htsjdk.variant.variantcontext

Class GenotypesContext

java.lang.Object

htsjdk.variant.variantcontext.GenotypesContext

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<Genotype>, java.util.Collection<Genotype>, java.util.List<Genotype>

Direct Known Subclasses:

LazyGenotypesContext

public class GenotypesContext
extends java.lang.Object
implements java.util.List<Genotype>, java.io.Serializable

Represents an ordered collection of Genotype objects

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static GenotypesContext	NO_GENOTYPES static constant value for an empty GenotypesContext.
protected java.util.ArrayList<Genotype>	notToBeDirectlyAccessedGenotypes An ArrayList of genotypes contained in this context WARNING: TO ENABLE THE LAZY VERSION OF THIS CLASS, NO METHODS SHOULD DIRECTLY ACCESS THIS VARIABLE.
protected java.util.List<java.lang.String>	sampleNamesInOrder sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order
protected java.util.Map<java.lang.String,java.lang.Integer>	sampleNameToOffset a map optimized for efficient lookup.
static long	serialVersionUID

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	GenotypesContext() Create an empty GenotypeContext
protected	GenotypesContext(java.util.ArrayList<Genotype> genotypes) Create an GenotypeContext containing genotypes
protected	GenotypesContext(java.util.ArrayList<Genotype> genotypes, java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset, java.util.List<java.lang.String> sampleNamesInOrder) Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names
protected	GenotypesContext(int n) Create an empty GenotypeContext, with initial capacity for n elements

Method Summary

Modifier and Type	Method and Description
boolean	add(Genotype genotype) Adds a single genotype to this context.
void	add(int i, Genotype genotype)
boolean	addAll(java.util.Collection<? extends Genotype> genotypes) Adds all of the genotypes to this context See add(Genotype) for important information about this functions constraints and performance costs
boolean	addAll(int i, java.util.Collection<? extends Genotype> genotypes)
void	checkImmutability()
void	clear()
boolean	contains(java.lang.Object o)
boolean	containsAll(java.util.Collection<?> objects)
boolean	containsSample(java.lang.String sample)
boolean	containsSamples(java.util.Collection<java.lang.String> samples)
static GenotypesContext	copy(java.util.Collection<Genotype> toCopy) Create a GenotypesContext containing the genotypes in iteration order contained in toCopy
static GenotypesContext	copy(GenotypesContext toCopy) Create a freshly allocated GenotypeContext containing the genotypes in toCopy
static GenotypesContext	create() Basic creation routine
static GenotypesContext	create(java.util.ArrayList<Genotype> genotypes) Create a fully resolved GenotypeContext containing genotypes
static GenotypesContext	create(java.util.ArrayList<Genotype> genotypes, java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset, java.util.List<java.lang.String> sampleNamesInOrder) Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names
static GenotypesContext	create(Genotype... genotypes) Create a fully resolved GenotypeContext containing genotypes
static GenotypesContext	create(int nGenotypes) Basic creation routine
protected void	ensureSampleNameMap()
protected void	ensureSampleOrdering()
Genotype	get(int i)
Genotype	get(java.lang.String sampleName) Gets sample associated with this sampleName, or null if none is found
protected java.util.ArrayList<Genotype>	getGenotypes()
int	getMaxPloidy(int defaultPloidy) What is the max ploidy among all samples? Returns defaultPloidy if no genotypes are present
java.util.Set<java.lang.String>	getSampleNames()
java.util.List<java.lang.String>	getSampleNamesOrderedByName()
GenotypesContext	immutable()
int	indexOf(java.lang.Object o)
protected void	invalidateSampleNameMap()
protected void	invalidateSampleOrdering()
boolean	isEmpty()
boolean	isLazyWithData()
boolean	isMutable()
java.lang.Iterable<Genotype>	iterateInSampleNameOrder() Iterate over the Genotypes in this context in their sample name order (A, B, C) regardless of the underlying order in the vector of genotypes
java.lang.Iterable<Genotype>	iterateInSampleNameOrder(java.lang.Iterable<java.lang.String> sampleNamesInOrder) Iterate over the Genotypes in this context in the order specified by sampleNamesInOrder
java.util.Iterator<Genotype>	iterator()
int	lastIndexOf(java.lang.Object o)
java.util.ListIterator<Genotype>	listIterator()
java.util.ListIterator<Genotype>	listIterator(int i)
Genotype	remove(int i) Note that remove requires us to invalidate our sample -> index cache.
boolean	remove(java.lang.Object o) See for important warning remove(int)
boolean	removeAll(java.util.Collection<?> objects)
Genotype	replace(Genotype genotype) Replaces the genotype in this context -- note for efficiency reasons we do not add the genotype if it's not present.
boolean	retainAll(java.util.Collection<?> objects)
Genotype	set(int i, Genotype genotype)
int	size()
java.util.List<Genotype>	subList(int i, int i1)
GenotypesContext	subsetToSamples(java.util.Set<java.lang.String> samples) Return a freshly allocated subcontext of this context containing only the samples listed in samples.
java.lang.Object[]	toArray()
<T> T[]	toArray(T[] ts)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

