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

Class FullCvTermEnricher<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>

All Implemented Interfaces:

CvTermEnricher<C>, MIEnricher<C>

Direct Known Subclasses:

FullCvTermUpdater

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

Provides full enrichment of cv term. - enrich minimal properties of CvTerm. See MinimalCvTermEnricher for more details - enrich xrefs of CvTerm. It will only add missing xrefs and not remove any existing xrefs using DefaultXrefComparator - enrich synonyms of CvTerm. It will only add missing synonyms and not remove any existing synonyms using DefaultAliasComparator - enrich annotations of CvTerm. It will only add missing annotations and not remove any existing annotations using DefaultAnnotationComparator

Since:

13/06/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
FullCvTermEnricher(CvTermFetcher<C> cvTermFetcher)	A constructor matching super.

Method Summary

Modifier and Type	Method	Description
protected void	processAnnotations(C cvTermToEnrich, C termFetched)	processAnnotations.
void	processCvTerm(C cvTermToEnrich, C termFetched)	A method that can be overridden to add to or change the behaviour of enrichment without effecting fetching.
protected void	processMinimalUpdates(C cvTermToEnrich, C termFetched)	processMinimalUpdates.
protected void	processSynonyms(C cvTermToEnrich, C termFetched)	processSynonyms.
protected void	processXrefs(C cvTermToEnrich, C cvTermFetched)	processXrefs.

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

enrich, find, getCvTermEnricherListener, getCvTermFetcher, getRetryCount, onEnrichedVersionNotFound, processFullName, processIdentifiers, setCvTermEnricherListener, 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

FullCvTermEnricher

public FullCvTermEnricher(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.

Method Detail

processCvTerm

public void processCvTerm(C cvTermToEnrich,
                          C termFetched)
                   throws EnricherException

A method that can be overridden to add to or change the behaviour of enrichment without effecting fetching. Strategy for the cvTerm enrichment. This method can be overwritten to change how the cvTerm is enriched.

Overrides:

processCvTerm in class MinimalCvTermEnricher<C extends CvTerm>

Parameters:

cvTermToEnrich - the CvTerm to enrich

termFetched - a C object.

Throws:

EnricherException - if any.

processMinimalUpdates

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

processMinimalUpdates.

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processAnnotations

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

processAnnotations.

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processSynonyms

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

processSynonyms.

Parameters:

cvTermToEnrich - a C object.

termFetched - a C object.

Throws:

EnricherException - if any.

processXrefs

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

processXrefs.

Parameters:

cvTermToEnrich - a C object.

cvTermFetched - a C object.

Throws:

EnricherException - if any.