Package ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentDao

All Superinterfaces:

BaseDao<ExpressionExperiment>, BaseVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>, CachedFilteringDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, CuratableDao<ExpressionExperiment>, FilteringDao<ExpressionExperiment>, FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

All Known Implementing Classes:

ExpressionExperimentDaoImpl

public interface ExpressionExperimentDao
extends CuratableDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>

Created by tesarst on 13/03/17.

Author:

tesarst

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	ExpressionExperimentDao.Identifiers

Field Summary

Fields

Modifier and Type	Field	Description
static final String	FREE_TEXT	Special indicator for free-text terms.
static final String	OBJECT_ALIAS
static final String	UNCATEGORIZED	Special indicator for an uncategorized term.

Method Summary

Modifier and Type	Method	Description
int	addRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors with the given quantitation type.
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.
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)
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> expressionExperimentIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris)	Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.
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<ExpressionExperiment> ees)
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperiment 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 expressionExperiment)
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.
CellLevelCharacteristics	getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
Category	getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)	Obtain the category of a cell-level characteristic.
Collection<CellLevelCharacteristics>	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
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.
Collection<CellTypeAssignment>	getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolIdentifier)
Collection<Protocol>	getCellTypeAssignmentProtocols()	Obtain all cell type assignment protocols currently used.
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment ee)
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
Collection<CellTypeAssignment>	getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, 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.
Collection<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 ee)	Obtain factor value-level annotations for a given subset.
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<QuantitationType,Collection<RawExpressionDataVector>>	getMissingValueVectors(ExpressionExperiment ee)	Obtain the missing value vectors for a given experiment.
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, boolean useCursorFetchIfSupported)	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.
CellTypeAssignment	getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)	Obtain the preferred assignment for the given quantitation type.
CellTypeAssignment	getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)	Obtain the preferred assignment for the given quantitation type without loading the indices.
QuantitationType	getPreferredQuantitationType(ExpressionExperiment ee)	Obtain the preferred quantitation type for the raw vectors, if available.
Collection<RawExpressionDataVector>	getPreferredRawDataVectors(ExpressionExperiment ee)	Obtain the preferred raw data vectors for a given experiment.
SingleCellDimension	getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
SingleCellDimension	getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
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 quantitationType)	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 includeProtocol, 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 includeProtocol, 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)
Map<ExpressionExperiment,Taxon>	getTaxa(Collection<ExpressionExperiment> ees)
Taxon	getTaxon(ExpressionExperiment 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.
boolean	hasProcessedExpressionData(ExpressionExperiment ee)	Test if the dataset has preferred expression data vectors.
ExpressionExperiment	load(Long id, CacheMode cacheMode)	Load an experiment by ID with a specific cache mode.
List<ExpressionExperimentDao.Identifiers>	loadAllIdentifiers()	Load all possible identifiers for all experiments.
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 loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)	Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
List<ExpressionExperiment>	loadWithRelationsAndCache(List<Long> ids)	Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).
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 useCursorFetchIfSupported, boolean createNewSession)	Obtain a stream over the vectors for a given QT.
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
void	thaw(ExpressionExperiment expressionExperiment)	Thaw everything.
void	thawLite(ExpressionExperiment expressionExperiment)	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 interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, 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.BrowsingDao

browse, browse

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

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

loadValueObjects, loadValueObjects

Field Details

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

• Constant Field Values

FREE_TEXT

static final String FREE_TEXT

Special indicator for free-text terms.

Free-text terms or categories have a null URI and a non-empty label.

UNCATEGORIZED

static final String UNCATEGORIZED

Special indicator for an uncategorized term.

Uncategorized terms (or the uncategorized category) has both null URI and label.

Method Details

load

ExpressionExperiment load(Long id,
 CacheMode cacheMode)

Load an experiment by ID with a specific cache mode.

