Class DifferentialExpressionResultServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<DifferentialExpressionAnalysisResult>

ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl

All Implemented Interfaces:

DifferentialExpressionResultService, BaseImmutableService<DifferentialExpressionAnalysisResult>, BaseReadOnlyService<DifferentialExpressionAnalysisResult>, BaseService<DifferentialExpressionAnalysisResult>

@Service
public class DifferentialExpressionResultServiceImpl
extends AbstractService<DifferentialExpressionAnalysisResult>
implements DifferentialExpressionResultService

Facade for DifferentialExpressionResultService.

Phase 3 service decomposition: the row-level result read cluster has been extracted to DifferentialExpressionResultReadService; this facade delegates reads to that bean while continuing to host the ACL @Secured annotations (which live on the DifferentialExpressionResultService interface) and the inherited BaseReadOnlyService surface (provided by AbstractService).

Author:

keshav

See Also:

• DifferentialExpressionResultService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao DERDao, DifferentialExpressionResultReadService readService)

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 resultSet, 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)

Methods inherited from class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, 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 BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Constructor Details

DifferentialExpressionResultServiceImpl

@Autowired
public DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao DERDao,
 DifferentialExpressionResultReadService readService)

Method Details

findByGeneAndExperimentAnalyzedIds

public 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)

Specified by:

findByGeneAndExperimentAnalyzedIds in interface DifferentialExpressionResultService

See Also:

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

findByExperimentAnalyzed

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

Specified by:

findByExperimentAnalyzed in interface DifferentialExpressionResultService

See Also:

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

findByGene

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

Specified by:

findByGene in interface DifferentialExpressionResultService

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean)

findByGene

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

Specified by:

findByGene in interface DifferentialExpressionResultService

See Also:

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

findByGeneAndExperimentAnalyzed

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

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultService

See Also:

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

findByGeneAndExperimentAnalyzed

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

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultService

See Also:

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

findGeneResultsByResultSetIdsAndGeneIds

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

Specified by:

findGeneResultsByResultSetIdsAndGeneIds in interface DifferentialExpressionResultService

See Also:

• DifferentialExpressionResultDao.findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection)

findByResultSet

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

Specified by:

findByResultSet in interface DifferentialExpressionResultService

See Also:

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

findContrastsByAnalysisResultIds

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

Specified by:

findContrastsByAnalysisResultIds in interface DifferentialExpressionResultService

See Also:

• DifferentialExpressionResultDao.findContrastsByAnalysisResultIds(Collection)