ubic.gemma.persistence.service.association

Interface Gene2GOAssociationDao

All Superinterfaces:

BaseDao<Gene2GOAssociation>

All Known Implementing Classes:

Gene2GOAssociationDaoImpl

public interface Gene2GOAssociationDao
extends BaseDao<Gene2GOAssociation>

See Also:

Gene2GOAssociation

Method Summary

Modifier and Type	Method and Description
Gene2GOAssociation	find(Gene2GOAssociation gene2GOAssociation) Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<Gene2GOAssociation>	findAssociationByGene(Gene gene)
Collection<Gene2GOAssociation>	findAssociationByGenes(Collection<Gene> genes)
Collection<Characteristic>	findByGene(Gene gene)
Map<Gene,Collection<Characteristic>>	findByGenes(Collection<Gene> needToFind)
Collection<Gene>	findByGoTerm(String goId, Taxon taxon)
Map<Taxon,Collection<Gene>>	findByGoTermsPerTaxon(Collection<String> termsToFetch)
Gene2GOAssociation	findOrCreate(Gene2GOAssociation gene2GOAssociation) Calls the find method, and if this method returns null, creates a new instance in the persistent storage.
Collection<Gene>	getGenes(Collection<String> ids)
Collection<Gene>	getGenes(Collection<String> ids, Taxon taxon)
void	removeAllInBatch() Remove all entities from persistent storage.

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

countAll, create, create, createInBatch, getElementClass, load, load, loadAll, remove, remove, remove, removeInBatch, save, save, saveInBatch, update, update, updateInBatch

Method Detail

find

Gene2GOAssociation find(Gene2GOAssociation gene2GOAssociation)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<Gene2GOAssociation>

Parameters:

gene2GOAssociation - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

findOrCreate

Gene2GOAssociation findOrCreate(Gene2GOAssociation gene2GOAssociation)

Description copied from interface: BaseDao

Calls the find method, and if this method returns null, creates a new instance in the persistent storage.

Specified by:

findOrCreate in interface BaseDao<Gene2GOAssociation>

Parameters:

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

Returns:

the given entity, guaranteed to be representing an entity present in the persistent storage.

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> needToFind)

findByGoTerm

Collection<Gene> findByGoTerm(String goId,
                              Taxon taxon)

findByGoTermsPerTaxon

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

getGenes

Collection<Gene> getGenes(Collection<String> ids)

getGenes

Collection<Gene> getGenes(Collection<String> ids,
                          @Nullable
                          Taxon taxon)

removeAllInBatch

void removeAllInBatch()

Description copied from interface: BaseDao

Remove all entities from persistent storage.

Specified by:

removeAllInBatch in interface BaseDao<Gene2GOAssociation>