The cache mode will be effective for the remainder of the Hibernate session.

loadAllIdentifiers

List<ExpressionExperimentDao.Identifiers> loadAllIdentifiers()

Load all possible identifiers for all experiments.

filterByTaxon

Collection<Long> filterByTaxon(Collection<Long> ids,
 Taxon taxon)

findByShortName

ExpressionExperiment findByShortName(String shortName)

findByName

Collection<ExpressionExperiment> findByName(String name)

findOneByName

@Nullable
ExpressionExperiment findOneByName(String name)

findByAccession

Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

findByAccession

Collection<ExpressionExperiment> findByAccession(String accession)

findOneByAccession

@Nullable
ExpressionExperiment findOneByAccession(String accession)

findByBibliographicReference

Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)

findByBioAssay

ExpressionExperiment findByBioAssay(BioAssay ba)

findByBioMaterial

Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)

findByBioMaterials

Map<ExpressionExperiment,Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> bms)

findByExpressedGene

Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
 Double rank)

findByDesign

ExpressionExperiment findByDesign(ExperimentalDesign ed)

findByFactor

ExpressionExperiment findByFactor(ExperimentalFactor ef)

findByFactorValue

ExpressionExperiment findByFactorValue(FactorValue fv)

findByFactorValue

ExpressionExperiment findByFactorValue(Long factorValueId)

findByFactorValues

Map<ExpressionExperiment,FactorValue> findByFactorValues(Collection<FactorValue> fvs)

findByGene

Collection<ExpressionExperiment> findByGene(Gene gene)

findByQuantitationType

ExpressionExperiment findByQuantitationType(QuantitationType quantitationType)

findByTaxon

Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

findByUpdatedLimit

List<ExpressionExperiment> findByUpdatedLimit(Collection<Long> ids,
 int limit)

findByUpdatedLimit

List<ExpressionExperiment> findByUpdatedLimit(int limit)

findUpdatedAfter

Collection<ExpressionExperiment> findUpdatedAfter(Date date)

Find experiments updated on or after a given date.

getAnnotationCounts

Map<Long,Long> getAnnotationCounts(Collection<Long> ids)

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment bas)

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(Collection<ExpressionExperiment> ees)

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee,
 QuantitationType qt,
 Class<? extends DataVector> dataVectorType)

getGenesUsedByPreferredVectors

Collection<Gene> getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)

Obtain genes used by the processed vectors of this dataset.

getTechnologyTypeUsageFrequency

Map<TechnologyType,Long> getTechnologyTypeUsageFrequency()

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.

getTechnologyTypeUsageFrequency

Map<TechnologyType,Long> getTechnologyTypeUsageFrequency(Collection<Long> eeIds)

Obtain the dataset usage frequency by technology type for the given dataset IDs.

Note: No ACL filtering is performed.

See Also:

• getTechnologyTypeUsageFrequency()

getArrayDesignsUsageFrequency

Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(int maxResults)

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.

getArrayDesignsUsageFrequency

Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(Collection<Long> eeIds,
 int maxResults)

Obtain dataset usage frequency by platform currently for the given dataset IDs.

Note: no ACL filtering is performed. Only administrator can see troubled platforms.

See Also:

• getArrayDesignsUsageFrequency(int)

getOriginalPlatformsUsageFrequency

Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(int maxResults)

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.

getOriginalPlatformsUsageFrequency

Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(Collection<Long> eeIds,
 int maxResults)

Obtain dataset usage frequency by platform currently for the given dataset IDs.

Note: no ACL filtering is performed. Only administrators can see troubled platforms.

See Also:

• getOriginalPlatformsUsageFrequency(int)

getAuditEvents

Map<Long,Collection<AuditEvent>> getAuditEvents(Collection<Long> ids)

getBioAssayDimensions

Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)

getBioAssayDimensionsFromSubSets

Collection<BioAssayDimension> getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)

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.

getBioAssayDimension

@Nullable
BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
 QuantitationType qt,
 Class<? extends BulkExpressionDataVector> dataVectorType)

Retrieve a dimension for a given experiment and quantitation type.

Parameters:

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 getBioAssayDimension(ExpressionExperiment, QuantitationType).

Throws:

NonUniqueResultException - if there is more than one dimension for the given set of vectors

getBioAssayDimension

@Nullable
BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
 QuantitationType qt)

Retrieve a dimension for a given experiment and quantitation type.

