Package org.snpeff.vcf

Class VcfLof

java.lang.Object

org.snpeff.vcf.VcfLof

Direct Known Subclasses:

VcfNmd

public class VcfLof
extends java.lang.Object

An 'LOF' entry in a vcf line

Author:

pablocingolani

Constructor Summary

Constructors

Constructor	Description
VcfLof(java.lang.String lofStr)
VcfLof(java.lang.String geneName, java.lang.String geneId, int numTranscripts, double percentAffected)
VcfLof(Gene gene, double percentAffected)
VcfLof(VcfEntry vcfEntry, java.lang.String lofStr)

Method Summary

Modifier and Type	Method	Description
static int	fieldNum(java.lang.String name)	Convert from field name to field number
java.lang.String	getGeneId()
java.lang.String	getGeneName()
int	getNumTranscripts()
double	getPercentAffected()
java.lang.String	getPercentAffectedStr()
VcfEntry	getVcfEntry()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfLof

public VcfLof(Gene gene,
              double percentAffected)

VcfLof

public VcfLof(java.lang.String lofStr)

VcfLof

public VcfLof(java.lang.String geneName,
              java.lang.String geneId,
              int numTranscripts,
              double percentAffected)

VcfLof

public VcfLof(VcfEntry vcfEntry,
              java.lang.String lofStr)

Method Detail

fieldNum

public static int fieldNum(java.lang.String name)

Convert from field name to field number

getGeneId

public java.lang.String getGeneId()

getGeneName

public java.lang.String getGeneName()

getNumTranscripts

public int getNumTranscripts()

getPercentAffected

public double getPercentAffected()

getPercentAffectedStr

public java.lang.String getPercentAffectedStr()

getVcfEntry

public VcfEntry getVcfEntry()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object