haplotype

Interface HapPair

All Known Implementing Classes:

BitHapPair, RevHapPair, WrappedHapPair

public interface HapPair

Interface HapPair represents a pair of haplotypes for a sample. The pair of haplotypes are guaranteed to have non-missing alleles at each marker.

All instances of HapPair are required to be immutable.

Method Summary

Modifier and Type	Method and Description
int	allele1(int marker) Returns the first allele for the specified marker.
int	allele2(int marker) Returns the second allele for the specified marker.
Marker	marker(int marker) Returns the specified marker.
Markers	markers() Returns the markers.
int	nMarkers() Returns the number of markers.
int	sampleIndex() Returns the index of the sample associated with this haplotype pair in the list of samples returned by this.samples().
Samples	samples() Returns the list of samples containing the sample associated with this haplotype pair.

Method Detail

allele1

int allele1(int marker)

Returns the first allele for the specified marker.

Parameters:

marker - a marker index

Returns:

the first allele for the specified marker

Throws:

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

allele2

int allele2(int marker)

Returns the second allele for the specified marker.

Parameters:

marker - a marker index

Returns:

the second allele for the specified marker

Throws:

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

markers

Markers markers()

Returns the markers.

Returns:

the markers

marker

Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - a marker index

Returns:

the specified marker

Throws:

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

nMarkers

int nMarkers()

Returns the number of markers.

Returns:

the number of markers

samples

Samples samples()

Returns the list of samples containing the sample associated with this haplotype pair.

Returns:

the list of samples containing the sample associated with this haplotype pair

sampleIndex

int sampleIndex()

Returns the index of the sample associated with this haplotype pair in the list of samples returned by this.samples().

Returns:

the index of the sample associated with this haplotype pair in the list of samples returned by this.samples()