pro.parseq.vcf.types

Class VcfFile

java.lang.Object

pro.parseq.vcf.types.VcfFile

public class VcfFile
extends Object

Class to hold VCF file data

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
VcfFile()

Method Summary

Modifier and Type	Method and Description
boolean	addDataLine(VcfLine dataLine)
boolean	addDataLineVariants(DataLine dataLine)
boolean	addLine(VcfLine line)
boolean	addMetaLine(Metadata metaLine)
boolean	addSampleName(String sampleName)
List<VcfLine>	getDataLines()
Map<String,Filter>	getFilters()
Map<String,Format>	getFormats()
Map<String,Information>	getInfos()
List<VcfLine>	getLines()
List<Metadata>	getMetaLines()
Map<String,List<Metadata>>	getOtherMetadata()
List<String>	getSampleNames()
List<Variant>	getVariants()
Filter	putFilter(Filter filter)
Format	putFormat(Format format)
Information	putInfo(Information info)
List<Metadata>	putOtherMetadata(Metadata other)
void	setDataLines(List<VcfLine> dataLines)
void	setFilters(Map<String,Filter> filters)
void	setFormats(Map<String,Format> formats)
void	setInfos(Map<String,Information> infos)
void	setLines(List<VcfLine> lines)
void	setMetaLines(List<Metadata> metaLines)
void	setOtherMetadata(Map<String,List<Metadata>> otherMetadata)
void	setSampleNames(List<String> sampleNames)
void	setVariants(List<Variant> variants)
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfFile

public VcfFile()

Method Detail

getLines

public List<VcfLine> getLines()

addLine

public boolean addLine(VcfLine line)

setLines

public void setLines(List<VcfLine> lines)

getMetaLines

public List<Metadata> getMetaLines()

addMetaLine

public boolean addMetaLine(Metadata metaLine)

setMetaLines

public void setMetaLines(List<Metadata> metaLines)

getDataLines

public List<VcfLine> getDataLines()

addDataLine

public boolean addDataLine(VcfLine dataLine)

setDataLines

public void setDataLines(List<VcfLine> dataLines)

getFilters

public Map<String,Filter> getFilters()

putFilter

public Filter putFilter(Filter filter)

setFilters

public void setFilters(Map<String,Filter> filters)

getFormats

public Map<String,Format> getFormats()

putFormat

public Format putFormat(Format format)

setFormats

public void setFormats(Map<String,Format> formats)

getInfos

public Map<String,Information> getInfos()

putInfo

public Information putInfo(Information info)

setInfos

public void setInfos(Map<String,Information> infos)

getOtherMetadata

public Map<String,List<Metadata>> getOtherMetadata()

putOtherMetadata

public List<Metadata> putOtherMetadata(Metadata other)

setOtherMetadata

public void setOtherMetadata(Map<String,List<Metadata>> otherMetadata)

getSampleNames

public List<String> getSampleNames()

addSampleName

public boolean addSampleName(String sampleName)

setSampleNames

public void setSampleNames(List<String> sampleNames)

getVariants

public List<Variant> getVariants()

addDataLineVariants

public boolean addDataLineVariants(DataLine dataLine)

setVariants

public void setVariants(List<Variant> variants)

size

public int size()