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

Class FullFeatureUpdater<F extends Feature>

java.lang.Object

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

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

psidev.psi.mi.jami.enricher.impl.full.FullFeatureUpdater<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:

FullFeatureEvidenceUpdater

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

Provides full updater of feature. - update minimal properties of feature (see MinimalFeatureUpdater) - update interaction dependency - update interaction effect - update xrefs - update aliases - update annotations - update linked features

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullFeatureUpdater()	Constructor for FullFeatureUpdater.
protected	FullFeatureUpdater(MinimalFeatureUpdater<F> minimalUpdater)	Constructor for FullFeatureUpdater.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher	getCvTermEnricher()	Gets the subEnricher for CvTerms.
FeatureEnricherListener<F>	getFeatureEnricherListener()	Retrieves the listener of feature changes.
protected MinimalFeatureUpdater<F>	getMinimalUpdater()	Getter for the field minimalUpdater.
void	onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
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	processRole(F featureToEnrich, F objectSource)	processRole.
protected void	processXrefs(F objectToEnrich, F cvTermFetched)	processXrefs.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setFeatureEnricherListener(FeatureEnricherListener<F> featureEnricherListener)	setFeatureEnricherListener.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.full.FullFeatureEnricher

enrich, mergeLinkedFeatures, processOtherProperties, processOtherProperties, processRole

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

enrich, enrich, onInvalidRange, onOutOfDateRange, processFeatureType, processFeatureType, processFullName, processIdentifiers, processMinimalUpdates, processMinimalUpdates, processRanges, processRanges, processRangeStatus, processShortLabel, setFeaturesWithRangesToUpdate, updateRangePositions

Methods inherited from class java.lang.Object

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

Constructor Detail

FullFeatureUpdater

public FullFeatureUpdater()

Constructor for FullFeatureUpdater.

FullFeatureUpdater

protected FullFeatureUpdater(MinimalFeatureUpdater<F> minimalUpdater)

Constructor for FullFeatureUpdater.

Parameters:

minimalUpdater - a MinimalFeatureUpdater object.

Method Detail

processLinkedFeatures

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

processLinkedFeatures.

Overrides:

processLinkedFeatures in class FullFeatureEnricher<F extends Feature>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processRole

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

processRole.

Overrides:

processRole in class FullFeatureEnricher<F extends Feature>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(F objectToEnrich,
                            F cvTermFetched)

processXrefs.

Overrides:

processXrefs in class FullFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

cvTermFetched - a F object.

processAnnotations

protected void processAnnotations(F objectToEnrich,
                                  F fetchedObject)

processAnnotations.

Overrides:

processAnnotations in class FullFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

fetchedObject - a F object.

processAliases

protected void processAliases(F objectToEnrich,
                              F termFetched)

processAliases.

Overrides:

processAliases in class FullFeatureEnricher<F extends Feature>

Parameters:

objectToEnrich - a F object.

termFetched - a F object.

setFeatureEnricherListener

public void setFeatureEnricherListener(FeatureEnricherListener<F> featureEnricherListener)

setFeatureEnricherListener.

Sets the listener of feature changes. Can be null.

Specified by:

setFeatureEnricherListener in interface FeatureEnricher<F extends Feature>

Overrides:

setFeatureEnricherListener in class MinimalFeatureEnricher<F extends Feature>

Parameters:

featureEnricherListener - a FeatureEnricherListener object.

getFeatureEnricherListener

public FeatureEnricherListener<F> getFeatureEnricherListener()

Retrieves the listener of feature changes. May be null if changes are not being listened to.

Specified by:

getFeatureEnricherListener in interface FeatureEnricher<F extends Feature>

Overrides:

getFeatureEnricherListener in class MinimalFeatureEnricher<F extends Feature>

Returns:

The current listener of feature changes.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher cvTermEnricher)

setCvTermEnricher.

Sets the subEnricher for CvTerms. Can be null.

Specified by:

setCvTermEnricher in interface FeatureEnricher<F extends Feature>

Overrides:

setCvTermEnricher in class MinimalFeatureEnricher<F extends Feature>

Parameters:

cvTermEnricher - a CvTermEnricher object.

getCvTermEnricher

public CvTermEnricher getCvTermEnricher()

Gets the subEnricher for CvTerms. Can be null.

Specified by:

getCvTermEnricher in interface FeatureEnricher<F extends Feature>

Overrides:

getCvTermEnricher in class MinimalFeatureEnricher<F extends Feature>

Returns:

The CvTerm enricher which is being used.

onSequenceUpdate

public void onSequenceUpdate(Protein protein,
                             String oldSequence)

Listen to the event where the sequence of a protein has been changed. If oldSequence is null, it means that the sequence has been initialised. If the sequence of the protein is null, it means that the sequence of the protein has been reset

Specified by:

onSequenceUpdate in interface PolymerChangeListener<F extends Feature>

Overrides:

onSequenceUpdate in class MinimalFeatureEnricher<F extends Feature>

Parameters:

protein - : updated polymer

oldSequence - : old sequence

onShortNameUpdate

public void onShortNameUpdate(Protein interactor,
                              String oldShortName)

Listens for the event where the shortName has been changed.

Specified by:

onShortNameUpdate in interface InteractorChangeListener<F extends Feature>

Overrides:

onShortNameUpdate in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

oldShortName - The old shortName.

onFullNameUpdate

public void onFullNameUpdate(Protein interactor,
                             String oldFullName)

Listens for the event where the fullName has been changed.

