Package haplotype

Class WrappedHapPair

java.lang.Object

haplotype.WrappedHapPair

All Implemented Interfaces:

HapPair

public final class WrappedHapPair
extends java.lang.Object
implements HapPair

Class WrappedHapPair is a HapPair instance that wraps a RefGTWindow object.

Constructor Summary

Constructors

Constructor	Description
WrappedHapPair(GT phasedGT, int hapPair)	Creates a WrappedHapPair instance representing the specified haplotype pair.

Method Summary

Modifier and Type	Method	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.
int	idIndex()	Returns the sample identifier index.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the markers.
int	nMarkers()	Returns the number of markers.

Methods inherited from interface haplotype.HapPair

Methods inherited from class java.lang.Object

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

Constructor Detail

WrappedHapPair

public WrappedHapPair(GT phasedGT,
                      int hapPair)

Creates a WrappedHapPair instance representing the specified haplotype pair.

Parameters:

phasedGT - the RefGTWindow object that will be "wrapped" by this

hapPair - a haplotype pair index

Throws:

java.lang.IllegalArgumentException - if phasedGT.isPhased() == false

java.lang.IllegalArgumentException - if hapPair < 0 || hapPair >= sampleHapPairs.nHapPairs()

java.lang.NullPointerException - if sampleHapPairs == null

Method Detail

allele1

public int allele1(int marker)

Description copied from interface: HapPair

Returns the first allele for the specified marker.

Specified by:

allele1 in interface HapPair

Parameters:

marker - a marker index

Returns:

the first allele for the specified marker

allele2

public int allele2(int marker)

Description copied from interface: HapPair

Returns the second allele for the specified marker.

Specified by:

allele2 in interface HapPair

Parameters:

marker - a marker index

Returns:

the second allele for the specified marker

markers

public Markers markers()

Description copied from interface: HapPair

Returns the markers.

Specified by:

markers in interface HapPair

Returns:

the markers

marker

public Marker marker(int marker)

Description copied from interface: HapPair

Returns the specified marker.

Specified by:

marker in interface HapPair

Parameters:

marker - a marker index

Returns:

the specified marker

nMarkers

public int nMarkers()

Description copied from interface: HapPair

Returns the number of markers.

Specified by:

nMarkers in interface HapPair

Returns:

the number of markers

idIndex

public int idIndex()

Description copied from interface: HapPair

Returns the sample identifier index.

Specified by:

idIndex in interface HapPair

Returns:

the sample identifier index