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

Class SingleCellExpressionExperimentServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl

All Implemented Interfaces:

SingleCellExpressionExperimentService

@Service
public class SingleCellExpressionExperimentServiceImpl
extends Object
implements SingleCellExpressionExperimentService

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService

SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionExperimentServiceImpl()

Method Summary

Modifier and Type	Method	Description
CellLevelCharacteristics	addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellTypeAssignment	addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cta)
int	addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Add single-cell data vectors.
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)	Obtain a CLC by name.
Category	getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Collection<CellLevelCharacteristics>	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Optional<CellLevelCharacteristics>	getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)	Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.
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 protocolName)	Obtain a cell type assignment by a protocol identifier.
Collection<Protocol>	getCellTypeAssignmentProtocols()	Obtain a collection of protocols used to assign cell types to single-cell vectors.
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment ee)	Obtain all the cell type labellings from all single-cell vectors.
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
Collection<CellTypeAssignment>	getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellTypeAssignment	getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellTypeAssignment	getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String ctaName)
Characteristic	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int cellIndex)
Characteristic[]	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int startIndex, int endIndexExclusive)
Characteristic	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int cellIndex)
Characteristic[]	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int startIndex, int endIndexExclusive)
Optional<ExperimentalFactor>	getCellTypeFactor(ExpressionExperiment ee)	Obtain the cell type factor.
List<Characteristic>	getCellTypes(ExpressionExperiment ee)	Obtain the cell types of a given single-cell dataset.
long	getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
Map<BioAssay,Long>	getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
long	getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of single-cell vectors for a given quantitation type.
Optional<CellTypeAssignment>	getPreferredCellTypeAssignment(ExpressionExperiment ee)	Obtain the preferred cell type labelling from the preferred single-cell vectors.
Optional<CellTypeAssignment>	getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Optional<Collection<SingleCellExpressionDataVector>>	getPreferredSingleCellDataVectors(ExpressionExperiment ee)	Obtain preferred single-cell vectors.
Optional<SingleCellDimension>	getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Obtain the preferred single-cell dimension without its cell IDs.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
Optional<QuantitationType>	getPreferredSingleCellQuantitationType(ExpressionExperiment ee)	Obtain the preferred single-cell quantitation type.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)	Obtain single-cell vectors for a particular sample.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
List<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain single-cell vectors for a given quantitation type.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
SingleCellExpressionDataVector	getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)	Obtain a single single-cell vector without initializing cell IDs.
SingleCellDimension	getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain a single-cell dimension used for a given dataset and QT.
List<SingleCellDimension>	getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by a given dataset.
List<SingleCellDimension>	getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellDimension	getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)	Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.
SingleCellDimension	getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
SingleCellExpressionDataMatrix<?>	getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
Collection<QuantitationType>	getSingleCellQuantitationTypes(ExpressionExperiment ee)
ExpressionExperiment	loadWithSingleCellVectors(Long id)	Load an experiment with its single-cell data vectors initialized.
ExperimentalFactor	recreateCellTypeFactor(ExpressionExperiment ee)	Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.
CellTypeAssignment	relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol protocol, String description)	Relabel the cell types of an existing set of single-cell vectors.
long	removeAllCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
long	removeAllCellTypeAssignments(ExpressionExperiment ee, QuantitationType qt)
void	removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)	Remove existing cell-level characteristics by QT.
void	removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	removeCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment by QT.
void	removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment.
void	removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
int	removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Remove single-cell data vectors for the given quantitation type.
int	replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Replace existing single-cell data vectors for the given quantitation type.
Optional<Stream<String>>	streamCellIds(ExpressionExperiment ee, boolean createNewSession)
Stream<String>	streamCellIds(ExpressionExperiment ee, QuantitationType qt, boolean createNewSession)
Stream<Characteristic>	streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	streamCellTypes(ExpressionExperiment ee, CellTypeAssignment cta, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)	Obtain a stream over single-cell vectors for a given quantitation type.
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
void	updateSparsityMetrics(ExpressionExperiment ee)	Update the sparsity metrics.