Throws:

NonUniqueResultException - if there is more than one dimension for the given set of vectors

getBioAssayDimensionById

@Nullable
BioAssayDimension getBioAssayDimensionById(ExpressionExperiment ee,
 Long dimensionId,
 Class<? extends BulkExpressionDataVector> dataVectorType)

Obtain a bioassay dimension by ID.

getBioMaterialCount

long getBioMaterialCount(ExpressionExperiment expressionExperiment)

getRawDataVectorCount

long getRawDataVectorCount(ExpressionExperiment ee)

getExperimentsWithOutliers

Collection<ExpressionExperiment> getExperimentsWithOutliers()

getLastArrayDesignUpdate

Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

getLastArrayDesignUpdate

@Nullable
Date getLastArrayDesignUpdate(ExpressionExperiment ee)

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

Obtain the count of distinct experiments per taxon.

Experiments are filtered by ACLs and troubled experiments are only visible to administrators.

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount(Collection<Long> ids)

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.

getPopulatedFactorCounts

Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)

getPopulatedFactorCountsExcludeBatch

Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)

getQuantitationTypeCount

Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)

getPreferredSingleCellQuantitationType

@Nullable
QuantitationType getPreferredSingleCellQuantitationType(ExpressionExperiment ee)

Obtain the preferred quantitation type for single cell data, if available.

getPreferredQuantitationType

@Nullable
QuantitationType getPreferredQuantitationType(ExpressionExperiment ee)

Obtain the preferred quantitation type for the raw vectors, if available.

getProcessedQuantitationType

@Nullable
QuantitationType getProcessedQuantitationType(ExpressionExperiment ee)

Obtain the quantitation type for the processed vectors, if available.

Throws:

NonUniqueResultException - if there is more than one set of processed vectors

hasProcessedExpressionData

boolean hasProcessedExpressionData(ExpressionExperiment ee)

Test if the dataset has preferred expression data vectors.

getSampleRemovalEvents

Map<ExpressionExperiment,Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

getSubSets

Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment)

getSubSets

Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment,
 BioAssayDimension bad)

getSubSetsByDimension

Map<BioAssayDimension,Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)

getSubSetById

@Nullable
ExpressionExperimentSubSet getSubSetById(ExpressionExperiment ee,
 Long subSetId)

getTaxa

Map<ExpressionExperiment,Taxon> getTaxa(Collection<ExpressionExperiment> ees)

getTaxon

@Nullable
Taxon getTaxon(ExpressionExperiment ee)

Determine the taxon for a given experiment or subset.

Returns:

a unique taxon for the dataset, or null if no taxon could be determined

loadWithRelationsAndCache

List<ExpressionExperiment> loadWithRelationsAndCache(List<Long> ids)

Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).

loadDetailsValueObjects

Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjects(@Nullable
 Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

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

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

Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(@Nullable
 Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.

loadDetailsValueObjectsByIds

List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)

Like loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.

loadDetailsValueObjectsByIdsWithCache

List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)

Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.

loadBlacklistedValueObjects

Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadLackingFactors

Collection<ExpressionExperiment> loadLackingFactors()

loadLackingTags

Collection<ExpressionExperiment> loadLackingTags()

thaw

void thaw(ExpressionExperiment expressionExperiment)

Thaw everything.

Includes thawLite(ExpressionExperiment) and raw/processed vectors.

Does not include single-cell vectors.

thawLiter

void thawLiter(ExpressionExperiment expressionExperiment)

Thaw experiment metadata.

thawLite

void thawLite(ExpressionExperiment expressionExperiment)

Thaw experiment metadata and bioassays.

Include thawLiter(ExpressionExperiment) and bioassays.

getAllAnnotations

Map<Class<? extends Identifiable>,List<Characteristic>> getAllAnnotations(ExpressionExperiment expressionExperiment,
 boolean useEe2c)

Obtain all annotations, grouped by applicable level.

Parameters:

useEe2c - use the EXPRESSION_EXPERIMENT2CHARACTERISTIC table to retrieve annotations

getExperimentAnnotations

Collection<Characteristic> getExperimentAnnotations(ExpressionExperiment expressionExperiment,
 boolean useEe2c)

Obtain experiment-level annotations.

Parameters:

useEe2c - use the EXPRESSION_EXPERIMENTE2CHARACTERISTIC table, TableMaintenanceUtil

getExperimentSubSetAnnotations

Collection<Characteristic> getExperimentSubSetAnnotations(ExpressionExperiment ee)

Obtain the subset annotations.

getBioMaterialAnnotations

List<Characteristic> getBioMaterialAnnotations(ExpressionExperiment expressionExperiment,
 boolean useEe2c)

Obtain sample-level annotations.

