java.lang.Object
- ubic.gemma.persistence.service.AbstractDao<O>
- - ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>
  - - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO>
    - - ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<C,VO>
      - ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
        
        ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<ExpressionExperiment>, BaseVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>, CachedFilteringDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, CuratableDao<ExpressionExperiment>, ExpressionExperimentDao, FilteringDao<ExpressionExperiment>, FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
```
@Repository
public class ExpressionExperimentDaoImpl
extends AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
implements ExpressionExperimentDao
```
Author:

pavlidis

See Also:

ExpressionExperiment

Nested Class Summary
- Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
  AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Field Summary
- Fields inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
  CURATION_DETAILS_ALIAS
- Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
  REPORT_SLOW_QUERY_AFTER_MS
- Fields inherited from class ubic.gemma.persistence.service.AbstractDao
  log
- Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
  FREE_TEXT, OBJECT_ALIAS, UNCATEGORIZED

Constructor Summary

Constructors
Constructor Description

ExpressionExperimentDaoImpl(SessionFactory sessionFactory)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`addRawDataVectors(ExpressionExperiment ee, QuantitationType newQt, Collection<RawExpressionDataVector> newVectors)`	Add raw data vectors with the given quantitation type.
`List<ExpressionExperiment>`	`browse(int start, int limit)`
`List<ExpressionExperiment>`	`browse(int start, int limit, String orderField, boolean descending)`
`protected void`	`configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer configurer)`	Register filterable properties.
`long`	`countBioMaterials(Filters filters)`	Count the number of biomaterials of datasets satisfying the given filters.
`int`	`createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`	Add processed data vectors
`void`	`createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)`	Create a single-cell dimension for a given experiment.
`void`	`deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)`	Delete the given single cell dimension.
`protected ExpressionExperimentValueObject`	`doLoadValueObject(ExpressionExperiment entity)`	Load a value object for a given entity.
`Collection<Long>`	`filterByTaxon(Collection<Long> ids, Taxon taxon)`
`ExpressionExperiment`	`find(ExpressionExperiment entity)`	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
`Collection<ExpressionExperiment>`	`findByAccession(String accession)`
`Collection<ExpressionExperiment>`	`findByAccession(DatabaseEntry accession)`
`Collection<ExpressionExperiment>`	`findByBibliographicReference(BibliographicReference bibRef)`
`ExpressionExperiment`	`findByBioAssay(BioAssay ba)`
`Collection<ExpressionExperiment>`	`findByBioMaterial(BioMaterial bm)`
`Map<ExpressionExperiment,Collection<BioMaterial>>`	`findByBioMaterials(Collection<BioMaterial> bms)`
`ExpressionExperiment`	`findByDesign(ExperimentalDesign ed)`
`Collection<ExpressionExperiment>`	`findByExpressedGene(Gene gene, Double rank)`
`ExpressionExperiment`	`findByFactor(ExperimentalFactor ef)`
`ExpressionExperiment`	`findByFactorValue(Long factorValueId)`
`ExpressionExperiment`	`findByFactorValue(FactorValue fv)`
`Map<ExpressionExperiment,FactorValue>`	`findByFactorValues(Collection<FactorValue> fvs)`
`Collection<ExpressionExperiment>`	`findByGene(Gene gene)`
`Collection<ExpressionExperiment>`	`findByName(String name)`
`ExpressionExperiment`	`findByQuantitationType(QuantitationType quantitationType)`
`ExpressionExperiment`	`findByShortName(String shortName)`
`Collection<ExpressionExperiment>`	`findByTaxon(Taxon taxon)`
`List<ExpressionExperiment>`	`findByUpdatedLimit(int limit)`
`List<ExpressionExperiment>`	`findByUpdatedLimit(Collection<Long> ids, int limit)`
`ExpressionExperiment`	`findOneByAccession(String accession)`
`ExpressionExperiment`	`findOneByName(String name)`
`Collection<ExpressionExperiment>`	`findUpdatedAfter(Date date)`	Find experiments updated on or after a given date.
`Map<Class<? extends Identifiable>,List<Characteristic>>`	`getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)`	Obtain all annotations, grouped by applicable level.
`Map<Long,Long>`	`getAnnotationCounts(Collection<Long> ids)`
`Map<Characteristic,Long>`	`getAnnotationsUsageFrequency(Collection<Long> eeIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris)`	We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.
`Map<ArrayDesign,Long>`	`getArrayDesignsUsageFrequency(int maxResults)`	Obtain dataset usage frequency by platform currently used.
`Map<ArrayDesign,Long>`	`getArrayDesignsUsageFrequency(Collection<Long> eeIds, int maxResults)`	Obtain dataset usage frequency by platform currently for the given dataset IDs.
`Collection<ArrayDesign>`	`getArrayDesignsUsed(Collection<? extends BioAssaySet> ees)`
`Collection<ArrayDesign>`	`getArrayDesignsUsed(BioAssaySet bas)`
`Collection<ArrayDesign>`	`getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)`
`Map<Long,Collection<AuditEvent>>`	`getAuditEvents(Collection<Long> ids)`
`BioAssayDimension`	`getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)`	Retrieve a dimension for a given experiment and quantitation type.
`BioAssayDimension`	`getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)`	Retrieve a dimension for a given experiment and quantitation type.
`BioAssayDimension`	`getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)`	Obtain a bioassay dimension by ID.
`Collection<BioAssayDimension>`	`getBioAssayDimensions(ExpressionExperiment expressionExperiment)`
`Collection<BioAssayDimension>`	`getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)`	Retrieve `BioAssayDimension` that are used by subsets of a given `ExpressionExperiment`.
`List<Characteristic>`	`getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)`	Obtain sample-level annotations.
`List<Characteristic>`	`getBioMaterialAnnotations(ExpressionExperimentSubSet subset)`
`long`	`getBioMaterialCount(ExpressionExperiment expressionExperiment)`
`Map<Characteristic,Long>`	`getCategoriesUsageFrequency(Collection<Long> eeIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)`
`Characteristic`	`getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)`	Obtain the characteristic at a given cell index.
`Characteristic[]`	`getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)`
`List<CellLevelCharacteristics>`	`getCellLevelCharacteristics(ExpressionExperiment ee)`	Obtain all cell-level characteristics from all single cell dimensions.
`List<CellLevelCharacteristics>`	`getCellLevelCharacteristics(ExpressionExperiment ee, Category category)`	Obtain all cell-level characteristics from all single cell dimensions matching the given category.
`List<CellLevelCharacteristics>`	`getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)`
`CellLevelCharacteristics`	`getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)`	Obtain a specific cell-level characteristic by ID.
`Category`	`getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)`	Obtain the category of a cell-level characteristic.
`CellTypeAssignment`	`getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)`	Obtain a cell type assignment by ID.
`CellTypeAssignment`	`getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)`	Obtain a cell type assignment by name.
`List<CellTypeAssignment>`	`getCellTypeAssignments(ExpressionExperiment ee)`
`List<CellTypeAssignment>`	`getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)`
`CellTypeAssignment`	`getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)`	Obtain a cell type assignment by ID without loading the indices.
`CellTypeAssignment`	`getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)`	Obtain a cell type assignment by name without loading the indices.
`Characteristic`	`getCellTypeAt(CellTypeAssignment cta, int cellIndex)`	Obtain the cell type at a given cell index.
`Characteristic[]`	`getCellTypeAt(CellTypeAssignment cta, int startIndex, int endIndexExclusive)`
`List<Characteristic>`	`getCellTypes(ExpressionExperiment ee)`
`List<Characteristic>`	`getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)`	Obtain experimental design-level annotations.
`List<Characteristic>`	`getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)`	Obtain experiment-level annotations.
`Collection<ExpressionExperiment>`	`getExperimentsLackingPublications()`
`Collection<Characteristic>`	`getExperimentSubSetAnnotations(ExpressionExperiment ee)`	Obtain the subset annotations.
`Collection<ExpressionExperiment>`	`getExperimentsWithOutliers()`
`List<Statement>`	`getFactorValueAnnotations(ExpressionExperiment ee)`	Obtain factor value-level annotations.
`List<Statement>`	`getFactorValueAnnotations(ExpressionExperimentSubSet subset)`	Obtain factor value-level annotations for a given subset.
`protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta`	`getFilterablePropertyMeta(String propertyName)`	Checks for special properties that are allowed to be referenced on certain objects.
`protected Query`	`getFilteringCountQuery(Filters filters)`	Produce a query that will be used to retrieve the size of `AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)`.
`protected Query`	`getFilteringIdQuery(Filters filters, Sort sort)`	Produce a query that will be used to retrieve IDs of `AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)`.