Methods inherited from class java.lang.Object

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

Constructor Details

SingleCellExpressionExperimentServiceImpl

public SingleCellExpressionExperimentServiceImpl()

Method Details

loadWithSingleCellVectors

@Transactional(readOnly=true)
public ExpressionExperiment loadWithSingleCellVectors(Long id)

Description copied from interface: SingleCellExpressionExperimentService

Load an experiment with its single-cell data vectors initialized.

The rest of the experiment is also initialized as per ExpressionExperimentDao.thawLite(ExpressionExperiment).

Specified by:

loadWithSingleCellVectors in interface SingleCellExpressionExperimentService

getSingleCellDataVectors

@Transactional(readOnly=true)
public List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType)

Description copied from interface: SingleCellExpressionExperimentService

Obtain single-cell vectors for a given quantitation type.

Specified by:

getSingleCellDataVectors in interface SingleCellExpressionExperimentService

getSingleCellDataVectors

@Transactional(readOnly=true)
public Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Specified by:

getSingleCellDataVectors in interface SingleCellExpressionExperimentService

getSingleCellDataVectors

@Transactional(readOnly=true)
public Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType)

Description copied from interface: SingleCellExpressionExperimentService

Obtain single-cell vectors for a particular sample.

Specified by:

getSingleCellDataVectors in interface SingleCellExpressionExperimentService

getSingleCellDataVectors

@Transactional(readOnly=true)
public Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Specified by:

getSingleCellDataVectors in interface SingleCellExpressionExperimentService

streamSingleCellDataVectors

@Transactional(readOnly=true)
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a stream over single-cell vectors for a given quantitation type.

Specified by:

streamSingleCellDataVectors in interface SingleCellExpressionExperimentService

streamSingleCellDataVectors

@Transactional(readOnly=true)
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Specified by:

streamSingleCellDataVectors in interface SingleCellExpressionExperimentService

streamSingleCellDataVectors

@Transactional(readOnly=true)
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Specified by:

streamSingleCellDataVectors in interface SingleCellExpressionExperimentService

streamSingleCellDataVectors

@Transactional(readOnly=true)
public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession)

Specified by:

streamSingleCellDataVectors in interface SingleCellExpressionExperimentService

getSingleCellDataVectorWithoutCellIds

@Transactional(readOnly=true)
public SingleCellExpressionDataVector getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee,
 QuantitationType quantitationType,
 CompositeSequence designElement)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a single single-cell vector without initializing cell IDs.

Specified by:

getSingleCellDataVectorWithoutCellIds in interface SingleCellExpressionExperimentService

See Also:

• SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType)

getNumberOfSingleCellDataVectors

@Transactional(readOnly=true)
public long getNumberOfSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Description copied from interface: SingleCellExpressionExperimentService

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

Specified by:

getNumberOfSingleCellDataVectors in interface SingleCellExpressionExperimentService

getNumberOfNonZeroes

@Transactional(readOnly=true)
public long getNumberOfNonZeroes(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getNumberOfNonZeroes in interface SingleCellExpressionExperimentService

getNumberOfNonZeroesBySample

@Transactional(readOnly=true)
public Map<BioAssay,Long> getNumberOfNonZeroesBySample(ExpressionExperiment ee,
 QuantitationType qt,
 int fetchSize,
 boolean useCursorFetchIfSupported)

Specified by:

getNumberOfNonZeroesBySample in interface SingleCellExpressionExperimentService

getPreferredSingleCellDataVectors

@Transactional(readOnly=true)
public Optional<Collection<SingleCellExpressionDataVector>> getPreferredSingleCellDataVectors(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain preferred single-cell vectors.

Specified by:

getPreferredSingleCellDataVectors in interface SingleCellExpressionExperimentService

getSingleCellQuantitationTypes

@Transactional(readOnly=true)
public Collection<QuantitationType> getSingleCellQuantitationTypes(ExpressionExperiment ee)

Specified by:

getSingleCellQuantitationTypes in interface SingleCellExpressionExperimentService

getPreferredSingleCellQuantitationType

@Transactional(readOnly=true)
public Optional<QuantitationType> getPreferredSingleCellQuantitationType(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the preferred single-cell quantitation type.

