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

Class MinimalFeatureUpdater<F extends Feature>

java.lang.Object

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

psidev.psi.mi.jami.enricher.impl.minimal.MinimalFeatureUpdater<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>

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

Provides minimal update of feature. - update shortName if different - update fullName if different - enrich feature type with CvTerm enricher if not null. It will override existing feature type if different using DefaultCvTermComparator - enrich identifiers. Add missing identifiers (using DefaultXrefComparator) and remove identifiers not in the feature source - shift ranges if the protein sequence change - Ignore all other properties of a feature

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalFeatureUpdater()

Method Summary

Modifier and Type	Method	Description
protected void	onInvalidRange(F feature, Range range, Collection<String> errorMessages)	onInvalidRange.
protected void	onOutOfDateRange(F feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
protected void	processFeatureType(F featureToEnrich, F objectSource)	processFeatureType.
protected void	processFullName(F objectToEnrich, F objectSource)	processFullName.
protected void	processIdentifiers(F objectToEnrich, F objectSource)	processIdentifiers.
protected void	processRanges(F objectToEnrich, F objectSource)	processRanges.
protected void	processShortLabel(F objectToEnrich, F objectSource)	processShortLabel.
protected boolean	updateRangePositions()	updateRangePositions.

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, onOrganismUpdate, onRemovedAlias, onRemovedAnnotation, onRemovedChecksum, onRemovedIdentifier, onRemovedXref, onSequenceUpdate, onShortNameUpdate, processFeatureType, processMinimalUpdates, processMinimalUpdates, processOtherProperties, processOtherProperties, processRanges, processRangeStatus, setCvTermEnricher, setFeatureEnricherListener, setFeaturesWithRangesToUpdate

Methods inherited from class java.lang.Object

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

Constructor Detail

MinimalFeatureUpdater

public MinimalFeatureUpdater()

Method Detail

updateRangePositions

protected boolean updateRangePositions()

updateRangePositions.

Overrides:

updateRangePositions in class MinimalFeatureEnricher<F extends Feature>

Returns:

a boolean.

onInvalidRange

protected void onInvalidRange(F feature,
                              Range range,
                              Collection<String> errorMessages)

onInvalidRange.

Overrides:

onInvalidRange in class MinimalFeatureEnricher<F extends Feature>

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

onOutOfDateRange

protected void onOutOfDateRange(F feature,
                                Range range,
                                Collection<String> errorMessages,
                                String oldSequence)

onOutOfDateRange.

Overrides:

onOutOfDateRange in class MinimalFeatureEnricher<F extends Feature>

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

oldSequence - a String object.

processRanges

protected void processRanges(F objectToEnrich,
                             F objectSource)
                      throws EnricherException

processRanges.

Overrides:

processRanges in class MinimalFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processFeatureType

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

processFeatureType.

Overrides:

processFeatureType in class MinimalFeatureEnricher<F extends Feature>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processShortLabel

protected void processShortLabel(F objectToEnrich,
                                 F objectSource)
                          throws EnricherException

processShortLabel.

Overrides:

processShortLabel in class MinimalFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processFullName

protected void processFullName(F objectToEnrich,
                               F objectSource)
                        throws EnricherException

processFullName.

Overrides:

processFullName in class MinimalFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processIdentifiers

protected void processIdentifiers(F objectToEnrich,
                                  F objectSource)
                           throws EnricherException

processIdentifiers.

Overrides:

processIdentifiers in class MinimalFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.