`protected Query`	`getFilteringQuery(Filters filters, Sort sort)`	Produce a query for retrieving value objects after applying a set of filters and a given ordering.
`Collection<Gene>`	`getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)`	Obtain genes used by the processed vectors of this dataset.
`Map<Long,Date>`	`getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)`
`Date`	`getLastArrayDesignUpdate(ExpressionExperiment ee)`
`Map<BioAssay,Long>`	`getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)`
`long`	`getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)`	Obtain the number of non-zeroes.
`Map<BioAssay,Long>`	`getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize)`	Obtain the number of non-zeroes by sample.
`long`	`getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)`	Obtain the number of single-cell vectors for a given QT.
`Map<ArrayDesign,Long>`	`getOriginalPlatformsUsageFrequency(int maxResults)`	Obtain dataset usage frequency by original platforms.
`Map<ArrayDesign,Long>`	`getOriginalPlatformsUsageFrequency(Collection<Long> eeIds, int maxResults)`	Obtain dataset usage frequency by platform currently for the given dataset IDs.
`Map<Taxon,Long>`	`getPerTaxonCount()`	Obtain the count of distinct experiments per taxon.
`Map<Taxon,Long>`	`getPerTaxonCount(Collection<Long> ids)`	Obtain the count of distinct experiments per taxon for experiments with the given IDs.
`Map<Long,Long>`	`getPopulatedFactorCounts(Collection<Long> ids)`
`Map<Long,Long>`	`getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)`
`CellTypeAssignment`	`getPreferredCellTypeAssignment(ExpressionExperiment ee)`	Obtain the preferred assignment of the preferred single-cell vectors.
`QuantitationType`	`getPreferredQuantitationType(ExpressionExperiment ee)`	Obtain the preferred quantitation type for the raw vectors, if available.
`SingleCellDimension`	`getPreferredSingleCellDimension(ExpressionExperiment ee)`	Obtain the preferred single cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
`SingleCellDimension`	`getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)`	Load a single-cell dimension without its cell IDs.
`QuantitationType`	`getPreferredSingleCellQuantitationType(ExpressionExperiment ee)`	Obtain the preferred quantitation type for single cell data, if available.
`Collection<ProcessedExpressionDataVector>`	`getProcessedDataVectors(ExpressionExperiment ee)`	Retrieve the processed vector for an experiment.
`Collection<ProcessedExpressionDataVector>`	`getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)`	Retrieve a slice of processed vectors for an experiment.
`QuantitationType`	`getProcessedQuantitationType(ExpressionExperiment ee)`	Obtain the quantitation type for the processed vectors, if available.
`Map<QuantitationType,Long>`	`getQuantitationTypeCount(ExpressionExperiment ee)`
`long`	`getRawDataVectorCount(ExpressionExperiment ee)`
`Collection<RawExpressionDataVector>`	`getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)`	Obtain a slice of the raw vectors for a given experiment and QT.
`Collection<RawExpressionDataVector>`	`getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)`	Obtain raw vectors for a given experiment and QT.
`Map<ExpressionExperiment,Collection<AuditEvent>>`	`getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)`
`List<SingleCellExpressionDataVector>`	`getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)`	Obtain a set of single-cell data vectors for the given quantitation type.
`List<SingleCellExpressionDataVector>`	`getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeCellIds, boolean includeData, boolean includeDataIndices)`	Obtain a set of single-cell data vectors for the given quantitation type.
`SingleCellExpressionDataVector`	`getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)`
`SingleCellDimension`	`getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)`	Obtain the single-cell dimension used by a specific QT.
`List<SingleCellDimension>`	`getSingleCellDimensions(ExpressionExperiment ee)`	Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.
`List<SingleCellDimension>`	`getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)`	Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.
`List<SingleCellDimension>`	`getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)`
`SingleCellDimension`	`getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)`	Load a single-cell dimension used by a specific QT without its cell IDs.
`SingleCellDimension`	`getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeCharacteristics, boolean includeIndices)`
`List<QuantitationType>`	`getSingleCellQuantitationTypes(ExpressionExperiment ee)`	Obtain a list of single-cell QTs.
`ExpressionExperimentSubSet`	`getSubSetById(ExpressionExperiment ee, Long subSetId)`
`Collection<ExpressionExperimentSubSet>`	`getSubSets(ExpressionExperiment expressionExperiment)`
`Collection<ExpressionExperimentSubSet>`	`getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)`
`Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>`	`getSubSetsByDimension(ExpressionExperiment expressionExperiment)`
`<T extends BioAssaySet> Map<T,Taxon>`	`getTaxa(Collection<T> bioAssaySets)`
`Taxon`	`getTaxon(BioAssaySet ee)`	Determine the taxon for a given experiment or subset.
`Map<TechnologyType,Long>`	`getTechnologyTypeUsageFrequency()`	Obtain the dataset usage frequency by technology type.
`Map<TechnologyType,Long>`	`getTechnologyTypeUsageFrequency(Collection<Long> eeIds)`	Obtain the dataset usage frequency by technology type for the given dataset IDs.
`protected TypedResultTransformer<ExpressionExperimentValueObject>`	`getValueObjectTransformer()`	Obtain a value object transformer for the results of `AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)`.
`boolean`	`hasProcessedExpressionData(ExpressionExperiment ee)`	Test if the dataset has preferred expression data vectors.
`protected void`	`initializeCachedFilteringResult(ExpressionExperiment ee)`	Initialize a result from `AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)` retrieved from the Hibernate `StandardQueryCache`.
`ExpressionExperiment`	`load(Long id, CacheMode cacheMode)`	Load an experiment by ID with a specific cache mode.
`SortedMap<String,String>`	`loadAllAccessionAndName()`
`SortedMap<Long,String>`	`loadAllIdAndName()`
`SortedSet<String>`	`loadAllName()`
`SortedMap<String,String>`	`loadAllShortNameAndName()`
`BioAssaySet`	`loadBioAssaySet(Long id)`
`Slice<ExpressionExperimentValueObject>`	`loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)`
`Slice<ExpressionExperimentDetailsValueObject>`	`loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)`	Special method for front-end access.
`List<ExpressionExperimentDetailsValueObject>`	`loadDetailsValueObjectsByIds(Collection<Long> ids)`	Like `ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int)`, but returning a list.
`List<ExpressionExperimentDetailsValueObject>`	`loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)`	Flavour of `ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection)`, but using the query cache.
`Slice<ExpressionExperimentDetailsValueObject>`	`loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)`	Flavour of `ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection)`, but using the query cache.
`Collection<ExpressionExperiment>`	`loadLackingFactors()`
`Collection<ExpressionExperiment>`	`loadLackingTags()`
`List<ExpressionExperimentValueObject>`	`loadValueObjects(Filters filters, Sort sort)`	Load VOs with minimal ordering and filtering.
`Slice<ExpressionExperimentValueObject>`	`loadValueObjects(Filters filters, Sort sort, int offset, int limit)`	Load VOs with ordering, filtering and offset/limit.
`List<ExpressionExperiment>`	`loadWithRelationsAndCache(List<Long> ids)`	Load datasets by IDs with the same relation as `CachedFilteringDao.loadWithCache(Filters, Sort)`.
`protected void`	`postProcessValueObjects(List<ExpressionExperimentValueObject> results)`	Post-process VOs in bulk.
`void`	`remove(ExpressionExperiment ee)`	Remove a persistent instance
`int`	`removeAllRawDataVectors(ExpressionExperiment ee)`	Remove all raw data vectors.
`int`	`removeAllSingleCellDataVectors(ExpressionExperiment ee)`	Remove all single-cell data vectors and their quantitation types.
`int`	`removeProcessedDataVectors(ExpressionExperiment ee)`	Remove processed data vectors.
`int`	`removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)`	Remove raw data vectors for a given quantitation type.
`int`	`removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean deleteQt)`	Remove the given single-cell data vectors.
`int`	`replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)`	Replace processed data vectors.
`int`	`replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)`	Replace raw data vectors for a given quantitation type.
`Stream<String>`	`streamCellIds(SingleCellDimension dimension, boolean createNewSession)`	Stream the cell IDs of a dimension.
`Stream<Characteristic>`	`streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)`
`Stream<Characteristic>`	`streamCellTypes(CellTypeAssignment cta, boolean createNewSession)`
`Stream<SingleCellExpressionDataVector>`	`streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)`	Obtain a stream over the vectors for a given QT.
`Stream<SingleCellExpressionDataVector>`	`streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)`
`void`	`thaw(ExpressionExperiment expressionExperiment)`	Thaw everything.
`void`	`thawLite(ExpressionExperiment ee)`	Thaw experiment metadata and bioassays.
`void`	`thawLiter(ExpressionExperiment expressionExperiment)`	Thaw experiment metadata.
`MeanVarianceRelation`	`updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)`
`void`	`updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)`	Update a single-cell dimensino for a given experiment.