Specified by:

getPreferredSingleCellQuantitationType in interface SingleCellExpressionExperimentService

getSingleCellExpressionDataMatrix

@Transactional(readOnly=true)
public SingleCellExpressionDataMatrix<?> getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 List<BioAssay> samples,
 QuantitationType quantitationType)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a single-cell expression data matrix for the given quantitation type.

Specified by:

getSingleCellExpressionDataMatrix in interface SingleCellExpressionExperimentService

getSingleCellExpressionDataMatrix

@Transactional(readOnly=true)
public SingleCellExpressionDataMatrix<?> getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 QuantitationType quantitationType)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a single-cell expression data matrix for the given quantitation type.

Specified by:

getSingleCellExpressionDataMatrix in interface SingleCellExpressionExperimentService

addSingleCellDataVectors

@Transactional
public int addSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<SingleCellExpressionDataVector> vectors,
 @Nullable
 String details)

Description copied from interface: SingleCellExpressionExperimentService

Add single-cell data vectors.

Specified by:

addSingleCellDataVectors in interface SingleCellExpressionExperimentService

Returns:

the number of vectors that were added

replaceSingleCellDataVectors

@Transactional
public int replaceSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<SingleCellExpressionDataVector> vectors,
 @Nullable
 String details)

Description copied from interface: SingleCellExpressionExperimentService

Replace existing single-cell data vectors for the given quantitation type.

Specified by:

replaceSingleCellDataVectors in interface SingleCellExpressionExperimentService

Parameters:

details - additional details to include in the audit event

Returns:

the number of vectors that were replaced

updateSparsityMetrics

@Transactional
public void updateSparsityMetrics(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Update the sparsity metrics.

If no preferred single-cell vectors are present, the sparsity metrics will be cleared.

Specified by:

updateSparsityMetrics in interface SingleCellExpressionExperimentService

removeSingleCellDataVectors

@Transactional
public int removeSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType)

Description copied from interface: SingleCellExpressionExperimentService

Remove single-cell data vectors for the given quantitation type.

Specified by:

removeSingleCellDataVectors in interface SingleCellExpressionExperimentService

Returns:

the number of vectors that were removed

getSingleCellDimensionWithCellLevelCharacteristics

@Transactional(readOnly=true)
public SingleCellDimension getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getSingleCellDimensionWithCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getSingleCellDimensionWithAssaysAndCellLevelCharacteristics

@Transactional(readOnly=true)
public SingleCellDimension getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

Description copied from interface: SingleCellExpressionExperimentService

Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.

Specified by:

getSingleCellDimensionWithAssaysAndCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getSingleCellDimensionWithoutCellIds

@Transactional(readOnly=true)
public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)

Specified by:

getSingleCellDimensionWithoutCellIds in interface SingleCellExpressionExperimentService

getSingleCellDimensions

@Transactional(readOnly=true)
public List<SingleCellDimension> getSingleCellDimensions(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain all the single-cell dimensions used by a given dataset.

Specified by:

getSingleCellDimensions in interface SingleCellExpressionExperimentService

getSingleCellDimensionsWithoutCellIds

@Transactional(readOnly=true)
public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)

Specified by:

getSingleCellDimensionsWithoutCellIds in interface SingleCellExpressionExperimentService

getSingleCellDimensionsWithoutCellIds

@Transactional(readOnly=true)
public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)

Specified by:

getSingleCellDimensionsWithoutCellIds in interface SingleCellExpressionExperimentService

getSingleCellDimension

@Transactional(readOnly=true)
public SingleCellDimension getSingleCellDimension(ExpressionExperiment ee,
 QuantitationType qt)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a single-cell dimension used for a given dataset and QT.

Specified by:

getSingleCellDimension in interface SingleCellExpressionExperimentService

getSingleCellDimensionWithoutCellIds

@Transactional(readOnly=true)
public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getSingleCellDimensionWithoutCellIds in interface SingleCellExpressionExperimentService

getPreferredSingleCellDimension

@Transactional(readOnly=true)
public Optional<SingleCellDimension> getPreferredSingleCellDimension(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the preferred single-cell dimension.

Cell type assignments and other cell-level characteristics are eagerly initialized.

