Package ubic.gemma.persistence.service.association

Interface Gene2GOAssociationService

All Superinterfaces:

BaseImmutableService<Gene2GOAssociation>, BaseReadOnlyService<Gene2GOAssociation>

All Known Implementing Classes:

Gene2GOAssociationServiceImpl

public interface Gene2GOAssociationService
extends BaseImmutableService<Gene2GOAssociation>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Gene2GOAssociation	create(Gene2GOAssociation gene2GOAssociation)	Creates the given entity in the persistent storage.
Collection<Gene2GOAssociation>	findAssociationByGene(Gene gene)
Collection<Gene2GOAssociation>	findAssociationByGenes(Collection<Gene> genes)
Collection<Characteristic>	findByGene(Gene gene)
Map<Gene,Collection<Characteristic>>	findByGenes(Collection<Gene> genes)
Collection<Gene>	findByGOTerm(String goID, Taxon taxon)
Collection<Gene>	findByGOTerms(Collection<String> termsToFetch, Taxon taxon)
Map<Taxon,Collection<Gene>>	findByGOTermsPerTaxon(Collection<String> termsToFetch)
Gene2GOAssociation	findOrCreate(Gene2GOAssociation gene2GOAssociation)	Does a search for the entity in the persistent storage, and if not found, creates it.
int	removeAll()	Remove all Gene2GO associations in batch.

Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService

create, remove, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Method Detail

findOrCreate

@Secured("GROUP_ADMIN")
Gene2GOAssociation findOrCreate(Gene2GOAssociation gene2GOAssociation)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<Gene2GOAssociation>

Parameters:

gene2GOAssociation - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Secured("GROUP_ADMIN")
Gene2GOAssociation create(Gene2GOAssociation gene2GOAssociation)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<Gene2GOAssociation>

Parameters:

gene2GOAssociation - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

findAssociationByGene

Collection<Gene2GOAssociation> findAssociationByGene(Gene gene)

findAssociationByGenes

Collection<Gene2GOAssociation> findAssociationByGenes(Collection<Gene> genes)

findByGene

Collection<Characteristic> findByGene(Gene gene)

findByGenes

Map<Gene,Collection<Characteristic>> findByGenes(Collection<Gene> genes)

findByGOTerm

Collection<Gene> findByGOTerm(String goID,
                              Taxon taxon)

removeAll

@Secured("GROUP_ADMIN")
int removeAll()

Remove all Gene2GO associations in batch.

findByGOTerms

Collection<Gene> findByGOTerms(Collection<String> termsToFetch,
                               @Nullable
                               Taxon taxon)

Parameters:

termsToFetch - terms

taxon - constraint

Returns:

all the genes that match any of the terms. Used to fetch genes associated with a term + children.

findByGOTermsPerTaxon

Map<Taxon,Collection<Gene>> findByGOTermsPerTaxon(Collection<String> termsToFetch)