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

Class MinimalOntologyTermEnricher

java.lang.Object

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

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

All Implemented Interfaces:

CvTermEnricher<OntologyTerm>, MIEnricher<OntologyTerm>

Direct Known Subclasses:

FullOntologyTermEnricher, MinimalOntologyTermUpdater

public class MinimalOntologyTermEnricher
extends AbstractMIEnricher<OntologyTerm>
implements CvTermEnricher<OntologyTerm>

Provides minimal enrichment of ontologYTerm. - enrich minimal properties of Cv Term. See description in MinimalCvTermEnricher - enrich children of a term. It will use DefaultCvTermComparator to compare children and add missing children without removing any existing children. It will enrich the children of the ontologyTerm It will ignore all other properties of an ontologyTerm

Since:

08/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	MinimalOntologyTermEnricher(OntologyTermFetcher cvTermFetcher)	A constructor matching super.
protected	MinimalOntologyTermEnricher(MinimalCvTermEnricher<OntologyTerm> cvEnricher)	Constructor for MinimalOntologyTermEnricher.

Method Summary

Modifier and Type	Method	Description
void	enrich(OntologyTerm objectToEnrich)	enrich.
void	enrich(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	enrich.
protected void	enrichChild(OntologyTerm objectToEnrich)	enrichChild.
protected void	enrichRelatedTerms(Collection<OntologyTerm> cvTermToEnrich)	enrichRelatedTerms.
OntologyTerm	find(OntologyTerm objectToEnrich)	find.
protected MinimalCvTermEnricher<OntologyTerm>	getCvEnricher()	Getter for the field cvEnricher.
CvTermEnricherListener<OntologyTerm>	getCvTermEnricherListener()	getCvTermEnricherListener.
CvTermFetcher<OntologyTerm>	getCvTermFetcher()	getCvTermFetcher.
protected void	mergeOntologyTerms(OntologyTerm termToEnrich, Collection<OntologyTerm> toEnrichTerms, Collection<OntologyTerm> fetchedTerms, boolean remove)	Takes two lists of ontology terms and produces a list of those to add and those to remove.
protected void	onEnrichedVersionNotFound(OntologyTerm cvTermToEnrich)	onEnrichedVersionNotFound.
protected void	processChildren(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processChildren.
protected void	processDefinition(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processDefinition.
protected void	processOntologyTerm(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	A method that can be overridden to add to or change the behaviour of enrichment without effecting fetching.
void	setCvTermEnricherListener(CvTermEnricherListener<OntologyTerm> listener)	setCvTermEnricherListener.

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

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

Constructor Detail

MinimalOntologyTermEnricher

public MinimalOntologyTermEnricher(OntologyTermFetcher 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.

MinimalOntologyTermEnricher

protected MinimalOntologyTermEnricher(MinimalCvTermEnricher<OntologyTerm> cvEnricher)

Constructor for MinimalOntologyTermEnricher.

Parameters:

cvEnricher - a MinimalCvTermEnricher object.

Method Detail

enrich

public void enrich(OntologyTerm objectToEnrich)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<OntologyTerm>

Overrides:

enrich in class AbstractMIEnricher<OntologyTerm>

Parameters:

objectToEnrich - a T object.

Throws:

EnricherException - if any.

processOntologyTerm

protected void processOntologyTerm(OntologyTerm cvTermToEnrich,
                                   OntologyTerm cvTermFetched)
                            throws EnricherException

A method that can be overridden to add to or change the behaviour of enrichment without effecting fetching.

Parameters:

cvTermToEnrich - the CvTerm to enrich

cvTermFetched - a OntologyTerm object.

Throws:

EnricherException - if any.

processDefinition

protected void processDefinition(OntologyTerm cvTermToEnrich,
                                 OntologyTerm cvTermFetched)
                          throws EnricherException

processDefinition.

Parameters:

cvTermToEnrich - a OntologyTerm object.

cvTermFetched - a OntologyTerm object.

Throws:

EnricherException - if any.

processChildren

protected void processChildren(OntologyTerm cvTermToEnrich,
                               OntologyTerm cvTermFetched)
                        throws EnricherException

processChildren.

Parameters:

cvTermToEnrich - a OntologyTerm object.

cvTermFetched - a OntologyTerm object.

Throws:

EnricherException - if any.

enrichRelatedTerms

protected void enrichRelatedTerms(Collection<OntologyTerm> cvTermToEnrich)
                           throws EnricherException

enrichRelatedTerms.

Parameters:

cvTermToEnrich - a Collection object.

Throws:

EnricherException - if any.

enrichChild

protected void enrichChild(OntologyTerm objectToEnrich)
                    throws EnricherException

enrichChild.

Parameters:

objectToEnrich - a OntologyTerm object.

Throws:

EnricherException - if any.

onEnrichedVersionNotFound

protected void onEnrichedVersionNotFound(OntologyTerm cvTermToEnrich)
                                  throws EnricherException

onEnrichedVersionNotFound.

Specified by:

onEnrichedVersionNotFound in class AbstractMIEnricher<OntologyTerm>

Parameters:

cvTermToEnrich - a T object.

Throws:

EnricherException - if any.

enrich

public void enrich(OntologyTerm cvTermToEnrich,
                   OntologyTerm cvTermFetched)
            throws EnricherException

enrich.

Specified by:

enrich in interface MIEnricher<OntologyTerm>

Specified by:

enrich in class AbstractMIEnricher<OntologyTerm>

Parameters:

cvTermToEnrich - a T object.

cvTermFetched - a T object.

Throws:

EnricherException - if any.

find

public OntologyTerm find(OntologyTerm objectToEnrich)
                  throws EnricherException

find.

Specified by:

find in class AbstractMIEnricher<OntologyTerm>

Parameters:

objectToEnrich - a T object.

Returns:

a T object.

Throws:

EnricherException - if any.

mergeOntologyTerms

protected void mergeOntologyTerms(OntologyTerm termToEnrich,
                                  Collection<OntologyTerm> toEnrichTerms,
                                  Collection<OntologyTerm> fetchedTerms,
                                  boolean remove)
                           throws EnricherException

Takes two lists of ontology terms and produces a list of those to add and those to remove. It will add in toEnrichTerms all xref from fetchedTerms that are not there. It will also remove extra identifiers from toEnrichTerms if remove boolean is true.

Parameters:

termToEnrich - The object to enrich

fetchedTerms - The new terms to be added.

remove - : if true, we remove terms that are not in enriched list

toEnrichTerms - a Collection object.

Throws:

EnricherException - if any.

getCvTermFetcher

public CvTermFetcher<OntologyTerm> getCvTermFetcher()

getCvTermFetcher.

Specified by:

getCvTermFetcher in interface CvTermEnricher<OntologyTerm>

Returns:

a CvTermFetcher object.

setCvTermEnricherListener

public void setCvTermEnricherListener(CvTermEnricherListener<OntologyTerm> listener)

setCvTermEnricherListener.

Specified by:

setCvTermEnricherListener in interface CvTermEnricher<OntologyTerm>

Parameters:

listener - a CvTermEnricherListener object.

getCvTermEnricherListener

public CvTermEnricherListener<OntologyTerm> getCvTermEnricherListener()

getCvTermEnricherListener.

Specified by:

getCvTermEnricherListener in interface CvTermEnricher<OntologyTerm>

Returns:

a CvTermEnricherListener object.

getCvEnricher

protected MinimalCvTermEnricher<OntologyTerm> getCvEnricher()

Getter for the field cvEnricher.

Returns:

a MinimalCvTermEnricher object.