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

Class ExpressionExperimentSubSetDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<ExpressionExperimentSubSet>

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl

All Implemented Interfaces:

BaseDao<ExpressionExperimentSubSet>, ExpressionExperimentSubSetDao

@Repository
public class ExpressionExperimentSubSetDaoImpl
extends AbstractDao<ExpressionExperimentSubSet>
implements ExpressionExperimentSubSetDao

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.

See Also:

• ExpressionExperimentSubSet

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSubSetDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
ExpressionExperimentSubSet	find(ExpressionExperimentSubSet entity)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<ExpressionExperimentSubSet>	findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<FactorValue>	getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValue used by the samples from this subset in the given factor.
ExpressionExperimentSubSet	loadWithBioAssays(Long id)
void	remove(ExpressionExperimentSubSet entity)	Remove a persistent instance

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

countAll, create, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Constructor Details

ExpressionExperimentSubSetDaoImpl

@Autowired
public ExpressionExperimentSubSetDaoImpl(SessionFactory sessionFactory)

Method Details

find

public ExpressionExperimentSubSet find(ExpressionExperimentSubSet entity)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<ExpressionExperimentSubSet>

Overrides:

find in class AbstractDao<ExpressionExperimentSubSet>

Parameters:

entity - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

loadWithBioAssays

@Nullable
public ExpressionExperimentSubSet loadWithBioAssays(Long id)

Specified by:

loadWithBioAssays in interface ExpressionExperimentSubSetDao

findByBioAssayIn

public Collection<ExpressionExperimentSubSet> findByBioAssayIn(Collection<BioAssay> bioAssays)

Specified by:

findByBioAssayIn in interface ExpressionExperimentSubSetDao

getFactorValuesUsed

public Collection<FactorValue> getFactorValuesUsed(ExpressionExperimentSubSet entity,
 ExperimentalFactor factor)

Description copied from interface: ExpressionExperimentSubSetDao

Obtain the FactorValue used by the samples from this subset in the given factor.

Specified by:

getFactorValuesUsed in interface ExpressionExperimentSubSetDao

getFactorValuesUsed

public Collection<FactorValue> getFactorValuesUsed(Long subSetId,
 Long experimentalFactor)

Specified by:

getFactorValuesUsed in interface ExpressionExperimentSubSetDao

See Also:

• ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor)

getArrayDesignsUsed

public Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperimentSubSet subset)

Specified by:

getArrayDesignsUsed in interface ExpressionExperimentSubSetDao

remove

public void remove(ExpressionExperimentSubSet entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<ExpressionExperimentSubSet>

Overrides:

remove in class AbstractDao<ExpressionExperimentSubSet>

Parameters:

entity - the entity to be removed