Interface DifferentialExpressionResultReadService

All Known Implementing Classes:

DifferentialExpressionResultReadServiceImpl

public interface DifferentialExpressionResultReadService

Read-only retrieval service for DifferentialExpressionAnalysisResult.

Phase 3 of the DifferentialExpressionResultService decomposition (strangler fig). This service houses the row-level result read cluster previously implemented directly on the DifferentialExpressionResultServiceImpl facade: findByExperimentAnalyzed, findByGene (x2), findByGeneAndExperimentAnalyzedIds, findByGeneAndExperimentAnalyzed (x2), findGeneResultsByResultSetIdsAndGeneIds, findByResultSet, and findContrastsByAnalysisResultIds. All methods delegate to DifferentialExpressionResultDao and orchestrate no write-side collaborators.

Distinct from DifferentialExpressionAnalysisReadService, which is the analysis-level decomp; this service is the row-level result decomp.

Callers should generally keep using DifferentialExpressionResultService as the facade -- the facade delegates to this service. Direct injection is appropriate where a class is logically read-only (REST endpoints, CLIs, browser controllers, intra-core readers).

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

See Also:

• DifferentialExpressionResultService

Method Summary

Modifier and Type	Method	Description
Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>>	findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)
Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)
Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)
Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionValueObject>	findByResultSet(ExpressionAnalysisResultSet ar, double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long, ContrastsValueObject>	findContrastsByAnalysisResultIds(Collection<Long> ids)
Map<Long, Map<Long, DiffExprGeneSearchResult>>	findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)

Method Details

findByExperimentAnalyzed

Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByExperimentAnalyzed(Collection, boolean, double, int)

findByGene

Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes)

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean)

findByGene

Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean, double, int)

findByGeneAndExperimentAnalyzedIds

List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzedIds(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecific,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets,
 Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap,
 Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap,
 Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap,
 double threshold,
 boolean initializeFactorValues)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean, boolean)

findByGeneAndExperimentAnalyzed

Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean)

findByGeneAndExperimentAnalyzed

Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int)

findGeneResultsByResultSetIdsAndGeneIds

Map<Long, Map<Long, DiffExprGeneSearchResult>> findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets,
 Collection<Long> geneIds)

See Also:

• DifferentialExpressionResultDao.findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection)

findByResultSet

List<DifferentialExpressionValueObject> findByResultSet(ExpressionAnalysisResultSet ar,
 double threshold,
 int maxResultsToReturn,
 int minNumberOfResults)

See Also:

• DifferentialExpressionResultDao.findByResultSet(ExpressionAnalysisResultSet, double, int, int)

findContrastsByAnalysisResultIds

Map<Long, ContrastsValueObject> findContrastsByAnalysisResultIds(Collection<Long> ids)

See Also:

• DifferentialExpressionResultDao.findContrastsByAnalysisResultIds(Collection)