Package org.snpeff.nextProt
Class NextProtXmlEntry
- java.lang.Object
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- org.snpeff.nextProt.NextProtXmlNode
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- org.snpeff.nextProt.NextProtXmlEntry
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public class NextProtXmlEntry extends NextProtXmlNode
Mimics the 'entry' in a NextProt XML file- Author:
- Pablo Cingolani
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Constructor Summary
Constructors Constructor Description NextProtXmlEntry(java.lang.String accession, NextProtHandler handler)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(NextProtXmlAnnotation ann)
Add an annotationvoid
addIsoformSequence(java.lang.String isoformAccession, java.lang.String sequence)
Add an Isoform sequencevoid
addMarkers(NextProtMarkerFactory markersFactory)
Create all Markers for this entryjava.util.List<NextProtXmlAnnotation>
getAnnotations()
NextProtHandler
getHandler()
java.util.Set<org.snpeff.nextProt.Identifier>
getIdentifiers()
NextProtXmlIsoform
getIsoform(java.lang.String isoformAccession)
Get or create an isoformjava.util.Map<java.lang.String,NextProtXmlIsoform>
getIsoformsByAccession()
NextProtXmlIsoform
getOrCreateIsoform(java.lang.String isoformAccession)
java.lang.String
toString()
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Methods inherited from class org.snpeff.nextProt.NextProtXmlNode
getAccession
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Constructor Detail
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NextProtXmlEntry
public NextProtXmlEntry(java.lang.String accession, NextProtHandler handler)
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Method Detail
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add
public void add(NextProtXmlAnnotation ann)
Add an annotation
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addIsoformSequence
public void addIsoformSequence(java.lang.String isoformAccession, java.lang.String sequence)
Add an Isoform sequence
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addMarkers
public void addMarkers(NextProtMarkerFactory markersFactory)
Create all Markers for this entry
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getAnnotations
public java.util.List<NextProtXmlAnnotation> getAnnotations()
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getHandler
public NextProtHandler getHandler()
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getIdentifiers
public java.util.Set<org.snpeff.nextProt.Identifier> getIdentifiers()
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getIsoform
public NextProtXmlIsoform getIsoform(java.lang.String isoformAccession)
Get or create an isoform
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getIsoformsByAccession
public java.util.Map<java.lang.String,NextProtXmlIsoform> getIsoformsByAccession()
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getOrCreateIsoform
public NextProtXmlIsoform getOrCreateIsoform(java.lang.String isoformAccession)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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