Specified by:

getPreferredSingleCellDimension in interface SingleCellExpressionExperimentService

getPreferredSingleCellDimensionWithoutCellIds

@Transactional(readOnly=true)
public Optional<SingleCellDimension> getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the preferred single-cell dimension without its cell IDs.

The returned object is not persistent since it's a projection.

Specified by:

getPreferredSingleCellDimensionWithoutCellIds in interface SingleCellExpressionExperimentService

getPreferredSingleCellDimensionWithoutCellIds

@Transactional(readOnly=true)
public Optional<SingleCellDimension> getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)

Specified by:

getPreferredSingleCellDimensionWithoutCellIds in interface SingleCellExpressionExperimentService

getPreferredSingleCellDimensionWithCellLevelCharacteristics

@Transactional(readOnly=true)
public Optional<SingleCellDimension> getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the preferred single-cell dimension.

Cell type assignments and other cell-level characteristics are eagerly initialized.

Specified by:

getPreferredSingleCellDimensionWithCellLevelCharacteristics in interface SingleCellExpressionExperimentService

streamCellIds

@Transactional(readOnly=true)
public Optional<Stream<String>> streamCellIds(ExpressionExperiment ee,
 boolean createNewSession)

Specified by:

streamCellIds in interface SingleCellExpressionExperimentService

streamCellIds

@Transactional(readOnly=true)
public Stream<String> streamCellIds(ExpressionExperiment ee,
 QuantitationType qt,
 boolean createNewSession)

Specified by:

streamCellIds in interface SingleCellExpressionExperimentService

streamCellTypes

@Transactional(readOnly=true)
public Stream<Characteristic> streamCellTypes(ExpressionExperiment ee,
 CellTypeAssignment cta,
 boolean createNewSession)

Specified by:

streamCellTypes in interface SingleCellExpressionExperimentService

getCellTypeAt

@Transactional(readOnly=true)
public Characteristic getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId,
 int cellIndex)

Specified by:

getCellTypeAt in interface SingleCellExpressionExperimentService

getCellTypeAt

@Transactional(readOnly=true)
public Characteristic[] getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId,
 int startIndex,
 int endIndexExclusive)

Specified by:

getCellTypeAt in interface SingleCellExpressionExperimentService

getCellTypeAt

@Transactional(readOnly=true)
public Characteristic getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName,
 int cellIndex)

Specified by:

getCellTypeAt in interface SingleCellExpressionExperimentService

getCellTypeAt

@Transactional(readOnly=true)
public Characteristic[] getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName,
 int startIndex,
 int endIndexExclusive)

Specified by:

getCellTypeAt in interface SingleCellExpressionExperimentService

getCellLevelCharacteristicsCategory

@Transactional(readOnly=true)
public Category getCellLevelCharacteristicsCategory(ExpressionExperiment ee,
 CellLevelCharacteristics clc)

Specified by:

getCellLevelCharacteristicsCategory in interface SingleCellExpressionExperimentService

streamCellLevelCharacteristics

@Transactional(readOnly=true)
public Stream<Characteristic> streamCellLevelCharacteristics(ExpressionExperiment ee,
 CellLevelCharacteristics clc,
 boolean createNewSession)

Specified by:

streamCellLevelCharacteristics in interface SingleCellExpressionExperimentService

relabelCellTypes

@Transactional
public CellTypeAssignment relabelCellTypes(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellDimension dimension,
 List<String> newCellTypeLabels,
 @Nullable
 Protocol protocol,
 @Nullable
 String description)

Description copied from interface: SingleCellExpressionExperimentService

Relabel the cell types of an existing set of single-cell vectors.

Specified by:

relabelCellTypes in interface SingleCellExpressionExperimentService

Parameters:

newCellTypeLabels - the new cell types labels, must match the number of cells

protocol - the protocol used to generate the new labelling, or null if unknown

Returns:

a new, preferred cell type labelling

addCellTypeAssignment

@Transactional
public CellTypeAssignment addCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellDimension dimension,
 CellTypeAssignment cta)

Specified by:

addCellTypeAssignment in interface SingleCellExpressionExperimentService

removeCellTypeAssignment

@Transactional
public void removeCellTypeAssignment(ExpressionExperiment ee,
 SingleCellDimension dimension,
 CellTypeAssignment cellTypeAssignment)

Description copied from interface: SingleCellExpressionExperimentService

Remove the given cell type assignment.

