org.broadinstitute.hellbender.tools.walkers.genotyper

Class HomogeneousPloidyModel

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel

All Implemented Interfaces:

PloidyModel, SampleList

public final class HomogeneousPloidyModel
extends java.lang.Object
implements PloidyModel

PloidyModel implementation tailored to work with a homogeneous constant ploidy across samples and positions.

Field Summary

Fields inherited from interface org.broadinstitute.hellbender.utils.genotyper.SampleList

EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
HomogeneousPloidyModel(SampleList sampleList, int ploidy) Constructs a homogeneous ploidy model given the sample list and ploidy.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getSample(int index) Returns the element given its index within the set.
int	indexOfSample(java.lang.String sample) Returns the index of an object.
boolean	isHomogeneous() Checks whether the ploidy is homogeneous across all samples.
int	numberOfSamples() Returns number of elements in the list.
int	samplePloidy(int sampleIndex) Return the assumed ploidy for a sample given its index.
int	totalPloidy() Sum of all ploidy across all samples.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.broadinstitute.hellbender.utils.genotyper.SampleList

asListOfSamples, asSetOfSamples, emptySampleList, equals, singletonSampleList

Constructor Detail

HomogeneousPloidyModel

public HomogeneousPloidyModel(SampleList sampleList,
                              int ploidy)

Constructs a homogeneous ploidy model given the sample list and ploidy.

Parameters:

sampleList - the sample list.

ploidy - the common ploidy for all samples in samples.

Throws:

java.lang.IllegalArgumentException - if sampleList is null, or ploidy is 0 or less.

Method Detail

numberOfSamples

public int numberOfSamples()

Description copied from interface: SampleList

Returns number of elements in the list.

Specified by:

numberOfSamples in interface SampleList

getSample

public java.lang.String getSample(int index)

Description copied from interface: SampleList

Returns the element given its index within the set.

Specified by:

getSample in interface SampleList

Parameters:

index - the target samples's index.

Returns:

never null; as null is not a valid element.

indexOfSample

public int indexOfSample(java.lang.String sample)

Description copied from interface: SampleList

Returns the index of an object.

Specified by:

indexOfSample in interface SampleList

Parameters:

sample - the sample of interest.

Returns:

-1 if such a sample is not an element of this set, otherwise is index in the set thus a values within [0,SampleList.numberOfSamples()).

samplePloidy

public int samplePloidy(int sampleIndex)

Description copied from interface: PloidyModel

Return the assumed ploidy for a sample given its index.

Specified by:

samplePloidy in interface PloidyModel

Parameters:

sampleIndex - target sample index.

Returns:

0 or greater.

isHomogeneous

public boolean isHomogeneous()

Description copied from interface: PloidyModel

Checks whether the ploidy is homogeneous across all samples.

Specified by:

isHomogeneous in interface PloidyModel

Returns:

true if all samples has the same ploidy.

totalPloidy

public int totalPloidy()

Description copied from interface: PloidyModel

Sum of all ploidy across all samples.

It must match the sum of all ploidies across samples.

Specified by:

totalPloidy in interface PloidyModel

Returns:

0 or greater.