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

Class FullFeatureEvidenceEnricher

java.lang.Object

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

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

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

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 FullFeatureEvidenceEnricher
extends FullFeatureEnricher<FeatureEvidence>

Provides full enrichment of feature evidence. - enrich full properties of feature. See FullFeatureEnricher - enrich detection methods if cv term enricher is not null

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullFeatureEvidenceEnricher()	Constructor for FullFeatureEvidenceEnricher.
protected	FullFeatureEvidenceEnricher(MinimalFeatureEvidenceEnricher minimalEnricher)	Constructor for FullFeatureEvidenceEnricher.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher	getCvTermEnricher()	Gets the subEnricher for CvTerms.
FeatureEnricherListener<FeatureEvidence>	getFeatureEnricherListener()	Retrieves the listener of feature changes.
protected MinimalFeatureEvidenceEnricher	getMinimalEnricher()	Getter for the field minimalEnricher.
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.
void	processMinimalUpdates(FeatureEvidence objectToEnrich, FeatureEvidence objectSource)	processMinimalUpdates.
protected void	processOtherProperties(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processOtherProperties.
protected void	processParameters(FeatureEvidence featureToEnrich, FeatureEvidence objectSource)	processParameters.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setFeatureEnricherListener(FeatureEnricherListener<FeatureEvidence> featureEnricherListener)	setFeatureEnricherListener.

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

enrich, mergeLinkedFeatures, processAliases, processAnnotations, processLinkedFeatures, processOtherProperties, processRole, processRole, processXrefs

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

enrich, enrich, onInvalidRange, onOutOfDateRange, processFeatureType, processFeatureType, processFullName, processIdentifiers, 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

FullFeatureEvidenceEnricher

public FullFeatureEvidenceEnricher()

Constructor for FullFeatureEvidenceEnricher.

FullFeatureEvidenceEnricher

protected FullFeatureEvidenceEnricher(MinimalFeatureEvidenceEnricher minimalEnricher)

Constructor for FullFeatureEvidenceEnricher.

Parameters:

minimalEnricher - a MinimalFeatureEvidenceEnricher object.

Method Detail

processMinimalUpdates

public void processMinimalUpdates(FeatureEvidence objectToEnrich,
                                  FeatureEvidence objectSource)
                           throws EnricherException

processMinimalUpdates.

Overrides:

processMinimalUpdates in class MinimalFeatureEnricher<FeatureEvidence>

Parameters:

objectToEnrich - a F object.

objectSource - a F 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.

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.

processOtherProperties

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

processOtherProperties.

Overrides:

processOtherProperties in class FullFeatureEnricher<FeatureEvidence>

Parameters:

featureToEnrich - a F object.

objectSource - a F object.

Throws:

EnricherException - if any.

processParameters

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

processParameters.

Parameters:

featureToEnrich - a FeatureEvidence object.

objectSource - a FeatureEvidence object.

Throws:

EnricherException - if any.

getMinimalEnricher

protected MinimalFeatureEvidenceEnricher getMinimalEnricher()

Getter for the field minimalEnricher.

Returns:

a MinimalFeatureEvidenceEnricher object.