Class DifferentialExpressionResultReadServiceImpl

java.lang.Object

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

All Implemented Interfaces:

DifferentialExpressionResultReadService

@Service("differentialExpressionResultReadService")
public class DifferentialExpressionResultReadServiceImpl
extends Object
implements DifferentialExpressionResultReadService

Implementation of DifferentialExpressionResultReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade DifferentialExpressionResultService 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:

• DifferentialExpressionResultService

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultReadServiceImpl(DifferentialExpressionResultDao DERDao)

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 Object

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

Constructor Details

DifferentialExpressionResultReadServiceImpl

@Autowired
public DifferentialExpressionResultReadServiceImpl(DifferentialExpressionResultDao DERDao)

Method Details

findByGeneAndExperimentAnalyzedIds

@Transactional(readOnly=true)
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 DifferentialExpressionResultReadService

See Also:

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

findByExperimentAnalyzed

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

Specified by:

findByExperimentAnalyzed in interface DifferentialExpressionResultReadService

See Also:

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

findByGene

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject, List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes)

Specified by:

findByGene in interface DifferentialExpressionResultReadService

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean)

findByGene

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

Specified by:

findByGene in interface DifferentialExpressionResultReadService

See Also:

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

findByGeneAndExperimentAnalyzed

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

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultReadService

See Also:

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

findByGeneAndExperimentAnalyzed

@Transactional(readOnly=true)
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 DifferentialExpressionResultReadService

See Also:

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

findGeneResultsByResultSetIdsAndGeneIds

@Transactional(readOnly=true)
public Map<Long, Map<Long, DiffExprGeneSearchResult>> findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets,
 Collection<Long> geneIds)

Specified by:

findGeneResultsByResultSetIdsAndGeneIds in interface DifferentialExpressionResultReadService

See Also:

• DifferentialExpressionResultDao.findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection)

findByResultSet

@Transactional(readOnly=true)
public List<DifferentialExpressionValueObject> findByResultSet(ExpressionAnalysisResultSet resultSet,
 double threshold,
 int maxResultsToReturn,
 int minNumberOfResults)

Specified by:

findByResultSet in interface DifferentialExpressionResultReadService

See Also:

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

findContrastsByAnalysisResultIds

@Transactional(readOnly=true)
public Map<Long, ContrastsValueObject> findContrastsByAnalysisResultIds(Collection<Long> ids)

Specified by:

findContrastsByAnalysisResultIds in interface DifferentialExpressionResultReadService

See Also:

• DifferentialExpressionResultDao.findContrastsByAnalysisResultIds(Collection)