Package phase

Class HmmUpdater

java.lang.Object

phase.HmmUpdater

public class HmmUpdater
extends java.lang.Object

Class HmmUpdater has static methods for next marker updates of forward and backward HMM values.

Method Summary

Modifier and Type	Method	Description
static void	bwdUpdate(float[] bwd, float pSwitch, float[] pMismatch, byte[] mismatch, int nStates)	Updates the backward values.
static float	fwdUpdate(float[] fwd, float sum, float pSwitch, float[] pMismatch, 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

Method Detail

fwdUpdate

public static float fwdUpdate(float[] fwd,
                              float sum,
                              float pSwitch,
                              float[] pMismatch,
                              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

pMismatch - two element array with emission probabilities for 0 or 1 mismatches between the observed and reference haplotype alleles

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.IllegalArgumentException - if pMismatch.length != 2

java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < nStates) and (mismatch[j] < 0 || mismatch[j] > 1)

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

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

bwdUpdate

public static void bwdUpdate(float[] bwd,
                             float pSwitch,
                             float[] pMismatch,
                             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

pMismatch - two element array with emission probabilities for 0 or 1 mismatches between alleles the observed and reference haplotype alleles

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

nStates - the number of states

Throws:

java.lang.IllegalArgumentException - if pMismatch.length != 2

java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < nStates) and (mismatch[j] < 0 || mismatch[j] > 1)

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

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