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, 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 and Description
Gene2GOAssociationServiceImpl(Gene2GOAssociationDao mainDao, CacheManager cacheManager)

Method Summary

Modifier and Type	Method and 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)

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, load, load, loadAll, loadOrFail, remove, remove, remove, removeAllInBatch, 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.association.Gene2GOAssociationService

create, findOrCreate, removeAllInBatch

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

create, remove, remove, remove, save, save, update, update

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

countAll, find, findOrFail, load, load, loadAll, loadOrFail

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

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