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

Class MinimalProteinUpdater

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

All Implemented Interfaces:

InteractorEnricher<Protein>, MIEnricher<Protein>, ProteinEnricher

Direct Known Subclasses:

FullProteinUpdater

public class MinimalProteinUpdater
extends AbstractInteractorUpdater<Protein>
implements ProteinEnricher

Updates a protein to the minimum level. As an updater, some data may be overwritten in the protein being enriched. See description of minimal 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 The protein fetcher is require to enrich proteins

Since:

13/06/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	UNIPROT_REMOVED_QUALIFIER	Constant UNIPROT_REMOVED_QUALIFIER="uniprot-removed-ac"

Constructor Summary

Constructors

Constructor	Description
MinimalProteinUpdater(ProteinFetcher proteinFetcher)	The only constructor which forces the setting of the fetcher If the cvTerm fetcher is null, an illegal state exception will be thrown at the next enrichment.

Method Summary

Modifier and Type	Method	Description
Protein	find(Protein objectToEnrich)	find.
ProteinMapper	getProteinMapper()	getProteinMapper.
protected void	processDeadUniprotIdentity(Protein proteinToEnrich, String oldUniprot)	processDeadUniprotIdentity.
void	setProteinMapper(ProteinMapper mapper)	setProteinMapper.

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

canEnrichInteractor, getInteractorEnricher, getListener, isFullEnrichment, 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, processOtherProperties, 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

Field Detail

UNIPROT_REMOVED_QUALIFIER

public static final String UNIPROT_REMOVED_QUALIFIER

Constant UNIPROT_REMOVED_QUALIFIER="uniprot-removed-ac"

See Also:

Constant Field Values

Constructor Detail

MinimalProteinUpdater

public MinimalProteinUpdater(ProteinFetcher proteinFetcher)

The only constructor which forces the setting of the fetcher If the cvTerm fetcher is null, an illegal state exception will be thrown at the next enrichment.

Parameters:

proteinFetcher - The protein fetcher to use.

Method Detail

processDeadUniprotIdentity

protected void processDeadUniprotIdentity(Protein proteinToEnrich,
                                          String oldUniprot)

processDeadUniprotIdentity.

Parameters:

proteinToEnrich - a Protein object.

oldUniprot - a String object.

find

public Protein find(Protein objectToEnrich)
             throws EnricherException

find.

Overrides:

find in class AbstractInteractorUpdater<Protein>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

getProteinMapper

public ProteinMapper getProteinMapper()

getProteinMapper.

Specified by:

getProteinMapper in interface ProteinEnricher

Returns:

a ProteinMapper object.

setProteinMapper

public void setProteinMapper(ProteinMapper mapper)

setProteinMapper.

Specified by:

setProteinMapper in interface ProteinEnricher

Parameters:

mapper - a ProteinMapper object.