Package org.snpeff.nextProt
Class NextProtMarkerFactory
java.lang.Object
org.snpeff.nextProt.NextProtMarkerFactory
Creates Markers from nextprot XML annotations
- Author:
- Pablo Cingolani
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionaddMarkers
(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, String trId) Create markers and add themvoid
Sequence conservations analysis.nextProt
(Transcript tr, String accession, String name, int aaStart, int aaEnd) Create a single NextProt markernextProt
(Transcript tr, NextProtXmlAnnotation annotation, Location location) Create a list of NextProt markers according to this annotationvoid
Save nextprot markers as databases
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Constructor Details
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NextProtMarkerFactory
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Method Details
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addMarkers
public Markers addMarkers(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, 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 -
getMarkers
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nextProt
Create a list of NextProt markers according to this annotation -
nextProt
Create a single NextProt marker -
saveDatabase
public void saveDatabase()Save nextprot markers as databases
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