Package ubic.gemma.persistence.service.association

Class Gene2GOAssociationDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<Gene2GOAssociation>

ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl

All Implemented Interfaces:

Gene2GOAssociationDao, BaseDao<Gene2GOAssociation>

@Repository
public class Gene2GOAssociationDaoImpl
extends AbstractDao<Gene2GOAssociation>
implements Gene2GOAssociationDao

Author:

pavlidis

See Also:

Gene2GOAssociation

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

elementClass, log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Gene2GOAssociationDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	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)
Collection<Gene>	getGenes(Collection<String> ids)
Collection<Gene>	getGenes(Collection<String> ids, Taxon taxon)
int	removeAll()

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

countAll, create, create, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.association.Gene2GOAssociationDao

findOrCreate

Constructor Detail

Gene2GOAssociationDaoImpl

@Autowired
protected Gene2GOAssociationDaoImpl(SessionFactory sessionFactory)

Method Detail

find

public 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>

Specified by:

find in interface Gene2GOAssociationDao

Overrides:

find in class AbstractDao<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.

findAssociationByGene

public Collection<Gene2GOAssociation> findAssociationByGene(Gene gene)

Specified by:

findAssociationByGene in interface Gene2GOAssociationDao

findAssociationByGenes

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

Specified by:

findAssociationByGenes in interface Gene2GOAssociationDao

findByGene

public Collection<Characteristic> findByGene(Gene gene)

Specified by:

findByGene in interface Gene2GOAssociationDao

findByGenes

public Map<Gene,Collection<Characteristic>> findByGenes(Collection<Gene> needToFind)

Specified by:

findByGenes in interface Gene2GOAssociationDao

findByGoTerm

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

Specified by:

findByGoTerm in interface Gene2GOAssociationDao

findByGoTermsPerTaxon

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

Specified by:

findByGoTermsPerTaxon in interface Gene2GOAssociationDao

getGenes

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

Specified by:

getGenes in interface Gene2GOAssociationDao

getGenes

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

Specified by:

getGenes in interface Gene2GOAssociationDao

removeAll

public int removeAll()

Specified by:

removeAll in interface Gene2GOAssociationDao