Uses of Interface
ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

Packages that use CellLevelCharacteristics

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata	This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.core.visualization
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.experiment

Uses of CellLevelCharacteristics in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	EntityLocator.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)
CellLevelCharacteristics	EntityLocatorImpl.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)

Uses of CellLevelCharacteristics in ubic.gemma.core.analysis.singleCell

Methods in ubic.gemma.core.analysis.singleCell that return CellLevelCharacteristics

Modifier and Type	Method	Description
static CellLevelCharacteristics	SingleCellMaskUtils.createMask(boolean[] mask)	Create a mask from a boolean array.

Methods in ubic.gemma.core.analysis.singleCell that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
static Set<CellLevelCharacteristics>	SingleCellSlicerUtils.sliceClcs(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)

Methods in ubic.gemma.core.analysis.singleCell with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	SingleCellSparsityMetrics.addExpressedCells(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] isExpressed)	Populate a boolean vector that indicates if a cell has at least one expressed gene.
static int	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int[]	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static int[]	SingleCellDescriptive.countFastWithUnknown(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingByFactorValueCharacteristics(CellLevelCharacteristics cta, ExperimentalFactor factor)	Map the cell types from a cell type assignment to factor values in a cell type factor.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue,ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
int	SingleCellSparsityMetrics.getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of cells with at least one gene expressed.
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of expressed cell by gene pairs.
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)
int	SingleCellSparsityMetrics.getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)	Calculate the number of genes expressed in at least one cell.
int	SingleCellSparsityMetrics.getNumberOfDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)
static double	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	SingleCellDescriptive.median(SingleCellExpressionDataVector vector, int column, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static boolean[]	SingleCellMaskUtils.parseMask(CellLevelCharacteristics mask)	Parse a mask from a CellLevelCharacteristics object.
static boolean[]	SingleCellMaskUtils.parseMask(CellLevelCharacteristics mask, boolean createArray)
static double	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.readMappingFromFile(CellLevelCharacteristics clc, ExperimentalFactor factor, Path cellTypeMappingFile)	Create a mapping of cell type assignments to factor values from a file.
static double[]	SingleCellDescriptive.sum(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	SingleCellDescriptive.sumWithUnknown(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static void	SingleCellMaskUtils.validateMask(CellLevelCharacteristics mask)	Validate a mask.
static void	CellLevelCharacteristicsMappingUtils.writeMapping(CellLevelCharacteristics cta, ExperimentalFactor factor, Map<Characteristic,FactorValue> cta2f, Writer dest)	Create a mapping of cell type assignments to factor values from a file.

Uses of CellLevelCharacteristics in ubic.gemma.core.analysis.singleCell.aggregate

Methods in ubic.gemma.core.analysis.singleCell.aggregate that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	SingleCellAggregationConfig.getMask()	Categorical mask to use on data.

Methods in ubic.gemma.core.analysis.singleCell.aggregate with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
static Collection<RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.aggregate(Collection<SingleCellExpressionDataVector> vectors, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics, boolean aggregateUnknownCharacteristics)	Aggregate a collection of vectors.
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellType2Factor, SingleCellAggregationConfig config)
static Function<SingleCellExpressionDataVector,RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.createAggregator(SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics, boolean aggregateUnknownCharacteristics)	Create an aggregator that can be used on a Stream of vectors.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)
SingleCellAggregationConfig.SingleCellAggregationConfigBuilder	SingleCellAggregationConfig.SingleCellAggregationConfigBuilder.mask(CellLevelCharacteristics mask)	Categorical mask to use on data.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)

Uses of CellLevelCharacteristics in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
Set<CellLevelCharacteristics>	AbstractDelegatingSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	AnnDataSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	MexSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	NullSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	SingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)

Uses of CellLevelCharacteristics in ubic.gemma.core.loader.expression.singleCell.metadata

Methods in ubic.gemma.core.loader.expression.singleCell.metadata that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
Set<CellLevelCharacteristics>	GenericMetadataSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)

Methods in ubic.gemma.core.loader.expression.singleCell.metadata with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	CellLevelCharacteristicsWriter.write(CellLevelCharacteristics cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write a single set of cell-level characteristics to a writer.

Method parameters in ubic.gemma.core.loader.expression.singleCell.metadata with type arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	CellLevelCharacteristicsWriter.write(Collection<CellLevelCharacteristics> cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write multiple sets of cell-level characteristics to a writer.