Methods inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
addEventsToMap, addNonTroubledFilter, distinctIfNecessary, formNativeNonTroubledClause, formNonTroubledClause, groupByIfNecessary, loadTroubledIds, updateCurationDetailsFromAuditEvent

Methods inherited from class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
count, countWithCache, getEntityTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
afterPropertiesSet, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyType, getSort

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractDao
countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao
countAll, create, create, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringDao
countWithCache, loadIdsWithCache, loadWithCache, loadWithCache

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringVoEnabledDao
loadValueObjectsWithCache, loadValueObjectsWithCache

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao
loadTroubledIds, updateCurationDetailsFromAuditEvent

Methods inherited from interface ubic.gemma.persistence.service.FilteringDao
count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

- Constructor Detail
  - ExpressionExperimentDaoImpl
```
@Autowired
public ExpressionExperimentDaoImpl(SessionFactory sessionFactory)
```
- Method Detail
  - load
```
public ExpressionExperiment load(Long id,
                                 CacheMode cacheMode)
```
    Description copied from interface: ExpressionExperimentDao
    
    Load an experiment by ID with a specific cache mode.
    The cache mode will be effective for the remainder of the Hibernate session.
    
    Specified by:
    
    load in interface ExpressionExperimentDao
  - loadAllIdAndName
```
public SortedMap<Long,String> loadAllIdAndName()
```
    Specified by:
    
    loadAllIdAndName in interface ExpressionExperimentDao
  - loadAllShortNameAndName
```
public SortedMap<String,String> loadAllShortNameAndName()
```
    Specified by:
    
    loadAllShortNameAndName in interface ExpressionExperimentDao
  - loadAllName
```
public SortedSet<String> loadAllName()
```
    Specified by:
    
    loadAllName in interface ExpressionExperimentDao
  - loadAllAccessionAndName
```
public SortedMap<String,String> loadAllAccessionAndName()
```
    Specified by:
    
    loadAllAccessionAndName in interface ExpressionExperimentDao
  - browse
```
public List<ExpressionExperiment> browse(int start,
                                         int limit)
```
    Specified by:
    
    browse in interface BrowsingDao<ExpressionExperiment>
  - browse
```
public List<ExpressionExperiment> browse(int start,
                                         int limit,
                                         String orderField,
                                         boolean descending)
```
    Specified by:
    
    browse in interface BrowsingDao<ExpressionExperiment>
  - loadBioAssaySet
```
public BioAssaySet loadBioAssaySet(Long id)
```
    Specified by:
    
    loadBioAssaySet in interface ExpressionExperimentDao
  - filterByTaxon
```
public Collection<Long> filterByTaxon(@Nullable
                                      Collection<Long> ids,
                                      Taxon taxon)
```
    Specified by:
    
    filterByTaxon in interface ExpressionExperimentDao
  - findByShortName
```
public ExpressionExperiment findByShortName(String shortName)
```
    Specified by:
    
    findByShortName in interface ExpressionExperimentDao
  - findByName
```
public Collection<ExpressionExperiment> findByName(String name)
```
    Specified by:
    
    findByName in interface ExpressionExperimentDao
  - findOneByName
```
public ExpressionExperiment findOneByName(String name)
```
    Specified by:
    
    findOneByName in interface ExpressionExperimentDao
  - find
```
public ExpressionExperiment find(ExpressionExperiment entity)
```
    Description copied from interface: BaseDao
    
    Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
    
    Specified by:
    
    find in interface BaseDao<ExpressionExperiment>
    
    Overrides:
    
    find in class AbstractDao<ExpressionExperiment>
    
    Parameters:
    
    entity - the entity to look for.
    
    Returns:
    
    an entity that was found in the persistent storage, or null if no such entity was found.
  - findByAccession
```
public Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)
```
    Specified by:
    
    findByAccession in interface ExpressionExperimentDao
  - findByAccession
```
public Collection<ExpressionExperiment> findByAccession(String accession)
```
    Specified by:
    
    findByAccession in interface ExpressionExperimentDao
  - findOneByAccession
```
@Nullable
public ExpressionExperiment findOneByAccession(String accession)
```
    Specified by:
    
    findOneByAccession in interface ExpressionExperimentDao
  - findByBibliographicReference
```
public Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)
```
    Specified by:
    
    findByBibliographicReference in interface ExpressionExperimentDao
  - findByBioAssay
```
public ExpressionExperiment findByBioAssay(BioAssay ba)
```
    Specified by:
    
    findByBioAssay in interface ExpressionExperimentDao
  - findByBioMaterial
```
public Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)
```
    Specified by:
    
    findByBioMaterial in interface ExpressionExperimentDao
  - findByBioMaterials
```
public Map<ExpressionExperiment,Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> bms)
```
    Specified by:
    
    findByBioMaterials in interface ExpressionExperimentDao
  - findByExpressedGene
```
public Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
                                                            Double rank)
```
    Specified by:
    
    findByExpressedGene in interface ExpressionExperimentDao
  - findByDesign
```
public ExpressionExperiment findByDesign(ExperimentalDesign ed)
```
    Specified by:
    
    findByDesign in interface ExpressionExperimentDao
  - findByFactor
```
public ExpressionExperiment findByFactor(ExperimentalFactor ef)
```
    Specified by:
    
    findByFactor in interface ExpressionExperimentDao
  - findByFactorValue
```
public ExpressionExperiment findByFactorValue(FactorValue fv)
```
    Specified by:
    
    findByFactorValue in interface ExpressionExperimentDao
  - findByFactorValue
```
public ExpressionExperiment findByFactorValue(Long factorValueId)
```
    Specified by:
    
    findByFactorValue in interface ExpressionExperimentDao
  - findByFactorValues
```
public Map<ExpressionExperiment,FactorValue> findByFactorValues(Collection<FactorValue> fvs)
```
    Specified by:
    
    findByFactorValues in interface ExpressionExperimentDao
  - findByGene
```
public Collection<ExpressionExperiment> findByGene(Gene gene)
```
    Specified by:
    
    findByGene in interface ExpressionExperimentDao
  - findByQuantitationType
```
public ExpressionExperiment findByQuantitationType(QuantitationType quantitationType)
```
    Specified by:
    
    findByQuantitationType in interface ExpressionExperimentDao
  - findByTaxon
```
public Collection<ExpressionExperiment> findByTaxon(Taxon taxon)
```
    Specified by:
    
    findByTaxon in interface ExpressionExperimentDao
  - findByUpdatedLimit
```
public List<ExpressionExperiment> findByUpdatedLimit(Collection<Long> ids,
                                                     int limit)
```
    Specified by:
    
    findByUpdatedLimit in interface ExpressionExperimentDao
  - findByUpdatedLimit
```
public List<ExpressionExperiment> findByUpdatedLimit(int limit)
```
    Specified by:
    
    findByUpdatedLimit in interface ExpressionExperimentDao
  - findUpdatedAfter
```
public Collection<ExpressionExperiment> findUpdatedAfter(@Nullable
                                                         Date date)
```
    Description copied from interface: ExpressionExperimentDao
    
    Find experiments updated on or after a given date.
    
    Specified by:
    
    findUpdatedAfter in interface ExpressionExperimentDao
  - getAnnotationCounts
```
public Map<Long,Long> getAnnotationCounts(Collection<Long> ids)
```
    Specified by:
    
    getAnnotationCounts in interface ExpressionExperimentDao
  - getAllAnnotations
```
public Map<Class<? extends Identifiable>,List<Characteristic>> getAllAnnotations(ExpressionExperiment expressionExperiment,
                                                                                       boolean useEe2c)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain all annotations, grouped by applicable level.
    
    Specified by:
    
    getAllAnnotations in interface ExpressionExperimentDao
    
    useEe2c - use the EXPRESSION_EXPERIMENT2CHARACTERISTIC table to retrieve annotations
  - getExperimentAnnotations
```
public List<Characteristic> getExperimentAnnotations(ExpressionExperiment expressionExperiment,
                                                     boolean useEe2c)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain experiment-level annotations.
    
