Package ubic.gemma.persistence.service.association

Class Gene2GOAssociationServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, Gene2GOAssociationService, BaseImmutableService<Gene2GOAssociation>, BaseReadOnlyService<Gene2GOAssociation>, BaseService<Gene2GOAssociation>

@Service
public class Gene2GOAssociationServiceImpl
extends AbstractService<Gene2GOAssociation>
implements Gene2GOAssociationService, org.springframework.beans.factory.InitializingBean

Author:

klc

See Also:

• Gene2GOAssociationService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
Gene2GOAssociationServiceImpl(Gene2GOAssociationDao mainDao, org.springframework.cache.CacheManager cacheManager)

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
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.
int	removeAll()	Remove all Gene2GO associations in batch.

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAll, 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.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, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.association.Gene2GOAssociationService

create, findOrCreate

Constructor Details

Gene2GOAssociationServiceImpl

@Autowired
public Gene2GOAssociationServiceImpl(Gene2GOAssociationDao mainDao,
 org.springframework.cache.CacheManager cacheManager)

Method Details

afterPropertiesSet

public void afterPropertiesSet()

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

findAssociationByGene

@Transactional(readOnly=true)
public Collection<Gene2GOAssociation> findAssociationByGene(Gene gene)

Specified by:

findAssociationByGene in interface Gene2GOAssociationService

findAssociationByGenes

@Transactional(readOnly=true)
public Collection<Gene2GOAssociation> findAssociationByGenes(Collection<Gene> genes)

Specified by:

findAssociationByGenes in interface Gene2GOAssociationService

findByGene

@Transactional(readOnly=true)
public Collection<Characteristic> findByGene(Gene gene)

Specified by:

findByGene in interface Gene2GOAssociationService

findByGenes

@Transactional(readOnly=true)
public Map<Gene,Collection<Characteristic>> findByGenes(Collection<Gene> genes)

Specified by:

findByGenes in interface Gene2GOAssociationService

findByGOTermUris

@Transactional(readOnly=true)
public Collection<Gene> findByGOTermUris(Collection<String> uris,
 @Nullable
 Taxon taxon)

Description copied from interface: Gene2GOAssociationService

Find all the genes that match any of the terms.

Used to fetch genes associated with a term + children.

Specified by:

findByGOTermUris in interface Gene2GOAssociationService

findByGOTermUrisPerTaxon

@Transactional(readOnly=true)
public Map<Taxon,Collection<Gene>> findByGOTermUrisPerTaxon(Collection<String> uris)

Description copied from interface: Gene2GOAssociationService

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

Specified by:

findByGOTermUrisPerTaxon in interface Gene2GOAssociationService

removeAll

@Transactional
public int removeAll()

Description copied from interface: Gene2GOAssociationService

Remove all Gene2GO associations in batch.

Specified by:

removeAll in interface Gene2GOAssociationService