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

Class FullFeatureEnricher<F extends Feature>

java.lang.Object

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

psidev.psi.mi.jami.enricher.impl.full.FullFeatureEnricher<F>

All Implemented Interfaces:

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

Direct Known Subclasses:

FullFeatureEvidenceEnricher, FullFeatureUpdater

public class FullFeatureEnricher<F extends Feature>
extends MinimalFeatureEnricher<F>

Provides full enrichment of feature. - enrich minimal properties of feature (see MinimalFeatureEnricher) - enrich interaction dependency - enrich interaction effect - enrich xrefs - enrich aliases - enrich annotations - enrich linked features

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
FullFeatureEnricher()	Constructor for FullFeatureEnricher.

Method Summary

Modifier and Type	Method	Description
void	enrich(F objectToEnrich)	Enrichment of a single feature.
protected void	mergeLinkedFeatures(F objectToEnrich, Collection<F> linkedFeaturesToEnrich, Collection<F> fetchedFeatures, boolean remove)	mergeLinkedFeatures.
protected void	processAliases(F objectToEnrich, F termFetched)	processAliases.
protected void	processAnnotations(F objectToEnrich, F fetchedObject)	processAnnotations.
protected void	processLinkedFeatures(F featureToEnrich, F objectSource)	processLinkedFeatures.
protected void	processOtherProperties(F featureToEnrich)	processOtherProperties.
protected void	processOtherProperties(F featureToEnrich, F objectSource)	processOtherProperties.
protected void	processRole(F featureToEnrich)	processRole.
protected void	processRole(F featureToEnrich, F objectSource)	processRole.
protected void	processXrefs(F objectToEnrich, F cvTermFetched)	processXrefs.

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

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

FullFeatureEnricher

public FullFeatureEnricher()

Constructor for FullFeatureEnricher.

Method Detail

enrich

public void enrich(F objectToEnrich)
            throws EnricherException

Enrichment of a single feature.

Specified by:

enrich in interface MIEnricher<F extends Feature>

Overrides:

enrich in class MinimalFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - The feature which is to be enriched.

Throws:

EnricherException - Thrown if problems are encountered in the fetcher

processOtherProperties

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

processOtherProperties.

Overrides:

processOtherProperties in class MinimalFeatureEnricher<F extends Feature>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processLinkedFeatures

protected void processLinkedFeatures(F featureToEnrich,
                                     F objectSource)
                              throws EnricherException

processLinkedFeatures.

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(F featureToEnrich)
                               throws EnricherException

processOtherProperties.

Overrides:

processOtherProperties in class MinimalFeatureEnricher<F extends Feature>

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processRole

protected void processRole(F featureToEnrich)
                    throws EnricherException

processRole.

Parameters:

featureToEnrich - a F object.

Throws:

EnricherException - if any.

processRole

protected void processRole(F featureToEnrich,
                           F objectSource)
                    throws EnricherException

processRole.

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(F objectToEnrich,
                            F cvTermFetched)
                     throws EnricherException

processXrefs.

Parameters:

objectToEnrich - a F object.

cvTermFetched - a F object.

Throws:

EnricherException - if any.

processAnnotations

protected void processAnnotations(F objectToEnrich,
                                  F fetchedObject)
                           throws EnricherException

processAnnotations.

Parameters:

objectToEnrich - a F object.

fetchedObject - a F object.

Throws:

EnricherException - if any.

processAliases

protected void processAliases(F objectToEnrich,
                              F termFetched)
                       throws EnricherException

processAliases.

Parameters:

objectToEnrich - a F object.

termFetched - a F object.

Throws:

EnricherException - if any.

mergeLinkedFeatures

protected void mergeLinkedFeatures(F objectToEnrich,
                                   Collection<F> linkedFeaturesToEnrich,
                                   Collection<F> fetchedFeatures,
                                   boolean remove)
                            throws EnricherException

mergeLinkedFeatures.

Parameters:

objectToEnrich - a F object.

linkedFeaturesToEnrich - a Collection object.

fetchedFeatures - a Collection object.

remove - a boolean.

Throws:

EnricherException - if any.