org.broadinstitute.hellbender.utils.genotyper

Interface SampleList

All Known Subinterfaces:

PloidyModel

All Known Implementing Classes:

GenotypingData, GenotypingLikelihoods, HeterogeneousPloidyModel, HomogeneousPloidyModel, IndexedSampleList, ReadLikelihoods, UnfilledReadsLikelihoods

public interface SampleList

An immutable, indexed set of samples.

Implementing classes must guarantee that the sample list will remain constant through the life of the object.

Field Summary

Fields

Modifier and Type	Field and Description
static SampleList	EMPTY_LIST

Method Summary

Modifier and Type	Method and Description
default java.util.List<java.lang.String>	asListOfSamples() Returns a List unmodifiable view of a sample-list
default java.util.Set<java.lang.String>	asSetOfSamples() Returns a Set unmodifiable view of the sample-list
static SampleList	emptySampleList() Empty list.
static boolean	equals(SampleList first, SampleList second) Checks whether two sample lists are in fact the same.
java.lang.String	getSample(int sampleIndex) Returns the element given its index within the set.
int	indexOfSample(java.lang.String sample) Returns the index of an object.
int	numberOfSamples() Returns number of elements in the list.
static SampleList	singletonSampleList(java.lang.String sampleName) Creates a list with a single sample.

Field Detail

EMPTY_LIST

static final SampleList EMPTY_LIST

Method Detail

emptySampleList

static SampleList emptySampleList()

Empty list.

Returns:

never null

numberOfSamples

int numberOfSamples()

Returns number of elements in the list.

indexOfSample

int indexOfSample(java.lang.String sample)

Returns the index of an object.

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,numberOfSamples()).

Throws:

java.lang.IllegalArgumentException - if sample is null.

getSample

java.lang.String getSample(int sampleIndex)

Returns the element given its index within the set.

Parameters:

sampleIndex - the target samples's index.

Returns:

never null; as null is not a valid element.

Throws:

java.lang.IllegalArgumentException - if index is not valid; in [0,numberOfSamples()).

equals

static boolean equals(SampleList first,
                      SampleList second)

Checks whether two sample lists are in fact the same.

Parameters:

first - one list to compare.

second - another list to compare.

Returns:

true iff both list are equal.

Throws:

java.lang.IllegalArgumentException - if if either list is null.

asListOfSamples

default java.util.List<java.lang.String> asListOfSamples()

Returns a List unmodifiable view of a sample-list

Returns:

Unmodifiable view of the sample list. Never null.

Throws:

java.lang.IllegalArgumentException - if list is null.

asSetOfSamples

default java.util.Set<java.lang.String> asSetOfSamples()

Returns a Set unmodifiable view of the sample-list

Returns:

Unmodifiable view of the sample set. Never null.

singletonSampleList

static SampleList singletonSampleList(java.lang.String sampleName)

Creates a list with a single sample.

Parameters:

sampleName - the sample name.

Returns:

never sampleName