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

Class MinimalGeneEnricher

java.lang.Object

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

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

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

All Implemented Interfaces:

InteractorEnricher<Gene>, MIEnricher<Gene>

Direct Known Subclasses:

FullGeneEnricher

public class MinimalGeneEnricher
extends AbstractInteractorEnricher<Gene>

A basic minimal enricher for genes. See description of minimal enrichment in AbstractInteractorEnricher. The GeneFetcher is required for enriching genes.

Since:

04/09/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalGeneEnricher(GeneFetcher fetcher)	Constructor for MinimalGeneEnricher.

Method Summary

Modifier and Type	Method	Description
protected boolean	canEnrichInteractor(Gene entityToEnrich, Gene fetchedEntity)	canEnrichInteractor.
Gene	find(Gene geneToEnrich)	find.
GeneFetcher	getInteractorFetcher()	getInteractorFetcher.
protected boolean	isFullEnrichment()	isFullEnrichment.
protected void	onCompletedEnrichment(Gene objectToEnrich)	onCompletedEnrichment.
protected void	onEnrichedVersionNotFound(Gene objectToEnrich)	onEnrichedVersionNotFound.
protected void	onInteractorCheckFailure(Gene objectToEnrich, Gene 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

MinimalGeneEnricher

public MinimalGeneEnricher(GeneFetcher fetcher)

Constructor for MinimalGeneEnricher.

Parameters:

fetcher - a GeneFetcher object.

Method Detail

getInteractorFetcher

public GeneFetcher getInteractorFetcher()

getInteractorFetcher.

Specified by:

getInteractorFetcher in interface InteractorEnricher<Gene>

Overrides:

getInteractorFetcher in class AbstractInteractorEnricher<Gene>

Returns:

a InteractorFetcher object.

find

public Gene find(Gene geneToEnrich)
          throws EnricherException

find.

Specified by:

find in class AbstractInteractorEnricher<Gene>

Parameters:

geneToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(Gene objectToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Overrides:

onEnrichedVersionNotFound in class AbstractInteractorEnricher<Gene>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

isFullEnrichment

protected boolean isFullEnrichment()

isFullEnrichment.

Specified by:

isFullEnrichment in class AbstractInteractorEnricher<Gene>

Returns:

a boolean.

onCompletedEnrichment

protected void onCompletedEnrichment(Gene objectToEnrich)

onCompletedEnrichment.

Specified by:

onCompletedEnrichment in class AbstractInteractorEnricher<Gene>

Parameters:

objectToEnrich - a T object.

onInteractorCheckFailure

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

onInteractorCheckFailure.

Specified by:

onInteractorCheckFailure in class AbstractInteractorEnricher<Gene>

Parameters:

objectToEnrich - a T object.

fetchedObject - a T object.

Throws:

EnricherException - if any.

canEnrichInteractor

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

canEnrichInteractor.

Overrides:

canEnrichInteractor in class AbstractInteractorEnricher<Gene>

Parameters:

entityToEnrich - a T object.

fetchedEntity - a T object.

Returns:

a boolean.

Throws:

EnricherException - if any.