NO_GENOTYPES

public static final GenotypesContext NO_GENOTYPES

static constant value for an empty GenotypesContext. Useful since so many VariantContexts have no genotypes

sampleNamesInOrder

protected java.util.List<java.lang.String> sampleNamesInOrder

sampleNamesInOrder a list of sample names, one for each genotype in genotypes, sorted in alphabetical order

sampleNameToOffset

protected java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset

a map optimized for efficient lookup. Each genotype in genotypes must have its sample name in sampleNameToOffset, with a corresponding integer value that indicates the offset of that genotype in the vector of genotypes

notToBeDirectlyAccessedGenotypes

protected java.util.ArrayList<Genotype> notToBeDirectlyAccessedGenotypes

An ArrayList of genotypes contained in this context WARNING: TO ENABLE THE LAZY VERSION OF THIS CLASS, NO METHODS SHOULD DIRECTLY ACCESS THIS VARIABLE. USE getGenotypes() INSTEAD.

Constructor Detail

GenotypesContext

protected GenotypesContext()

Create an empty GenotypeContext

GenotypesContext

protected GenotypesContext(int n)

Create an empty GenotypeContext, with initial capacity for n elements

GenotypesContext

protected GenotypesContext(java.util.ArrayList<Genotype> genotypes)

Create an GenotypeContext containing genotypes

GenotypesContext

protected GenotypesContext(java.util.ArrayList<Genotype> genotypes,
                           java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset,
                           java.util.List<java.lang.String> sampleNamesInOrder)

Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names

Parameters:

genotypes - our genotypes in arbitrary

sampleNameToOffset - map optimized for efficient lookup. Each genotype in genotypes must have its sample name in sampleNameToOffset, with a corresponding integer value that indicates the offset of that genotype in the vector of genotypes

sampleNamesInOrder - a list of sample names, one for each genotype in genotypes, sorted in alphabetical order.

Method Detail

create

public static final GenotypesContext create()

Basic creation routine

Returns:

an empty, mutable GenotypeContext

create

public static final GenotypesContext create(int nGenotypes)

Basic creation routine

Returns:

an empty, mutable GenotypeContext with initial capacity for nGenotypes

create

public static final GenotypesContext create(java.util.ArrayList<Genotype> genotypes,
                                            java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset,
                                            java.util.List<java.lang.String> sampleNamesInOrder)

Create a fully resolved GenotypeContext containing genotypes, sample lookup table, and sorted sample names

Parameters:

genotypes - our genotypes in arbitrary

sampleNameToOffset - map optimized for efficient lookup. Each genotype in genotypes must have its sample name in sampleNameToOffset, with a corresponding integer value that indicates the offset of that genotype in the vector of genotypes

sampleNamesInOrder - a list of sample names, one for each genotype in genotypes, sorted in alphabetical order.

