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 AbstractService

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao expressionExperimentSubSetDao, ExpressionExperimentSubSetReadService expressionExperimentSubSetReadService, 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(Collection<ExpressionExperimentSubSet> entities)
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 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 Object

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

Methods inherited from interface BaseImmutableService

create

Methods inherited from interface BaseReadOnlyService

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

Methods inherited from interface BaseService

save, save, update, update

Methods inherited from interface ExpressionExperimentSubSetService

create, find, findOrCreate, load, loadAll

Constructor Details

ExpressionExperimentSubSetServiceImpl

@Autowired
public ExpressionExperimentSubSetServiceImpl(ExpressionExperimentSubSetDao expressionExperimentSubSetDao,
 ExpressionExperimentSubSetReadService expressionExperimentSubSetReadService,
 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

See Also:

• BaseDao.remove(Identifiable)

remove

public void remove(Collection<ExpressionExperimentSubSet> entities)

Specified by:

remove in interface BaseImmutableService<ExpressionExperimentSubSet>

Overrides:

remove in class AbstractService<ExpressionExperimentSubSet>

See Also:

• BaseDao.remove(Collection)