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

Class FullParticipantEvidenceUpdater<P extends ParticipantEvidence>

java.lang.Object

psidev.psi.mi.jami.enricher.impl.minimal.MinimalEntityEnricher<P,F>

psidev.psi.mi.jami.enricher.impl.minimal.MinimalParticipantEnricher<P,FeatureEvidence>

psidev.psi.mi.jami.enricher.impl.minimal.MinimalParticipantEvidenceEnricher<P>

psidev.psi.mi.jami.enricher.impl.full.FullParticipantEvidenceEnricher<P>

psidev.psi.mi.jami.enricher.impl.full.FullParticipantEvidenceUpdater<P>

All Implemented Interfaces:

EntityEnricher<P,FeatureEvidence>, MIEnricher<P>, ParticipantEnricher<P,FeatureEvidence>, ParticipantEvidenceEnricher<P>

Direct Known Subclasses:

FullExperimentalParticipantPoolUpdater

public class FullParticipantEvidenceUpdater<P extends ParticipantEvidence>
extends FullParticipantEvidenceEnricher<P>

Created with IntelliJ IDEA.

Since:

28/06/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullParticipantEvidenceUpdater()	Constructor for FullParticipantEvidenceUpdater.
protected	FullParticipantEvidenceUpdater(MinimalParticipantEvidenceUpdater<P> participantEnricher)	Constructor for FullParticipantEvidenceUpdater.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher<CvTerm>	getCvTermEnricher()	The current CvTerm enricher, If null, CvTerms will not be enriched.
FeatureEnricher<FeatureEvidence>	getFeatureEnricher()	The current enricher used for features.
CompositeInteractorEnricher	getInteractorEnricher()	Getter for the field interactorEnricher.
protected MinimalParticipantEvidenceUpdater<P>	getMinimalUpdater()	Getter for the field minimalUpdater.
EntityEnricherListener	getParticipantEnricherListener()	The current listener that participant changes are reported to.
protected void	processAliases(P objectToEnrich, P objectSource)	processAliases.
void	processBiologicalRole(P objectToEnrich, P objectSource)	processBiologicalRole.
protected void	processConfidences(P participantEvidenceToEnrich, P objectSource)	processConfidences.
protected void	processExperimentalPreparations(P participantEvidenceToEnrich, P objectSource)	processExperimentalPreparations.
void	processExperimentalRole(P participantEvidenceToEnrich, P objectSource)	processExperimentalRole.
void	processFeatures(P objectToEnrich, P objectSource)	processFeatures.
void	processIdentificationMethods(P participantEvidenceToEnrich, P objectSource)	processIdentificationMethods.
void	processInteractor(P objectToEnrich, P objectSource)	processInteractor.
protected void	processParameters(P participantEvidenceToEnrich, P objectSource)	processParameters.
protected void	processXrefs(P participantEvidenceToEnrich, P objectSource)	processXrefs.
void	setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)	setCvTermEnricher.
void	setFeatureEnricher(FeatureEnricher<FeatureEvidence> featureEnricher)	setFeatureEnricher.
void	setInteractorEnricher(CompositeInteractorEnricher interactorEnricher)	setInteractorEnricher.
void	setParticipantEnricherListener(EntityEnricherListener listener)	setParticipantEnricherListener.

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

mergeExperimentalPreparations, processExperimentalPreparations, processOtherProperties, processOtherProperties

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

getOrganismEnricher, mergeIdentificationMethods, processExperimentalRole, processExpressedInOrganism, processExpressedInOrganism, processIdentificationMethods, setOrganismEnricher

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

enrich, processBiologicalRole

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

enrich, enrich, processFeatures, processInteractor

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.enricher.MIEnricher

enrich, enrich, enrich

Constructor Detail

FullParticipantEvidenceUpdater

public FullParticipantEvidenceUpdater()

Constructor for FullParticipantEvidenceUpdater.

FullParticipantEvidenceUpdater

protected FullParticipantEvidenceUpdater(MinimalParticipantEvidenceUpdater<P> participantEnricher)

Constructor for FullParticipantEvidenceUpdater.

Parameters:

participantEnricher - a MinimalParticipantEvidenceUpdater object.

Method Detail

processExperimentalPreparations

protected void processExperimentalPreparations(P participantEvidenceToEnrich,
                                               P objectSource)
                                        throws EnricherException

processExperimentalPreparations.

Overrides:

processExperimentalPreparations in class FullParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processParameters

protected void processParameters(P participantEvidenceToEnrich,
                                 P objectSource)
                          throws EnricherException

processParameters.

