Package org.pharmgkb.parser.vcf

Class MemoryMappedVcfDataStore

java.lang.Object

org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

public class MemoryMappedVcfDataStore
extends Object

See MemoryMappedVcfLineParser.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MemoryMappedVcfDataStore.Genotype
protected static class	MemoryMappedVcfDataStore.Locus

Constructor Summary

Constructors

Constructor	Description
MemoryMappedVcfDataStore()

Method Summary

Modifier and Type	Method	Description
Collection<VcfPosition>	getAllPositions()
Collection<List<VcfSample>>	getAllSamples()
MemoryMappedVcfDataStore.Genotype	getGenotypeAtLocus(String chromosome, long position, int sampleIndex)
MemoryMappedVcfDataStore.Genotype	getGenotypeAtLocus(String chromosome, long position, String sampleId)
MemoryMappedVcfDataStore.Genotype	getGenotypeForId(String positionId, int sampleIndex)
MemoryMappedVcfDataStore.Genotype	getGenotypeForId(String positionId, String sampleId)
protected Map<String,VcfPosition>	getIdToPosition()
protected Map<String,List<VcfSample>>	getIdToSamples()
protected Map<MemoryMappedVcfDataStore.Locus,VcfPosition>	getLocusToPosition()
protected Map<MemoryMappedVcfDataStore.Locus,List<VcfSample>>	getLocusToSamples()
VcfMetadata	getMetadata()
VcfPosition	getPositionAtLocus(String chromosome, long position)
VcfPosition	getPositionForId(String id)
VcfSample	getSampleAtLocus(String chromosome, long position, int sampleIndex)
VcfSample	getSampleAtLocus(String chromosome, long position, String sampleId)
VcfSample	getSampleForId(String positionId, int sampleIndex)
VcfSample	getSampleForId(String positionId, String sampleId)
List<VcfSample>	getSamplesAtLocus(String chromosome, long position)
List<VcfSample>	getSamplesForId(String id)
protected void	setIdToPosition(Map<String,VcfPosition> idToPosition)
protected void	setIdToSamples(Map<String,List<VcfSample>> idToSamples)
protected void	setLocusToPosition(Map<MemoryMappedVcfDataStore.Locus,VcfPosition> locusToPosition)
protected void	setLocusToSamples(Map<MemoryMappedVcfDataStore.Locus,List<VcfSample>> locusToSamples)
protected void	setMetadata(VcfMetadata metadata)

Methods inherited from class java.lang.Object

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

Constructor Details

MemoryMappedVcfDataStore

public MemoryMappedVcfDataStore()

Method Details

getAllPositions

@Nullable
public Collection<VcfPosition> getAllPositions()

Returns:

Every position read, or null if none no lines read.

getAllSamples

@Nullable
public Collection<List<VcfSample>> getAllSamples()

Returns:

The samples for every VCF record read, or null if no lines were read.

getMetadata

@Nullable
public VcfMetadata getMetadata()

Returns:

The metadata, or null if no lines were read.

setMetadata

protected void setMetadata(VcfMetadata metadata)

getPositionForId

@Nullable
public VcfPosition getPositionForId(@Nonnull
 String id)

getSamplesForId

@Nullable
public List<VcfSample> getSamplesForId(@Nonnull
 String id)

getPositionAtLocus

@Nullable
public VcfPosition getPositionAtLocus(@Nonnull
 String chromosome,
 long position)

getSamplesAtLocus

@Nullable
public List<VcfSample> getSamplesAtLocus(@Nonnull
 String chromosome,
 long position)

getSampleForId

@Nullable
public VcfSample getSampleForId(@Nonnull
 String positionId,
 @Nonnull
 String sampleId)

getSampleForId

@Nullable
public VcfSample getSampleForId(@Nonnull
 String positionId,
 int sampleIndex)

getSampleAtLocus

@Nullable
public VcfSample getSampleAtLocus(@Nonnull
 String chromosome,
 long position,
 @Nonnull
 String sampleId)

getSampleAtLocus

@Nullable
public VcfSample getSampleAtLocus(@Nonnull
 String chromosome,
 long position,
 int sampleIndex)

getGenotypeForId

@Nullable
public MemoryMappedVcfDataStore.Genotype getGenotypeForId(@Nonnull
 String positionId,
 String sampleId)

getGenotypeAtLocus

@Nullable
public MemoryMappedVcfDataStore.Genotype getGenotypeAtLocus(@Nonnull
 String chromosome,
 long position,
 String sampleId)

getGenotypeForId

@Nullable
public MemoryMappedVcfDataStore.Genotype getGenotypeForId(@Nonnull
 String positionId,
 int sampleIndex)

getGenotypeAtLocus

@Nullable
public MemoryMappedVcfDataStore.Genotype getGenotypeAtLocus(@Nonnull
 String chromosome,
 long position,
 int sampleIndex)

getIdToPosition

protected Map<String,VcfPosition> getIdToPosition()

setIdToPosition

protected void setIdToPosition(Map<String,VcfPosition> idToPosition)

getLocusToPosition

protected Map<MemoryMappedVcfDataStore.Locus,VcfPosition> getLocusToPosition()

setLocusToPosition

protected void setLocusToPosition(Map<MemoryMappedVcfDataStore.Locus,VcfPosition> locusToPosition)

getIdToSamples

protected Map<String,List<VcfSample>> getIdToSamples()

setIdToSamples

protected void setIdToSamples(Map<String,List<VcfSample>> idToSamples)

getLocusToSamples

protected Map<MemoryMappedVcfDataStore.Locus,List<VcfSample>> getLocusToSamples()

setLocusToSamples

protected void setLocusToSamples(Map<MemoryMappedVcfDataStore.Locus,List<VcfSample>> locusToSamples)