Package org.snpeff.nextProt

Class NextProtXmlIsoform

java.lang.Object

org.snpeff.nextProt.NextProtXmlNode

org.snpeff.nextProt.NextProtXmlIsoform

public class NextProtXmlIsoform
extends NextProtXmlNode

Mimics the 'isoform-mapping' in a NextProt XML file

Author:

Pablo Cingolani

Constructor Summary

Constructors

Constructor	Description
NextProtXmlIsoform(java.lang.String accession)

Method Summary

Modifier and Type	Method	Description
void	addProteinMapping(org.xml.sax.Attributes attributes)	Add a transcript mapping
void	addTranscriptMapping(org.xml.sax.Attributes attributes)	Add a protein mapping
java.util.Set<java.lang.String>	getProteinIds()
java.lang.String	getSequence()
java.util.Set<java.lang.String>	getTranscriptIds()
void	setSequence(java.lang.String sequence)	Add an Isoform sequence
java.lang.String	toString()

Methods inherited from class org.snpeff.nextProt.NextProtXmlNode

getAccession

Methods inherited from class java.lang.Object

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

Constructor Detail

NextProtXmlIsoform

public NextProtXmlIsoform(java.lang.String accession)

Method Detail

addProteinMapping

public void addProteinMapping(org.xml.sax.Attributes attributes)

Add a transcript mapping

addTranscriptMapping

public void addTranscriptMapping(org.xml.sax.Attributes attributes)

Add a protein mapping

getProteinIds

public java.util.Set<java.lang.String> getProteinIds()

getSequence

public java.lang.String getSequence()

getTranscriptIds

public java.util.Set<java.lang.String> getTranscriptIds()

setSequence

public void setSequence(java.lang.String sequence)

Add an Isoform sequence

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object