Uses of Class
ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector

Packages that use BulkExpressionDataVector

Package	Description
ubic.gemma.core.analysis.preprocess.slice	This package provides capabilities for slicing BulkExpressionDataVector.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.visualization
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment

Uses of BulkExpressionDataVector in ubic.gemma.core.analysis.preprocess.slice

Methods in ubic.gemma.core.analysis.preprocess.slice with type parameters of type BulkExpressionDataVector

Modifier and Type	Method	Description
static <T extends BulkExpressionDataVector> Function<T,T>	BulkDataSlicerUtils.createSlicer(List<BioAssay> assays, Class<T> vectorType)	Create a slicer function for bulk data vectors that can be applied on a Stream.
static <T extends BulkExpressionDataVector> Collection<T>	BulkDataSlicerUtils.slice(Collection<T> vectors, List<BioAssay> assays, Class<T> vectorType)	Slice a collection of bulk data vectors.

Uses of BulkExpressionDataVector in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix with type parameters of type BulkExpressionDataVector

Modifier and Type	Method	Description
static <T extends BulkExpressionDataVector> List<T>	BulkExpressionDataMatrixUtils.toVectors(BulkExpressionDataMatrix<?> matrix, Class<T> vectorType)	Convert a BulkExpressionDataMatrix to a collection of BulkExpressionDataVector.

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
protected Collection<BulkExpressionDataVector>	AbstractMultiAssayExpressionDataMatrix.selectVectors(Collection<? extends BulkExpressionDataVector> vectors, Collection<QuantitationType> qTypes)
protected Collection<BulkExpressionDataVector>	AbstractMultiAssayExpressionDataMatrix.selectVectors(Collection<? extends BulkExpressionDataVector> vectors, List<QuantitationType> qTypes)

Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
static BulkExpressionDataMatrix<?>	BulkExpressionDataMatrix.getMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Create a bulk expression data matrix from a collection of vectors.
static MultiAssayBulkExpressionDataMatrix<?>	MultiAssayBulkExpressionDataMatrix.getMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Create a matrix using all the vectors, which are assumed to share the same representation.
protected void	AbstractMultiAssayExpressionDataMatrix.selectVectors(Collection<? extends BulkExpressionDataVector> vectors)	Selects all the vectors passed in (uses them to initialize the data)
protected Collection<BulkExpressionDataVector>	AbstractMultiAssayExpressionDataMatrix.selectVectors(Collection<? extends BulkExpressionDataVector> vectors, Collection<QuantitationType> qTypes)
protected Collection<BulkExpressionDataVector>	AbstractMultiAssayExpressionDataMatrix.selectVectors(Collection<? extends BulkExpressionDataVector> vectors, List<QuantitationType> qTypes)
protected abstract void	AbstractMultiAssayExpressionDataMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)
protected void	EmptyExpressionMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)
protected void	ExpressionDataBooleanMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)
protected void	ExpressionDataDoubleMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Populate this matrix from a given collection of BulkExpressionDataVectors.
protected void	ExpressionDataIntegerMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)
protected void	ExpressionDataStringMatrix.vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BulkExpressionDataVector

Modifier	Constructor	Description
protected	AbstractBulkExpressionDataMatrix(List<? extends BulkExpressionDataVector> vectors)
	BulkExpressionDataDoubleMatrix(List<? extends BulkExpressionDataVector> vectors)
	BulkExpressionDataIntMatrix(List<BulkExpressionDataVector> vectors)
	ExpressionDataBooleanMatrix(Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataBooleanMatrix(Collection<? extends BulkExpressionDataVector> vectors, List<QuantitationType> qtypes)
	ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, Collection<QuantitationType> quantitationTypes)
	ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataIntegerMatrix(Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataStringMatrix(Collection<? extends BulkExpressionDataVector> vectors)
	ExpressionDataStringMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
	TwoChannelExpressionDataMatrixBuilder(Collection<? extends BulkExpressionDataVector> vectors)

Uses of BulkExpressionDataVector in ubic.gemma.core.datastructure.matrix.io

Method parameters in ubic.gemma.core.datastructure.matrix.io with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
int	JsonMatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,String[]> geneAnnotations)	Alternate method that uses annotations in string form (e.g., read from another file).

Uses of BulkExpressionDataVector in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
Slice<? extends BulkExpressionDataVector>	ExpressionDataHeatmap.getVectors()

Method parameters in ubic.gemma.core.visualization with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperiment ee, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a given set of vectors.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a subset.

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

Subclasses of BulkExpressionDataVector in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
class	RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.

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

Modifier	Constructor	Description
	BooleanVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject badvo, ArrayDesignValueObject advo)
protected	DataVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtVo, BioAssayDimensionValueObject badvo, ArrayDesignValueObject advo, Collection<Long> genes)
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject badVo, ArrayDesignValueObject advo, Collection<Long> genes)
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject vectorsBadVo, ArrayDesignValueObject advo, Collection<Long> genes, BioAssayDimensionValueObject dimToMatch)	Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.

Uses of BulkExpressionDataVector in ubic.gemma.persistence.service.common.quantitationtype

Method parameters in ubic.gemma.persistence.service.common.quantitationtype with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)	Retrieve all the QTs associated with the given experiment and dimension.
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> dataVectorTypes)
Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)

Uses of BulkExpressionDataVector in ubic.gemma.persistence.service.expression.bioAssayData

Classes in ubic.gemma.persistence.service.expression.bioAssayData with type parameters of type BulkExpressionDataVector

Modifier and Type	Class	Description
class	AbstractBulkExpressionDataVectorService<T extends BulkExpressionDataVector>
class	AbstractDesignElementDataVectorDao<T extends BulkExpressionDataVector>
interface	BulkExpressionDataVectorService<T extends BulkExpressionDataVector>

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return BulkExpressionDataVector

Modifier and Type	Method	Description
BulkExpressionDataVector	RawAndProcessedExpressionDataVectorDaoImpl.find(BulkExpressionDataVector entity)
BulkExpressionDataVector	RawAndProcessedExpressionDataVectorDaoImpl.load(Long id)

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.findAndThaw(BioAssayDimension bioAssayDimension)
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorDaoImpl.load(Collection<Long> ids)
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorService.thaw(Collection<BulkExpressionDataVector> vectors)	Thaw both raw and processed vectors.
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.thaw(Collection<BulkExpressionDataVector> vectors)	Deprecated.

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type BulkExpressionDataVector

Modifier and Type	Method	Description
BulkExpressionDataVector	RawAndProcessedExpressionDataVectorDaoImpl.find(BulkExpressionDataVector entity)

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorService.thaw(Collection<BulkExpressionDataVector> vectors)	Thaw both raw and processed vectors.
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.thaw(Collection<BulkExpressionDataVector> vectors)	Deprecated.

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

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type BulkExpressionDataVector

Modifier and Type	Method	Description
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)	Retrieve a dimension for a given experiment and quantitation type.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)	Obtain a bioassay dimension by ID.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)