This uses the EE2C table under the hood.

getBioMaterialAnnotations

List<Characteristic> getBioMaterialAnnotations(ExpressionExperimentSubSet expressionExperiment)

getExperimentalDesignAnnotations

List<Characteristic> getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment,
 boolean useEe2c)

Obtain experimental design-level annotations.

This is equivalent to the subject components of getFactorValueAnnotations(ExpressionExperiment) for now, but other annotations from the experimental design might be included in the future.

getFactorValueAnnotations

List<Statement> getFactorValueAnnotations(ExpressionExperiment ee)

Obtain factor value-level annotations.

getFactorValueAnnotations

List<Statement> getFactorValueAnnotations(ExpressionExperimentSubSet ee)

Obtain factor value-level annotations for a given subset.

getCategoriesUsageFrequency

Map<Characteristic,Long> getCategoriesUsageFrequency(@Nullable
 Collection<Long> eeIds,
 @Nullable
 Collection<String> excludedCategoryUris,
 @Nullable
 Collection<String> excludedTermUris,
 @Nullable
 Collection<String> retainedTermUris,
 int maxResults)

getAnnotationsUsageFrequency

Map<Characteristic,Long> getAnnotationsUsageFrequency(@Nullable
 Collection<Long> expressionExperimentIds,
 @Nullable
 Class<? extends Identifiable> level,
 int maxResults,
 int minFrequency,
 @Nullable
 String category,
 @Nullable
 Collection<String> excludedCategoryUris,
 @Nullable
 Collection<String> excludedTermUris,
 @Nullable
 Collection<String> retainedTermUris)

Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.

This is meant as a counterpart to CharacteristicService.findExperimentsByUris(Collection, Taxon, int, boolean, boolean) to answer the reverse question: which annotations can be used to filter a given set of datasets?

Parameters:

expressionExperimentIds - 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

Collection<ExpressionExperiment> getExperimentsLackingPublications()

updateMeanVarianceRelation

MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
 MeanVarianceRelation mvr)

countBioMaterials

long countBioMaterials(@Nullable
 Filters filters)

Count the number of biomaterials of datasets satisfying the given filters.

The result is stored in the standard query cache.

getRawDataVectors

Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

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.

getRawDataVectors

Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 List<BioAssay> assays,
 QuantitationType qt)

Obtain a slice of the raw vectors for a given experiment and QT.

getPreferredRawDataVectors

Collection<RawExpressionDataVector> getPreferredRawDataVectors(ExpressionExperiment ee)

Obtain the preferred raw data vectors for a given experiment.

getMissingValueVectors

Map<QuantitationType,Collection<RawExpressionDataVector>> getMissingValueVectors(ExpressionExperiment ee)

Obtain the missing value vectors for a given experiment.

addRawDataVectors

int addRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 Collection<RawExpressionDataVector> newVectors)

Add raw data vectors with the given quantitation type.

Returns:

the number of raw data vectors created

removeAllRawDataVectors

int removeAllRawDataVectors(ExpressionExperiment ee)

Remove all raw data vectors.

All affected QTs are removed.

removeRawDataVectors

int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 boolean keepDimension)

Remove raw data vectors for a given quantitation type.

Unused BioAssayDimension are removed unless keepDimension is set to true.

Parameters:

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, replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) can be used.

Returns:

the number of removed raw vectors

replaceRawDataVectors

int replaceRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 Collection<RawExpressionDataVector> vectors)

Replace raw data vectors for a given quantitation type.

Returns:

the number of replaced raw vectors

getProcessedDataVectors

@Nullable
Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee)

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.

Returns:

the processed vectors, or null if there are no processed vectors

See Also:

• getProcessedQuantitationType(ExpressionExperiment)

getProcessedDataVectors

@Nullable
Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee,
 List<BioAssay> assays)

Retrieve a slice of processed vectors for an experiment.

Returns:

the processed vectors, or null if there are no processed vectors

createProcessedDataVectors

int createProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Add processed data vectors

The number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated.

Returns:

the number of created processed vectors

removeProcessedDataVectors

int removeProcessedDataVectors(ExpressionExperiment ee)

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.

Returns:

the number of removed processed vectors

replaceProcessedDataVectors

int replaceProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Replace processed data vectors.

