main

Class ConstrainedAlleleProbs

java.lang.Object

main.ConstrainedAlleleProbs

All Implemented Interfaces:

AlleleProbs

public class ConstrainedAlleleProbs
extends java.lang.Object
implements AlleleProbs

Class ConstrainedAlleleProbs is a wrapper for an AlleleProbs instance that changes the wrapped haplotype allele probabilities for a subset of markers.

Instances of class ConstrainedAlleleProbs are immutable.

Constructor Summary

Constructors

Constructor and Description
ConstrainedAlleleProbs(SampleHapPairs shp, AlleleProbs alProbs, int[] indexMap) Construct a new ConstrainedAlleleProbs instance.

Method Summary

Modifier and Type	Method and Description
int	allele1(int marker, int sample) Returns the marker allele with maximum probability for the first haplotype of the specified sample.
int	allele2(int marker, int sample) Returns the marker allele with maximum probability for the second haplotype of the specified sample.
float	alProb1(int marker, int sample, int allele) Returns the probability that the specified marker allele is present on the first haplotype of the specified sample.
float	alProb2(int marker, int sample, int allele) Returns the probability that the specified marker allele is present on the second haplotype of the specified sample.
float	gtProb(int marker, int sample, int allele1, int allele2) Returns the phased genotype probability, equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2)).
boolean	isImputed(int marker) Returns true if the specified marker is not present in the input data and returns false otherwise.
Marker	marker(int marker) Returns the specified marker.
Markers	markers() Returns the list of markers.
int	nMarkers() Returns the number of markers.
int	nSamples() Returns the number of samples.
Samples	samples() Returns the list of samples.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConstrainedAlleleProbs

public ConstrainedAlleleProbs(SampleHapPairs shp,
                              AlleleProbs alProbs,
                              int[] indexMap)

Construct a new ConstrainedAlleleProbs instance. The alleles in the specified SampleHapPairs object will have probability 1 in the new ConstrainedAlleleProbs object. All other allele probabilities in the constructed object are determined by the wrapped AlleleProbs object.

Parameters:

shp - phased haplotype pairs for a subset of markers

alProbs - the allele probabilities

indexMap - an array of length alProbs.nMarkers() whose j-th element is the index of marker alProbs.marker(j) in shp.markers(), or is -1 if the marker is not present in shp.markers()

Throws:

java.lang.IllegalArgumentException - if alProbs.nMarkers() != indexMap.length

java.lang.IllegalArgumentException - if (indexMap[j] != -1 && alProbs.marker(j).equals(shp.marker(indexMap[j])) == false) for any j satisfying (0 <= j && j < indexMap.length)

java.lang.NullPointerException - if shp == null || alProbs == null || indexMap == null

Method Detail

isImputed

public boolean isImputed(int marker)

Returns true if the specified marker is not present in the input data and returns false otherwise.

Parameters:

marker - a marker index

Returns:

true if the specified marker is not present in the input target data

Throws:

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

alProb1

public float alProb1(int marker,
                     int sample,
                     int allele)

Description copied from interface: AlleleProbs

Returns the probability that the specified marker allele is present on the first haplotype of the specified sample.

Specified by:

alProb1 in interface AlleleProbs

Parameters:

marker - a marker index

sample - a sample index

allele - an allele index

Returns:

the probability that the specified marker allele is present on the first haplotype of the specified sample

alProb2

public float alProb2(int marker,
                     int sample,
                     int allele)

Description copied from interface: AlleleProbs

Returns the probability that the specified marker allele is present on the second haplotype of the specified sample.

Specified by:

alProb2 in interface AlleleProbs

Parameters:

marker - a marker index

sample - a sample index

allele - an allele index

Returns:

the probability that the specified marker allele is present on the second haplotype of the specified sample.

gtProb

public float gtProb(int marker,
                    int sample,
                    int allele1,
                    int allele2)

Description copied from interface: AlleleProbs

Returns the phased genotype probability, equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2)).

Specified by:

gtProb in interface AlleleProbs

Parameters:

marker - a marker index

sample - a sample index

allele1 - allele index of the allele on the first haplotype

allele2 - allele index of the allele on the second haplotype

Returns:

the phased genotype probability equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2))

allele1

public int allele1(int marker,
                   int sample)

Description copied from interface: AlleleProbs

Returns the marker allele with maximum probability for the first haplotype of the specified sample. If more than one allele has maximum probability, one of the alleles with maximum probability will be returned.

Specified by:

allele1 in interface AlleleProbs

Parameters:

marker - a marker index

sample - a sample index

Returns:

the marker allele with maximum probability for the first haplotype of the specified sample

allele2

public int allele2(int marker,
                   int sample)

Description copied from interface: AlleleProbs

Returns the marker allele with maximum probability for the second haplotype of the specified sample. If more than one allele has maximum probability, one of the alleles with maximum probability will be returned.

Specified by:

allele2 in interface AlleleProbs

Parameters:

marker - a marker index

sample - a sample index

Returns:

the marker allele with maximum probability for the second haplotype of the specified sample

nMarkers

public int nMarkers()

Description copied from interface: AlleleProbs

Returns the number of markers.

Specified by:

nMarkers in interface AlleleProbs

Returns:

the number of markers

markers

public Markers markers()

Description copied from interface: AlleleProbs

Returns the list of markers.

Specified by:

markers in interface AlleleProbs

Returns:

the list of markers

marker

public Marker marker(int marker)

Description copied from interface: AlleleProbs

Returns the specified marker.

Specified by:

marker in interface AlleleProbs

Parameters:

marker - a marker index

Returns:

the specified marker

nSamples

public int nSamples()

Description copied from interface: AlleleProbs

Returns the number of samples.

Specified by:

nSamples in interface AlleleProbs

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: AlleleProbs

Returns the list of samples.

Specified by:

samples in interface AlleleProbs

Returns:

the list of samples