    Specified by:
    
    getExperimentAnnotations in interface ExpressionExperimentDao
    
    useEe2c - use the EXPRESSION_EXPERIMENTE2CHARACTERISTIC table, TableMaintenanceUtil
  - getExperimentSubSetAnnotations
```
public Collection<Characteristic> getExperimentSubSetAnnotations(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the subset annotations.
    
    Specified by:
    
    getExperimentSubSetAnnotations in interface ExpressionExperimentDao
  - getBioMaterialAnnotations
```
public List<Characteristic> getBioMaterialAnnotations(ExpressionExperiment expressionExperiment,
                                                      boolean useEe2c)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain sample-level annotations.
    This uses the EE2C table under the hood.
    
    Specified by:
    
    getBioMaterialAnnotations in interface ExpressionExperimentDao
  - getBioMaterialAnnotations
```
public List<Characteristic> getBioMaterialAnnotations(ExpressionExperimentSubSet subset)
```
    Specified by:
    
    getBioMaterialAnnotations in interface ExpressionExperimentDao
  - getExperimentalDesignAnnotations
```
public List<Characteristic> getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment,
                                                             boolean useEe2c)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain experimental design-level annotations.
    This is equivalent to the subject components of ExpressionExperimentDao.getFactorValueAnnotations(ExpressionExperiment) for now, but other annotations from the experimental design might be included in the future.
    
    Specified by:
    
    getExperimentalDesignAnnotations in interface ExpressionExperimentDao
  - getFactorValueAnnotations
```
public List<Statement> getFactorValueAnnotations(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain factor value-level annotations.
    
    Specified by:
    
    getFactorValueAnnotations in interface ExpressionExperimentDao
  - getFactorValueAnnotations
```
public List<Statement> getFactorValueAnnotations(ExpressionExperimentSubSet subset)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain factor value-level annotations for a given subset.
    
    Specified by:
    
    getFactorValueAnnotations in interface ExpressionExperimentDao
  - getCategoriesUsageFrequency
```
public Map<Characteristic,Long> getCategoriesUsageFrequency(@Nullable
                                                                  Collection<Long> eeIds,
                                                                  @Nullable
                                                                  Collection<String> excludedCategoryUris,
                                                                  @Nullable
                                                                  Collection<String> excludedTermUris,
                                                                  @Nullable
                                                                  Collection<String> retainedTermUris,
                                                                  int maxResults)
```
    Specified by:
    
    getCategoriesUsageFrequency in interface ExpressionExperimentDao
  - getAnnotationsUsageFrequency
```
public Map<Characteristic,Long> getAnnotationsUsageFrequency(@Nullable
                                                                   Collection<Long> eeIds,
                                                                   @Nullable
                                                                   Class<? extends Identifiable> level,
                                                                   int maxResults,
                                                                   int minFrequency,
                                                                   @Nullable
                                                                   String category,
                                                                   @Nullable
                                                                   Collection<String> excludedCategoryUris,
                                                                   @Nullable
                                                                   Collection<String> excludedTermUris,
                                                                   @Nullable
                                                                   Collection<String> retainedTermUris)
```
    We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.
    
    Specified by:
    
    getAnnotationsUsageFrequency in interface ExpressionExperimentDao
    
    Parameters:
    
    eeIds - IDs of ExpressionExperiment to use for restricting annotations, or null to consider everything
    
    level - applicable annotation level, one of ExpressionExperiment, ExperimentalDesign or BioMaterial
    
    maxResults - maximum number of annotations to return, or -1 to return everything
    
    minFrequency - minimum usage frequency to be reported (0 effectively allows everything)
    
    category - a category URI or free text category to restrict the results to, or null to consider everything, empty string to consider uncategorized terms
    
    retainedTermUris - a collection of term to retain even if they don't meet the minimum frequency criteria
  - getExperimentsLackingPublications
```
public Collection<ExpressionExperiment> getExperimentsLackingPublications()
```
    Specified by:
    
    getExperimentsLackingPublications in interface ExpressionExperimentDao
  - updateMeanVarianceRelation
```
public MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
                                                       MeanVarianceRelation mvr)
```
    Specified by:
    
    updateMeanVarianceRelation in interface ExpressionExperimentDao
  - countBioMaterials
```
public long countBioMaterials(@Nullable
                              Filters filters)
```
    Description copied from interface: ExpressionExperimentDao
    
    Count the number of biomaterials of datasets satisfying the given filters.
    The result is stored in the standard query cache.
    
    Specified by:
    
    countBioMaterials in interface ExpressionExperimentDao
  - getArrayDesignsUsed
```
public Collection<ArrayDesign> getArrayDesignsUsed(BioAssaySet bas)
```
    Specified by:
    
    getArrayDesignsUsed in interface ExpressionExperimentDao
  - getArrayDesignsUsed
```
public Collection<ArrayDesign> getArrayDesignsUsed(Collection<? extends BioAssaySet> ees)
```
    Specified by:
    
    getArrayDesignsUsed in interface ExpressionExperimentDao
  - getArrayDesignsUsed
```
public Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee,
                                                   QuantitationType qt,
                                                   Class<? extends DataVector> dataVectorType)
```
    Specified by:
    
    getArrayDesignsUsed in interface ExpressionExperimentDao
  - getGenesUsedByPreferredVectors
```
public Collection<Gene> getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain genes used by the processed vectors of this dataset.
    
    Specified by:
    
    getGenesUsedByPreferredVectors in interface ExpressionExperimentDao
  - getTechnologyTypeUsageFrequency
```
public Map<TechnologyType,Long> getTechnologyTypeUsageFrequency()
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the dataset usage frequency by technology type.
    If a dataset was switched to a platform of a different technology type, it is counted toward both.
    
    Specified by:
    
    getTechnologyTypeUsageFrequency in interface ExpressionExperimentDao
  - getTechnologyTypeUsageFrequency
```
public Map<TechnologyType,Long> getTechnologyTypeUsageFrequency(Collection<Long> eeIds)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the dataset usage frequency by technology type for the given dataset IDs.
    Note: No ACL filtering is performed.
    
    Specified by:
    
    getTechnologyTypeUsageFrequency in interface ExpressionExperimentDao
    
    See Also:
    
    ExpressionExperimentDao.getTechnologyTypeUsageFrequency()
  - getArrayDesignsUsageFrequency
```
public Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(int maxResults)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain dataset usage frequency by platform currently used.
    Note that a dataset counts toward all the platforms mentioned through its BioAssay.
    This method uses ACLs and the troubled status to only displays the counts of datasets the current user is entitled to see. Only administrator can see troubled platforms.
    
    Specified by:
    
    getArrayDesignsUsageFrequency in interface ExpressionExperimentDao
  - getArrayDesignsUsageFrequency
```
public Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(Collection<Long> eeIds,
                                                                 int maxResults)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain dataset usage frequency by platform currently for the given dataset IDs.
    Note: no ACL filtering is performed. Only administrator can see troubled platforms.
    
    Specified by:
    
    getArrayDesignsUsageFrequency in interface ExpressionExperimentDao
    
    See Also:
    
    ExpressionExperimentDao.getArrayDesignsUsageFrequency(int)
  - getOriginalPlatformsUsageFrequency
```
public Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(int maxResults)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain dataset usage frequency by original platforms.
    Note that a dataset counts toward all the platforms mentioned through its BioAssay. Datasets whose platform hasn't been switched (i.e. the original is the same as the current one) are ignored.
    This method uses ACLs and the troubled status to only displays the counts of datasets the current user is entitled to see. Only administrators can see troubled platforms.
    
    Specified by:
    
    getOriginalPlatformsUsageFrequency in interface ExpressionExperimentDao
  - getOriginalPlatformsUsageFrequency
```
public Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(Collection<Long> eeIds,
                                                                      int maxResults)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain dataset usage frequency by platform currently for the given dataset IDs.
    Note: no ACL filtering is performed. Only administrators can see troubled platforms.
    
