Package haplotype

Interface HapPairs

All Known Implementing Classes:

WrappedHapPairs

public interface HapPairs

Interface HapPairs represents a list of haplotype pairs. Each haplotype pair is guaranteed to have two non-missing alleles at each marker.

All instances of HapPairs are required to be immutable.

Method Summary

Modifier and Type	Method	Description
int	allele(int marker, int haplotype)	Returns the allele for the specified marker and haplotype.
int	allele1(int marker, int hapPair)	Returns the first allele for the specified marker and haplotype pair.
int	allele2(int marker, int hapPair)	Returns the second allele for the specified marker and haplotype pair.
int	idIndex(int hapPair)	Returns the sample identifier index for the specified haplotype pair.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the markers.
int	nHapPairs()	Returns the number of haplotype pairs.
int	nHaps()	Returns the number of haplotypes.
int	nMarkers()	Returns the number of markers.

Method Detail

allele

int allele(int marker,
           int haplotype)

Returns the allele for the specified marker and haplotype.

Parameters:

marker - a marker index

haplotype - a haplotype index

Returns:

the allele for the specified marker and haplotype

Throws:

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

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

allele1

int allele1(int marker,
            int hapPair)

Returns the first allele for the specified marker and haplotype pair.

Parameters:

marker - a marker index

hapPair - a haplotype pair index

Returns:

the first allele for the specified marker and haplotype pair

Throws:

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

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

allele2

int allele2(int marker,
            int hapPair)

Returns the second allele for the specified marker and haplotype pair.

Parameters:

marker - a marker index

hapPair - a haplotype pair index

Returns:

the second allele for the specified marker and haplotype pair

Throws:

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

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

nMarkers

int nMarkers()

Returns the number of markers.

Returns:

the number of markers

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()

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

idIndex

int idIndex(int hapPair)

Returns the sample identifier index for the specified haplotype pair.

Parameters:

hapPair - a haplotype pair index

Returns:

the sample identifier index for the specified haplotype pair

Throws:

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