Uses of CellLevelCharacteristics in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	ExpressionDataHeatmap.getCellLevelCharacteristics()

Methods in ubic.gemma.core.visualization with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	ExpressionDataHeatmap.setCellLevelCharacteristics(CellLevelCharacteristics cellLevelCharacteristics)
void	SingleCellDataBoxplot.setCellLevelCharacteristics(CellLevelCharacteristics cellLevelCharacteristics)

Uses of CellLevelCharacteristics in ubic.gemma.model.expression.bioAssayData

Classes in ubic.gemma.model.expression.bioAssayData that implement CellLevelCharacteristics

Modifier and Type	Class	Description
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.

Fields in ubic.gemma.model.expression.bioAssayData with type parameters of type CellLevelCharacteristics

Modifier and Type	Field	Description
static final Comparator<CellLevelCharacteristics>	CellLevelCharacteristics.COMPARATOR

Methods in ubic.gemma.model.expression.bioAssayData that return CellLevelCharacteristics

Modifier and Type	Method	Description
static CellLevelCharacteristics	CellLevelCharacteristics.Factory.newInstance(String name, String description, List<Characteristic> characteristics, int[] indices)

Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
Set<CellLevelCharacteristics>	SingleCellDimension.getCellLevelCharacteristics()	Set of cell-level characteristics.

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, DoubleBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static float[]	SingleCellExpressionDataVectorUtils.getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static float[]	SingleCellExpressionDataVectorUtils.getSampleDataAsFloats(SingleCellExpressionDataVector vector, FloatBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static int[]	SingleCellExpressionDataVectorUtils.getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int[]	SingleCellExpressionDataVectorUtils.getSampleDataAsInts(SingleCellExpressionDataVector vector, IntBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	SingleCellExpressionDataVectorUtils.getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	SingleCellExpressionDataVectorUtils.getSampleDataAsLongs(SingleCellExpressionDataVector vector, LongBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)

Method parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	SingleCellDimension.setCellLevelCharacteristics(Set<CellLevelCharacteristics> cellLevelCharacteristics)	Set of cell-level characteristics.

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type CellLevelCharacteristics

Modifier	Constructor	Description
	CellLevelCharacteristicsValueObject(CellLevelCharacteristics cellLevelCharacteristics, boolean excludeCharacteristicIds)

Uses of CellLevelCharacteristics in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	SingleCellExpressionExperimentService.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)	Obtain a specific cell-level characteristic by ID.
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)	Obtain a CLC by name.
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee)	Obtain all cell-level characteristics from all single-cell dimensions.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain all cell-level characteristics from all single-cell dimensions matching the given category.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
Collection<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Collection<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Optional<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)	Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.
Optional<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	SingleCellExpressionExperimentService.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
Characteristic	ExpressionExperimentDao.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)	Obtain the characteristic at a given cell index.
Characteristic[]	ExpressionExperimentDao.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)
Characteristic	ExpressionExperimentDaoImpl.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)
Characteristic[]	ExpressionExperimentDaoImpl.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)
Category	ExpressionExperimentDao.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)	Obtain the category of a cell-level characteristic.
Category	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentService.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)	Remove existing cell-level characteristics by QT.
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
Stream<Characteristic>	ExpressionExperimentDao.streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	ExpressionExperimentDaoImpl.streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentService.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentServiceImpl.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)

Uses of CellLevelCharacteristics in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
EntityUrlBuilder.ExpressionExperimentWebUrl	EntityUrlBuilder.ExpressionExperimentWebUrl.showSingleCellExpressionData(QuantitationType quantitationType, CompositeSequence designElement, List<BioAssay> assays, CellLevelCharacteristics cellLevelCharacteristics, Characteristic focusedCharacteristic)

Uses of CellLevelCharacteristics in ubic.gemma.web.controller.expression.experiment

Methods in ubic.gemma.web.controller.expression.experiment that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	SingleCellExpressionDataModel.getCellLevelCharacteristics1()

Methods in ubic.gemma.web.controller.expression.experiment that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
Collection<CellLevelCharacteristics>	SingleCellExpressionDataModel.getCellLevelCharacteristics()

Constructors in ubic.gemma.web.controller.expression.experiment with parameters of type CellLevelCharacteristics

Modifier	Constructor	Description
	CellLevelCharacteristicsEditForm(CellLevelCharacteristics clc)
	SingleCellExpressionDataModel(ExpressionExperiment expressionExperiment, Collection<CellTypeAssignment> cellTypeAssignments, Collection<CellLevelCharacteristics> cellLevelCharacteristics, QuantitationType quantitationType, CompositeSequence designElement, Gene gene, Long[] assayIds, CellTypeAssignment cellTypeAssignment, CellLevelCharacteristics cellLevelCharacteristics1, Characteristic focusedCharacteristic, String keywords, String font)