Package org.snpeff.nextProt
Class NextProtMarkerFactory
- java.lang.Object
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- org.snpeff.nextProt.NextProtMarkerFactory
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public class NextProtMarkerFactory extends java.lang.Object
Creates Markers from nextprot XML annotations- Author:
- Pablo Cingolani
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Constructor Summary
Constructors Constructor Description NextProtMarkerFactory(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Markers
addMarkers(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, java.lang.String trId)
Create markers and add themvoid
conservation()
Sequence conservations analysis.Markers
getMarkers()
Markers
nextProt(Transcript tr, java.lang.String accession, java.lang.String name, int aaStart, int aaEnd)
Create a single NextProt markerMarkers
nextProt(Transcript tr, NextProtXmlAnnotation annotation, Location location)
Create a list of NextProt markers according to this annotationvoid
saveDatabase()
Save nextprot markers as databases
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Constructor Detail
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NextProtMarkerFactory
public NextProtMarkerFactory(Config config)
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Method Detail
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addMarkers
public Markers addMarkers(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, java.lang.String trId)
Create markers and add them- Returns:
- New markers created
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conservation
public void conservation()
Sequence conservations analysis. Tag highly conserved NextProt markers
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getMarkers
public Markers getMarkers()
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nextProt
public Markers nextProt(Transcript tr, NextProtXmlAnnotation annotation, Location location)
Create a list of NextProt markers according to this annotation
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nextProt
public Markers nextProt(Transcript tr, java.lang.String accession, java.lang.String name, int aaStart, int aaEnd)
Create a single NextProt marker
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saveDatabase
public void saveDatabase()
Save nextprot markers as databases
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