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

Class MinimalBioactiveEntityEnricher

java.lang.Object

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

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

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

All Implemented Interfaces:

InteractorEnricher<BioactiveEntity>, MIEnricher<BioactiveEntity>

Direct Known Subclasses:

FullBioactiveEntityEnricher

public class MinimalBioactiveEntityEnricher
extends AbstractInteractorEnricher<BioactiveEntity>

A basic minimal enricher for bioactive entities. See description of minimal enrichment in AbstractInteractorEnricher. The bioactive entities fetcher is required for enriching bioactive entities.

Since:

07/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalBioactiveEntityEnricher(BioactiveEntityFetcher fetcher)	The only constructor, fulfilling the requirement of a bioactiveEntity fetcher.

Method Summary

Modifier and Type	Method	Description
protected boolean	canEnrichInteractor(BioactiveEntity entityToEnrich, BioactiveEntity fetchedEntity)	canEnrichInteractor.
BioactiveEntity	find(BioactiveEntity objectToEnrich)	find.
BioactiveEntityFetcher	getInteractorFetcher()	Returns the current fetcher which is being used to collect information about entities for enrichment.
protected boolean	isFullEnrichment()	isFullEnrichment.
protected void	onCompletedEnrichment(BioactiveEntity objectToEnrich)	onCompletedEnrichment.
protected void	onEnrichedVersionNotFound(BioactiveEntity objectToEnrich)	onEnrichedVersionNotFound.
protected void	onInteractorCheckFailure(BioactiveEntity objectToEnrich, BioactiveEntity fetchedObject)	onInteractorCheckFailure.

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.MIEnricher

enrich, enrich

Constructor Detail

MinimalBioactiveEntityEnricher

public MinimalBioactiveEntityEnricher(BioactiveEntityFetcher fetcher)

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

Parameters:

fetcher - The fetcher used to collect bioactiveEntity records.

Method Detail

getInteractorFetcher

public BioactiveEntityFetcher getInteractorFetcher()

Returns the current fetcher which is being used to collect information about entities for enrichment.

Specified by:

getInteractorFetcher in interface InteractorEnricher<BioactiveEntity>

Overrides:

getInteractorFetcher in class AbstractInteractorEnricher<BioactiveEntity>

Returns:

The current fetcher.

find

public BioactiveEntity find(BioactiveEntity objectToEnrich)
                     throws EnricherException

find.

Specified by:

find in class AbstractInteractorEnricher<BioactiveEntity>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(BioactiveEntity objectToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Overrides:

onEnrichedVersionNotFound in class AbstractInteractorEnricher<BioactiveEntity>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

isFullEnrichment

protected boolean isFullEnrichment()

isFullEnrichment.

Specified by:

isFullEnrichment in class AbstractInteractorEnricher<BioactiveEntity>

Returns:

a boolean.

onCompletedEnrichment

protected void onCompletedEnrichment(BioactiveEntity objectToEnrich)

onCompletedEnrichment.

Specified by:

onCompletedEnrichment in class AbstractInteractorEnricher<BioactiveEntity>

Parameters:

objectToEnrich - a T object.

onInteractorCheckFailure

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

onInteractorCheckFailure.

Specified by:

onInteractorCheckFailure in class AbstractInteractorEnricher<BioactiveEntity>

Parameters:

objectToEnrich - a T object.

fetchedObject - a T object.

Throws:

EnricherException - if any.

canEnrichInteractor

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

canEnrichInteractor.

Overrides:

canEnrichInteractor in class AbstractInteractorEnricher<BioactiveEntity>

Parameters:

entityToEnrich - a T object.

fetchedEntity - a T object.

Returns:

a boolean.

Throws:

EnricherException - if any.