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

Class ExpressionExperimentSubSetServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl

All Implemented Interfaces:

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

@Service
public class ExpressionExperimentSubSetServiceImpl
extends AbstractService<ExpressionExperimentSubSet>
implements ExpressionExperimentSubSetService

Author:

pavlidis

See Also:

• ExpressionExperimentSubSetService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao expressionExperimentSubSetDao, DifferentialExpressionAnalysisService differentialExpressionAnalysisService)

Method Summary

Modifier and Type	Method	Description
Collection<ExpressionExperimentSubSet>	findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<FactorValueValueObject>	getFactorValuesUsed(Long subSetId, Long experimentalFactor)
Collection<FactorValue>	getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
ExpressionExperimentSubSet	loadWithBioAssays(Long id)
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<ExpressionExperimentSubSet> entities)	Removes all the given entities from persistent storage.
void	remove(ExpressionExperimentSubSet subset)	doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting experiment set members

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, save, save, streamAll, streamAll, 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.BaseImmutableService

create

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

Methods inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService

create, find, findOrCreate, load, loadAll

Constructor Details

ExpressionExperimentSubSetServiceImpl

@Autowired
public ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao expressionExperimentSubSetDao,
 DifferentialExpressionAnalysisService differentialExpressionAnalysisService)

Method Details

findByBioAssayIn

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSubSet> findByBioAssayIn(Collection<BioAssay> bioAssays)

Specified by:

findByBioAssayIn in interface ExpressionExperimentSubSetService

getFactorValuesUsed

@Transactional(readOnly=true)
public Collection<FactorValue> getFactorValuesUsed(ExpressionExperimentSubSet entity,
 ExperimentalFactor factor)

Specified by:

getFactorValuesUsed in interface ExpressionExperimentSubSetService

Parameters:

entity - entity

factor - factor

Returns:

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

getFactorValuesUsed

@Transactional(readOnly=true)
public Collection<FactorValueValueObject> getFactorValuesUsed(Long subSetId,
 Long experimentalFactor)

Specified by:

getFactorValuesUsed in interface ExpressionExperimentSubSetService

getArrayDesignsUsed

@Transactional(readOnly=true)
public Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperimentSubSet subset)

Specified by:

getArrayDesignsUsed in interface ExpressionExperimentSubSetService

loadWithBioAssays

@Transactional(readOnly=true)
public ExpressionExperimentSubSet loadWithBioAssays(Long id)

Specified by:

loadWithBioAssays in interface ExpressionExperimentSubSetService

remove

@Transactional
public void remove(ExpressionExperimentSubSet subset)

doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting experiment set members

Specified by:

remove in interface BaseImmutableService<ExpressionExperimentSubSet>

Specified by:

remove in interface ExpressionExperimentSubSetService

Overrides:

remove in class AbstractService<ExpressionExperimentSubSet>

Parameters:

subset - subset

remove

public void remove(Collection<ExpressionExperimentSubSet> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<ExpressionExperimentSubSet>

Overrides:

remove in class AbstractService<ExpressionExperimentSubSet>

Parameters:

entities - the entities to be removed.

remove

public 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<ExpressionExperimentSubSet>

Overrides:

remove in class AbstractService<ExpressionExperimentSubSet>

Parameters:

id - the ID of entity to be removed.