Interface DifferentialExpressionAnalysisReadService

All Known Implementing Classes:

DifferentialExpressionAnalysisReadServiceImpl

public interface DifferentialExpressionAnalysisReadService

Read-only retrieval service for DifferentialExpressionAnalysis.

Phase 3 of the DifferentialExpressionAnalysisService decomposition (strangler fig). This service houses the read-side cluster previously implemented directly on the DifferentialExpressionAnalysisServiceImpl facade: loadWithExperimentAnalyzed, findByName, findByFactor, findExperimentsWithAnalyses, findByExperimentAndAnalysisId, the thaw variants, canDelete, findByExperimentIds, findByExperiment, findByExperiments, and getExperimentsWithAnalysis. All methods delegate to the relevant DAOs with no orchestration of write-side collaborators.

Callers should generally keep using DifferentialExpressionAnalysisService 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 DifferentialExpressionAnalysisService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• DifferentialExpressionAnalysisService

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Collection<DifferentialExpressionAnalysis>	findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
DifferentialExpressionAnalysis	findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpressionAnalysisValueObject>>	findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, boolean includeAssays)
Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> experimentIds, boolean includeSubSets)
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)	Load an analysis by ID and eagerly initialize its experimentAnalyzed.
Collection<DifferentialExpressionAnalysis>	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)	Thaw a collection of DifferentialExpressionAnalysis for full traversal.
DifferentialExpressionAnalysis	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)	Thaw a single DifferentialExpressionAnalysis for full traversal.
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)	Thaw a single DifferentialExpressionAnalysis including all its result sets, results and contrasts.

Method Details

loadWithExperimentAnalyzed

@Nullable
DifferentialExpressionAnalysis loadWithExperimentAnalyzed(Long id)

Load an analysis by ID and eagerly initialize its experimentAnalyzed.

findByName

Collection<DifferentialExpressionAnalysis> findByName(String name)

See Also:

• DifferentialExpressionAnalysisDao.findByName(String)

findByFactor

Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

See Also:

• DifferentialExpressionAnalysisDao.findByFactor(ExperimentalFactor)

findExperimentsWithAnalyses

Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

See Also:

• DifferentialExpressionAnalysisDao.findExperimentsWithAnalyses(Gene)

findByExperimentAndAnalysisId

@Nullable
DifferentialExpressionAnalysis findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment,
 boolean includeSubSets,
 Long analysisId)

See Also:

• DifferentialExpressionAnalysisDao.findByExperimentAndAnalysisId(ExpressionExperiment, boolean, Long)

thaw

@CheckReturnValue
Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

Thaw a collection of DifferentialExpressionAnalysis for full traversal.

thaw

@CheckReturnValue
DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Thaw a single DifferentialExpressionAnalysis for full traversal.

thawFully

@CheckReturnValue
DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Thaw a single DifferentialExpressionAnalysis including all its result sets, results and contrasts.

canDelete

boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Returns:

true if the analysis can be deleted (no other entity is keeping it around).

findByExperimentIds

Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpressionAnalysisValueObject>> findByExperimentIds(Collection<Long> experimentIds,
 boolean includeSubSets,
 boolean includeAssays)

See Also:

• DifferentialExpressionAnalysisService.findByExperimentIds(Collection, boolean, boolean)

findByExperiment

Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experimentAnalyzed,
 boolean includeSubSets)

See Also:

• DifferentialExpressionAnalysisDao.findByExperiment(ExpressionExperiment, boolean)

findByExperiments

Map<ExpressionExperiment, Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> experiments,
 boolean includeSubSets)

See Also:

• DifferentialExpressionAnalysisDao.findByExperiments(Collection, boolean)

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentIds,
 boolean includeSubSets)

See Also:

• DifferentialExpressionAnalysisDao.getExperimentsWithAnalysis(Collection, boolean)