Package imp

Class ImpStates

java.lang.Object

imp.ImpStates

public final class ImpStates
extends java.lang.Object

Class ImpStates identifies a list of pseudo-reference haplotypes for a target haplotype. Each pseudo-reference haplotype is a one-dimensional mosaic of reference haplotype segments.

Instances of ImpStates are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
ImpStates(ImpIbs ibsHaps)	Constructs a new ImpStates object from the specified data.

Method Summary

Modifier and Type	Method	Description
int	ibsStates(int targHap, int[][] hapIndices, boolean[][] alMatch)	Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j].
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

ImpStates

public ImpStates(ImpIbs ibsHaps)

Constructs a new ImpStates object from the specified data.

Parameters:

ibsHaps - the IBS haplotype segments

Throws:

java.lang.NullPointerException - if impData == null || 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 targHap,
                     int[][] hapIndices,
                     boolean[][] alMatch)

Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j]. The number of HMM states states at each marker is returned.

Parameters:

targHap - the haplotype index

hapIndices - the two-dimensional array in which reference haplotype indices for each HMM state will be stored

alMatch - the two-dimensional array in which allele match status between the target haplotype and HMM state will be stored

Returns:

the number of HMM states at each marker

Throws:

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

java.lang.IndexOutOfBoundsException - if (hapIndices.length < this.impData().nClusters()) or if any hapIndices[j].length is less than the number of HMM states at a marker for any j satisfying (0 <= j && j < this.nClusters())

java.lang.IndexOutOfBoundsException - if (alMatch.length < this.impdata().nClusters()) or if any alMatch[j].length is less than the number of HMM states at a marker for any j satisfying (0 <= j && j < this.nClusters())

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

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