Package htsjdk.variant.variantcontext

Class LazyGenotypesContext

java.lang.Object

htsjdk.variant.variantcontext.GenotypesContext

htsjdk.variant.variantcontext.LazyGenotypesContext

All Implemented Interfaces:

Serializable, Iterable<Genotype>, Collection<Genotype>, List<Genotype>

public class LazyGenotypesContext
extends GenotypesContext

Lazy-loading GenotypesContext. A lazy-loading context has access to the VCFParser and a unparsed string of genotype data. If the user attempts to manipulate the genotypes contained in this context, we decode the data and become a full blown GenotypesContext. However, if the user never does this we are spared a lot of expense decoding the genotypes unnecessarily.

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	LazyGenotypesContext.LazyData	Returns the data used in the full GenotypesContext constructor GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)
static interface	LazyGenotypesContext.LazyParser	Simple lazy parser interface.

Field Summary

Fields inherited from class htsjdk.variant.variantcontext.GenotypesContext

NO_GENOTYPES, notToBeDirectlyAccessedGenotypes, sampleNamesInOrder, sampleNameToOffset, serialVersionUID

Constructor Summary

Constructors

Constructor	Description
LazyGenotypesContext(LazyGenotypesContext.LazyParser parser, Object unparsedGenotypeData, int nUnparsedGenotypes)	Creates a new lazy loading genotypes context using the LazyParser to create genotypes data on demand.

Method Summary

Modifier and Type	Method	Description
void	decode()	Force us to decode the genotypes, if not already done
protected void	ensureSampleNameMap()	Overrides the ensure* functionality.
protected void	ensureSampleOrdering()
protected ArrayList<Genotype>	getGenotypes()	Overrides the genotypes accessor.
Object	getUnparsedGenotypeData()
protected void	invalidateSampleNameMap()
protected void	invalidateSampleOrdering()
boolean	isEmpty()
int	size()

Methods inherited from class htsjdk.variant.variantcontext.GenotypesContext

add, add, addAll, addAll, checkImmutability, clear, contains, containsAll, containsSample, containsSamples, copy, copy, create, create, create, create, create, get, get, getMaxPloidy, getSampleNames, getSampleNamesOrderedByName, immutable, indexOf, isLazyWithData, isMutable, iterateInSampleNameOrder, iterateInSampleNameOrder, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, replace, retainAll, set, subList, subsetToSamples, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Constructor Details

LazyGenotypesContext

public LazyGenotypesContext(LazyGenotypesContext.LazyParser parser,
 Object unparsedGenotypeData,
 int nUnparsedGenotypes)

Creates a new lazy loading genotypes context using the LazyParser to create genotypes data on demand.

Parameters:

parser - the parser to be used to load on-demand genotypes data

unparsedGenotypeData - the encoded genotypes data that we will decode if necessary

nUnparsedGenotypes - the number of genotypes that will be produced if / when we actually decode the genotypes data

Method Details

getGenotypes

protected ArrayList<Genotype> getGenotypes()

Overrides the genotypes accessor. If we haven't already, decode the genotypes data and store the decoded results in the appropriate variables. Otherwise we just returned the decoded result directly. Note some care needs to be taken here as the value in notToBeDirectlyAccessedGenotypes may diverge from what would be produced by decode, if after the first decode the genotypes themselves are replaced

Overrides:

getGenotypes in class GenotypesContext

Returns:

decode

public void decode()

Force us to decode the genotypes, if not already done

ensureSampleNameMap

protected void ensureSampleNameMap()

Overrides the ensure* functionality. If the data hasn't been loaded yet and we want to build the cache, just decode it and we're done. If we've already decoded the data, though, go through the super class

Overrides:

ensureSampleNameMap in class GenotypesContext

ensureSampleOrdering

protected void ensureSampleOrdering()

Overrides:

ensureSampleOrdering in class GenotypesContext

invalidateSampleNameMap

protected void invalidateSampleNameMap()

Overrides:

invalidateSampleNameMap in class GenotypesContext

invalidateSampleOrdering

protected void invalidateSampleOrdering()

Overrides:

invalidateSampleOrdering in class GenotypesContext

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<Genotype>

Specified by:

isEmpty in interface List<Genotype>

Overrides:

isEmpty in class GenotypesContext

size

public int size()

Specified by:

size in interface Collection<Genotype>

Specified by:

size in interface List<Genotype>

Overrides:

size in class GenotypesContext

getUnparsedGenotypeData

public Object getUnparsedGenotypeData()