haplotype

Class BasicHapPairs

java.lang.Object

haplotype.BasicHapPairs

All Implemented Interfaces:

HapPairs

public final class BasicHapPairs
extends java.lang.Object
implements HapPairs

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

Instances of class BasicHapPairs are immutable.

Constructor Summary

Constructors

Constructor and Description
BasicHapPairs(java.util.List<HapPair> hapPairList) Constructs a new BasicHapPairs instance corresponding to the specified list of haplotype pairs.

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.
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.
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(int hapPair) Returns a list of samples containing the sample associated with the specified 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

BasicHapPairs

public BasicHapPairs(java.util.List<HapPair> hapPairList)

Constructs a new BasicHapPairs instance corresponding to the specified list of haplotype pairs.

Parameters:

hapPairList - a list of haplotype pairs

Throws:

java.lang.IllegalArgumentException - if hapPairList.isEmpty() == true

java.lang.NullPointerException - if (hapPairList == null || hapPairList[j] == null) for any j satisfying (0 <= j && j < hapPairsList.size())

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

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()

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