Returns:

an mutable GenotypeContext containing genotypes with already present lookup data

create

public static final GenotypesContext create(java.util.ArrayList<Genotype> genotypes)

Create a fully resolved GenotypeContext containing genotypes

Parameters:

genotypes - our genotypes in arbitrary

Returns:

an mutable GenotypeContext containing genotypes

create

public static final GenotypesContext create(Genotype... genotypes)

Create a fully resolved GenotypeContext containing genotypes

Parameters:

genotypes - our genotypes in arbitrary

Returns:

an mutable GenotypeContext containing genotypes

copy

public static final GenotypesContext copy(GenotypesContext toCopy)

Create a freshly allocated GenotypeContext containing the genotypes in toCopy

Parameters:

toCopy - the GenotypesContext to copy

Returns:

an mutable GenotypeContext containing genotypes

copy

public static final GenotypesContext copy(java.util.Collection<Genotype> toCopy)

Create a GenotypesContext containing the genotypes in iteration order contained in toCopy

Parameters:

toCopy - the collection of genotypes

Returns:

an mutable GenotypeContext containing genotypes

immutable

public final GenotypesContext immutable()

isMutable

public boolean isMutable()

checkImmutability

public final void checkImmutability()

invalidateSampleNameMap

protected void invalidateSampleNameMap()

invalidateSampleOrdering

protected void invalidateSampleOrdering()

ensureSampleOrdering

protected void ensureSampleOrdering()

ensureSampleNameMap

protected void ensureSampleNameMap()

isLazyWithData

public boolean isLazyWithData()

getGenotypes

protected java.util.ArrayList<Genotype> getGenotypes()

clear

public void clear()

Specified by:

clear in interface java.util.Collection<Genotype>

Specified by:

clear in interface java.util.List<Genotype>

size

public int size()

Specified by:

size in interface java.util.Collection<Genotype>

Specified by:

size in interface java.util.List<Genotype>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection<Genotype>

Specified by:

isEmpty in interface java.util.List<Genotype>

add

public boolean add(Genotype genotype)

Adds a single genotype to this context. There are many constraints on this input, and important impacts on the performance of other functions provided by this context. First, the sample name of genotype must be unique within this context. However, this is not enforced in the code itself, through you will invalid the contract on this context if you add duplicate samples and are running with CoFoJa enabled. Second, adding genotype also updates the sample name -> index map, so add() followed by containsSample and related function is an efficient series of operations. Third, adding the genotype invalidates the sorted list of sample names, to add() followed by any of the SampleNamesInOrder operations is inefficient, as each SampleNamesInOrder must rebuild the sorted list of sample names at an O(n log n) cost.

Specified by:

add in interface java.util.Collection<Genotype>

Specified by:

add in interface java.util.List<Genotype>

Parameters:

genotype -

Returns:

add

public void add(int i,
                Genotype genotype)

Specified by:

add in interface java.util.List<Genotype>

addAll

public boolean addAll(java.util.Collection<? extends Genotype> genotypes)

Adds all of the genotypes to this context See add(Genotype) for important information about this functions constraints and performance costs

Specified by:

addAll in interface java.util.Collection<Genotype>

Specified by:

addAll in interface java.util.List<Genotype>

Parameters:

genotypes -

Returns:

addAll

public boolean addAll(int i,
                      java.util.Collection<? extends Genotype> genotypes)

Specified by:

addAll in interface java.util.List<Genotype>

contains

public boolean contains(java.lang.Object o)

Specified by:

contains in interface java.util.Collection<Genotype>

Specified by:

contains in interface java.util.List<Genotype>

containsAll

public boolean containsAll(java.util.Collection<?> objects)

Specified by:

containsAll in interface java.util.Collection<Genotype>

Specified by:

containsAll in interface java.util.List<Genotype>

get

public Genotype get(int i)

Specified by:

get in interface java.util.List<Genotype>

getMaxPloidy

public int getMaxPloidy(int defaultPloidy)

What is the max ploidy among all samples? Returns defaultPloidy if no genotypes are present

Parameters:

defaultPloidy - the default ploidy, if all samples are no-called

Returns:

get

public Genotype get(java.lang.String sampleName)

Gets sample associated with this sampleName, or null if none is found

Parameters:

sampleName -

Returns:

indexOf

public int indexOf(java.lang.Object o)

Specified by:

indexOf in interface java.util.List<Genotype>

iterator

public java.util.Iterator<Genotype> iterator()

Specified by:

iterator in interface java.lang.Iterable<Genotype>

Specified by:

iterator in interface java.util.Collection<Genotype>

Specified by:

iterator in interface java.util.List<Genotype>

lastIndexOf

public int lastIndexOf(java.lang.Object o)

