch.length < nStates

java.lang.NullPointerException - if fwd == null || mismatch == null

bwdUpdate

public void bwdUpdate(float[] bwd,
                      float pSwitch,
                      byte[] mismatch,
                      int nStates)

Updates the backward values.

Parameters:

bwd - the array of backward values that will be updated

pSwitch - the probability of jumping to a random state

mismatch - the number of allele mismatches (0 or 1) for each HMM state

nStates - the number of states

Throws:

java.lang.IndexOutOfBoundsException - if bwd.length < nStates || mismatch.length < nStates

java.lang.NullPointerException - if bwd == null || mismatch == null

fwdUpdate

public double fwdUpdate(double[] fwd,
                        double sum,
                        double pSwitch,
                        byte[] mismatch,
                        int nStates)

Updates the forward values and returns the sum of the updated forward values.

Parameters:

fwd - the array of forward values that will be updated

pSwitch - the probability of jumping to a random state

sum - the sum of forward values in the specified array

mismatch - the number of allele mismatches (0 or 1) for each HMM state

nStates - the number of states

Returns:

the sum of the updated forward values

Throws:

java.lang.IndexOutOfBoundsException - if fwd.length < nStates || mismatch.length < nStates

java.lang.NullPointerException - if fwd == null || mismatch == null

bwdUpdate

public void bwdUpdate(double[] bwd,
                      double pSwitch,
                      byte[] mismatch,
                      int nStates)

Updates the backward values.

Parameters:

bwd - the array of backward values that will be updated

pSwitch - the probability of jumping to a random state

mismatch - the number of allele mismatches (0 or 1) for each HMM state

nStates - the number of states

Throws:

java.lang.IndexOutOfBoundsException - if bwd.length < nStates || mismatch.length < nStates

java.lang.NullPointerException - if bwd == null || mismatch == null