Specified by:

onFullNameUpdate in interface InteractorChangeListener<F extends Feature>

Overrides:

onFullNameUpdate in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

oldFullName - The old fullName.

onOrganismUpdate

public void onOrganismUpdate(Protein interactor,
                             Organism o)

Listen to the event where the organism of a interactor has been initialised. This event happens when a interactor does not have any organisms

Specified by:

onOrganismUpdate in interface InteractorChangeListener<F extends Feature>

Overrides:

onOrganismUpdate in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

o - a Organism object.

onInteractorTypeUpdate

public void onInteractorTypeUpdate(Protein interactor,
                                   CvTerm old)

Listen to the event where the interactor type has been initialised. This event happens when a interactor does not have any interactor types

Specified by:

onInteractorTypeUpdate in interface InteractorChangeListener<F extends Feature>

Overrides:

onInteractorTypeUpdate in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

old - a CvTerm object.

onAddedAlias

public void onAddedAlias(Protein o,
                         Alias added)

Listen to the event where an alias has been added to the object aliases.

Specified by:

onAddedAlias in interface AliasesChangeListener<F extends Feature>

Overrides:

onAddedAlias in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

added - The added alias.

onRemovedAlias

public void onRemovedAlias(Protein o,
                           Alias removed)

Listen to the event where an alias has been removed from the object aliases.

Specified by:

onRemovedAlias in interface AliasesChangeListener<F extends Feature>

Overrides:

onRemovedAlias in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed alias.

onAddedAnnotation

public void onAddedAnnotation(Protein o,
                              Annotation added)

Listen to the event where an annotation has been added to the object annotations.

Specified by:

onAddedAnnotation in interface AnnotationsChangeListener<F extends Feature>

Overrides:

onAddedAnnotation in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - : the parent of this annotation

added - : the added annotation

onRemovedAnnotation

public void onRemovedAnnotation(Protein o,
                                Annotation removed)

Listen to the event where an annotation has been removed from the object annotations.

Specified by:

onRemovedAnnotation in interface AnnotationsChangeListener<F extends Feature>

Overrides:

onRemovedAnnotation in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - : the parent of this annotation

removed - : the removed annotation

onAddedChecksum

public void onAddedChecksum(Protein interactor,
                            Checksum added)

Listen to the event where a checksum has been added to the interactor checksums.

Specified by:

onAddedChecksum in interface ChecksumsChangeListener<F extends Feature>

Overrides:

onAddedChecksum in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

added - The added checksum.

onRemovedChecksum

public void onRemovedChecksum(Protein interactor,
                              Checksum removed)

Listen to the event where a checksum has been removed from the interactor checksums.

Specified by:

onRemovedChecksum in interface ChecksumsChangeListener<F extends Feature>

Overrides:

onRemovedChecksum in class MinimalFeatureEnricher<F extends Feature>

Parameters:

interactor - The interactor which has changed.

removed - The removed checksum.

onAddedIdentifier

public void onAddedIdentifier(Protein o,
                              Xref added)

Listen to the event where an identifier has been added to the protein identifiers.

Specified by:

onAddedIdentifier in interface IdentifiersChangeListener<F extends Feature>

Overrides:

onAddedIdentifier in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

added - The added identifier

onRemovedIdentifier

public void onRemovedIdentifier(Protein o,
                                Xref removed)

Listen to the event where an identifier has been removed from the protein identifiers.

Specified by:

onRemovedIdentifier in interface IdentifiersChangeListener<F extends Feature>

Overrides:

onRemovedIdentifier in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed identifier.

onAddedXref

public void onAddedXref(Protein o,
                        Xref added)

Listen to the event where a xref has been added to the protein xrefs.

Specified by:

onAddedXref in interface XrefsChangeListener<F extends Feature>

Overrides:

onAddedXref in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

added - The added Xref.

onRemovedXref

public void onRemovedXref(Protein o,
                          Xref removed)

Listen to the event where a xref has been removed from the interactor xrefs.

Specified by:

onRemovedXref in interface XrefsChangeListener<F extends Feature>

Overrides:

onRemovedXref in class MinimalFeatureEnricher<F extends Feature>

Parameters:

o - The object which has changed.

removed - The removed Xref.

onEnrichmentComplete

public void onEnrichmentComplete(Protein object,
                                 EnrichmentStatus status,
                                 String message)

onEnrichmentComplete.

Specified by:

onEnrichmentComplete in interface EnricherListener<F extends Feature>

Overrides:

onEnrichmentComplete in class MinimalFeatureEnricher<F extends Feature>

Parameters:

object - a T object.

status - a EnrichmentStatus object.

message - a String object.

onEnrichmentError

public void onEnrichmentError(Protein object,
                              String message,
                              Exception e)

onEnrichmentError.

Specified by:

onEnrichmentError in interface EnricherListener<F extends Feature>

Overrides:

onEnrichmentError in class MinimalFeatureEnricher<F extends Feature>

Parameters:

object - a T object.

message - a String object.

e - a Exception object.

getMinimalUpdater

protected MinimalFeatureUpdater<F> getMinimalUpdater()

Getter for the field minimalUpdater.

Returns:

a MinimalFeatureUpdater object.