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

Class MinimalFeatureEvidenceEnricher

java.lang.Object

psidev.psi.mi.jami.enricher.impl.minimal.MinimalFeatureEnricher<FeatureEvidence>

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

All Implemented Interfaces:

EventListener, FeatureEnricher<FeatureEvidence>, EnricherListener<Protein>, InteractorEnricherListener<Protein>, ProteinEnricherListener, MIEnricher<FeatureEvidence>, ProteinListeningFeatureEnricher<FeatureEvidence>, AliasesChangeListener<Protein>, AnnotationsChangeListener<Protein>, ChecksumsChangeListener<Protein>, IdentifiersChangeListener<Protein>, InteractorChangeListener<Protein>, PolymerChangeListener<Protein>, ProteinChangeListener, XrefsChangeListener<Protein>

Direct Known Subclasses:

MinimalFeatureEvidenceUpdater

public class MinimalFeatureEvidenceEnricher
extends MinimalFeatureEnricher<FeatureEvidence>

Provides minimal enrichment of feature evidence. - enrich minimal properties of feature. See MinimalFeatureEnricher - enrich detection methods if cv term enricher is not null - Ignore all other properties of a feature

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalFeatureEvidenceEnricher()

Method Summary

Modifier and Type	Method	Description
protected void	mergeDetectionMethods(FeatureEvidence termToEnrich, Collection<CvTerm> toEnrichTerms, Collection<CvTerm> fetchedTerms, boolean remove)	Takes two lists of detection methods and produces a list of those to add and those to remove.
protected void	processDetectionMethods(FeatureEvidence featureToEnrich)	processDetectionMethods.
protected void	processDetectionMethods(FeatureEvidence featureToEnrich, FeatureEvidence source)	processDetectionMethods.
protected void	processOtherProperties(FeatureEvidence featureToEnrich)	processOtherProperties.
protected void	processOtherProperties(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processOtherProperties.

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

enrich, enrich, enrich, getCvTermEnricher, getFeatureEnricherListener, onAddedAlias, onAddedAnnotation, onAddedChecksum, onAddedIdentifier, onAddedXref, onEnrichmentComplete, onEnrichmentError, onFullNameUpdate, onInteractorTypeUpdate, onInvalidRange, onOrganismUpdate, onOutOfDateRange, onRemovedAlias, onRemovedAnnotation, onRemovedChecksum, onRemovedIdentifier, onRemovedXref, onSequenceUpdate, onShortNameUpdate, processFeatureType, processFeatureType, processFullName, processIdentifiers, processMinimalUpdates, processMinimalUpdates, processRanges, processRanges, processRangeStatus, processShortLabel, setCvTermEnricher, setFeatureEnricherListener, setFeaturesWithRangesToUpdate, updateRangePositions

Methods inherited from class java.lang.Object

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

Constructor Detail

MinimalFeatureEvidenceEnricher

public MinimalFeatureEvidenceEnricher()

Method Detail

processOtherProperties

protected void processOtherProperties(FeatureEvidence featureToEnrich)
                               throws EnricherException

processOtherProperties.

Overrides:

processOtherProperties in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(FeatureEvidence featureToEnrich,
                                      FeatureEvidence objectSource)
                               throws EnricherException

processOtherProperties.

Overrides:

processOtherProperties in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processDetectionMethods

protected void processDetectionMethods(FeatureEvidence featureToEnrich)
                                throws EnricherException

processDetectionMethods.

Parameters:

featureToEnrich - a FeatureEvidence object.

Throws:

EnricherException - if any.

processDetectionMethods

protected void processDetectionMethods(FeatureEvidence featureToEnrich,
                                       FeatureEvidence source)
                                throws EnricherException

processDetectionMethods.

Parameters:

featureToEnrich - a FeatureEvidence object.

source - a FeatureEvidence object.

Throws:

EnricherException - if any.

mergeDetectionMethods

protected void mergeDetectionMethods(FeatureEvidence termToEnrich,
                                     Collection<CvTerm> toEnrichTerms,
                                     Collection<CvTerm> fetchedTerms,
                                     boolean remove)
                              throws EnricherException

Takes two lists of detection methods and produces a list of those to add and those to remove. It will add in toEnrichTerms all detection methods from fetchedTerms that are not there. It will also remove extra detection methods from toEnrichTerms if remove boolean is true.

Parameters:

termToEnrich - The object to enrich

fetchedTerms - The new terms to be added.

remove - : if true, we remove terms that are not in enriched list

toEnrichTerms - a Collection object.

Throws:

EnricherException - if any.