    Specified by:
    
    getOriginalPlatformsUsageFrequency in interface ExpressionExperimentDao
    
    See Also:
    
    ExpressionExperimentDao.getOriginalPlatformsUsageFrequency(int)
  - getAuditEvents
```
public Map<Long,Collection<AuditEvent>> getAuditEvents(Collection<Long> ids)
```
    Specified by:
    
    getAuditEvents in interface ExpressionExperimentDao
  - getBioAssayDimensions
```
public Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)
```
    Specified by:
    
    getBioAssayDimensions in interface ExpressionExperimentDao
  - getBioAssayDimensionsFromSubSets
```
public Collection<BioAssayDimension> getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)
```
    Description copied from interface: ExpressionExperimentDao
    
    Retrieve BioAssayDimension that are used by subsets of a given ExpressionExperiment.
    This covers cases where BAs in a subset are not the same as the BAs in the experiment such as for single-cell data where we use sub-assays.
    
    Specified by:
    
    getBioAssayDimensionsFromSubSets in interface ExpressionExperimentDao
  - getBioAssayDimension
```
public BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
                                              QuantitationType qt,
                                              Class<? extends BulkExpressionDataVector> dataVectorType)
```
    Description copied from interface: ExpressionExperimentDao
    
    Retrieve a dimension for a given experiment and quantitation type.
    
    Specified by:
    
    getBioAssayDimension in interface ExpressionExperimentDao
    
    dataVectorType - the type of data vectors to consider, this is necessary because otherwise all the vector tables would have to be looked at. If you do nto know the type of vector, use ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment, QuantitationType).
  - getBioAssayDimension
```
public BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
                                              QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Retrieve a dimension for a given experiment and quantitation type.
    
    Specified by:
    
    getBioAssayDimension in interface ExpressionExperimentDao
  - getBioAssayDimensionById
```
public BioAssayDimension getBioAssayDimensionById(ExpressionExperiment ee,
                                                  Long dimensionId,
                                                  Class<? extends BulkExpressionDataVector> dataVectorType)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a bioassay dimension by ID.
    
    Specified by:
    
    getBioAssayDimensionById in interface ExpressionExperimentDao
  - getBioMaterialCount
```
public long getBioMaterialCount(ExpressionExperiment expressionExperiment)
```
    Specified by:
    
    getBioMaterialCount in interface ExpressionExperimentDao
  - getRawDataVectorCount
```
public long getRawDataVectorCount(ExpressionExperiment ee)
```
    Specified by:
    
    getRawDataVectorCount in interface ExpressionExperimentDao
    
    Parameters:
    
    ee - the expression experiment
    
    Returns:
    
    count of RAW vectors.
  - getExperimentsWithOutliers
```
public Collection<ExpressionExperiment> getExperimentsWithOutliers()
```
    Specified by:
    
    getExperimentsWithOutliers in interface ExpressionExperimentDao
  - getLastArrayDesignUpdate
```
public Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
```
    Specified by:
    
    getLastArrayDesignUpdate in interface ExpressionExperimentDao
  - getLastArrayDesignUpdate
```
public Date getLastArrayDesignUpdate(ExpressionExperiment ee)
```
    Specified by:
    
    getLastArrayDesignUpdate in interface ExpressionExperimentDao
  - getPerTaxonCount
```
public Map<Taxon,Long> getPerTaxonCount()
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the count of distinct experiments per taxon.
    Experiments are filtered by ACLs and troubled experiments are only visible to administrators.
    
    Specified by:
    
    getPerTaxonCount in interface ExpressionExperimentDao
  - getPerTaxonCount
```
public Map<Taxon,Long> getPerTaxonCount(Collection<Long> ids)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the count of distinct experiments per taxon for experiments with the given IDs.
    Experiments are not filtered by ACLs and toubled experiments are only visible to administrators.
    
    Specified by:
    
    getPerTaxonCount in interface ExpressionExperimentDao
  - getPopulatedFactorCounts
```
public Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)
```
    Specified by:
    
    getPopulatedFactorCounts in interface ExpressionExperimentDao
  - getPopulatedFactorCountsExcludeBatch
```
public Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
```
    Specified by:
    
    getPopulatedFactorCountsExcludeBatch in interface ExpressionExperimentDao
  - getQuantitationTypeCount
```
public Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)
```
    Specified by:
    
    getQuantitationTypeCount in interface ExpressionExperimentDao
  - getPreferredSingleCellQuantitationType
```
public QuantitationType getPreferredSingleCellQuantitationType(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the preferred quantitation type for single cell data, if available.
    
    Specified by:
    
    getPreferredSingleCellQuantitationType in interface ExpressionExperimentDao
  - getPreferredQuantitationType
```
public QuantitationType getPreferredQuantitationType(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the preferred quantitation type for the raw vectors, if available.
    
    Specified by:
    
    getPreferredQuantitationType in interface ExpressionExperimentDao
  - getProcessedQuantitationType
```
public QuantitationType getProcessedQuantitationType(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the quantitation type for the processed vectors, if available.
    
    Specified by:
    
    getProcessedQuantitationType in interface ExpressionExperimentDao
  - hasProcessedExpressionData
```
public boolean hasProcessedExpressionData(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Test if the dataset has preferred expression data vectors.
    
    Specified by:
    
    hasProcessedExpressionData in interface ExpressionExperimentDao
  - getSampleRemovalEvents
```
public Map<ExpressionExperiment,Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
```
    Specified by:
    
    getSampleRemovalEvents in interface ExpressionExperimentDao
  - getSubSets
```
public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment)
```
    Specified by:
    
    getSubSets in interface ExpressionExperimentDao
  - getSubSets
```
public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment,
                                                         BioAssayDimension bad)
```
    Specified by:
    
    getSubSets in interface ExpressionExperimentDao
  - getSubSetsByDimension
```
public Map<BioAssayDimension,Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)
```
    Specified by:
    
    getSubSetsByDimension in interface ExpressionExperimentDao
  - getSubSetById
```
public ExpressionExperimentSubSet getSubSetById(ExpressionExperiment ee,
                                                Long subSetId)
```
    Specified by:
    
    getSubSetById in interface ExpressionExperimentDao
  - getTaxa
```
public <T extends BioAssaySet> Map<T,Taxon> getTaxa(Collection<T> bioAssaySets)
```
    Specified by:
    
