Package psidev.psi.mi.jami.enricher.impl.full

Class FullProteinUpdater

java.lang.Object

psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher<T>

psidev.psi.mi.jami.enricher.impl.AbstractInteractorEnricher<T>

psidev.psi.mi.jami.enricher.impl.AbstractInteractorUpdater<Protein>

psidev.psi.mi.jami.enricher.impl.minimal.MinimalProteinUpdater

psidev.psi.mi.jami.enricher.impl.full.FullProteinUpdater

All Implemented Interfaces:

InteractorEnricher<Protein>, MIEnricher<Protein>, ProteinEnricher

public class FullProteinUpdater
extends MinimalProteinUpdater

Full updater of proteins. As an updater, some data may be overwritten in the protein being enriched. See description of full update in AbstractInteractorUpdater If the protein remapper is not null and the enricher cannot find a uniprot identifier, it will remap to uniprot using the proteinMapper. In case of dead uniprot entries, it will move the dead uniprot identifier to the xrefs and add a qualifier 'uniprot-removed-ac' and add a caution in the annotations. If the remapping is successfull, it will remove any cautions left because of dead entry and set the uniprot identifier of the protein - update sequence of polymer. If the sequence of the polymer to enrich is different from the one of the fetched polymer, it will enrich it with the sequence of the fetched polymer

Since:

20/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.enricher.impl.minimal.MinimalProteinUpdater

UNIPROT_REMOVED_QUALIFIER

Constructor Summary

Constructors

Constructor	Description
FullProteinUpdater(ProteinFetcher proteinFetcher)	Constructor for FullProteinUpdater.

Method Summary

Modifier and Type	Method	Description
protected boolean	isFullEnrichment()	isFullEnrichment.
protected void	processOtherProperties(Protein proteinToEnrich, Protein fetched)	processOtherProperties.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.minimal.MinimalProteinUpdater

find, getProteinMapper, processDeadUniprotIdentity, setProteinMapper

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractInteractorUpdater

canEnrichInteractor, getInteractorEnricher, getListener, onCompletedEnrichment, onEnrichedVersionNotFound, onInteractorCheckFailure, processAliases, processAnnotations, processChecksums, processFullName, processIdentifiers, processInteractorType, processOrganism, processShortLabel, processXrefs, setListener

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractInteractorEnricher

enrich, getCvTermEnricher, getInteractorFetcher, getOrganismEnricher, getRetryCount, processInteractorType, processOrganism, setCvTermEnricher, setOrganismEnricher, setRetryCount

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher

enrich, enrich

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.enricher.InteractorEnricher

getCvTermEnricher, getInteractorFetcher, getListener, getOrganismEnricher, setCvTermEnricher, setListener, setOrganismEnricher

Methods inherited from interface psidev.psi.mi.jami.enricher.MIEnricher

enrich, enrich, enrich

Constructor Detail

FullProteinUpdater

public FullProteinUpdater(ProteinFetcher proteinFetcher)

Constructor for FullProteinUpdater.

Parameters:

proteinFetcher - a ProteinFetcher object.

Method Detail

isFullEnrichment

protected boolean isFullEnrichment()

isFullEnrichment.

Overrides:

isFullEnrichment in class AbstractInteractorUpdater<Protein>

Returns:

a boolean.

processOtherProperties

protected void processOtherProperties(Protein proteinToEnrich,
                                      Protein fetched)

processOtherProperties.

Overrides:

processOtherProperties in class AbstractInteractorEnricher<Protein>

Parameters:

proteinToEnrich - a T object.

fetched - a T object.