Interface ExpressionExperimentSubSetReadService

All Known Implementing Classes:

ExpressionExperimentSubSetReadServiceImpl

public interface ExpressionExperimentSubSetReadService

Read-only retrieval service for ExpressionExperimentSubSet objects in the context of a parent ExpressionExperiment.

Phase 3 of the ExpressionExperimentService decomposition (strangler fig). This service houses the subset-retrieval cluster previously implemented directly on the ExpressionExperimentServiceImpl facade: getSubSets*, getSubSetById*, and the getSubSetsByFactorValue* variants. All methods delegate to ExpressionExperimentDao (and occasionally call Hibernate.initialize(Object) or Thaws for eager-loading) with no orchestration of write-side collaborators.

Callers should generally keep using ExpressionExperimentService as the facade — the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring construction cycle through the heavier facade.

ACL / @Secured annotations live on ExpressionExperimentService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

This service also houses the read methods that used to live on ExpressionExperimentSubSetService (the standalone subset CRUD service): findByBioAssayIn(Collection), getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor), getFactorValuesUsedAsVO(Long, Long), getArrayDesignsUsed(ExpressionExperimentSubSet), loadSubSet(Long), loadSubSetWithBioAssays(Long). The standalone ExpressionExperimentSubSetService now delegates these reads here, keeping its facade ACL annotations in place.

See Also:

• ExpressionExperimentService
• ExpressionExperimentSubSetService

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 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.

Method Details

getSubSetsWithBioAssays

Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)

Obtain all the subsets for a given dataset.

getSubSetsWithBioAssays

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.

getSubSetsWithCharacteristics

Collection<ExpressionExperimentSubSet> getSubSetsWithCharacteristics(ExpressionExperiment ee)

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

getSubSetsByDimension

Map<BioAssayDimension, Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)

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

getSubSetsByDimensionWithBioAssays

Map<BioAssayDimension, Set<ExpressionExperimentSubSet>> getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)

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

getSubSets

Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Obtain the subsets for a particular dimension.

getSubSetsWithBioAssays

Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

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

getSubSetsByFactorValue

Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

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

getSubSetsByFactorValue

@Nullable
Map<FactorValue, ExpressionExperimentSubSet> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 ExperimentalFactor experimentalFactor,
 BioAssayDimension dimension)

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

getSubSetsByFactorValueWithCharacteristicsAndBioAssays

@Nullable
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.

getSubSetByIdWithCharacteristics

@Nullable
ExpressionExperimentSubSet getSubSetByIdWithCharacteristics(ExpressionExperiment ee,
 Long subSetId)

Obtain a particular subset by ID, with characteristics initialized.

getSubSetByIdWithCharacteristicsAndBioAssays

@Nullable
ExpressionExperimentSubSet getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee,
 Long subSetId)

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

loadSubSet

@Nullable
ExpressionExperimentSubSet loadSubSet(Long id)

Load a subset by ID, without initializing collections.

See Also:

• ExpressionExperimentSubSetService.load(Long)

loadSubSetWithBioAssays

@Nullable
ExpressionExperimentSubSet loadSubSetWithBioAssays(Long id)

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

See Also:

• ExpressionExperimentSubSetService.loadWithBioAssays(Long)

findByBioAssayIn

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

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

See Also:

• ExpressionExperimentSubSetService.findByBioAssayIn(Collection)

getFactorValuesUsed

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

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

See Also:

• ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet, ExperimentalFactor)

getFactorValuesUsedAsVO

Collection<FactorValueValueObject> getFactorValuesUsedAsVO(Long subSetId,
 Long experimentalFactor)

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

See Also:

• ExpressionExperimentSubSetService.getFactorValuesUsed(Long, Long)

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperimentSubSet subset)

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

See Also:

• ExpressionExperimentSubSetService.getArrayDesignsUsed(ExpressionExperimentSubSet)