    getTaxa in interface ExpressionExperimentDao
  - getTaxon
```
public Taxon getTaxon(BioAssaySet ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Determine the taxon for a given experiment or subset.
    
    Specified by:
    
    getTaxon in interface ExpressionExperimentDao
    
    Returns:
    
    a unique taxon for the dataset, or null if no taxon could be determined
  - loadWithRelationsAndCache
```
public List<ExpressionExperiment> loadWithRelationsAndCache(List<Long> ids)
```
    Description copied from interface: ExpressionExperimentDao
    
    Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).
    
    Specified by:
    
    loadWithRelationsAndCache in interface ExpressionExperimentDao
  - loadDetailsValueObjects
```
public Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjects(@Nullable
                                                                             Collection<Long> ids,
                                                                             @Nullable
                                                                             Taxon taxon,
                                                                             @Nullable
                                                                             Sort sort,
                                                                             int offset,
                                                                             int limit)
```
    Description copied from interface: ExpressionExperimentDao
    
    Special method for front-end access. This is partly redundant with FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int); however, it fills in more information, returns ExpressionExperimentDetailsValueObject
    
    Specified by:
    
    loadDetailsValueObjects in interface ExpressionExperimentDao
    
    Parameters:
    
    ids - only list specific ids, or null to ignore
    
    taxon - only list EEs in the specified taxon, or null to ignore
    
    sort - the field to order the results by.
    
    offset - offset
    
    limit - maximum number of results to return
    
    Returns:
    
    a list of EE details VOs representing experiments matching the given arguments.
  - loadDetailsValueObjectsByIdsWithCache
```
public Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(@Nullable
                                                                                           Collection<Long> ids,
                                                                                           @Nullable
                                                                                           Taxon taxon,
                                                                                           @Nullable
                                                                                           Sort sort,
                                                                                           int offset,
                                                                                           int limit)
```
    Description copied from interface: ExpressionExperimentDao
    
    Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
    
    Specified by:
    
    loadDetailsValueObjectsByIdsWithCache in interface ExpressionExperimentDao
  - loadDetailsValueObjectsByIds
```
public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)
```
    Description copied from interface: ExpressionExperimentDao
    
    Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
    
    Specified by:
    
    loadDetailsValueObjectsByIds in interface ExpressionExperimentDao
  - loadDetailsValueObjectsByIdsWithCache
```
public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
```
    Description copied from interface: ExpressionExperimentDao
    
    Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
    
    Specified by:
    
    loadDetailsValueObjectsByIdsWithCache in interface ExpressionExperimentDao
  - loadBlacklistedValueObjects
```
public Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable
                                                                          Filters filters,
                                                                          @Nullable
                                                                          Sort sort,
                                                                          int offset,
                                                                          int limit)
```
    Specified by:
    
    loadBlacklistedValueObjects in interface ExpressionExperimentDao
  - loadLackingFactors
```
public Collection<ExpressionExperiment> loadLackingFactors()
```
    Specified by:
    
    loadLackingFactors in interface ExpressionExperimentDao
  - loadLackingTags
```
public Collection<ExpressionExperiment> loadLackingTags()
```
    Specified by:
    
    loadLackingTags in interface ExpressionExperimentDao
  - doLoadValueObject
```
protected ExpressionExperimentValueObject doLoadValueObject(ExpressionExperiment entity)
```
    Description copied from class: AbstractVoEnabledDao
    
    Load a value object for a given entity.
    This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.
    
    Specified by:
    
    doLoadValueObject in class AbstractVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - postProcessValueObjects
```
protected void postProcessValueObjects(List<ExpressionExperimentValueObject> results)
```
    Description copied from class: AbstractVoEnabledDao
    
    Post-process VOs in bulk.
    Use this as an opportunity to load extra informations that could not be populated in the initial AbstractVoEnabledDao.doLoadValueObject(Identifiable) or AbstractVoEnabledDao.doLoadValueObjects(Collection)
    
    Overrides:
    
    postProcessValueObjects in class AbstractVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - loadValueObjects
```
public List<ExpressionExperimentValueObject> loadValueObjects(@Nullable
                                                              Filters filters,
                                                              @Nullable
                                                              Sort sort)
```
    Description copied from interface: FilteringVoEnabledDao
    
    Load VOs with minimal ordering and filtering.
    Use this as an alternative to FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int) if you do not intend to provide pagination capabilities.
    
    Specified by:
    
    loadValueObjects in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    Overrides:
    
    loadValueObjects in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    See Also:
    
    FilteringDao.load(Filters, Sort), FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)
  - loadValueObjects
```
public Slice<ExpressionExperimentValueObject> loadValueObjects(@Nullable
                                                               Filters filters,
                                                               @Nullable
                                                               Sort sort,
                                                               int offset,
                                                               int limit)
```
    Description copied from interface: FilteringVoEnabledDao
    
    Load VOs with ordering, filtering and offset/limit.
    Consider using FilteringDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode) to produce the filters and sort safely from user input.
    
    Specified by:
    
    loadValueObjects in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    Overrides:
    
    loadValueObjects in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    Parameters:
    
    filters - filters applied on the search. The properties mentioned in the Filter must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".
    
    sort - an object property and direction to order by. This property must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".
    
    offset - an offset from which entities are retrieved when sorted according to the sort argument, or 0 to ignore
    
    limit - a limit on the number of returned results, or -1 to ignore
    
    Returns:
    
    a slice of the relevant data
    
    See Also:
    
    FilteringDao.load(Filters, Sort, int, int)
  - getValueObjectTransformer
```
protected TypedResultTransformer<ExpressionExperimentValueObject> getValueObjectTransformer()
```
    Description copied from class: AbstractQueryFilteringVoEnabledDao
    
    Obtain a value object transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
    By default, it will process the first element of the tuple with AbstractVoEnabledDao.doLoadValueObjects(Collection) and then post-process the resulting VOs with AbstractVoEnabledDao.postProcessValueObjects(List).
    
    Overrides:
    
    getValueObjectTransformer in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - remove
```
public void remove(ExpressionExperiment ee)
```
    Description copied from interface: BaseDao
    
    Remove a persistent instance
    
    Specified by:
    
    remove in interface BaseDao<ExpressionExperiment>
    
    Overrides:
    
    remove in class AbstractDao<ExpressionExperiment>
    
    Parameters:
    
    ee - the entity to be removed
  - thaw
```
public void thaw(ExpressionExperiment expressionExperiment)
```
    Description copied from interface: ExpressionExperimentDao
    
    Thaw everything.
    Includes ExpressionExperimentDao.thawLite(ExpressionExperiment) and raw/processed vectors.
    Does not include single-cell vectors.
    
    Specified by:
    
    thaw in interface ExpressionExperimentDao
  - thawLite
```
public void thawLite(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Thaw experiment metadata and bioassays.
    Include ExpressionExperimentDao.thawLiter(ExpressionExperiment) and bioassays.
    
    Specified by:
    
    thawLite in interface ExpressionExperimentDao
  - thawLiter
```
public void thawLiter(ExpressionExperiment expressionExperiment)
```
    Description copied from interface: ExpressionExperimentDao
    
    Thaw experiment metadata.
    
    Specified by:
    
    thawLiter in interface ExpressionExperimentDao
  - getSingleCellDimensions
```
public List<SingleCellDimension> getSingleCellDimensions(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.
    
    Specified by:
    
    getSingleCellDimensions in interface ExpressionExperimentDao
  - getSingleCellDimensionsWithoutCellIds
```
public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.
    Cell IDs are not loaded.
    
    Specified by:
    
    getSingleCellDimensionsWithoutCellIds in interface ExpressionExperimentDao
  - getSingleCellDimensionsWithoutCellIds
```
public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee,
                                                                       boolean includeBioAssays,
                                                                       boolean includeCtas,
                                                                       boolean includeClcs,
                                                                       boolean includeCharacteristics,
                                                                       boolean includeIndices)
```
    Specified by:
    
    getSingleCellDimensionsWithoutCellIds in interface ExpressionExperimentDao
  - getSingleCellDimension
```
public SingleCellDimension getSingleCellDimension(ExpressionExperiment ee,
                                                  QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the single-cell dimension used by a specific QT.
    
    Specified by:
    
    getSingleCellDimension in interface ExpressionExperimentDao
  - getSingleCellDimensionWithoutCellIds
```
public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
                                                                QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Load a single-cell dimension used by a specific QT without its cell IDs.
    
    Specified by:
    
    getSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
  - getSingleCellDimensionWithoutCellIds
```
public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
                                                                QuantitationType qt,
                                                                boolean includeBioAssays,
                                                                boolean includeCtas,
                                                                boolean includeClcs,
                                                                boolean includeCharacteristics,
                                                                boolean includeIndices)
```
    Specified by:
    
    getSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
  - getPreferredSingleCellDimension
```
public SingleCellDimension getPreferredSingleCellDimension(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the preferred single cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
    
    Specified by:
    
    getPreferredSingleCellDimension in interface ExpressionExperimentDao
  - getPreferredSingleCellDimensionWithoutCellIds
```
public SingleCellDimension getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Load a single-cell dimension without its cell IDs.
    
    Specified by:
    
    getPreferredSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
  - createSingleCellDimension
```
public void createSingleCellDimension(ExpressionExperiment ee,
                                      SingleCellDimension singleCellDimension)
```
    Description copied from interface: ExpressionExperimentDao
    
    Create a single-cell dimension for a given experiment.
    
    Specified by:
    
    createSingleCellDimension in interface ExpressionExperimentDao
  - updateSingleCellDimension
```
public void updateSingleCellDimension(ExpressionExperiment ee,
                                      SingleCellDimension singleCellDimension)
```
    Description copied from interface: ExpressionExperimentDao
    
    Update a single-cell dimensino for a given experiment.
    
    Specified by:
    
    updateSingleCellDimension in interface ExpressionExperimentDao
  - deleteSingleCellDimension
```
public void deleteSingleCellDimension(ExpressionExperiment ee,
                                      SingleCellDimension singleCellDimension)
```
    Description copied from interface: ExpressionExperimentDao
    
    Delete the given single cell dimension.
    
    Specified by:
    
    deleteSingleCellDimension in interface ExpressionExperimentDao
  - streamCellIds
```
public Stream<String> streamCellIds(SingleCellDimension dimension,
                                    boolean createNewSession)
```
    Description copied from interface: ExpressionExperimentDao
    
    Stream the cell IDs of a dimension.
    
    Specified by:
    
    streamCellIds in interface ExpressionExperimentDao
    
    createNewSession - create a new session held by the stream, allowing to use the stream beyond the lifetime current session. If you set this to true, make absolutely sure that the resulting stream is closed.
    
