Class ExpressionExperimentSubSetReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl

All Implemented Interfaces:

ExpressionExperimentSubSetReadService

@Service("expressionExperimentSubSetReadService")
public class ExpressionExperimentSubSetReadServiceImpl
extends Object
implements ExpressionExperimentSubSetReadService

Implementation of ExpressionExperimentSubSetReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade ExpressionExperimentService interface — this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• ExpressionExperimentService

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSubSetReadServiceImpl(ExpressionExperimentDao expressionExperimentDao, ExpressionExperimentSubSetDao expressionExperimentSubSetDao)

Method Summary

Modifier and Type	Method	Description
Collection<ExpressionExperimentSubSet>	findByBioAssayIn(Collection<BioAssay> bioAssays)	Find every subset that contains any of the supplied bio-assays.
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperimentSubSet subset)	Obtain the array designs used by the assays in the subset.
Collection<FactorValue>	getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValues used by samples in the given subset for the given factor.
Collection<FactorValueValueObject>	getFactorValuesUsedAsVO(Long subSetId, Long experimentalFactor)	VO-form variant of ExpressionExperimentSubSetReadService.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) accepting plain IDs.
ExpressionExperimentSubSet	getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized.
ExpressionExperimentSubSet	getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized and assays thawed.
Collection<ExpressionExperimentSubSet>	getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset, with assays thawed.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.
Map<FactorValue, ExpressionExperimentSubSet>	getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor.
Map<FactorValue, ExpressionExperimentSubSet>	getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Collection<ExpressionExperimentSubSet>	getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension, with assays lightly thawed.
Collection<ExpressionExperimentSubSet>	getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset, with characteristics initialized.
ExpressionExperimentSubSet	loadSubSet(Long id)	Load a subset by ID, without initializing collections.
ExpressionExperimentSubSet	loadSubSetWithBioAssays(Long id)	Load a subset by ID with its bio-assays initialized.

Methods inherited from class Object

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

Constructor Details

ExpressionExperimentSubSetReadServiceImpl

@Autowired
public ExpressionExperimentSubSetReadServiceImpl(ExpressionExperimentDao expressionExperimentDao,
 ExpressionExperimentSubSetDao expressionExperimentSubSetDao)

Method Details

getSubSetsWithBioAssays

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain all the subsets for a given dataset.

Specified by:

getSubSetsWithBioAssays in interface ExpressionExperimentSubSetReadService

getSubSetsWithBioAssays

@Transactional(readOnly=true)
public Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>> getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)

Description copied from interface: ExpressionExperimentSubSetReadService

Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.

Specified by:

getSubSetsWithBioAssays in interface ExpressionExperimentSubSetReadService

getSubSetsWithCharacteristics

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSubSet> getSubSetsWithCharacteristics(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain all the subsets for a given dataset, with characteristics initialized.

Specified by:

getSubSetsWithCharacteristics in interface ExpressionExperimentSubSetReadService

getSubSetsByDimension

@Transactional(readOnly=true)
public Map<BioAssayDimension, Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain all the subsets organized by dimension for a given dataset.

Specified by:

getSubSetsByDimension in interface ExpressionExperimentSubSetReadService

getSubSetsByDimensionWithBioAssays

@Transactional(readOnly=true)
public Map<BioAssayDimension, Set<ExpressionExperimentSubSet>> getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain all the subsets organized by dimension for a given dataset, with assays thawed.

Specified by:

getSubSetsByDimensionWithBioAssays in interface ExpressionExperimentSubSetReadService

getSubSets

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain the subsets for a particular dimension.

Specified by:

getSubSets in interface ExpressionExperimentSubSetReadService

getSubSetsWithBioAssays

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain the subsets for a particular dimension, with assays lightly thawed.

Specified by:

getSubSetsWithBioAssays in interface ExpressionExperimentSubSetReadService

getSubSetsByFactorValue

@Transactional(readOnly=true)
public Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Description copied from interface: ExpressionExperimentSubSetReadService

Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.

Specified by:

getSubSetsByFactorValue in interface ExpressionExperimentSubSetReadService

getSubSetsByFactorValue

@Transactional(readOnly=true)
public Map<FactorValue, ExpressionExperimentSubSet> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 ExperimentalFactor experimentalFactor,
 BioAssayDimension dimension)

Description copied from interface: ExpressionExperimentSubSetReadService

Reconstitute the FV-to-subset mapping for a given experiment and factor.

Specified by:

getSubSetsByFactorValue in interface ExpressionExperimentSubSetReadService

getSubSetsByFactorValueWithCharacteristicsAndBioAssays

@Transactional(readOnly=true)
public Map<FactorValue, ExpressionExperimentSubSet> getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment,
 ExperimentalFactor experimentalFactor,
 BioAssayDimension dimension)

Description copied from interface: ExpressionExperimentSubSetReadService

Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.

Specified by:

getSubSetsByFactorValueWithCharacteristicsAndBioAssays in interface ExpressionExperimentSubSetReadService

getSubSetByIdWithCharacteristics

@Transactional(readOnly=true)
public ExpressionExperimentSubSet getSubSetByIdWithCharacteristics(ExpressionExperiment ee,
 Long subSetId)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain a particular subset by ID, with characteristics initialized.

Specified by:

getSubSetByIdWithCharacteristics in interface ExpressionExperimentSubSetReadService

getSubSetByIdWithCharacteristicsAndBioAssays

@Transactional(readOnly=true)
public ExpressionExperimentSubSet getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee,
 Long subSetId)

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain a particular subset by ID, with characteristics initialized and assays thawed.

Specified by:

getSubSetByIdWithCharacteristicsAndBioAssays in interface ExpressionExperimentSubSetReadService

loadSubSet

@Nullable
@Transactional(readOnly=true)
public ExpressionExperimentSubSet loadSubSet(Long id)

Description copied from interface: ExpressionExperimentSubSetReadService

Load a subset by ID, without initializing collections.

Specified by:

loadSubSet in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.load(Long)

loadSubSetWithBioAssays

@Nullable
@Transactional(readOnly=true)
public ExpressionExperimentSubSet loadSubSetWithBioAssays(Long id)

Description copied from interface: ExpressionExperimentSubSetReadService

Load a subset by ID with its bio-assays initialized.

Specified by:

loadSubSetWithBioAssays in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.loadWithBioAssays(Long)

findByBioAssayIn

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

Description copied from interface: ExpressionExperimentSubSetReadService

Find every subset that contains any of the supplied bio-assays.

Specified by:

findByBioAssayIn in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.findByBioAssayIn(Collection)

getFactorValuesUsed

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

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain the FactorValues used by samples in the given subset for the given factor.

Specified by:

getFactorValuesUsed in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor)

getFactorValuesUsedAsVO

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

Description copied from interface: ExpressionExperimentSubSetReadService

VO-form variant of ExpressionExperimentSubSetReadService.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor) accepting plain IDs.

Specified by:

getFactorValuesUsedAsVO in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.getFactorValuesUsed(Long, Long)

getArrayDesignsUsed

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

Description copied from interface: ExpressionExperimentSubSetReadService

Obtain the array designs used by the assays in the subset.

Specified by:

getArrayDesignsUsed in interface ExpressionExperimentSubSetReadService

See Also:

• ExpressionExperimentSubSetService.getArrayDesignsUsed(ExpressionExperimentSubSet)