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

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 Detail

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)