Package org.snpeff.nextProt

Class NextProtXmlEntry

java.lang.Object

org.snpeff.nextProt.NextProtXmlNode

org.snpeff.nextProt.NextProtXmlEntry

public class NextProtXmlEntry
extends NextProtXmlNode

Mimics the 'entry' in a NextProt XML file

Author:

Pablo Cingolani

Constructor Summary

Constructors

Constructor	Description
NextProtXmlEntry(java.lang.String accession, NextProtHandler handler)

Method Summary

Modifier and Type	Method	Description
void	add(NextProtXmlAnnotation ann)	Add an annotation
void	addIsoformSequence(java.lang.String isoformAccession, java.lang.String sequence)	Add an Isoform sequence
void	addMarkers(NextProtMarkerFactory markersFactory)	Create all Markers for this entry
java.util.List<NextProtXmlAnnotation>	getAnnotations()
NextProtHandler	getHandler()
java.util.Set<org.snpeff.nextProt.Identifier>	getIdentifiers()
NextProtXmlIsoform	getIsoform(java.lang.String isoformAccession)	Get or create an isoform
java.util.Map<java.lang.String,NextProtXmlIsoform>	getIsoformsByAccession()
NextProtXmlIsoform	getOrCreateIsoform(java.lang.String isoformAccession)
java.lang.String	toString()

Methods inherited from class org.snpeff.nextProt.NextProtXmlNode

getAccession

Methods inherited from class java.lang.Object

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

Constructor Detail

NextProtXmlEntry

public NextProtXmlEntry(java.lang.String accession,
                        NextProtHandler handler)

Method Detail

add

public void add(NextProtXmlAnnotation ann)

Add an annotation

addIsoformSequence

public void addIsoformSequence(java.lang.String isoformAccession,
                               java.lang.String sequence)

Add an Isoform sequence

addMarkers

public void addMarkers(NextProtMarkerFactory markersFactory)

Create all Markers for this entry

getAnnotations

public java.util.List<NextProtXmlAnnotation> getAnnotations()

getHandler

public NextProtHandler getHandler()

getIdentifiers

public java.util.Set<org.snpeff.nextProt.Identifier> getIdentifiers()

getIsoform

public NextProtXmlIsoform getIsoform(java.lang.String isoformAccession)

Get or create an isoform

getIsoformsByAccession

public java.util.Map<java.lang.String,NextProtXmlIsoform> getIsoformsByAccession()

getOrCreateIsoform

public NextProtXmlIsoform getOrCreateIsoform(java.lang.String isoformAccession)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object