Package ubic.gemma.persistence.service.genome.taxon

Interface TaxonService

All Superinterfaces:

BaseImmutableService<Taxon>, BaseReadOnlyService<Taxon>, BaseService<Taxon>, BaseVoEnabledService<Taxon,TaxonValueObject>, FilteringService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>

All Known Implementing Classes:

TaxonServiceImpl

public interface TaxonService
extends BaseService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Taxon	findByCommonName(String commonName)
Taxon	findByNcbiId(Integer ncbiId)
Taxon	findByScientificName(String scientificName)
Taxon	findOrCreate(Taxon taxon)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<TaxonValueObject>	getTaxaWithArrays()
Collection<TaxonValueObject>	getTaxaWithDatasets()
Collection<TaxonValueObject>	getTaxaWithEvidence()
Collection<TaxonValueObject>	getTaxaWithGenes()
Collection<Taxon>	loadAllTaxaWithGenes()
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<Taxon> entities)	Removes all the given entities from persistent storage.
void	remove(Taxon taxon)	Removes the given entity from the persistent storage.
void	update(Collection<Taxon> entities)	Updates all entities in the given collection in the persistent storage.
void	update(Taxon taxon)	Updates the given entity in the persistent storage.

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

create, 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

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Detail

findByCommonName

Taxon findByCommonName(String commonName)

findByScientificName

Taxon findByScientificName(String scientificName)

findByNcbiId

Taxon findByNcbiId(Integer ncbiId)

findOrCreate

@Secured("GROUP_USER")
Taxon findOrCreate(Taxon taxon)

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<Taxon>

Parameters:

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

Returns:

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

remove

@Secured("GROUP_USER")
void remove(Collection<Taxon> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<Taxon>

Parameters:

entities - 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<Taxon>

Parameters:

id - the ID of entity to be removed.

remove

@Secured("GROUP_USER")
void remove(Taxon taxon)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<Taxon>

Parameters:

taxon - the entity to be removed.

update

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

Description copied from interface: BaseService

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

Specified by:

update in interface BaseService<Taxon>

Parameters:

entities - the entities to be updated.

update

@Secured("GROUP_USER")
void update(Taxon taxon)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<Taxon>

Parameters:

taxon - the entity to be updated.

loadAllTaxaWithGenes

Collection<Taxon> loadAllTaxaWithGenes()

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithEvidence

Collection<TaxonValueObject> getTaxaWithEvidence()

getTaxaWithGenes

Collection<TaxonValueObject> getTaxaWithGenes()

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithDatasets

Collection<TaxonValueObject> getTaxaWithDatasets()

Returns:

collection of taxa that have expression experiments available.

getTaxaWithArrays

Collection<TaxonValueObject> getTaxaWithArrays()

Returns:

List of taxa with array designs in gemma