Package org.snpeff.nextProt

Class NextProtMarkerFactory

java.lang.Object

org.snpeff.nextProt.NextProtMarkerFactory

public class NextProtMarkerFactory
extends java.lang.Object

Creates Markers from nextprot XML annotations

Author:

Pablo Cingolani

Constructor Summary

Constructors

Constructor	Description
NextProtMarkerFactory(Config config)

Method Summary

Modifier and Type	Method	Description
Markers	addMarkers(NextProtXmlEntry entry, NextProtXmlIsoform isoform, NextProtXmlAnnotation annotation, Location location, java.lang.String trId)	Create markers and add them
void	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 marker
Markers	nextProt(Transcript tr, NextProtXmlAnnotation annotation, Location location)	Create a list of NextProt markers according to this annotation
void	saveDatabase()	Save nextprot markers as databases

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NextProtMarkerFactory

public NextProtMarkerFactory(Config config)

Method Detail

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

conservation

public void conservation()

Sequence conservations analysis. Tag highly conserved NextProt markers

getMarkers

public Markers getMarkers()

nextProt

public Markers nextProt(Transcript tr,
                        NextProtXmlAnnotation annotation,
                        Location location)

Create a list of NextProt markers according to this annotation

nextProt

public Markers nextProt(Transcript tr,
                        java.lang.String accession,
                        java.lang.String name,
                        int aaStart,
                        int aaEnd)

Create a single NextProt marker

saveDatabase

public void saveDatabase()

Save nextprot markers as databases