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

Class ExpressionAnalysisResultSetServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

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

All Implemented Interfaces:

AnalysisResultSetService<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, ExpressionAnalysisResultSetService, BaseImmutableService<ExpressionAnalysisResultSet>, BaseReadOnlyService<ExpressionAnalysisResultSet>, BaseService<ExpressionAnalysisResultSet>, BaseVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>, FilteringService<ExpressionAnalysisResultSet>, FilteringVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

@Service
public class ExpressionAnalysisResultSetServiceImpl
extends AbstractFilteringVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>
implements ExpressionAnalysisResultSetService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
ExpressionAnalysisResultSetServiceImpl(ExpressionAnalysisResultSetDao voDao)

Method Summary

Modifier and Type	Method	Description
long	countResults(ExpressionAnalysisResultSet ears)
long	countResults(ExpressionAnalysisResultSet ears, double threshold)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Baseline	getBaseline(ExpressionAnalysisResultSet ears)
Map<ExpressionAnalysisResultSet,Baseline>	getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> rsIds, boolean initializeFactorValues)
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)
Map<Long,List<Gene>>	loadResultIdToGenesMap(ExpressionAnalysisResultSet resultSet)
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet ears, boolean includeFactorValuesInContrasts, boolean queryByResult, boolean includeTaxonInGenes)
ExpressionAnalysisResultSet	loadWithAnalysis(Long id)
ExpressionAnalysisResultSet	loadWithExperimentAnalyzed(Long id)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, int offset, int limit)
ExpressionAnalysisResultSet	thaw(ExpressionAnalysisResultSet ears)

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

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, remove, remove, remove, save, save, 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.BaseImmutableService

create, create, findOrCreate, remove, remove, remove

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

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

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

save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Detail

ExpressionAnalysisResultSetServiceImpl

@Autowired
public ExpressionAnalysisResultSetServiceImpl(ExpressionAnalysisResultSetDao voDao)

Method Detail

loadWithAnalysis

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet loadWithAnalysis(Long id)

Specified by:

loadWithAnalysis in interface ExpressionAnalysisResultSetService

loadWithResultsAndContrasts

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value)

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetService

loadWithResultsAndContrasts

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
                                                               int offset,
                                                               int limit)

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetService

loadWithResultsAndContrasts

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
                                                               double threshold,
                                                               int offset,
                                                               int limit)

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetService

countResults

@Transactional(readOnly=true)
public long countResults(ExpressionAnalysisResultSet ears)

Specified by:

countResults in interface ExpressionAnalysisResultSetService

countResults

@Transactional(readOnly=true)
public long countResults(ExpressionAnalysisResultSet ears,
                         double threshold)

Specified by:

countResults in interface ExpressionAnalysisResultSetService

thaw

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet thaw(ExpressionAnalysisResultSet ears)

Specified by:

thaw in interface ExpressionAnalysisResultSetService

loadWithExperimentAnalyzed

@Transactional(readOnly=true)
public ExpressionAnalysisResultSet loadWithExperimentAnalyzed(Long id)

Specified by:

loadWithExperimentAnalyzed in interface ExpressionAnalysisResultSetService

loadValueObjectWithResults

@Transactional(readOnly=true)
public DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet ears,
                                                                                     boolean includeFactorValuesInContrasts,
                                                                                     boolean queryByResult,
                                                                                     boolean includeTaxonInGenes)

Specified by:

loadValueObjectWithResults in interface ExpressionAnalysisResultSetService

loadResultIdToGenesMap

@Transactional(readOnly=true)
public Map<Long,List<Gene>> loadResultIdToGenesMap(ExpressionAnalysisResultSet resultSet)

Specified by:

loadResultIdToGenesMap in interface ExpressionAnalysisResultSetService

findByBioAssaySetInAndDatabaseEntryInLimit

@Transactional(readOnly=true)
public Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
                                                                                                            Collection<BioAssaySet> bioAssaySets,
                                                                                                            @Nullable
                                                                                                            Collection<DatabaseEntry> externalIds,
                                                                                                            @Nullable
                                                                                                            Filters filters,
                                                                                                            int offset,
                                                                                                            int limit,
                                                                                                            @Nullable
                                                                                                            Sort sort)

Specified by:

findByBioAssaySetInAndDatabaseEntryInLimit in interface ExpressionAnalysisResultSetService

getBaseline

@Transactional(readOnly=true)
public Baseline getBaseline(ExpressionAnalysisResultSet ears)

Specified by:

getBaseline in interface ExpressionAnalysisResultSetService

getBaselinesForInteractions

@Transactional(readOnly=true)
public Map<ExpressionAnalysisResultSet,Baseline> getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets,
                                                                                   boolean initializeFactorValues)

Specified by:

getBaselinesForInteractions in interface ExpressionAnalysisResultSetService

getBaselinesForInteractionsByIds

@Transactional(readOnly=true)
public Map<Long,Baseline> getBaselinesForInteractionsByIds(Collection<Long> rsIds,
                                                                 boolean initializeFactorValues)

Specified by:

getBaselinesForInteractionsByIds in interface ExpressionAnalysisResultSetService

loadPvalueDistribution

@Transactional(readOnly=true)
public Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)

Specified by:

loadPvalueDistribution in interface ExpressionAnalysisResultSetService