org.pharmgkb.parser.vcf

Class MemoryMappedVcfDataStore

java.lang.Object

org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

public class MemoryMappedVcfDataStore
extends java.lang.Object

See MemoryMappedVcfLineParser.

Nested Class Summary

Nested Classes

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

Constructor Summary

Constructors

Constructor and Description
MemoryMappedVcfDataStore()

Method Summary

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

MemoryMappedVcfDataStore

public MemoryMappedVcfDataStore()

Method Detail

getAllPositions

@Nullable
public java.util.Collection<VcfPosition> getAllPositions()

Returns:

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

getAllSamples

@Nullable
public java.util.Collection<java.util.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
                                               java.lang.String id)

getSamplesForId

@Nullable
public java.util.List<VcfSample> getSamplesForId(@Nonnull
                                                            java.lang.String id)

getPositionAtLocus

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

getSamplesAtLocus

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

getSampleForId

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

getSampleForId

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

getSampleAtLocus

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

getSampleAtLocus

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

getGenotypeForId

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

getGenotypeAtLocus

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

getGenotypeForId

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

getGenotypeAtLocus

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

getIdToPosition

protected java.util.Map<java.lang.String,VcfPosition> getIdToPosition()

setIdToPosition

protected void setIdToPosition(java.util.Map<java.lang.String,VcfPosition> idToPosition)

getLocusToPosition

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

setLocusToPosition

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

getIdToSamples

protected java.util.Map<java.lang.String,java.util.List<VcfSample>> getIdToSamples()

setIdToSamples

protected void setIdToSamples(java.util.Map<java.lang.String,java.util.List<VcfSample>> idToSamples)

getLocusToSamples

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

setLocusToSamples

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