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Class LowMemHapAlleleProbs

java.lang.Object

main.LowMemHapAlleleProbs

All Implemented Interfaces:

HapAlleleProbs

public class LowMemHapAlleleProbs
extends java.lang.Object
implements HapAlleleProbs

Class LowMemHapAlleleProbs stores allele probabilities for a haplotype.

Instances of class LowMemHapAlleleProbs are immutable.

Constructor Summary

Constructors

Constructor and Description
LowMemHapAlleleProbs(Markers markers, Samples samples, int hap, float[] alleleProbs) Constructs a new LowMemHapAlleleProbs instance.

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.
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

LowMemHapAlleleProbs

public LowMemHapAlleleProbs(Markers markers,
                            Samples samples,
                            int hap,
                            float[] alleleProbs)

Constructs a new LowMemHapAlleleProbs instance. The alleleProbs array lists the probability of each allele for each marker, sorted first by marker index, and then by allele index.

Parameters:

markers - the markers

samples - the samples

hap - the haplotype index

alleleProbs - the allele probabilities

Throws:

java.lang.IllegalArgumentException - if alleleProbs.length != markers.sumAlleles()

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= 2*samples.nSamples()

java.lang.NullPointerException - if markers == null || samples == null

Method Detail

allele

public float allele(int marker,
                    int allele)

Description copied from interface: HapAlleleProbs

Returns the specified allele probability.

Specified by:

allele in interface HapAlleleProbs

Parameters:

marker - a marker index

allele - an allele index

Returns:

the specified allele probability

alleleWithMaxProb

public int alleleWithMaxProb(int marker)

Description copied from interface: HapAlleleProbs

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.

Specified by:

alleleWithMaxProb in interface HapAlleleProbs

Parameters:

marker - a marker index

Returns:

the allele with maximum posterior probability

nMarkers

public int nMarkers()

Description copied from interface: HapAlleleProbs

Returns the number of markers.

Specified by:

nMarkers in interface HapAlleleProbs

Returns:

the number of markers

markers

public Markers markers()

Description copied from interface: HapAlleleProbs

Returns the list of markers.

Specified by:

markers in interface HapAlleleProbs

Returns:

the list of markers

marker

public Marker marker(int marker)

Description copied from interface: HapAlleleProbs

Returns the specified marker.

Specified by:

marker in interface HapAlleleProbs

Parameters:

marker - a marker index

Returns:

the specified marker

hapIndex

public int hapIndex()

Description copied from interface: HapAlleleProbs

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

Specified by:

hapIndex in interface HapAlleleProbs

Returns:

the haplotype index

samples

public Samples samples()

Description copied from interface: HapAlleleProbs

Returns the list of samples.

Specified by:

samples in interface HapAlleleProbs

Returns:

the list of 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