Package phase

Class HmmStateProbs

java.lang.Object

phase.HmmStateProbs

public class HmmStateProbs
extends java.lang.Object

Class HmmStateProbs has a method that returns the reference haplotype and probability associated with each HMM state.

Instances of class HmmStateProbs are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
HmmStateProbs(LowFreqPhaseIbs phaseIbs)	Creates a HmmStateProbs instance from the specified data.

Method Summary

Modifier and Type	Method	Description
int	maxStates()	Returns the maximum number of HMM states.
int	nMarkers()	Returns the number of markers
int	nTargHaps()	Returns the number of target haplotypes.
int	run(int targHap, int[][] refHaps, float[][] stateProbs)	Stores the HMM reference haplotypes and states probabilities for the specified target haplotype, and returns the number of HMM states per marker.

Methods inherited from class java.lang.Object

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

Constructor Detail

HmmStateProbs

public HmmStateProbs(LowFreqPhaseIbs phaseIbs)

Creates a HmmStateProbs instance from the specified data.

Parameters:

phaseIbs - the IBS haplotypes

Throws:

java.lang.NullPointerException - if phaseIbs == null

Method Detail

run

public int run(int targHap,
               int[][] refHaps,
               float[][] stateProbs)

Stores the HMM reference haplotypes and states probabilities for the specified target haplotype, and returns the number of HMM states per marker. The contract for this method is undefined if the number of elements in any row of the specified arrays is not greater than or equal to this.maxStates().

Parameters:

targHap - a target haplotype index

refHaps - the array in which the reference haplotype corresponding to each hidden state will be stored

stateProbs - the array in which the estimated probability of each hidden state will be stored

Returns:

the number of hidden states at each marker

Throws:

java.lang.IndexOutOfBoundsException - if targHap < 0 || targHap >= this.nTargHaps()

java.lang.IndexOutOfBoundsException - if refHaps.length < this.nMarkers()

java.lang.IndexOutOfBoundsException - if stateProbs.length < this.nMarkers()

java.lang.NullPointerException - if refHaps == null || stateProbs == null

nMarkers

public int nMarkers()

Returns the number of markers

Returns:

the number of markers

nTargHaps

public int nTargHaps()

Returns the number of target haplotypes.

Returns:

the number of target haplotypes

maxStates

public int maxStates()

Returns the maximum number of HMM states.

Returns:

the maximum number of HMM states