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>	findByGOTermUris(Collection<String> uris, Taxon taxon)	Find all the genes that match any of the terms.
Map<Taxon,Collection<Gene>>	findByGOTermUrisPerTaxon(Collection<String> uris)	Find all genes associated with a given set of GO terms, grouped by taxon.
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, streamAll, streamAll

Method Details

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)

findByGOTermUris

Collection<Gene> findByGOTermUris(Collection<String> uris,
 @Nullable
 Taxon taxon)

Find all the genes that match any of the terms.

Used to fetch genes associated with a term + children.

findByGOTermUrisPerTaxon

Map<Taxon,Collection<Gene>> findByGOTermUrisPerTaxon(Collection<String> uris)

Find all genes associated with a given set of GO terms, grouped by taxon.

removeAll

@Secured("GROUP_ADMIN")
int removeAll()

Remove all Gene2GO associations in batch.