haplotype

Interface SampleHapPairs

All Superinterfaces:

HapPairs

All Known Implementing Classes:

BasicSampleHapPairs, GLSampleHapPairs, RefHapPairs, RevSampleHapPairs

public interface SampleHapPairs
extends HapPairs

Interface SampleHapPairs represents a list of samples and a haplotype pair for each sample. Each haplotype pair is guaranteed to have two non-missing alleles at each marker.

All instances of SampleHapPairs are required to be immutable.

Method Summary

Modifier and Type	Method and Description
int	alleleCount(int marker, int allele) Returns the number of haplotypes that carry the specified allele.
int	hapIndex(int marker, int allele, int copy) Returns index of the haplotype that carries the specified copy of the specified allele.
int	majorAllele(int marker) Returns the index of the major allele.
int	nAlleles(int marker) Returns the number of marker alleles.
int	nSamples() Returns the number of samples.
Samples	samples() Returns the samples.
boolean	storesNonMajorIndices(int marker) Returns true if this object stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.

Methods inherited from interface haplotype.HapPairs

allele, allele1, allele2, marker, markers, nHapPairs, nHaps, nMarkers, sampleIndex, samples

Method Detail

samples

Samples samples()

Returns the samples. The k-th sample corresponds to the k-th haplotype pair.

Returns:

the samples

nSamples

int nSamples()

Returns the number of samples.

Returns:

the number of samples

nAlleles

int nAlleles(int marker)

Returns the number of marker alleles.

Parameters:

marker - a marker index

Returns:

the number of marker alleles.

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

storesNonMajorIndices

boolean storesNonMajorIndices(int marker)

Returns true if this object stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.

Parameters:

marker - a marker index

Returns:

true if this object stores the indices of haplotypes that carry non-major alleles

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

majorAllele

int majorAllele(int marker)

Returns the index of the major allele.

Parameters:

marker - a marker index

Returns:

the index of the major allele

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.UnsupportedOperationException - if storesNonMajorIndices(marker) == false

alleleCount

int alleleCount(int marker,
                int allele)

Returns the number of haplotypes that carry the specified allele.

Parameters:

marker - a marker index

allele - an allele index

Returns:

the number of haplotypes that carry the specified allele

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.IllegalArgumentException - if allele == this.majorAllele()

java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()

java.lang.UnsupportedOperationException - if storesNonMajorIndices(marker) == false

hapIndex

int hapIndex(int marker,
             int allele,
             int copy)

Returns index of the haplotype that carries the specified copy of the specified allele.

Parameters:

marker - a marker index

allele - an allele index

copy - a copy index.

Returns:

index of the haplotype that carries the specified allele.

Throws:

java.lang.IllegalArgumentException - if allele == this.majorAllele()

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()

java.lang.IndexOutOfBoundsException - if copy < 0 || copy >= this.alleleCount(allele)

java.lang.UnsupportedOperationException - if storesNonMajorIndices(marker) == false