The QT is reused and the number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated. Unused dimensions are removed.

Returns:

the number of vectors replaced

getSingleCellDimensions

List<SingleCellDimension> getSingleCellDimensions(ExpressionExperiment ee)

Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.

getSingleCellDimensionsWithoutCellIds

List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)

Obtain all the single cell dimensions used by the single-cell vectors of a given experiment.

Cell IDs are not loaded.

getSingleCellDimensionsWithoutCellIds

List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee,
 boolean includeBioAssays,
 boolean includeCtas,
 boolean includeClcs,
 boolean includeProtocol,
 boolean includeCharacteristics,
 boolean includeIndices)

getSingleCellDimension

@Nullable
SingleCellDimension getSingleCellDimension(ExpressionExperiment ee,
 QuantitationType quantitationType)

Obtain the single-cell dimension used by a specific QT.

getSingleCellDimensionWithoutCellIds

@Nullable
SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt)

Load a single-cell dimension used by a specific QT without its cell IDs.

getSingleCellDimensionWithoutCellIds

@Nullable
SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt,
 boolean includeBioAssays,
 boolean includeCtas,
 boolean includeClcs,
 boolean includeProtocol,
 boolean includeCharacteristics,
 boolean includeIndices)

getPreferredSingleCellDimension

@Nullable
SingleCellDimension getPreferredSingleCellDimension(ExpressionExperiment ee)

Obtain the preferred single cell dimension, that is the dimension associated to the preferred set of single-cell vectors.

getPreferredSingleCellDimensionWithoutCellIds

@Nullable
SingleCellDimension getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)

Load a single-cell dimension without its cell IDs.

getPreferredSingleCellDimensionsWithoutCellIds

@Nullable
SingleCellDimension getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee,
 boolean includeBioAssays,
 boolean includeCtas,
 boolean includeClcs,
 boolean includeProtocol,
 boolean includeCharacteristics,
 boolean includeIndices)

createSingleCellDimension

void createSingleCellDimension(ExpressionExperiment ee,
 SingleCellDimension singleCellDimension)

Create a single-cell dimension for a given experiment.

Throws:

IllegalArgumentException - if the single-cell dimension is invalid

updateSingleCellDimension

void updateSingleCellDimension(ExpressionExperiment ee,
 SingleCellDimension singleCellDimension)

Update a single-cell dimensino for a given experiment.

Throws:

IllegalArgumentException - if the single-cell dimension is invalid

deleteSingleCellDimension

void deleteSingleCellDimension(ExpressionExperiment ee,
 SingleCellDimension singleCellDimension)

Delete the given single cell dimension.

streamCellIds

@Nullable
Stream<String> streamCellIds(SingleCellDimension dimension,
 boolean createNewSession)

Stream the cell IDs of a dimension.

Parameters:

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

@Nullable
Stream<Characteristic> streamCellTypes(CellTypeAssignment cta,
 boolean createNewSession)

getCellLevelCharacteristicsCategory

@Nullable
Category getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)

Obtain the category of a cell-level characteristic.

This handles the case where the characteristics were not loaded (i.e. using getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean)).

streamCellLevelCharacteristics

@Nullable
Stream<Characteristic> streamCellLevelCharacteristics(CellLevelCharacteristics clc,
 boolean createNewSession)

getCellTypeAt

@Nullable
Characteristic getCellTypeAt(CellTypeAssignment cta,
 int cellIndex)

Obtain the cell type at a given cell index.

getCellTypeAt

Characteristic[] getCellTypeAt(CellTypeAssignment cta,
 int startIndex,
 int endIndexExclusive)

getCellLevelCharacteristicAt

@Nullable
Characteristic getCellLevelCharacteristicAt(CellLevelCharacteristics clc,
 int cellIndex)

Obtain the characteristic at a given cell index.

getCellLevelCharacteristicAt

Characteristic[] getCellLevelCharacteristicAt(CellLevelCharacteristics clc,
 int startIndex,
 int endIndexExclusive)

getCellTypeAssignments

List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment ee)

getCellTypeAssignments

List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

getCellTypeAssignmentsWithoutIndices

Collection<CellTypeAssignment> getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

getPreferredCellTypeAssignment

@Nullable
CellTypeAssignment getPreferredCellTypeAssignment(ExpressionExperiment ee)
                                           throws NonUniqueResultException

Obtain the preferred assignment of the preferred single-cell vectors.

