haplotype

Class BitHapPair

java.lang.Object

haplotype.BitHapPair

All Implemented Interfaces:

HapPair

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

Class BitHapPair represents a pair of haplotypes for a sample. The class stores alleles using java.util.BitSet objects.

Instances of class BitHapPair are immutable.

Constructor Summary

Constructors

Constructor and Description
BitHapPair(Markers markers, Samples samples, int sampleIndex, int[] alleles1, int[] alleles2) Constructs a new BitHapPair instance.

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.
java.lang.String	toString() Returns a string representation of this.

Methods inherited from class java.lang.Object

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

Constructor Detail

BitHapPair

public BitHapPair(Markers markers,
                  Samples samples,
                  int sampleIndex,
                  int[] alleles1,
                  int[] alleles2)

Constructs a new BitHapPair instance.

Parameters:

markers - the sequence of markers

samples - the list of samples

sampleIndex - the sample index

alleles1 - the sequence of allele indices for the first haplotype

alleles2 - the sequence of alleles indices for the second haplotype

Throws:

java.lang.IllegalArgumentException - if alleles1.length != markers.nMarkers() || alleles2.length != markers.nMarkers()

java.lang.IllegalArgumentException - if alleles1[k] < 0 || allele1[k] >= markers.marker(k).nAlleles() for some k satisfying 0 <= k && k < markers.nMarkers()

java.lang.IllegalArgumentException - if alleles2[k] < 0 || allele2[k] >= markers.marker(k).nAlleles() for some k satisfying 0 <= k && k < markers.nMarkers()

java.lang.IndexOutOfBoundsException - if sampleIndex < 0 || sampleIndex >= samples.nSamples()

java.lang.NullPointerException - if marker == null || samples == null || alleles1 == null || allele2 == 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

samples

public Samples samples()

Description copied from interface: HapPair

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

Specified by:

samples in interface HapPair

Returns:

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

sampleIndex

public int sampleIndex()

Description copied from interface: HapPair

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

Specified by:

sampleIndex in interface HapPair

Returns:

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

toString

public java.lang.String toString()

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this