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

Class MinimalProteinEnricher

java.lang.Object

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

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

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

All Implemented Interfaces:

InteractorEnricher<Protein>, MIEnricher<Protein>, ProteinEnricher

Direct Known Subclasses:

FullProteinEnricher

public class MinimalProteinEnricher
extends AbstractInteractorEnricher<Protein>
implements ProteinEnricher

Enriches a protein to the minimum level. As an enricher, no data will be overwritten in the protein being enriched. See description of minimal enrichment in AbstractInteractorEnricher 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 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:

14/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	CAUTION_MESSAGE	Constant CAUTION_MESSAGE="This sequence has been withdrawn from U"{trunked}

Constructor Summary

Constructors

Constructor	Description
MinimalProteinEnricher(ProteinFetcher fetcher)	The only constructor, fulfilling the requirement of a protein fetcher.

Method Summary

Modifier and Type	Method	Description
protected boolean	canEnrichInteractor(Protein entityToEnrich, Protein fetchedEntity)	canEnrichInteractor.
Protein	find(Protein proteinToEnrich)	find.
ProteinFetcher	getInteractorFetcher()	The fetcher to be used for used to collect data.
ProteinMapper	getProteinMapper()	The protein remapper has no default and can be left null
protected boolean	isFullEnrichment()	isFullEnrichment.
protected void	onCompletedEnrichment(Protein objectToEnrich)	onCompletedEnrichment.
protected void	onEnrichedVersionNotFound(Protein objectToEnrich)	onEnrichedVersionNotFound.
protected void	onInteractorCheckFailure(Protein objectToEnrich, Protein fetchedObject)	onInteractorCheckFailure.
protected void	processDeadUniprotIdentity(Protein proteinToEnrich, Xref uniprotIdentity)	processDeadUniprotIdentity.
protected boolean	remapProtein(Protein proteinToEnrich)	Attempts to remap the protein using the provided proteinRemapper.
void	setProteinMapper(ProteinMapper proteinMapper)	setProteinMapper.

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

enrich, getCvTermEnricher, getListener, getOrganismEnricher, getRetryCount, processAliases, processAnnotations, processChecksums, processFullName, processIdentifiers, processInteractorType, processInteractorType, processOrganism, processOrganism, processOtherProperties, processShortLabel, processXrefs, setCvTermEnricher, setListener, 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, getListener, getOrganismEnricher, setCvTermEnricher, setListener, setOrganismEnricher

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

enrich, enrich, enrich

Field Detail

CAUTION_MESSAGE

public static final String CAUTION_MESSAGE

Constant CAUTION_MESSAGE="This sequence has been withdrawn from U"{trunked}

See Also:

Constant Field Values

Constructor Detail

MinimalProteinEnricher

public MinimalProteinEnricher(ProteinFetcher fetcher)

The only constructor, fulfilling the requirement of a protein fetcher. If the protein fetcher is null, an illegal state exception will be thrown at the next enrichment.

Parameters:

fetcher - The fetcher used to collect protein records.

Method Detail

getInteractorFetcher

public ProteinFetcher getInteractorFetcher()

The fetcher to be used for used to collect data.

Specified by:

getInteractorFetcher in interface InteractorEnricher<Protein>

Overrides:

getInteractorFetcher in class AbstractInteractorEnricher<Protein>

Returns:

The fetcher which is currently being used for fetching.

setProteinMapper

public void setProteinMapper(ProteinMapper proteinMapper)

setProteinMapper.

The protein mapper to be used when a protein doesn't have a uniprot id or the uniprotID is dead.

Specified by:

setProteinMapper in interface ProteinEnricher

Parameters:

proteinMapper - a ProteinMapper object.

getProteinMapper

public ProteinMapper getProteinMapper()

The protein remapper has no default and can be left null

Specified by:

getProteinMapper in interface ProteinEnricher

Returns:

The current remapper.

find

public Protein find(Protein proteinToEnrich)
             throws EnricherException

find.

Specified by:

find in class AbstractInteractorEnricher<Protein>

Parameters:

proteinToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(Protein objectToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Overrides:

onEnrichedVersionNotFound in class AbstractInteractorEnricher<Protein>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

isFullEnrichment

protected boolean isFullEnrichment()

isFullEnrichment.

Specified by:

isFullEnrichment in class AbstractInteractorEnricher<Protein>

Returns:

a boolean.

onCompletedEnrichment

protected void onCompletedEnrichment(Protein objectToEnrich)

onCompletedEnrichment.

Specified by:

onCompletedEnrichment in class AbstractInteractorEnricher<Protein>

Parameters:

objectToEnrich - a T object.

onInteractorCheckFailure

protected void onInteractorCheckFailure(Protein objectToEnrich,
                                        Protein fetchedObject)
                                 throws EnricherException

onInteractorCheckFailure.

Specified by:

onInteractorCheckFailure in class AbstractInteractorEnricher<Protein>

Parameters:

objectToEnrich - a T object.

fetchedObject - a T object.

Throws:

EnricherException - if any.

canEnrichInteractor

protected boolean canEnrichInteractor(Protein entityToEnrich,
                                      Protein fetchedEntity)
                               throws EnricherException

canEnrichInteractor.

Overrides:

canEnrichInteractor in class AbstractInteractorEnricher<Protein>

Parameters:

entityToEnrich - a T object.

fetchedEntity - a T object.

Returns:

a boolean.

Throws:

EnricherException - if any.

processDeadUniprotIdentity

protected void processDeadUniprotIdentity(Protein proteinToEnrich,
                                          Xref uniprotIdentity)

processDeadUniprotIdentity.

Parameters:

proteinToEnrich - a Protein object.

uniprotIdentity - a Xref object.

remapProtein

protected boolean remapProtein(Protein proteinToEnrich)
                        throws EnricherException

Attempts to remap the protein using the provided proteinRemapper. If one has not been included, this method returns false and reports a failure to the listener. If after remapping, the protein still has no entry, this entry returns false.

Parameters:

proteinToEnrich - The protein to find a remapping for.

Returns:

Whether the remapping was successful.

Throws:

EnricherException - if any.