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

Class MinimalExperimentEnricher

java.lang.Object

psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher<Experiment>

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

All Implemented Interfaces:

ExperimentEnricher, MIEnricher<Experiment>

Direct Known Subclasses:

FullExperimentEnricher, MinimalExperimentUpdater

public class MinimalExperimentEnricher
extends AbstractMIEnricher<Experiment>
implements ExperimentEnricher

Provides minimal enrichment of experiment. - enrich publication using Publication enricher if not null. Will not override an existing publication with the publication loaded with the fetched experiment - enrich interaction detection method using CvTerm enricher if not null. Will not override an existing interaction detection method with the interaction detection method loaded with the fetched interaction detection method - enrich host organism using Organism enricher if not null. Will not override an existing host organism with the host organism loaded with the fetched experiment It will ignore all other properties of a Experiment

Since:

13/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalExperimentEnricher()	Constructor for MinimalExperimentEnricher.

Method Summary

Modifier and Type	Method	Description
void	enrich(Collection<Experiment> objects)	enrich.
void	enrich(Experiment experimentToEnrich, Experiment objectSource)	enrich.
Experiment	find(Experiment objectToEnrich)	find.
CvTermEnricher	getCvTermEnricher()	Gets the subEnricher for CvTerms.
ExperimentEnricherListener	getExperimentEnricherListener()	Gets current ExperimentEnricherListener.
OrganismEnricher	getOrganismEnricher()	Getter for the field organismEnricher.
PublicationEnricher	getPublicationEnricher()	Sets the subEnricher for publications.
protected void	onEnrichedVersionNotFound(Experiment experimentToEnrich)	onEnrichedVersionNotFound.
void	processExperiment(Experiment experimentToEnrich)	processExperiment.
void	processExperiment(Experiment experimentToEnrich, Experiment objectSource)	processExperiment.
protected void	processInteractionDetectionMethod(Experiment experimentToEnrich)	processInteractionDetectionMethod.
protected void	processInteractionDetectionMethod(Experiment experimentToEnrich, Experiment objectSource)	processInteractionDetectionMethod.
protected void	processOrganism(Experiment experimentToEnrich)	processOrganism.
protected void	processOrganism(Experiment experimentToEnrich, Experiment objectSource)	processOrganism.
protected void	processOtherProperties(Experiment experimentToEnrich)	processOtherProperties.
protected void	processOtherProperties(Experiment experimentToEnrich, Experiment objectSource)	processOtherProperties.
protected void	processPublication(Experiment experimentToEnrich)	processPublication.
protected void	processPublication(Experiment experimentToEnrich, Experiment objectSource)	processPublication.
void	setCvTermEnricher(CvTermEnricher cvTermEnricher)	setCvTermEnricher.
void	setExperimentEnricherListener(ExperimentEnricherListener listener)	setExperimentEnricherListener.
void	setOrganismEnricher(OrganismEnricher organismEnricher)	setOrganismEnricher.
void	setPublicationEnricher(PublicationEnricher publicationEnricher)	setPublicationEnricher.

Methods inherited from class psidev.psi.mi.jami.enricher.impl.AbstractMIEnricher

enrich

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

Constructor Detail

MinimalExperimentEnricher

public MinimalExperimentEnricher()

Constructor for MinimalExperimentEnricher.

Method Detail

processOrganism

protected void processOrganism(Experiment experimentToEnrich)
                        throws EnricherException

processOrganism.

Parameters:

experimentToEnrich - a Experiment object.

Throws:

EnricherException - if any.

processInteractionDetectionMethod

protected void processInteractionDetectionMethod(Experiment experimentToEnrich)
                                          throws EnricherException

processInteractionDetectionMethod.

Parameters:

experimentToEnrich - a Experiment object.

Throws:

EnricherException - if any.

processPublication

protected void processPublication(Experiment experimentToEnrich)
                           throws EnricherException

processPublication.

Parameters:

experimentToEnrich - a Experiment object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(Experiment experimentToEnrich)
                               throws EnricherException

processOtherProperties.

Parameters:

experimentToEnrich - a Experiment object.

