vcf

Interface HapsMarker

All Superinterfaces:

MarkerContainer

All Known Subinterfaces:

VcfEmission

All Known Implementing Classes:

BitSetGT, BitSetRefGT, ByteArrayRefGT, LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT, VcfRecord

public interface HapsMarker
extends MarkerContainer

Interface HapsMarker represents marker alleles for a list of haplotype pairs.

All instances of HapsMarkers are required to be immutable.

Method Summary

Modifier and Type	Method and Description
int	allele(int haplotype) Returns the allele on the specified haplotype.
int	allele1(int hapPair) Returns the first allele for the specified haplotype pair.
int	allele2(int hapPair) Returns the second allele for the specified haplotype pair.
Marker	marker() Returns the marker.
int	nHapPairs() Returns the number of haplotype pairs.
int	nHaps() Returns the number of haplotypes.

Method Detail

allele

int allele(int haplotype)

Returns the allele on the specified haplotype.

Parameters:

haplotype - a haplotype index

Returns:

the allele on the specified haplotype

Throws:

java.lang.IndexOutOfBoundsException - if haplotype < 0 || haplotype >= this.nHaps()

allele1

int allele1(int hapPair)

Returns the first allele for the specified haplotype pair.

Parameters:

hapPair - a haplotype pair index

Returns:

the first allele for the specified haplotype pair

Throws:

java.lang.IndexOutOfBoundsException - if hapPair < 0 || hapPair >= this.nHapPairs()

allele2

int allele2(int hapPair)

Returns the second allele for the specified haplotype pair.

Parameters:

hapPair - a haplotype pair index

Returns:

the second allele for the specified haplotype pair

Throws:

java.lang.IndexOutOfBoundsException - if hapPair < 0 || hapPair >= this.nHapPairs()

marker

Marker marker()

Returns the marker.

Specified by:

marker in interface MarkerContainer

Returns:

the marker

nHaps

int nHaps()

Returns the number of haplotypes. The returned value is equal to 2*this.nHapPairs().

Returns:

the number of haplotypes

nHapPairs

int nHapPairs()

Returns the number of haplotype pairs. The returned value is equal to this.nHaps()/2.

Returns:

the number of haplotype pairs