vcf

Interface AL

All Known Implementing Classes:

HbdAL

public interface AL

Interface AL (Allele Likelihoods) represents allele likelihoods for a set of haplotypes.

Instances of class AL are required to be immutable.

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

Method Detail

al

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.

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

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

java.lang.IndexOutOfBoundsException - if haplotype < 0 || haplotype >= this.nHaps()

java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.marker(marker).nAlleles()

allele

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.

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

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()

nMarkers

int nMarkers()

Returns the number of markers.

Returns:

the number of markers

marker

Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - the marker index

Returns:

the specified marker

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()

markers

Markers markers()

Returns the list of markers.

Returns:

the list of markers

nSamples

int nSamples()

Returns the number of samples.

Returns:

the number of samples

samples

Samples samples()

Returns the list of samples.

Returns:

the list of samples

nHaps

int nHaps()

Returns the number of haplotypes.

Returns:

the number of haplotypes

errProb

float errProb()

Returns the allelic error probability.

Returns:

the allelic error probability

toString

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