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

Class FullCvTermUpdater<C extends CvTerm>

java.lang.Object

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

psidev.psi.mi.jami.enricher.impl.minimal.MinimalCvTermEnricher<C>

psidev.psi.mi.jami.enricher.impl.full.FullCvTermEnricher<C>

psidev.psi.mi.jami.enricher.impl.full.FullCvTermUpdater<C>

All Implemented Interfaces:

CvTermEnricher<C>, MIEnricher<C>

public class FullCvTermUpdater<C extends CvTerm>
extends FullCvTermEnricher<C>

Provides full update of cv term. - update minimal properties of CvTerm. See MinimalCvTermUpdater for more details - update xrefs of CvTerm. It will add missing xrefs and remove all existing xrefs that are not in the fetched CvTerm using DefaultXrefComparator - update synonyms of CvTerm. It will add missing synonyms and remove all existing synonyms that are not in the fetched CvTerm using DefaultAliasComparator - update annotations of CvTerm. It will add missing annotations and remove all existing annotations that are not in the fetched CvTerm using DefaultAnnotationComparator

Since:

13/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	FullCvTermUpdater(CvTermFetcher<C> cvTermFetcher)	A constructor matching super.
protected	FullCvTermUpdater(MinimalCvTermUpdater<C> minimalCvTermUpdater)	Constructor for FullCvTermUpdater.

Method Summary

Modifier and Type	Method	Description
C	find(C cvTermToEnrich)	find.
CvTermEnricherListener<C>	getCvTermEnricherListener()	The current CvTermEnricherListener.
CvTermFetcher<C>	getCvTermFetcher()	The fetcher to be used for used for fetcher.
protected MinimalCvTermUpdater<C>	getMinimalCvTermUpdater()	Getter for the field minimalCvTermUpdater.
int	getRetryCount()	Getter for the field retryCount.
protected void	processAnnotations(C cvTermToEnrich, C termFetched)	processAnnotations.
protected void	processMinimalUpdates(C cvTermToEnrich, C termFetched)	processMinimalUpdates.
protected void	processSynonyms(C cvTermToEnrich, C termFetched)	processSynonyms.
protected void	processXrefs(C cvTermToEnrich, C cvTermFetched)	processXrefs.
void	setCvTermEnricherListener(CvTermEnricherListener<C> listener)	setCvTermEnricherListener.
void	setRetryCount(int retryCount)	Setter for the field retryCount.

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

processCvTerm

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

enrich, onEnrichedVersionNotFound, processFullName, processIdentifiers

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

FullCvTermUpdater

public FullCvTermUpdater(CvTermFetcher<C> cvTermFetcher)

A constructor matching super.

Parameters:

cvTermFetcher - The fetcher to initiate the enricher with. If null, an illegal state exception will be thrown at the next enrichment.

FullCvTermUpdater

protected FullCvTermUpdater(MinimalCvTermUpdater<C> minimalCvTermUpdater)

Constructor for FullCvTermUpdater.

Parameters:

minimalCvTermUpdater - a MinimalCvTermUpdater object.

Method Detail

processMinimalUpdates

protected void processMinimalUpdates(C cvTermToEnrich,
                                     C termFetched)
                              throws EnricherException

processMinimalUpdates.

Overrides:

processMinimalUpdates in class FullCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processAnnotations

protected void processAnnotations(C cvTermToEnrich,
                                  C termFetched)
                           throws EnricherException

processAnnotations.

Overrides:

processAnnotations in class FullCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processSynonyms

protected void processSynonyms(C cvTermToEnrich,
                               C termFetched)
                        throws EnricherException

processSynonyms.

Overrides:

processSynonyms in class FullCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processXrefs

protected void processXrefs(C cvTermToEnrich,
                            C cvTermFetched)
                     throws EnricherException

processXrefs.

Overrides:

processXrefs in class FullCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - a C object.

cvTermFetched - a C object.

Throws:

EnricherException - if any.

setCvTermEnricherListener

public void setCvTermEnricherListener(CvTermEnricherListener<C> listener)

setCvTermEnricherListener.

The cvTermEnricherListener to be used. It will be fired at all points where a change is made to the cvTerm

Specified by:

setCvTermEnricherListener in interface CvTermEnricher<C extends CvTerm>

Overrides:

setCvTermEnricherListener in class MinimalCvTermEnricher<C extends CvTerm>

Parameters:

listener - a CvTermEnricherListener object.

getCvTermFetcher

public CvTermFetcher<C> getCvTermFetcher()

The fetcher to be used for used for fetcher.

Specified by:

getCvTermFetcher in interface CvTermEnricher<C extends CvTerm>

Overrides:

getCvTermFetcher in class MinimalCvTermEnricher<C extends CvTerm>

Returns:

The fetcher which is being used for fetching.

getCvTermEnricherListener

public CvTermEnricherListener<C> getCvTermEnricherListener()

The current CvTermEnricherListener.

Specified by:

getCvTermEnricherListener in interface CvTermEnricher<C extends CvTerm>

Overrides:

getCvTermEnricherListener in class MinimalCvTermEnricher<C extends CvTerm>

Returns:

the current listener. May be null.

getRetryCount

public int getRetryCount()

Getter for the field retryCount.

Overrides:

getRetryCount in class MinimalCvTermEnricher<C extends CvTerm>

Returns:

a int.

setRetryCount

public void setRetryCount(int retryCount)

Setter for the field retryCount.

Overrides:

setRetryCount in class MinimalCvTermEnricher<C extends CvTerm>

Parameters:

retryCount - a int.

find

public C find(C cvTermToEnrich)
       throws EnricherException

find.

Overrides:

find in class MinimalCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

getMinimalCvTermUpdater

protected MinimalCvTermUpdater<C> getMinimalCvTermUpdater()

Getter for the field minimalCvTermUpdater.

Returns:

a MinimalCvTermUpdater object.