Package haplotype

Class WrappedHapPairs

java.lang.Object

haplotype.WrappedHapPairs

All Implemented Interfaces:

HapPairs

public class WrappedHapPairs
extends java.lang.Object
implements HapPairs

Class WrappedHapPairs is a HapPairs instance obtain by wrapping a PhasedGT object.

Instances of WrappedHapPairs are immutable.

Constructor Summary

Constructors

Constructor	Description
WrappedHapPairs(PhasedGT phasedGT)	Constructs a new WrappedHapPairs instance.

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WrappedHapPairs

public WrappedHapPairs(PhasedGT phasedGT)

Constructs a new WrappedHapPairs instance.

Parameters:

phasedGT - the object to be wrapped by this

Throws:

java.lang.NullPointerException - if phasedGT == null

Method Detail

allele

public int allele(int marker,
                  int haplotype)

Description copied from interface: HapPairs

Returns the allele for the specified marker and haplotype.

Specified by:

allele in interface HapPairs

Parameters:

marker - a marker index

haplotype - a haplotype index

Returns:

the allele for the specified marker and haplotype

allele1

public int allele1(int marker,
                   int hapPair)

Description copied from interface: HapPairs

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

Specified by:

allele1 in interface HapPairs

Parameters:

marker - a marker index

hapPair - a haplotype pair index

Returns:

the first allele for the specified marker and haplotype pair

allele2

public int allele2(int marker,
                   int hapPair)

Description copied from interface: HapPairs

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

Specified by:

allele2 in interface HapPairs

Parameters:

marker - a marker index

hapPair - a haplotype pair index

Returns:

the second allele for the specified marker and haplotype pair

nMarkers

public int nMarkers()

Description copied from interface: HapPairs

Returns the number of markers.

Specified by:

nMarkers in interface HapPairs

Returns:

the number of markers

markers

public Markers markers()

Description copied from interface: HapPairs

Returns the markers.

Specified by:

markers in interface HapPairs

Returns:

the markers

marker

public Marker marker(int marker)

Description copied from interface: HapPairs

Returns the specified marker.

Specified by:

marker in interface HapPairs

Parameters:

marker - a marker index

Returns:

the specified marker

nHaps

public int nHaps()

Description copied from interface: HapPairs

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

Specified by:

nHaps in interface HapPairs

Returns:

the number of haplotypes

nHapPairs

public int nHapPairs()

Description copied from interface: HapPairs

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

Specified by:

nHapPairs in interface HapPairs

Returns:

the number of haplotype pairs

idIndex

public int idIndex(int hapPair)

Description copied from interface: HapPairs

Returns the sample identifier index for the specified haplotype pair.

Specified by:

idIndex in interface HapPairs

Parameters:

hapPair - a haplotype pair index

Returns:

the sample identifier index for the specified haplotype pair