    Returns:
    
    a stream of cell IDs, or null if the dimension is not found
  - streamCellTypes
```
public Stream<Characteristic> streamCellTypes(CellTypeAssignment cta,
                                              boolean createNewSession)
```
    Specified by:
    
    streamCellTypes in interface ExpressionExperimentDao
  - getCellLevelCharacteristicsCategory
```
public Category getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the category of a cell-level characteristic.
    This handles the case where the characteristics were not loaded (i.e. using ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean)).
    
    Specified by:
    
    getCellLevelCharacteristicsCategory in interface ExpressionExperimentDao
  - getCellTypeAt
```
public Characteristic getCellTypeAt(CellTypeAssignment cta,
                                    int cellIndex)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the cell type at a given cell index.
    
    Specified by:
    
    getCellTypeAt in interface ExpressionExperimentDao
  - getCellTypeAt
```
public Characteristic[] getCellTypeAt(CellTypeAssignment cta,
                                      int startIndex,
                                      int endIndexExclusive)
```
    Specified by:
    
    getCellTypeAt in interface ExpressionExperimentDao
  - getCellLevelCharacteristicAt
```
public Characteristic getCellLevelCharacteristicAt(CellLevelCharacteristics clc,
                                                   int cellIndex)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the characteristic at a given cell index.
    
    Specified by:
    
    getCellLevelCharacteristicAt in interface ExpressionExperimentDao
  - getCellLevelCharacteristicAt
```
public Characteristic[] getCellLevelCharacteristicAt(CellLevelCharacteristics clc,
                                                     int startIndex,
                                                     int endIndexExclusive)
```
    Specified by:
    
    getCellLevelCharacteristicAt in interface ExpressionExperimentDao
  - streamCellLevelCharacteristics
```
public Stream<Characteristic> streamCellLevelCharacteristics(CellLevelCharacteristics clc,
                                                             boolean createNewSession)
```
    Specified by:
    
    streamCellLevelCharacteristics in interface ExpressionExperimentDao
  - getCellTypeAssignments
```
public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment ee)
```
    Specified by:
    
    getCellTypeAssignments in interface ExpressionExperimentDao
  - getCellTypeAssignments
```
public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment expressionExperiment,
                                                       QuantitationType qt)
```
    Specified by:
    
    getCellTypeAssignments in interface ExpressionExperimentDao
  - getPreferredCellTypeAssignment
```
public CellTypeAssignment getPreferredCellTypeAssignment(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the preferred assignment of the preferred single-cell vectors.
    
    Specified by:
    
    getPreferredCellTypeAssignment in interface ExpressionExperimentDao
  - getCellTypeAssignment
```
public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
                                                QuantitationType qt,
                                                Long ctaId)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a cell type assignment by ID.
    
    Specified by:
    
    getCellTypeAssignment in interface ExpressionExperimentDao
  - getCellTypeAssignmentWithoutIndices
```
public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment,
                                                              QuantitationType qt,
                                                              Long ctaId)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a cell type assignment by ID without loading the indices.
    
    Specified by:
    
    getCellTypeAssignmentWithoutIndices in interface ExpressionExperimentDao
  - getCellTypeAssignment
```
public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
                                                QuantitationType qt,
                                                String ctaName)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a cell type assignment by name.
    
    Specified by:
    
    getCellTypeAssignment in interface ExpressionExperimentDao
  - getCellTypeAssignmentWithoutIndices
```
public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment,
                                                              QuantitationType qt,
                                                              String ctaName)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a cell type assignment by name without loading the indices.
    
    Specified by:
    
    getCellTypeAssignmentWithoutIndices in interface ExpressionExperimentDao
  - getCellLevelCharacteristics
```
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain all cell-level characteristics from all single cell dimensions.
    
    Specified by:
    
    getCellLevelCharacteristics in interface ExpressionExperimentDao
  - getCellLevelCharacteristics
```
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee,
                                                                  Category category)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain all cell-level characteristics from all single cell dimensions matching the given category.
    
    Specified by:
    
    getCellLevelCharacteristics in interface ExpressionExperimentDao
  - getCellLevelCharacteristics
```
public CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee,
                                                            QuantitationType qt,
                                                            Long clcId)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a specific cell-level characteristic by ID.
    When using this method, no CellTypeAssignment can be returned as those are stored in a different table.
    
    Specified by:
    
    getCellLevelCharacteristics in interface ExpressionExperimentDao
  - getCellLevelCharacteristics
```
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
                                                                  QuantitationType qt)
```
    Specified by:
    
    getCellLevelCharacteristics in interface ExpressionExperimentDao
  - getCellTypes
```
public List<Characteristic> getCellTypes(ExpressionExperiment ee)
```
    Specified by:
    
    getCellTypes in interface ExpressionExperimentDao
  - getSingleCellQuantitationTypes
```
public List<QuantitationType> getSingleCellQuantitationTypes(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a list of single-cell QTs.
    
    Specified by:
    
    getSingleCellQuantitationTypes in interface ExpressionExperimentDao
  - getSingleCellDataVectors
```
public List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment expressionExperiment,
                                                                     QuantitationType quantitationType)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a set of single-cell data vectors for the given quantitation type.
    
    Specified by:
    
    getSingleCellDataVectors in interface ExpressionExperimentDao
  - getSingleCellDataVectors
```
public List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
                                                                     QuantitationType quantitationType,
                                                                     boolean includeCellIds,
                                                                     boolean includeData,
                                                                     boolean includeDataIndices)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a set of single-cell data vectors for the given quantitation type.
    
    Specified by:
    
    getSingleCellDataVectors in interface ExpressionExperimentDao
  - streamSingleCellDataVectors
```
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
                                                                          QuantitationType quantitationType,
                                                                          int fetchSize,
                                                                          boolean createNewSession)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a stream over the vectors for a given QT.
    
    Specified by:
    
    streamSingleCellDataVectors in interface ExpressionExperimentDao
    
    fetchSize - number of vectors to fetch at once
    
    createNewSession - create a new session held by the stream. If you set this to true, make absolutely sure that the resulting stream is closed because it is attached to a Session object.
    
    See Also:
    
    QueryUtils.stream(Query, int)
  - streamSingleCellDataVectors
```
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
                                                                          QuantitationType quantitationType,
                                                                          int fetchSize,
                                                                          boolean createNewSession,
                                                                          boolean includeCellIds,
                                                                          boolean includeData,
                                                                          boolean includeDataIndices)
```
    Specified by:
    
    streamSingleCellDataVectors in interface ExpressionExperimentDao
  - getSingleCellDataVectorWithoutCellIds
```
public SingleCellExpressionDataVector getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee,
                                                                            QuantitationType quantitationType,
                                                                            CompositeSequence designElement)
```
    Specified by:
    
    getSingleCellDataVectorWithoutCellIds in interface ExpressionExperimentDao
  - getNumberOfSingleCellDataVectors
```
public long getNumberOfSingleCellDataVectors(ExpressionExperiment ee,
                                             QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the number of single-cell vectors for a given QT.
    
    Specified by:
    
    getNumberOfSingleCellDataVectors in interface ExpressionExperimentDao
  - getNumberOfNonZeroes
```
public long getNumberOfNonZeroes(ExpressionExperiment ee,
                                 QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the number of non-zeroes.
    
    Specified by:
    
    getNumberOfNonZeroes in interface ExpressionExperimentDao
  - getNumberOfNonZeroesBySample
```
public Map<BioAssay,Long> getNumberOfNonZeroesBySample(ExpressionExperiment ee,
                                                             QuantitationType qt,
                                                             int fetchSize)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain the number of non-zeroes by sample.
    This is quite costly because the indices of each vector has to be examined.
    
    Specified by:
    
    getNumberOfNonZeroesBySample in interface ExpressionExperimentDao
  - removeSingleCellDataVectors
```
public int removeSingleCellDataVectors(ExpressionExperiment ee,
                                       QuantitationType quantitationType,
                                       boolean deleteQt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Remove the given single-cell data vectors.
    
    Specified by:
    
    removeSingleCellDataVectors in interface ExpressionExperimentDao
    
    quantitationType - quantitation to remove
    
    deleteQt - if true, detach the QT from the experiment and delete it TODO: add a replaceSingleCellDataVectors to avoid needing this
  - removeAllSingleCellDataVectors
```
public int removeAllSingleCellDataVectors(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Remove all single-cell data vectors and their quantitation types.
    
