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

Class FullOrganismUpdater

java.lang.Object

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

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

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

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

All Implemented Interfaces:

MIEnricher<Organism>, OrganismEnricher

public class FullOrganismUpdater
extends MinimalOrganismUpdater

Provides full update of a Organism. - update minimal properties of organism. See details in MinimalOrganismUpdater - if cvTermEnricher is not null, will update cellType, tissue and compartment. It will override cellType, tissue and compartment with the ones loaded with the fetched organism if they are different from the ones in the fetched organism. (See DefaultCvTermComparator)

Since:

24/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
FullOrganismUpdater(OrganismFetcher organismFetcher)	Constructor for FullOrganismUpdater.

Method Summary

Modifier and Type	Method	Description
CvTermEnricher<CvTerm>	getCvTermEnricher()	getCvTermEnricher.
protected void	processAliases(Organism organismToEnrich, Organism organismFetched)	processAliases.
protected void	processCellType(Organism entityToEnrich, Organism fetched)	processCellType.
protected void	processCompartment(Organism entityToEnrich, Organism fetched)	processCompartment.
protected void	processOtherProperties(Organism organismToEnrich, Organism organismFetched)	processOtherProperties.
protected void	processTissue(Organism entityToEnrich, Organism fetched)	processTissue.
void	setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)	setCvTermEnricher.

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

processCommonName, processScientificName, processTaxid

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

enrich, find, getOrganismEnricherListener, getOrganismFetcher, getRetryCount, onEnrichedVersionNotFound, setOrganismEnricherListener, setRetryCount

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

enrich, 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, enrich

Constructor Detail

FullOrganismUpdater

public FullOrganismUpdater(OrganismFetcher organismFetcher)

Constructor for FullOrganismUpdater.

Parameters:

organismFetcher - a OrganismFetcher object.

Method Detail

getCvTermEnricher

public CvTermEnricher<CvTerm> getCvTermEnricher()

getCvTermEnricher.

Specified by:

getCvTermEnricher in interface OrganismEnricher

Overrides:

getCvTermEnricher in class MinimalOrganismEnricher

Returns:

a CvTermEnricher object.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher<CvTerm> cvEnricher)

setCvTermEnricher.

Specified by:

setCvTermEnricher in interface OrganismEnricher

Overrides:

setCvTermEnricher in class MinimalOrganismEnricher

Parameters:

cvEnricher - a CvTermEnricher object.

processOtherProperties

protected void processOtherProperties(Organism organismToEnrich,
                                      Organism organismFetched)
                               throws EnricherException

processOtherProperties.

Overrides:

processOtherProperties in class MinimalOrganismEnricher

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.

Throws:

EnricherException - if any.

processAliases

protected void processAliases(Organism organismToEnrich,
                              Organism organismFetched)
                       throws EnricherException

processAliases.

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.

Throws:

EnricherException - if any.

processCellType

protected void processCellType(Organism entityToEnrich,
                               Organism fetched)
                        throws EnricherException

processCellType.

Parameters:

entityToEnrich - a Organism object.

fetched - a Organism object.

Throws:

EnricherException - if any.

processTissue

protected void processTissue(Organism entityToEnrich,
                             Organism fetched)
                      throws EnricherException

processTissue.

Parameters:

entityToEnrich - a Organism object.

fetched - a Organism object.

Throws:

EnricherException - if any.

processCompartment

protected void processCompartment(Organism entityToEnrich,
                                  Organism fetched)
                           throws EnricherException

processCompartment.

Parameters:

entityToEnrich - a Organism object.

fetched - a Organism object.

Throws:

EnricherException - if any.