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:

InitializingBean, Gene2GOAssociationService, BaseImmutableService<Gene2GOAssociation>, BaseReadOnlyService<Gene2GOAssociation>, BaseService<Gene2GOAssociation>

@Service
public class Gene2GOAssociationServiceImpl
extends AbstractService<Gene2GOAssociation>
implements Gene2GOAssociationService, 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, 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>	findByGOTerm(String goID, Taxon taxon)
Collection<Gene>	findByGOTerms(Collection<String> termsToFetch, Taxon taxon)
Map<Taxon,Collection<Gene>>	findByGOTermsPerTaxon(Collection<String> termsToFetch)
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, 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.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

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

create, findOrCreate

Constructor Detail

Gene2GOAssociationServiceImpl

@Autowired
public Gene2GOAssociationServiceImpl(Gene2GOAssociationDao mainDao,
                                     CacheManager cacheManager)

Method Detail

afterPropertiesSet

public void afterPropertiesSet()

Specified by:

afterPropertiesSet in interface 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

findByGOTerm

@Transactional(readOnly=true)
public Collection<Gene> findByGOTerm(String goID,
                                     Taxon taxon)

Specified by:

findByGOTerm 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

findByGOTerms

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

Specified by:

findByGOTerms in interface Gene2GOAssociationService

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

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

Specified by:

findByGOTermsPerTaxon in interface Gene2GOAssociationService