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

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

Author:

keshav

See Also:

• DifferentialExpressionResultService

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultServiceImpl(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 ubic.gemma.persistence.service.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 java.lang.Object

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

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

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

Constructor Details

DifferentialExpressionResultServiceImpl

@Autowired
public DifferentialExpressionResultServiceImpl(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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

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 DifferentialExpressionResultService

See Also:

• DifferentialExpressionResultDao.findContrastsByAnalysisResultIds(Collection)