Package ubic.gemma.persistence.service.genome.gene

Class GeneProductServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledService<GeneProduct,GeneProductValueObject>

ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl

All Implemented Interfaces:

BaseImmutableService<GeneProduct>, BaseReadOnlyService<GeneProduct>, BaseService<GeneProduct>, BaseVoEnabledService<GeneProduct,GeneProductValueObject>, GeneProductService

@Service
public class GeneProductServiceImpl
extends AbstractVoEnabledService<GeneProduct,GeneProductValueObject>
implements GeneProductService

See Also:

• GeneProductService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
GeneProductServiceImpl(AnnotationAssociationDao annotationAssociationDao, BioSequenceDao bioSequenceDao, BlatAssociationDao blatAssociationDao, GeneProductDao geneProductDao)

Method Summary

Modifier and Type	Method	Description
Collection<GeneProduct>	findByName(String name, Taxon taxon)
Collection<Gene>	getGenesByName(String search)
Collection<Gene>	getGenesByNcbiId(String search)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<GeneProduct> toRemove)	Removes all the given entities from persistent storage.
void	remove(GeneProduct entity)	Removes the given entity from the persistent storage.
GeneProduct	thaw(GeneProduct existing)

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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, 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

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.BaseService

save, save

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.genome.gene.GeneProductService

create, findOrCreate, update, update

Constructor Details

GeneProductServiceImpl

@Autowired
public GeneProductServiceImpl(AnnotationAssociationDao annotationAssociationDao,
 BioSequenceDao bioSequenceDao,
 BlatAssociationDao blatAssociationDao,
 GeneProductDao geneProductDao)

Method Details

getGenesByName

@Transactional(readOnly=true)
public Collection<Gene> getGenesByName(String search)

Specified by:

getGenesByName in interface GeneProductService

Parameters:

search - name

Returns:

all the genes that share the given gene product name

getGenesByNcbiId

@Transactional(readOnly=true)
public Collection<Gene> getGenesByNcbiId(String search)

Specified by:

getGenesByNcbiId in interface GeneProductService

Parameters:

search - ncbiID

Returns:

all the genes that share the given gene product ncbi id

findByName

@Transactional(readOnly=true)
public Collection<GeneProduct> findByName(String name,
 Taxon taxon)

Specified by:

findByName in interface GeneProductService

thaw

@Transactional(readOnly=true)
public GeneProduct thaw(GeneProduct existing)

Specified by:

thaw in interface GeneProductService

remove

@Transactional
public void remove(GeneProduct entity)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneProduct>

Specified by:

remove in interface GeneProductService

Overrides:

remove in class AbstractService<GeneProduct>

Parameters:

entity - the entity to be removed.

remove

@Transactional
public void remove(Collection<GeneProduct> toRemove)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneProduct>

Specified by:

remove in interface GeneProductService

Overrides:

remove in class AbstractService<GeneProduct>

Parameters:

toRemove - the entities to be removed.

remove

public void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneProduct>

Specified by:

remove in interface GeneProductService

Overrides:

remove in class AbstractService<GeneProduct>

Parameters:

id - the ID of entity to be removed.