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

Class MinimalOrganismEnricher

java.lang.Object

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

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

All Implemented Interfaces:

MIEnricher<Organism>, OrganismEnricher

Direct Known Subclasses:

FullOrganismEnricher, MinimalOrganismUpdater

public class MinimalOrganismEnricher
extends AbstractMIEnricher<Organism>
implements OrganismEnricher

Provides minimum enrichment of a Organism. - enrich common name if not set. Does not override it with fetched organism common name if already set. - enrich scientific name if not set. Does not override it with fetched organism scientific name if already set. The organism fetcher is required for enriching organism

Since:

22/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
MinimalOrganismEnricher(OrganismFetcher organismFetcher)	Constructor for MinimalOrganismEnricher.

Method Summary

Modifier and Type	Method	Description
void	enrich(Organism organismToEnrich, Organism organismFetched)	enrich.
Organism	find(Organism objectToEnrich)	find.
CvTermEnricher<CvTerm>	getCvTermEnricher()	getCvTermEnricher.
OrganismEnricherListener	getOrganismEnricherListener()	getOrganismEnricherListener.
OrganismFetcher	getOrganismFetcher()	getOrganismFetcher.
int	getRetryCount()	Getter for the field retryCount.
protected void	onEnrichedVersionNotFound(Organism objectToEnrich)	onEnrichedVersionNotFound.
protected void	processCommonName(Organism organismToEnrich, Organism organismFetched)	processCommonName.
protected void	processOtherProperties(Organism organismToEnrich, Organism organismFetched)	processOtherProperties.
protected void	processScientificName(Organism organismToEnrich, Organism organismFetched)	processScientificName.
protected void	processTaxid(Organism organismToEnrich, Organism organismFetched)	processTaxid.
void	setCvTermEnricher(CvTermEnricher<CvTerm> enricher)	setCvTermEnricher.
void	setOrganismEnricherListener(OrganismEnricherListener organismEnricherListener)	setOrganismEnricherListener.
void	setRetryCount(int retryCount)	Setter for the field retryCount.

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

MinimalOrganismEnricher

public MinimalOrganismEnricher(OrganismFetcher organismFetcher)

Constructor for MinimalOrganismEnricher.

Parameters:

organismFetcher - a OrganismFetcher object.

Method Detail

getRetryCount

public int getRetryCount()

Getter for the field retryCount.

Returns:

a int.

setRetryCount

public void setRetryCount(int retryCount)

Setter for the field retryCount.

Parameters:

retryCount - a int.

getOrganismFetcher

public OrganismFetcher getOrganismFetcher()

getOrganismFetcher.

Specified by:

getOrganismFetcher in interface OrganismEnricher

Returns:

The current organism fetcher

setOrganismEnricherListener

public void setOrganismEnricherListener(OrganismEnricherListener organismEnricherListener)

setOrganismEnricherListener.

Specified by:

setOrganismEnricherListener in interface OrganismEnricher

Parameters:

organismEnricherListener - a OrganismEnricherListener object.

setCvTermEnricher

public void setCvTermEnricher(CvTermEnricher<CvTerm> enricher)

setCvTermEnricher.

Specified by:

setCvTermEnricher in interface OrganismEnricher

Parameters:

enricher - a CvTermEnricher object.

getOrganismEnricherListener

public OrganismEnricherListener getOrganismEnricherListener()

getOrganismEnricherListener.

Specified by:

getOrganismEnricherListener in interface OrganismEnricher

Returns:

a OrganismEnricherListener object.

getCvTermEnricher

public CvTermEnricher<CvTerm> getCvTermEnricher()

getCvTermEnricher.

Specified by:

getCvTermEnricher in interface OrganismEnricher

Returns:

a CvTermEnricher object.

find

public Organism find(Organism objectToEnrich)
              throws EnricherException

find.

Specified by:

find in class AbstractMIEnricher<Organism>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(Organism objectToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Specified by:

onEnrichedVersionNotFound in class AbstractMIEnricher<Organism>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

enrich

public void enrich(Organism organismToEnrich,
                   Organism organismFetched)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<Organism>

Specified by:

enrich in class AbstractMIEnricher<Organism>

Parameters:

organismToEnrich - a T object.

organismFetched - a T object.

Throws:

EnricherException - if any.

processTaxid

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

processTaxid.

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.

Throws:

EnricherException - if any.

processOtherProperties

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

processOtherProperties.

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.

Throws:

EnricherException - if any.

processCommonName

protected void processCommonName(Organism organismToEnrich,
                                 Organism organismFetched)

processCommonName.

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.

processScientificName

protected void processScientificName(Organism organismToEnrich,
                                     Organism organismFetched)

processScientificName.

Parameters:

organismToEnrich - a Organism object.

organismFetched - a Organism object.