Package phase

Class PhaseStates

java.lang.Object

phase.PhaseStates

public final class PhaseStates
extends java.lang.Object

Class PhaseStates identifies a rolling window of reference haplotypes for a target sample.

Instances of PhaseStates are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
PhaseStates(PhaseIbs ibsHaps)	Constructs a new PhaseIbs object from the specified data.

Method Summary

Modifier and Type	Method	Description
int	ibsStates(int sample, int[][] stateAlleles)	Identifies the HMM state alleles for the specified sample.
int	nStates()	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

PhaseStates

public PhaseStates(PhaseIbs ibsHaps)

Constructs a new PhaseIbs object from the specified data.

Parameters:

ibsHaps - IBS haplotype segments

Throws:

java.lang.IllegalArgumentException - if nHapsPerStep < 1

java.lang.NullPointerException - if ibsStates == null

Method Detail

nStates

public int nStates()

Returns the number of HMM states per marker.

Returns:

the number of HMM states per marker

ibsStates

public int ibsStates(int sample,
                     int[][] stateAlleles)

Identifies the HMM state alleles for the specified sample. The j-th state allele for the m-th marker will be stored in stateAlleles[m][j].

Parameters:

sample - the sample index

stateAlleles - the two-dimensional array in which state alleles will be stored

Returns:

the number of state alleles at each marker

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.hapPairs().nSamples()

java.lang.IndexOutOfBoundsException - if stateAlleles.length < this.hapPairs().nMarkers() or if stateAlleles[j].length < this.nStates() for any j satisfying (0 <= j && j < this.hapPairs().nMarkers())

java.lang.NullPointerException - if stateAlleles == null or if stateAlleles[j] == null for any j satisfying (0 <= j && j < this.hapPairs().nMarkers())