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)
ExpressionExperimentSubSet	find(ExpressionExperimentSubSet entity)
Collection<ExpressionExperimentSubSet>	findByBioAssayIn(Collection<BioAssay> bioAssays)
ExpressionExperimentSubSet	findOrCreate(ExpressionExperimentSubSet entity)
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<FactorValueValueObject>	getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
ExpressionExperimentSubSet	load(Long id)
Collection<ExpressionExperimentSubSet>	loadAll()
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

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

countAll, findOrFail, getElementClass, load, loadOrFail, loadOrFail, 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)

Specified by:

find in interface BaseReadOnlyService<ExpressionExperimentSubSet>

See Also:

• BaseDao.find(Identifiable)

findOrCreate

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

Specified by:

findOrCreate in interface BaseImmutableService<ExpressionExperimentSubSet>

See Also:

• BaseDao.findOrCreate(Identifiable)

findByBioAssayIn

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

create

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

Specified by:

create in interface BaseImmutableService<ExpressionExperimentSubSet>

See Also:

• BaseDao.create(Identifiable)

load

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

Specified by:

load in interface BaseReadOnlyService<ExpressionExperimentSubSet>

See Also:

• BaseDao.load(Long)

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()

Specified by:

loadAll in interface BaseReadOnlyService<ExpressionExperimentSubSet>

See Also:

• BaseDao.loadAll()

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

See Also:

• BaseDao.remove(Identifiable)

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)