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

Interface ExpressionAnalysisResultSetDao

All Superinterfaces:

AnalysisResultSetDao<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, BaseDao<ExpressionAnalysisResultSet>, BaseVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>, FilteringDao<ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

All Known Implementing Classes:

ExpressionAnalysisResultSetDaoImpl

public interface ExpressionAnalysisResultSetDao
extends AnalysisResultSetDao<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

See Also:

ExpressionAnalysisResultSet

Method Summary

Modifier and Type	Method and Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters objectFilters, int offset, int limit, Sort sort) Retrieve result sets associated to a set of BioAssaySet and external database entries.
Map<DifferentialExpressionAnalysisResult,List<Gene>>	loadResultToGenesMap(ExpressionAnalysisResultSet resultSet) Load a DifferentialExpressionAnalysisResult to Gene multi-map.
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet resultSet) Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id)
void	thaw(ExpressionAnalysisResultSet resultSet) Thaw a result set's analysis, experiment analyzed and experimental factors.
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

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

loadValueObjectsPreFilter, loadValueObjectsPreFilter

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

getElementClass, getObjectAlias

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

countAll, create, create, find, findOrCreate, load, load, loadAll, remove, remove, remove, removeAll, save, save, update, update

Method Detail

loadWithResultsAndContrasts

ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id)

thaw

void thaw(ExpressionAnalysisResultSet resultSet)

Thaw a result set's analysis, experiment analyzed and experimental factors. If you need to load the probe, contrasts, etc. use loadWithResultsAndContrasts(Long) instead which is optimized for that purpose.

thawFully

DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

canDelete

boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

loadValueObjectWithResults

DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet resultSet)

Load an analysis result set with its all of its associated results.

See Also:

BaseVoEnabledDao.loadValueObject(Identifiable)

loadResultToGenesMap

Map<DifferentialExpressionAnalysisResult,List<Gene>> loadResultToGenesMap(ExpressionAnalysisResultSet resultSet)

Load a DifferentialExpressionAnalysisResult to Gene multi-map. This is much faster than navigating through the probe's alignments, transcripts and then genes as it uses the internal GENE2CS table described in TableMaintenanceUtil.updateGene2CsEntries(). Note: Not all probes have associated genes, so you should use Map.getOrDefault(Object, Object) with an empty collection to handle this case.

findByBioAssaySetInAndDatabaseEntryInLimit

Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
                                                                                                     Collection<BioAssaySet> bioAssaySets,
                                                                                                     @Nullable
                                                                                                     Collection<DatabaseEntry> databaseEntries,
                                                                                                     @Nullable
                                                                                                     Filters objectFilters,
                                                                                                     int offset,
                                                                                                     int limit,
                                                                                                     @Nullable
                                                                                                     Sort sort)

Retrieve result sets associated to a set of BioAssaySet and external database entries.

Parameters:

bioAssaySets - related BioAssaySet, or any if null

databaseEntries - related external identifier associated to the BioAssaySet, or any if null

objectFilters - list of object filters

limit - maximum number of results to return

sort - field and direction by which the collection is ordered