haplotype

Class RefHapPairs

java.lang.Object

haplotype.RefHapPairs

All Implemented Interfaces:

HapPairs, SampleHapPairs

public class RefHapPairs
extends java.lang.Object
implements SampleHapPairs

Class RefHapPairs stores a list of samples and a haplotype pair for each sample.

Instances of class RefHapPairs are immutable.

Constructor Summary

Constructors

Constructor and Description
RefHapPairs(Markers markers, Samples samples, VcfEmission[] refVcfRecs) Constructs a new RefHapPairs instance.

Method Summary

Modifier and Type	Method and 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	alleleCount(int marker, int allele) Returns the number of haplotypes that carry the specified allele.
int	hapIndex(int marker, int allele, int copy) Returns index of the haplotype that carries the specified copy of the specified allele.
int	majorAllele(int marker) Returns the index of the major allele.
Marker	marker(int marker) Returns the specified marker.
Markers	markers() Returns the markers.
int	nAlleles(int marker) Returns the number of marker alleles.
int	nHapPairs() Returns the number of haplotype pairs.
int	nHaps() Returns the number of haplotypes.
int	nMarkers() Returns the number of markers.
int	nSamples() Returns the number of samples.
int	sampleIndex(int hapPair) Returns the index of the sample associated with the specified haplotype pair in the list of samples returned by this.samples().
Samples	samples() Returns the samples.
Samples	samples(int hapPair) Returns a list of samples containing the sample associated with the specified haplotype pair
boolean	storesNonMajorIndices(int marker) Returns true if this object stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.

Methods inherited from class java.lang.Object

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

Constructor Detail

RefHapPairs

public RefHapPairs(Markers markers,
                   Samples samples,
                   VcfEmission[] refVcfRecs)

Constructs a new RefHapPairs instance.

Parameters:

markers - the sequence of markers

samples - the sequence of samples

refVcfRecs - the sequence of per-marker genotype data

Throws:

java.lang.IllegalArgumentException - if markers.nMarkers() != refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].samples().equals(samples) == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].marker().equals(markers.marker(k)) == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].isRefData() == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.NullPointerException - if markers == null || samples == null || refVcfRecs == null || refVcfRecs[k] == null for any k satisfying 0 <= k && k <= refVcfRecs.length

Method Detail

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

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

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

nSamples

public int nSamples()

Description copied from interface: SampleHapPairs

Returns the number of samples.

Specified by:

nSamples in interface SampleHapPairs

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: SampleHapPairs

Returns the samples. The k-th sample corresponds to the k-th haplotype pair.

Specified by:

samples in interface SampleHapPairs

Returns:

the samples

samples

public Samples samples(int hapPair)

Description copied from interface: HapPairs

Returns a list of samples containing the sample associated with the specified haplotype pair

Specified by:

samples in interface HapPairs

Parameters:

hapPair - a haplotype pair index

Returns:

a list of samples containing the sample associated with the specified haplotype pair

sampleIndex

public int sampleIndex(int hapPair)

Description copied from interface: HapPairs

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

Specified by:

sampleIndex in interface HapPairs

Parameters:

hapPair - a haplotype pair index

Returns:

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

nAlleles

public int nAlleles(int marker)

Description copied from interface: SampleHapPairs

Returns the number of marker alleles.

Specified by:

nAlleles in interface SampleHapPairs

Parameters:

marker - a marker index

Returns:

the number of marker alleles.

storesNonMajorIndices

public boolean storesNonMajorIndices(int marker)

Description copied from interface: SampleHapPairs

Returns true if this object stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.

Specified by:

storesNonMajorIndices in interface SampleHapPairs

Parameters:

marker - a marker index

Returns:

true if this object stores the indices of haplotypes that carry non-major alleles

majorAllele

public int majorAllele(int marker)

Description copied from interface: SampleHapPairs

Returns the index of the major allele.

Specified by:

majorAllele in interface SampleHapPairs

Parameters:

marker - a marker index

Returns:

the index of the major allele

alleleCount

public int alleleCount(int marker,
                       int allele)

Description copied from interface: SampleHapPairs

Returns the number of haplotypes that carry the specified allele.

Specified by:

alleleCount in interface SampleHapPairs

Parameters:

marker - a marker index

allele - an allele index

Returns:

the number of haplotypes that carry the specified allele

hapIndex

public int hapIndex(int marker,
                    int allele,
                    int copy)

Description copied from interface: SampleHapPairs

Returns index of the haplotype that carries the specified copy of the specified allele.

Specified by:

hapIndex in interface SampleHapPairs

Parameters:

marker - a marker index

allele - an allele index

copy - a copy index.

Returns:

index of the haplotype that carries the specified allele.