Package org.snpeff.nextProt
Class NextProtXmlAnnotation
- java.lang.Object
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- org.snpeff.nextProt.NextProtXmlNode
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- org.snpeff.nextProt.NextProtXmlAnnotation
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public class NextProtXmlAnnotation extends NextProtXmlNode
Mimics the 'annotation' tag in a NextProt XML file- Author:
- Pablo Cingolani
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Constructor Summary
Constructors Constructor Description NextProtXmlAnnotation(NextProtXmlEntry entry, java.lang.String category)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addMarkers(NextProtMarkerFactory markersFactory)
Create all markers for this annotationjava.lang.String
description()
java.lang.String
getCategory()
CvTerm
getCvTerm()
java.lang.String
getDescription()
java.util.List<Location>
getLocations()
boolean
hasCvTerm()
boolean
isEmpty()
void
locationBeginPos(org.xml.sax.Attributes attributes)
void
locationEnd()
End of location tagvoid
locationEndPos(org.xml.sax.Attributes attributes)
void
locationIsoformStart(java.lang.String accession)
void
locationStart(org.xml.sax.Attributes attributes)
java.lang.String
name()
Return an annotation "name" Clean up characters to make them compatible with VCF annotationsvoid
setCvTerm(CvTerm cvTerm)
void
setDescription(java.lang.String description)
java.lang.String
toString()
java.lang.String
toString(java.lang.String prefix)
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Methods inherited from class org.snpeff.nextProt.NextProtXmlNode
getAccession
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Constructor Detail
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NextProtXmlAnnotation
public NextProtXmlAnnotation(NextProtXmlEntry entry, java.lang.String category)
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Method Detail
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addMarkers
public void addMarkers(NextProtMarkerFactory markersFactory)
Create all markers for this annotation
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description
public java.lang.String description()
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getCategory
public java.lang.String getCategory()
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getCvTerm
public CvTerm getCvTerm()
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setCvTerm
public void setCvTerm(CvTerm cvTerm)
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getDescription
public java.lang.String getDescription()
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setDescription
public void setDescription(java.lang.String description)
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getLocations
public java.util.List<Location> getLocations()
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hasCvTerm
public boolean hasCvTerm()
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isEmpty
public boolean isEmpty()
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locationBeginPos
public void locationBeginPos(org.xml.sax.Attributes attributes)
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locationEnd
public void locationEnd()
End of location tag
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locationEndPos
public void locationEndPos(org.xml.sax.Attributes attributes)
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locationIsoformStart
public void locationIsoformStart(java.lang.String accession)
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locationStart
public void locationStart(org.xml.sax.Attributes attributes)
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name
public java.lang.String name()
Return an annotation "name" Clean up characters to make them compatible with VCF annotations
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toString
public java.lang.String toString(java.lang.String prefix)
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