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

Interface GeneProductService

All Superinterfaces:

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

All Known Implementing Classes:

GeneProductServiceImpl

public interface GeneProductService
extends BaseService<GeneProduct>, BaseVoEnabledService<GeneProduct,GeneProductValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
GeneProduct	create(GeneProduct entity)	Creates the given entity in the persistent storage.
Collection<GeneProduct>	findByName(String name, Taxon taxon)
GeneProduct	findOrCreate(GeneProduct geneProduct)	Does a search for the entity in the persistent storage, and if not found, creates it.
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 geneProduct)
void	update(Collection<GeneProduct> entities)	Updates all entities in the given collection in the persistent storage.
void	update(GeneProduct entity)	Updates the given entity in the persistent storage.

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

Method Details

findOrCreate

@Secured("GROUP_USER")
GeneProduct findOrCreate(GeneProduct geneProduct)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<GeneProduct>

Parameters:

geneProduct - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Secured("GROUP_USER")
GeneProduct create(GeneProduct entity)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<GeneProduct>

Parameters:

entity - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

@Secured("GROUP_ADMIN")
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>

Parameters:

toRemove - the entities to be removed.

remove

@Secured("GROUP_ADMIN")
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>

Parameters:

id - the ID of entity to be removed.

remove

@Secured("GROUP_ADMIN")
void remove(GeneProduct entity)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneProduct>

Parameters:

entity - the entity to be removed.

update

@Secured("GROUP_USER")
void update(Collection<GeneProduct> entities)

Description copied from interface: BaseService

Updates all entities in the given collection in the persistent storage.

Specified by:

update in interface BaseService<GeneProduct>

Parameters:

entities - the entities to be updated.

update

@Secured("GROUP_USER")
void update(GeneProduct entity)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<GeneProduct>

Parameters:

entity - the entity to be updated.

getGenesByName

Collection<Gene> getGenesByName(String search)

Parameters:

search - name

Returns:

all the genes that share the given gene product name

getGenesByNcbiId

Collection<Gene> getGenesByNcbiId(String search)

Parameters:

search - ncbiID

Returns:

all the genes that share the given gene product ncbi id

findByName

Collection<GeneProduct> findByName(String name,
 Taxon taxon)

thaw

GeneProduct thaw(GeneProduct geneProduct)