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

Class FullOrganismEnricher

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.full.FullOrganismEnricher

All Implemented Interfaces:

MIEnricher<Organism>, OrganismEnricher

public class FullOrganismEnricher
extends MinimalOrganismEnricher

Provides full enrichment of a Organism. - enrich minimal properties of organism. See details in MinimalOrganismEnricher - if cvTermEnricher is not null, will enrich cellType, tissue and compartment but does not override any celltype, tissue, compartment with the one loaded with the fetched organism The organism fetcher is required for enriching organism

Since:

13/06/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
FullOrganismEnricher(OrganismFetcher organismFetcher)	Constructor for FullOrganismEnricher.

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.MinimalOrganismEnricher

enrich, find, getOrganismEnricherListener, getOrganismFetcher, getRetryCount, onEnrichedVersionNotFound, processCommonName, processScientificName, processTaxid, 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

FullOrganismEnricher

public FullOrganismEnricher(OrganismFetcher organismFetcher)

Constructor for FullOrganismEnricher.

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.