Throws:

EnricherException - if any.

enrich

public void enrich(Collection<Experiment> objects)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<Experiment>

Overrides:

enrich in class AbstractMIEnricher<Experiment>

Parameters:

objects - a Collection object.

Throws:

EnricherException - if any.

enrich

public void enrich(Experiment experimentToEnrich,
                   Experiment objectSource)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<Experiment>

Specified by:

enrich in class AbstractMIEnricher<Experiment>

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

processExperiment

public void processExperiment(Experiment experimentToEnrich,
                              Experiment objectSource)
                       throws EnricherException

processExperiment.

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

find

public Experiment find(Experiment objectToEnrich)
                throws EnricherException

find.

Specified by:

find in class AbstractMIEnricher<Experiment>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(Experiment experimentToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Specified by:

onEnrichedVersionNotFound in class AbstractMIEnricher<Experiment>

Parameters:

experimentToEnrich - a T object.

Throws:

EnricherException - if any.

processExperiment

public void processExperiment(Experiment experimentToEnrich)
                       throws EnricherException

processExperiment.

Parameters:

experimentToEnrich - a Experiment object.

Throws:

EnricherException - if any.

processOtherProperties

protected void processOtherProperties(Experiment experimentToEnrich,
                                      Experiment objectSource)
                               throws EnricherException

processOtherProperties.

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

processInteractionDetectionMethod

protected void processInteractionDetectionMethod(Experiment experimentToEnrich,
                                                 Experiment objectSource)
                                          throws EnricherException

processInteractionDetectionMethod.

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

processPublication

protected void processPublication(Experiment experimentToEnrich,
                                  Experiment objectSource)
                           throws EnricherException

processPublication.

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

processOrganism

protected void processOrganism(Experiment experimentToEnrich,
                               Experiment objectSource)
                        throws EnricherException

processOrganism.

Parameters:

experimentToEnrich - a Experiment object.

objectSource - a Experiment object.

Throws:

EnricherException - if any.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher cvTermEnricher)

setCvTermEnricher.

Sets the subEnricher for CvTerms. Can be null.

Specified by:

setCvTermEnricher in interface ExperimentEnricher

Parameters:

cvTermEnricher - a CvTermEnricher object.

getCvTermEnricher

public CvTermEnricher getCvTermEnricher()

Gets the subEnricher for CvTerms. Can be null.

Specified by:

getCvTermEnricher in interface ExperimentEnricher

Returns:

The CvTerm enricher which is being used.

getPublicationEnricher

public PublicationEnricher getPublicationEnricher()

Sets the subEnricher for publications. Can be null.

Specified by:

getPublicationEnricher in interface ExperimentEnricher

Returns:

The publications enricher which is being used.

setPublicationEnricher

public void setPublicationEnricher(PublicationEnricher publicationEnricher)

setPublicationEnricher.

Gets the publications for organisms. Can be null.

Specified by:

setPublicationEnricher in interface ExperimentEnricher

Parameters:

publicationEnricher - a PublicationEnricher object.

getExperimentEnricherListener

public ExperimentEnricherListener getExperimentEnricherListener()

Gets current ExperimentEnricherListener. Can be null.

Specified by:

getExperimentEnricherListener in interface ExperimentEnricher

Returns:

The listener which is currently beign used.

setExperimentEnricherListener

public void setExperimentEnricherListener(ExperimentEnricherListener listener)

setExperimentEnricherListener.

Sets the ExperimentEnricherListener. Can be null.

Specified by:

setExperimentEnricherListener in interface ExperimentEnricher

Parameters:

listener - a ExperimentEnricherListener object.

getOrganismEnricher

public OrganismEnricher getOrganismEnricher()

Getter for the field organismEnricher.

Specified by:

getOrganismEnricher in interface ExperimentEnricher

Returns:

a OrganismEnricher object.

setOrganismEnricher

public void setOrganismEnricher(OrganismEnricher organismEnricher)

setOrganismEnricher.

Specified by:

setOrganismEnricher in interface ExperimentEnricher

Parameters:

organismEnricher - a OrganismEnricher object.