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

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

save, save, update, update

Method Detail

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.

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

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)