Package org.snpeff.nextProt
Class NextProtXmlIsoform
- java.lang.Object
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- org.snpeff.nextProt.NextProtXmlNode
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- org.snpeff.nextProt.NextProtXmlIsoform
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public class NextProtXmlIsoform extends NextProtXmlNode
Mimics the 'isoform-mapping' in a NextProt XML file- Author:
- Pablo Cingolani
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Constructor Summary
Constructors Constructor Description NextProtXmlIsoform(java.lang.String accession)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addProteinMapping(org.xml.sax.Attributes attributes)
Add a transcript mappingvoid
addTranscriptMapping(org.xml.sax.Attributes attributes)
Add a protein mappingjava.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 sequencejava.lang.String
toString()
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Methods inherited from class org.snpeff.nextProt.NextProtXmlNode
getAccession
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Method Detail
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addProteinMapping
public void addProteinMapping(org.xml.sax.Attributes attributes)
Add a transcript mapping
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addTranscriptMapping
public void addTranscriptMapping(org.xml.sax.Attributes attributes)
Add a protein mapping
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getProteinIds
public java.util.Set<java.lang.String> getProteinIds()
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getSequence
public java.lang.String getSequence()
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getTranscriptIds
public java.util.Set<java.lang.String> getTranscriptIds()
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setSequence
public void setSequence(java.lang.String sequence)
Add an Isoform sequence
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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