Package vcf

Class PhasedGTWrapper

java.lang.Object

vcf.PhasedGTWrapper

All Implemented Interfaces:

GT, PhasedGT

public class PhasedGTWrapper
extends java.lang.Object
implements PhasedGT

Class PhasedGTWrapper wraps a GT instance which satisfies gt.isPhased() == true.

Instances of class PhasedGTWrapper are immutable.

Constructor Summary

Constructors

Constructor	Description
PhasedGTWrapper(GT gt)	Constructs a new PhasedGTWrapper instance from the specified data.

Method Summary

Modifier and Type	Method	Description
int	allele1(int marker, int hapPair)	Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
int	allele2(int marker, int hapPair)	Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the list of markers.
int	nHaps()	Returns the number of haplotypes.
int	nMarkers()	Returns the number of markers.
int	nSamples()	Returns the number of samples.
Samples	samples()	Returns the list of samples.

Methods inherited from interface vcf.GT

allele, gl, isGTData

Methods inherited from class java.lang.Object

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

Methods inherited from interface vcf.PhasedGT

alProb1, alProb2, gtProb, isPhased, isPhased, isPhased

Constructor Detail

PhasedGTWrapper

public PhasedGTWrapper(GT gt)

Constructs a new PhasedGTWrapper instance from the specified data.

Parameters:

gt - the phased, non-missing genotypes to be wrapped

Throws:

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

java.lang.NullPointerException - if gt == null

Method Detail

samples

public Samples samples()

Description copied from interface: GT

Returns the list of samples.

Specified by:

samples in interface GT

Returns:

the list of samples

nSamples

public int nSamples()

Description copied from interface: GT

Returns the number of samples.

Specified by:

nSamples in interface GT

Returns:

the number of samples

allele1

public int allele1(int marker,
                   int hapPair)

Description copied from interface: GT

Returns the first allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.

Specified by:

allele1 in interface GT

Parameters:

marker - the marker index

hapPair - the sample index

Returns:

the first allele for the specified marker and sample

allele2

public int allele2(int marker,
                   int hapPair)

Description copied from interface: GT

Returns the second allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.

Specified by:

allele2 in interface GT

Parameters:

marker - the marker index

hapPair - the sample index

Returns:

the allele for the specified marker and sample

nMarkers

public int nMarkers()

Description copied from interface: GT

Returns the number of markers.

Specified by:

nMarkers in interface GT

Returns:

the number of markers

markers

public Markers markers()

Description copied from interface: GT

Returns the list of markers.

Specified by:

markers in interface GT

Returns:

the list of markers

marker

public Marker marker(int marker)

Description copied from interface: GT

Returns the specified marker.

Specified by:

marker in interface GT

Parameters:

marker - a marker index

Returns:

the specified marker

nHaps

public int nHaps()

Description copied from interface: GT

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

Specified by:

nHaps in interface GT

Returns:

the number of haplotypes