Specified by:

lastIndexOf in interface java.util.List<Genotype>

listIterator

public java.util.ListIterator<Genotype> listIterator()

Specified by:

listIterator in interface java.util.List<Genotype>

listIterator

public java.util.ListIterator<Genotype> listIterator(int i)

Specified by:

listIterator in interface java.util.List<Genotype>

remove

public Genotype remove(int i)

Note that remove requires us to invalidate our sample -> index cache. The loop: GenotypesContext gc = ... for ( sample in samples ) if ( gc.containsSample(sample) ) gc.remove(sample) is extremely inefficient, as each call to remove invalidates the cache and containsSample requires us to rebuild it, an O(n) operation. If you must remove many samples from the GC, use either removeAll or retainAll to avoid this O(n * m) operation.

Specified by:

remove in interface java.util.List<Genotype>

Parameters:

i -

Returns:

remove

public boolean remove(java.lang.Object o)

See for important warning remove(int)

Specified by:

remove in interface java.util.Collection<Genotype>

Specified by:

remove in interface java.util.List<Genotype>

Parameters:

o -

Returns:

removeAll

public boolean removeAll(java.util.Collection<?> objects)

Specified by:

removeAll in interface java.util.Collection<Genotype>

Specified by:

removeAll in interface java.util.List<Genotype>

retainAll

public boolean retainAll(java.util.Collection<?> objects)

Specified by:

retainAll in interface java.util.Collection<Genotype>

Specified by:

retainAll in interface java.util.List<Genotype>

set

public Genotype set(int i,
                    Genotype genotype)

Specified by:

set in interface java.util.List<Genotype>

replace

public Genotype replace(Genotype genotype)

Replaces the genotype in this context -- note for efficiency reasons we do not add the genotype if it's not present. The return value will be null indicating this happened. Note this operation is preserves the map cache Sample -> Offset but invalidates the sorted list of samples. Using replace within a loop containing any of the SampleNameInOrder operation requires an O(n log n) resorting after each replace operation.

Parameters:

genotype - a non null genotype to bind in this context

Returns:

null if genotype was not added, otherwise returns the previous genotype

subList

public java.util.List<Genotype> subList(int i,
                                        int i1)

Specified by:

subList in interface java.util.List<Genotype>

toArray

public java.lang.Object[] toArray()

Specified by:

toArray in interface java.util.Collection<Genotype>

Specified by:

toArray in interface java.util.List<Genotype>

toArray

public <T> T[] toArray(T[] ts)

Specified by:

toArray in interface java.util.Collection<Genotype>

Specified by:

toArray in interface java.util.List<Genotype>

iterateInSampleNameOrder

public java.lang.Iterable<Genotype> iterateInSampleNameOrder(java.lang.Iterable<java.lang.String> sampleNamesInOrder)

Iterate over the Genotypes in this context in the order specified by sampleNamesInOrder

Parameters:

sampleNamesInOrder - a Iterable of String, containing exactly one entry for each Genotype sample name in this context

Returns:

a Iterable over the genotypes in this context.

iterateInSampleNameOrder

public java.lang.Iterable<Genotype> iterateInSampleNameOrder()

Iterate over the Genotypes in this context in their sample name order (A, B, C) regardless of the underlying order in the vector of genotypes

Returns:

a Iterable over the genotypes in this context.

getSampleNames

public java.util.Set<java.lang.String> getSampleNames()

Returns:

The set of sample names for all genotypes in this context, in arbitrary order

getSampleNamesOrderedByName

public java.util.List<java.lang.String> getSampleNamesOrderedByName()

Returns:

The set of sample names for all genotypes in this context, in their natural ordering (A, B, C)

containsSample

public boolean containsSample(java.lang.String sample)

containsSamples

public boolean containsSamples(java.util.Collection<java.lang.String> samples)

subsetToSamples

public GenotypesContext subsetToSamples(java.util.Set<java.lang.String> samples)

Return a freshly allocated subcontext of this context containing only the samples listed in samples. Note that samples can contain names not in this context, they will just be ignored.

Parameters:

samples -

Returns:

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object