Overrides:

processParameters in class FullParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processConfidences

protected void processConfidences(P participantEvidenceToEnrich,
                                  P objectSource)
                           throws EnricherException

processConfidences.

Overrides:

processConfidences in class FullParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(P participantEvidenceToEnrich,
                            P objectSource)
                     throws EnricherException

processXrefs.

Overrides:

processXrefs in class FullParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processIdentificationMethods

public void processIdentificationMethods(P participantEvidenceToEnrich,
                                         P objectSource)
                                  throws EnricherException

processIdentificationMethods.

Overrides:

processIdentificationMethods in class MinimalParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processExperimentalRole

public void processExperimentalRole(P participantEvidenceToEnrich,
                                    P objectSource)
                             throws EnricherException

processExperimentalRole.

Overrides:

processExperimentalRole in class MinimalParticipantEvidenceEnricher<P extends ParticipantEvidence>

Parameters:

participantEvidenceToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processInteractor

public void processInteractor(P objectToEnrich,
                              P objectSource)
                       throws EnricherException

processInteractor.

Overrides:

processInteractor in class MinimalParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

objectToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processFeatures

public void processFeatures(P objectToEnrich,
                            P objectSource)
                     throws EnricherException

processFeatures.

Overrides:

processFeatures in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

objectToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processBiologicalRole

public void processBiologicalRole(P objectToEnrich,
                                  P objectSource)
                           throws EnricherException

processBiologicalRole.

Overrides:

processBiologicalRole in class MinimalParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

objectToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

processAliases

protected void processAliases(P objectToEnrich,
                              P objectSource)
                       throws EnricherException

processAliases.

Overrides:

processAliases in class MinimalParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

objectToEnrich - a P object.

objectSource - a P object.

Throws:

EnricherException - if any.

setParticipantEnricherListener

public void setParticipantEnricherListener(EntityEnricherListener listener)

setParticipantEnricherListener.

Sets the listener for Participant events. If null, events will not be reported.

Specified by:

setParticipantEnricherListener in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

setParticipantEnricherListener in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

listener - a EntityEnricherListener object.

getParticipantEnricherListener

public EntityEnricherListener getParticipantEnricherListener()

The current listener that participant changes are reported to. If null, events are not being reported.

Specified by:

getParticipantEnricherListener in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

getParticipantEnricherListener in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Returns:

TThe current listener. Can be null.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher<CvTerm> cvTermEnricher)

setCvTermEnricher.

Sets the enricher for CvTerms. If null, cvTerms are not being enriched.

Specified by:

setCvTermEnricher in interface ParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

setCvTermEnricher in class MinimalParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

cvTermEnricher - a CvTermEnricher object.

getCvTermEnricher

public CvTermEnricher<CvTerm> getCvTermEnricher()

The current CvTerm enricher, If null, CvTerms will not be enriched.

Specified by:

getCvTermEnricher in interface ParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

getCvTermEnricher in class MinimalParticipantEnricher<P extends ParticipantEvidence,FeatureEvidence>

Returns:

The new enricher for CvTerms. Can be null.

setFeatureEnricher

public void setFeatureEnricher(FeatureEnricher<FeatureEvidence> featureEnricher)

setFeatureEnricher.

Will attempt to add the featureEnricher as a proteinListener if this is valid. If the proteinEnricher already has a listener, this will be preserved using a listener manager.

Specified by:

setFeatureEnricher in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

setFeatureEnricher in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

featureEnricher - a FeatureEnricher object.

getFeatureEnricher

public FeatureEnricher<FeatureEvidence> getFeatureEnricher()

The current enricher used for features. If null, features are not currently being enriched.

Specified by:

getFeatureEnricher in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

getFeatureEnricher in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Returns:

The current enricher. May be null.

setInteractorEnricher

public void setInteractorEnricher(CompositeInteractorEnricher interactorEnricher)

setInteractorEnricher.

Specified by:

setInteractorEnricher in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

setInteractorEnricher in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Parameters:

interactorEnricher - a CompositeInteractorEnricher object.

getInteractorEnricher

public CompositeInteractorEnricher getInteractorEnricher()

Getter for the field interactorEnricher.

Specified by:

getInteractorEnricher in interface EntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Overrides:

getInteractorEnricher in class MinimalEntityEnricher<P extends ParticipantEvidence,FeatureEvidence>

Returns:

a CompositeInteractorEnricher object.

getMinimalUpdater

protected MinimalParticipantEvidenceUpdater<P> getMinimalUpdater()

Getter for the field minimalUpdater.

Returns:

a MinimalParticipantEvidenceUpdater object.