If the cell type labelling is preferred and applies to the preferred vectors as per SingleCellExpressionExperimentService.getPreferredCellTypeAssignment(ExpressionExperiment), the cell type factor will be removed.

Specified by:

removeCellTypeAssignment in interface SingleCellExpressionExperimentService

removeCellTypeAssignment

@Transactional
public void removeCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt,
 CellTypeAssignment cellTypeAssignment)

Description copied from interface: SingleCellExpressionExperimentService

Remove the given cell type assignment by QT.

Specified by:

removeCellTypeAssignment in interface SingleCellExpressionExperimentService

See Also:

• SingleCellExpressionExperimentService.removeCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment)

removeCellTypeAssignmentByName

@Transactional
public void removeCellTypeAssignmentByName(ExpressionExperiment ee,
 SingleCellDimension dimension,
 String name)

Specified by:

removeCellTypeAssignmentByName in interface SingleCellExpressionExperimentService

removeAllCellTypeAssignments

@Transactional
public long removeAllCellTypeAssignments(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

removeAllCellTypeAssignments in interface SingleCellExpressionExperimentService

getCellTypeAssignments

@Transactional(readOnly=true)
public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain all the cell type labellings from all single-cell vectors.

Specified by:

getCellTypeAssignments in interface SingleCellExpressionExperimentService

getCellTypeAssignments

@Transactional(readOnly=true)
public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

Specified by:

getCellTypeAssignments in interface SingleCellExpressionExperimentService

getCellTypeAssignment

@Transactional(readOnly=true)
public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long ctaId)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a cell type assignment by ID.

Specified by:

getCellTypeAssignment in interface SingleCellExpressionExperimentService

Returns:

that cell type assignmente, or null if none is found

getCellTypeAssignment

@Transactional(readOnly=true)
public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String ctaName)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a cell type assignment by name.

Specified by:

getCellTypeAssignment in interface SingleCellExpressionExperimentService

Returns:

that cell type assignmente, or null if none is found

getCellTypeAssignmentWithoutIndices

@Transactional(readOnly=true)
public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId)

Specified by:

getCellTypeAssignmentWithoutIndices in interface SingleCellExpressionExperimentService

getCellTypeAssignmentWithoutIndices

@Transactional(readOnly=true)
public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName)

Specified by:

getCellTypeAssignmentWithoutIndices in interface SingleCellExpressionExperimentService

getCellTypeAssignmentsWithoutIndices

@Transactional(readOnly=true)
public Collection<CellTypeAssignment> getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getCellTypeAssignmentsWithoutIndices in interface SingleCellExpressionExperimentService

getCellTypeAssignmentProtocols

@Transactional(readOnly=true)
public Collection<Protocol> getCellTypeAssignmentProtocols()

Description copied from interface: SingleCellExpressionExperimentService

Obtain a collection of protocols used to assign cell types to single-cell vectors.

Specified by:

getCellTypeAssignmentProtocols in interface SingleCellExpressionExperimentService

getCellTypeAssignmentByProtocol

@Transactional(readOnly=true)
public Collection<CellTypeAssignment> getCellTypeAssignmentByProtocol(ExpressionExperiment ee,
 QuantitationType qt,
 String protocolName)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a cell type assignment by a protocol identifier.

Specified by:

getCellTypeAssignmentByProtocol in interface SingleCellExpressionExperimentService

getPreferredCellTypeAssignment

@Transactional(readOnly=true)
public Optional<CellTypeAssignment> getPreferredCellTypeAssignment(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the preferred cell type labelling from the preferred single-cell vectors.

Specified by:

getPreferredCellTypeAssignment in interface SingleCellExpressionExperimentService

getPreferredCellTypeAssignment

@Transactional(readOnly=true)
public Optional<CellTypeAssignment> getPreferredCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getPreferredCellTypeAssignment in interface SingleCellExpressionExperimentService

getPreferredCellTypeAssignmentWithoutIndices

@Transactional(readOnly=true)
public Optional<CellTypeAssignment> getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getPreferredCellTypeAssignmentWithoutIndices in interface SingleCellExpressionExperimentService

addCellLevelCharacteristics

@Transactional
public CellLevelCharacteristics addCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDimension scd,
 CellLevelCharacteristics clc)

Description copied from interface: SingleCellExpressionExperimentService

Add new cell-level characteristics.

