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

Class MinimalFeatureEvidenceUpdater

java.lang.Object

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

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

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

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>

public class MinimalFeatureEvidenceUpdater
extends MinimalFeatureEvidenceEnricher

Provides minimal update of feature evidence. - update minimal properties of feature. See MinimalFeatureUpdater - update 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

Modifier	Constructor	Description
	MinimalFeatureEvidenceUpdater()	Constructor for MinimalFeatureEvidenceUpdater.
protected	MinimalFeatureEvidenceUpdater(MinimalFeatureUpdater<FeatureEvidence> minimalUpdater)	Constructor for MinimalFeatureEvidenceUpdater.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher	getCvTermEnricher()	Gets the subEnricher for CvTerms.
FeatureEnricherListener<FeatureEvidence>	getFeatureEnricherListener()	Retrieves the listener of feature changes.
protected MinimalFeatureUpdater<FeatureEvidence>	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.
protected void	onInvalidRange(FeatureEvidence feature, Range range, Collection<String> errorMessages)	onInvalidRange.
void	onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
protected void	onOutOfDateRange(FeatureEvidence feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
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	processDetectionMethods(FeatureEvidence featureToEnrich, FeatureEvidence source)	processDetectionMethods.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)	setFeatureEnricherListener.
protected boolean	updateRangePositions()	updateRangePositions.

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

mergeDetectionMethods, processDetectionMethods, processOtherProperties, processOtherProperties

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

enrich, enrich, enrich, processFeatureType, processFeatureType, processFullName, processIdentifiers, processMinimalUpdates, processMinimalUpdates, processRanges, processRanges, processRangeStatus, processShortLabel, setFeaturesWithRangesToUpdate

Methods inherited from class java.lang.Object

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

Constructor Detail

MinimalFeatureEvidenceUpdater

public MinimalFeatureEvidenceUpdater()

Constructor for MinimalFeatureEvidenceUpdater.

MinimalFeatureEvidenceUpdater

protected MinimalFeatureEvidenceUpdater(MinimalFeatureUpdater<FeatureEvidence> minimalUpdater)

Constructor for MinimalFeatureEvidenceUpdater.

Parameters:

minimalUpdater - a MinimalFeatureUpdater object.

Method Detail

processDetectionMethods

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

processDetectionMethods.

Overrides:

processDetectionMethods in class MinimalFeatureEvidenceEnricher

Parameters:

featureToEnrich - a FeatureEvidence object.

source - a FeatureEvidence object.

Throws:

EnricherException - if any.

setFeatureEnricherListener

public void setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)

setFeatureEnricherListener.

Sets the listener of feature changes. Can be null.

Specified by:

setFeatureEnricherListener in interface FeatureEnricher<FeatureEvidence>

Overrides:

setFeatureEnricherListener in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

featureEnricherListener - a FeatureEnricherListener object.

getFeatureEnricherListener

public FeatureEnricherListener<FeatureEvidence> getFeatureEnricherListener()

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

Specified by:

getFeatureEnricherListener in interface FeatureEnricher<FeatureEvidence>

Overrides:

getFeatureEnricherListener in class MinimalFeatureEnricher<FeatureEvidence>

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<FeatureEvidence>

Overrides:

setCvTermEnricher in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

cvTermEnricher - a CvTermEnricher object.

getCvTermEnricher

public CvTermEnricher getCvTermEnricher()

Gets the subEnricher for CvTerms. Can be null.

Specified by:

getCvTermEnricher in interface FeatureEnricher<FeatureEvidence>

Overrides:

getCvTermEnricher in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onSequenceUpdate in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onShortNameUpdate in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onFullNameUpdate in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onOrganismUpdate in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onInteractorTypeUpdate in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onAddedAlias in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onRemovedAlias in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onAddedAnnotation in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onRemovedAnnotation in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onAddedChecksum in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onRemovedChecksum in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onAddedIdentifier in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onRemovedIdentifier in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onAddedXref in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onRemovedXref in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

o - The object which has changed.

removed - The removed Xref.

updateRangePositions

protected boolean updateRangePositions()

updateRangePositions.

Overrides:

updateRangePositions in class MinimalFeatureEnricher<FeatureEvidence>

Returns:

a boolean.

onInvalidRange

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

onInvalidRange.

Overrides:

onInvalidRange in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

onOutOfDateRange

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

onOutOfDateRange.

Overrides:

onOutOfDateRange in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

feature - a F object.

range - a Range object.

errorMessages - a Collection object.

oldSequence - a String object.

onEnrichmentComplete

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

onEnrichmentComplete.

Specified by:

onEnrichmentComplete in interface EnricherListener<Protein>

Overrides:

onEnrichmentComplete in class MinimalFeatureEnricher<FeatureEvidence>

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<Protein>

Overrides:

onEnrichmentError in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

object - a T object.

message - a String object.

e - a Exception object.

getMinimalUpdater

protected MinimalFeatureUpdater<FeatureEvidence> getMinimalUpdater()

Getter for the field minimalUpdater.

Returns:

a MinimalFeatureUpdater object.