    Specified by:
    
    removeAllSingleCellDataVectors in interface ExpressionExperimentDao
  - getNumberOfDesignElementsPerSample
```
public Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
```
    Specified by:
    
    getNumberOfDesignElementsPerSample in interface ExpressionExperimentDao
  - getFilteringQuery
```
protected Query getFilteringQuery(@Nullable
                                  Filters filters,
                                  @Nullable
                                  Sort sort)
```
    Description copied from class: AbstractQueryFilteringVoEnabledDao
    
    Produce a query for retrieving value objects after applying a set of filters and a given ordering.
    Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().
    The make the cached query (i.e. AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.
    
    Specified by:
    
    getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    Returns:
    
    a Query that produce a list of AbstractQueryFilteringVoEnabledDao
  - initializeCachedFilteringResult
```
protected void initializeCachedFilteringResult(ExpressionExperiment ee)
```
    Description copied from class: AbstractQueryFilteringVoEnabledDao
    
    Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
    Lazy-loaded relations that are fetched in AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.
    
    Specified by:
    
    initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - getFilteringIdQuery
```
protected Query getFilteringIdQuery(@Nullable
                                    Filters filters,
                                    @Nullable
                                    Sort sort)
```
    Description copied from class: AbstractQueryFilteringVoEnabledDao
    
    Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
    
    Overrides:
    
    getFilteringIdQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - getFilteringCountQuery
```
protected Query getFilteringCountQuery(@Nullable
                                       Filters filters)
```
    Description copied from class: AbstractQueryFilteringVoEnabledDao
    
    Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
    
    Overrides:
    
    getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    Returns:
    
    a Query which must return a single Long value
  - configureFilterableProperties
```
protected void configureFilterableProperties(AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer configurer)
```
    Description copied from class: AbstractFilteringVoEnabledDao
    
    Register filterable properties.
    
    Overrides:
    
    configureFilterableProperties in class AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
  - getFilterablePropertyMeta
```
protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta getFilterablePropertyMeta(String propertyName)
```
    Checks for special properties that are allowed to be referenced on certain objects. E.g. characteristics on EEs. Obtain various meta-information used to infer what to use in a Filter or Sort.
    This is used by AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode).
    Include filtering by lastUpdated, troubled and needsAttention from the associated curation details.
    
    Overrides:
    
    getFilterablePropertyMeta in class AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
    
    See Also:
    
    AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String), AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, Collection), FilteringDao.getSort(String, Sort.Direction, Sort.NullMode)
  - getRawDataVectors
```
public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
                                                             QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain raw vectors for a given experiment and QT.
    This is preferable to using ExpressionExperiment.getRawExpressionDataVectors() as it only loads vectors relevant to the given QT.
    
    Specified by:
    
    getRawDataVectors in interface ExpressionExperimentDao
  - getRawDataVectors
```
public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
                                                             List<BioAssay> assays,
                                                             QuantitationType qt)
```
    Description copied from interface: ExpressionExperimentDao
    
    Obtain a slice of the raw vectors for a given experiment and QT.
    
    Specified by:
    
    getRawDataVectors in interface ExpressionExperimentDao
  - addRawDataVectors
```
public int addRawDataVectors(ExpressionExperiment ee,
                             QuantitationType newQt,
                             Collection<RawExpressionDataVector> newVectors)
```
    Description copied from interface: ExpressionExperimentDao
    
    Add raw data vectors with the given quantitation type.
    
    Specified by:
    
    addRawDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the number of raw data vectors created
  - removeAllRawDataVectors
```
public int removeAllRawDataVectors(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Remove all raw data vectors.
    All affected QTs are removed.
    
    Specified by:
    
    removeAllRawDataVectors in interface ExpressionExperimentDao
  - removeRawDataVectors
```
public int removeRawDataVectors(ExpressionExperiment ee,
                                QuantitationType qt,
                                boolean keepDimension)
```
    Description copied from interface: ExpressionExperimentDao
    
    Remove raw data vectors for a given quantitation type.
    Unused BioAssayDimension are removed unless keepDimension is set to true.
    
    Specified by:
    
    removeRawDataVectors in interface ExpressionExperimentDao
    
    keepDimension - keep the BioAssayDimension if it is not used by any other vectors. Use this only if you intend to reuse the dimension for another set of vectors. Alternatively, ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) can be used.
    
    Returns:
    
    the number of removed raw vectors
  - replaceRawDataVectors
```
public int replaceRawDataVectors(ExpressionExperiment ee,
                                 QuantitationType qt,
                                 Collection<RawExpressionDataVector> vectors)
```
    Description copied from interface: ExpressionExperimentDao
    
    Replace raw data vectors for a given quantitation type.
    
    Specified by:
    
    replaceRawDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the number of replaced raw vectors
  - getProcessedDataVectors
```
public Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Retrieve the processed vector for an experiment.
    Unlike ExpressionExperiment.getProcessedExpressionDataVectors(), this is guaranteed to return only one set of vectors and will raise a NonUniqueResultException if there is more than one processed QTs.
    
    Specified by:
    
    getProcessedDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the processed vectors, or null if there are no processed vectors
    
    See Also:
    
    ExpressionExperimentDao.getProcessedQuantitationType(ExpressionExperiment)
  - getProcessedDataVectors
```
public Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee,
                                                                         List<BioAssay> assays)
```
    Description copied from interface: ExpressionExperimentDao
    
    Retrieve a slice of processed vectors for an experiment.
    
    Specified by:
    
    getProcessedDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the processed vectors, or null if there are no processed vectors
  - createProcessedDataVectors
```
public int createProcessedDataVectors(ExpressionExperiment ee,
                                      Collection<ProcessedExpressionDataVector> vectors)
```
    Description copied from interface: ExpressionExperimentDao
    
    Add processed data vectors
    The number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated.
    
    Specified by:
    
    createProcessedDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the number of created processed vectors
  - removeProcessedDataVectors
```
public int removeProcessedDataVectors(ExpressionExperiment ee)
```
    Description copied from interface: ExpressionExperimentDao
    
    Remove processed data vectors.
    Their corresponding QT is detached from the experiment and removed. The number of vectors (i.e. ExpressionExperiment.getNumberOfDataVectors() is set to zero. Unused dimensions are removed.
    
    Specified by:
    
    removeProcessedDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the number of removed processed vectors
  - replaceProcessedDataVectors
```
public int replaceProcessedDataVectors(ExpressionExperiment ee,
                                       Collection<ProcessedExpressionDataVector> vectors)
```
    Description copied from interface: ExpressionExperimentDao
    
    Replace processed data vectors.
    The QT is reused and the number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated. Unused dimensions are removed.
    
    Specified by:
    
    replaceProcessedDataVectors in interface ExpressionExperimentDao
    
    Returns:
    
    the number of vectors replaced

Class ExpressionExperimentDaoImpl

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

Field Summary

Fields inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

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

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

Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

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

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

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

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

Methods inherited from class java.lang.Object

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

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

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

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

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao

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

Constructor Detail

ExpressionExperimentDaoImpl

Method Detail

load

loadAllIdAndName

loadAllShortNameAndName

loadAllName

loadAllAccessionAndName

browse

browse

loadBioAssaySet

filterByTaxon

findByShortName

findByName

findOneByName

find

findByAccession

findByAccession

findOneByAccession

findByBibliographicReference

findByBioAssay

findByBioMaterial

findByBioMaterials

findByExpressedGene

findByDesign

findByFactor

findByFactorValue

findByFactorValue

findByFactorValues

findByGene

findByQuantitationType

findByTaxon

findByUpdatedLimit

findByUpdatedLimit

findUpdatedAfter

getAnnotationCounts

getAllAnnotations

getExperimentAnnotations

getExperimentSubSetAnnotations

getBioMaterialAnnotations

getBioMaterialAnnotations

getExperimentalDesignAnnotations

getFactorValueAnnotations

getFactorValueAnnotations

getCategoriesUsageFrequency

getAnnotationsUsageFrequency

getExperimentsLackingPublications

updateMeanVarianceRelation

countBioMaterials

getArrayDesignsUsed

getArrayDesignsUsed

getArrayDesignsUsed

getGenesUsedByPreferredVectors

getTechnologyTypeUsageFrequency

getTechnologyTypeUsageFrequency

getArrayDesignsUsageFrequency

getArrayDesignsUsageFrequency

getOriginalPlatformsUsageFrequency