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Interface HapAlleleProbs

All Known Implementing Classes:

LowMemHapAlleleProbs

public interface HapAlleleProbs

Interface HapAlleleProbs stores allele probabilities for a haplotype.

All instances of HapAlleleProbs are required to be immutable.

Method Summary

Modifier and Type	Method and Description
float	allele(int marker, int allele) Returns the specified allele probability.
int	alleleWithMaxProb(int marker) Returns the allele with maximum posterior probability.
int	hapIndex() Returns the haplotype index.
Marker	marker(int marker) Returns the specified marker.
Markers	markers() Returns the list of markers.
int	nMarkers() Returns the number of markers.
Samples	samples() Returns the list of samples.

Method Detail

allele

float allele(int marker,
             int allele)

Returns the specified allele probability.

Parameters:

marker - a marker index

allele - an allele index

Returns:

the specified allele probability

Throws:

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

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

alleleWithMaxProb

int alleleWithMaxProb(int marker)

Returns the allele with maximum posterior probability. If more than one allele has maximum posterior probability, one of the alleles with maximum posterior probability will be returned.

Parameters:

marker - a marker index

Returns:

the allele with maximum posterior probability

Throws:

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

nMarkers

int nMarkers()

Returns the number of markers.

Returns:

the number of markers

markers

Markers markers()

Returns the list of markers.

Returns:

the list of markers

marker

Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - a marker index

Returns:

the specified marker

Throws:

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

hapIndex

int hapIndex()

Returns the haplotype index. The two haplotypes for sample k have indices 2*k and 2*k + 1.

Returns:

the haplotype index

samples

Samples samples()

Returns the list of samples.

Returns:

the list of samples