Specified by:

addCellLevelCharacteristics in interface SingleCellExpressionExperimentService

removeCellLevelCharacteristics

@Transactional
public void removeCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDimension scd,
 CellLevelCharacteristics clc)

Description copied from interface: SingleCellExpressionExperimentService

Remove existing cell-level characteristics.

Specified by:

removeCellLevelCharacteristics in interface SingleCellExpressionExperimentService

removeCellLevelCharacteristics

@Transactional
public void removeCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 CellLevelCharacteristics clc)

Description copied from interface: SingleCellExpressionExperimentService

Remove existing cell-level characteristics by QT.

Specified by:

removeCellLevelCharacteristics in interface SingleCellExpressionExperimentService

removeCellLevelCharacteristicsByName

@Transactional
public void removeCellLevelCharacteristicsByName(ExpressionExperiment ee,
 SingleCellDimension dimension,
 String name)

Specified by:

removeCellLevelCharacteristicsByName in interface SingleCellExpressionExperimentService

removeAllCellLevelCharacteristics

@Transactional
public long removeAllCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

removeAllCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getCellLevelCharacteristics

@Transactional(readOnly=true)
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee)

Specified by:

getCellLevelCharacteristics in interface SingleCellExpressionExperimentService

See Also:

• ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment)

getCellLevelCharacteristics

@Transactional(readOnly=true)
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee,
 Category category)

Description copied from interface: SingleCellExpressionExperimentService

Obtain CLC for given category.

Specified by:

getCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getCellLevelCharacteristics

@Transactional(readOnly=true)
public CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long id)

Specified by:

getCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getCellLevelCharacteristics

@Transactional(readOnly=true)
public CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 String name)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a CLC by name.

Specified by:

getCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getCellLevelCharacteristics

@Transactional(readOnly=true)
public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

Specified by:

getCellLevelCharacteristics in interface SingleCellExpressionExperimentService

getCellLevelCharacteristicsWithoutIndices

@Transactional(readOnly=true)
public CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 Long clcId)

Specified by:

getCellLevelCharacteristicsWithoutIndices in interface SingleCellExpressionExperimentService

getCellLevelCharacteristicsWithoutIndices

@Transactional(readOnly=true)
public CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 String clcName)

Specified by:

getCellLevelCharacteristicsWithoutIndices in interface SingleCellExpressionExperimentService

getCellLevelCharacteristicsWithoutIndices

@Transactional(readOnly=true)
public Collection<CellLevelCharacteristics> getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getCellLevelCharacteristicsWithoutIndices in interface SingleCellExpressionExperimentService

getCellLevelMask

@Transactional(readOnly=true)
public Optional<CellLevelCharacteristics> getCellLevelMask(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

Description copied from interface: SingleCellExpressionExperimentService

Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.

Specified by:

getCellLevelMask in interface SingleCellExpressionExperimentService

getCellTypes

@Transactional(readOnly=true)
public List<Characteristic> getCellTypes(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the cell types of a given single-cell dataset.

Only the cell types applicable to the preferred single-cell vectors and labelling are returned.

Specified by:

getCellTypes in interface SingleCellExpressionExperimentService

getCellTypeFactor

public Optional<ExperimentalFactor> getCellTypeFactor(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Obtain the cell type factor.

Specified by:

getCellTypeFactor in interface SingleCellExpressionExperimentService

Returns:

a cell type factor, or null of none exist

recreateCellTypeFactor

@Transactional
public ExperimentalFactor recreateCellTypeFactor(ExpressionExperiment ee)

Description copied from interface: SingleCellExpressionExperimentService

Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.

Analyses involving the factor are removed and samples mentioning the factor values are updated as per ExperimentalFactorService.remove(ExperimentalFactor).

Specified by:

recreateCellTypeFactor in interface SingleCellExpressionExperimentService

Returns:

the created cell type factor