Package imp

Class StateProbsFactory

java.lang.Object

imp.StateProbsFactory

public class StateProbsFactory
extends java.lang.Object

Class StateProbsFactory stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.

Instances of class StateProbsFactory are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
StateProbsFactory(int nTargMarkers)	Creates an StateProbsFactory instance from the specified data.

Method Summary

Modifier and Type	Method	Description
int	nTargMarkers()	Returns the number of target marker.
StateProbs	stateProbs(int targHap, int nStates, int[][] hapIndices, float[][] stateProbs)	Stores the reference haplotypes and state probabilities that will be used to imputed missing state probabilities using linear interpolation.

Methods inherited from class java.lang.Object

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

Constructor Detail

StateProbsFactory

public StateProbsFactory(int nTargMarkers)

Creates an StateProbsFactory instance from the specified data.

Parameters:

nTargMarkers - the number of target markers

Throws:

java.lang.IllegalArgumentException - if nTargMarkers <= 0

Method Detail

nTargMarkers

public int nTargMarkers()

Returns the number of target marker.

Returns:

the number of target marker

stateProbs

public StateProbs stateProbs(int targHap,
                             int nStates,
                             int[][] hapIndices,
                             float[][] stateProbs)

Stores the reference haplotypes and state probabilities that will be used to imputed missing state probabilities using linear interpolation. If a HMM state probability at a marker or the following marker are greater than or equal to Math.min(0.005f, 1.0f/nStates), then the reference haplotype, the state probability at the marker, and the state probability at the succeeding marker are stored.

Parameters:

targHap - a target data haplotype index

nStates - the number of HMM states at each marker

hapIndices - the reference haplotype indices corresponding to each state at each marker

stateProbs - the HMM state probabilities at each marker

Returns:

the state probabilities

Throws:

java.lang.IllegalArgumentException - if hapIndices.length != this.nTargMarkers()

java.lang.IllegalArgumentException - if stateProbs.length != this.nTargMarkers()

java.lang.IndexOutOfBoundsException - if there exists j satisfying (0 <= j && j <= this.nTargMarkers()) such that (hapIndices[j].length < nStates || stateProbs[j].length < nStates)

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

java.lang.NullPointerException - if there exists j satisfying (0 <= j && j <= this.nTargMarkers()) such that (hapIndices[j] == null || stateProbs[j] == null)