vcf

Class HbdAL

java.lang.Object

vcf.HbdAL

All Implemented Interfaces:

AL

public final class HbdAL
extends java.lang.Object
implements AL

Class HbdAL represents allele emission probabilities for a set of haplotype pairs under a homozygosity by descent (HBD) model.

Instances of class HbdAL are immutable.

Constructor Summary

Constructors

Constructor and Description
HbdAL(GL gl) Constructs an HbdAL instance.

Method Summary

Modifier and Type	Method and Description
float	al(int marker, int haplotype, int allele) Returns the probability of the observed data if the specified allele is the true allele for the specified marker and haplotype.
int	allele(int marker, int haplotype) Returns the allele on the specified haplotype if the allele emission probabilities are determined by a called allele, and returns -1 otherwise.
float	errProb() Returns the allelic error probability.
Marker	marker(int markerIndex) 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.
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

HbdAL

public HbdAL(GL gl)

Constructs an HbdAL instance.

Parameters:

gl - genotype emission probabilities.

Throws:

java.lang.NullPointerException - if gl==null.

Method Detail

al

public float al(int marker,
                int haplotype,
                int allele)

Description copied from interface: AL

Returns the probability of the observed data if the specified allele is the true allele for the specified marker and haplotype.

Specified by:

al in interface AL

Parameters:

marker - a marker index

haplotype - a haplotype index

allele - a allele index

Returns:

the probability of the observed data if the specified allele is the true allele for the specified marker and haplotype

allele

public int allele(int marker,
                  int haplotype)

Description copied from interface: AL

Returns the allele on the specified haplotype if the allele emission probabilities are determined by a called allele, and returns -1 otherwise.

Specified by:

allele in interface AL

Parameters:

marker - a marker index

haplotype - a haplotype index

Returns:

the allele on the specified haplotype if the allele emission probabilities are determined by a called allele, and returns -1 otherwise

nMarkers

public int nMarkers()

Description copied from interface: AL

Returns the number of markers.

Specified by:

nMarkers in interface AL

Returns:

the number of markers

marker

public Marker marker(int markerIndex)

Description copied from interface: AL

Returns the specified marker.

Specified by:

marker in interface AL

Parameters:

markerIndex - the marker index

Returns:

the specified marker

markers

public Markers markers()

Description copied from interface: AL

Returns the list of markers.

Specified by:

markers in interface AL

Returns:

the list of markers

nSamples

public int nSamples()

Description copied from interface: AL

Returns the number of samples.

Specified by:

nSamples in interface AL

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: AL

Returns the list of samples.

Specified by:

samples in interface AL

Returns:

the list of samples

nHaps

public int nHaps()

Description copied from interface: AL

Returns the number of haplotypes.

Specified by:

nHaps in interface AL

Returns:

the number of haplotypes

errProb

public float errProb()

Description copied from interface: AL

Returns the allelic error probability.

Specified by:

errProb in interface AL

Returns:

the allelic error probability

toString

public java.lang.String toString()

Description copied from interface: AL

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

Specified by:

toString in interface AL

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this