Throws:

NonUniqueResultException - if there are multiple preferred cell-type labellings

getPreferredCellTypeAssignment

@Nullable
CellTypeAssignment getPreferredCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt)
                                           throws NonUniqueResultException

Obtain the preferred assignment for the given quantitation type.

Throws:

NonUniqueResultException - if there are multiple preferred cell-type labellings

getPreferredCellTypeAssignmentWithoutIndices

@Nullable
CellTypeAssignment getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)
                                                         throws NonUniqueResultException

Obtain the preferred assignment for the given quantitation type without loading the indices.

Throws:

NonUniqueResultException - if there are multiple preferred cell-type labellings

getCellTypeAssignment

@Nullable
CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long ctaId)

Obtain a cell type assignment by ID.

getCellTypeAssignmentWithoutIndices

@Nullable
CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long ctaId)

Obtain a cell type assignment by ID without loading the indices.

getCellTypeAssignment

@Nullable
CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String ctaName)

Obtain a cell type assignment by name.

getCellTypeAssignmentProtocols

Collection<Protocol> getCellTypeAssignmentProtocols()

Obtain all cell type assignment protocols currently used.

getCellTypeAssignmentByProtocol

@Nullable
Collection<CellTypeAssignment> getCellTypeAssignmentByProtocol(ExpressionExperiment ee,
 QuantitationType qt,
 String protocolIdentifier)

getCellTypeAssignmentWithoutIndices

@Nullable
CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String ctaName)

Obtain a cell type assignment by name without loading the indices.

getCellLevelCharacteristics

List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee)

Obtain all cell-level characteristics from all single cell dimensions.

getCellLevelCharacteristics

List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee,
 Category category)

Obtain all cell-level characteristics from all single cell dimensions matching the given category.

getCellLevelCharacteristics

@Nullable
CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 Long clcId)

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.

getCellLevelCharacteristics

@Nullable
CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 String clcName)

getCellLevelCharacteristics

List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

getCellLevelCharacteristics

List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Category category)

getCellLevelCharacteristicsWithoutIndices

@Nullable
CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 Long clcId)

getCellLevelCharacteristicsWithoutIndices

@Nullable
CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 String clcName)

getCellLevelCharacteristicsWithoutIndices

Collection<CellLevelCharacteristics> getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

getCellTypes

List<Characteristic> getCellTypes(ExpressionExperiment ee)

getSingleCellQuantitationTypes

List<QuantitationType> getSingleCellQuantitationTypes(ExpressionExperiment ee)

Obtain a list of single-cell QTs.

getSingleCellDataVectors

List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment expressionExperiment,
 QuantitationType quantitationType)

Obtain a set of single-cell data vectors for the given quantitation type.

getSingleCellDataVectors

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.

streamSingleCellDataVectors

Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession)

Obtain a stream over the vectors for a given QT.

Parameters:

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, Class, int, boolean, boolean)

streamSingleCellDataVectors

Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession,
 boolean includeCellIds,
 boolean includeData,
 boolean includeDataIndices)

getSingleCellDataVectorWithoutCellIds

SingleCellExpressionDataVector getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee,
 QuantitationType quantitationType,
 CompositeSequence designElement)

getNumberOfSingleCellDataVectors

long getNumberOfSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Obtain the number of single-cell vectors for a given QT.

getNumberOfNonZeroes

long getNumberOfNonZeroes(ExpressionExperiment ee,
 QuantitationType qt)

Obtain the number of non-zeroes.

getNumberOfNonZeroesBySample

Map<BioAssay,Long> getNumberOfNonZeroesBySample(ExpressionExperiment ee,
 QuantitationType qt,
 int fetchSize,
 boolean useCursorFetchIfSupported)

Obtain the number of non-zeroes by sample.

This is quite costly because the indices of each vector has to be examined.

removeSingleCellDataVectors

int removeSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 boolean deleteQt)

Remove the given single-cell data vectors.

Parameters:

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

int removeAllSingleCellDataVectors(ExpressionExperiment ee)

Remove all single-cell data vectors and their quantitation types.

getNumberOfDesignElementsPerSample

Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)