Package ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentSubSetService

All Superinterfaces:

BaseImmutableService<ExpressionExperimentSubSet>, BaseReadOnlyService<ExpressionExperimentSubSet>, BaseService<ExpressionExperimentSubSet>

All Known Implementing Classes:

ExpressionExperimentSubSetServiceImpl

public interface ExpressionExperimentSubSetService
extends BaseService<ExpressionExperimentSubSet>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
ExpressionExperimentSubSet	create(ExpressionExperimentSubSet expressionExperimentSubSet)	Creates the given entity in the persistent storage.
ExpressionExperimentSubSet	find(ExpressionExperimentSubSet entity)	Does a search for the entity in the persistent storage
Collection<ExpressionExperimentSubSet>	findByBioAssayIn(Collection<BioAssay> bioAssays)
ExpressionExperimentSubSet	findOrCreate(ExpressionExperimentSubSet entity)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<FactorValueValueObject>	getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
ExpressionExperimentSubSet	load(Long id)	Loads object with given ID.
Collection<ExpressionExperimentSubSet>	loadAll()	Loads all the entities of specific type.
ExpressionExperimentSubSet	loadWithBioAssays(Long id)
void	remove(ExpressionExperimentSubSet entity)	Deletes an experiment subset and all of its associated DifferentialExpressionAnalysis objects.

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

create, remove, remove

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

countAll, findOrFail, getElementClass, load, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

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

save, save, update, update

Method Details

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperimentSubSet find(ExpressionExperimentSubSet entity)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage

Specified by:

find in interface BaseReadOnlyService<ExpressionExperimentSubSet>

Parameters:

entity - the entity to be searched for

Returns:

the version of entity retrieved from the persistent storage, if found, otherwise null.

findOrCreate

@Secured("GROUP_USER")
ExpressionExperimentSubSet findOrCreate(ExpressionExperimentSubSet entity)

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<ExpressionExperimentSubSet>

Parameters:

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

Returns:

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

findByBioAssayIn

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSubSet> findByBioAssayIn(Collection<BioAssay> bioAssays)

create

@Secured("GROUP_USER")
ExpressionExperimentSubSet create(ExpressionExperimentSubSet expressionExperimentSubSet)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<ExpressionExperimentSubSet>

Parameters:

expressionExperimentSubSet - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperimentSubSet load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<ExpressionExperimentSubSet>

Parameters:

id - the ID of entity to be loaded.

Returns:

the entity with matching ID, or null if the entity does not exist or if the passed ID was null

loadWithBioAssays

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperimentSubSet loadWithBioAssays(Long id)

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSubSet> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<ExpressionExperimentSubSet>

Returns:

collection of all entities currently available in the persistent storage.

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(ExpressionExperimentSubSet entity)

Deletes an experiment subset and all of its associated DifferentialExpressionAnalysis objects. This method is similar to ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl.handleDelete(ExpressionExperiment) but it doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting of experiment set members.

Specified by:

remove in interface BaseImmutableService<ExpressionExperimentSubSet>

Parameters:

entity - the subset to remove

getFactorValuesUsed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<FactorValue> getFactorValuesUsed(ExpressionExperimentSubSet entity,
 ExperimentalFactor factor)

Parameters:

entity - entity

factor - factor

Returns:

the factor values of the given factor that are relevant to the subset.

getFactorValuesUsed

Collection<FactorValueValueObject> getFactorValuesUsed(Long subSetId,
 Long experimentalFactor)

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperimentSubSet subset)