Uses of Interface
ubic.gemma.core.loader.util.mapper.BioAssayMapper

Packages that use BioAssayMapper

Package	Description
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.geo.singleCell	This package contains specific logic for dealing with single-cell data from GEO.
ubic.gemma.core.loader.expression.sequencing	This package contains interfaces and classes for loading sequencing 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.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.

Uses of BioAssayMapper in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression with parameters of type BioAssayMapper

Modifier and Type	Method	Description
void	AbstractDelegatingDataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)
void	DataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)	Set the strategy used for mapping BioAssay to sample names from the data.

Uses of BioAssayMapper in ubic.gemma.core.loader.expression.geo.singleCell

Classes in ubic.gemma.core.loader.expression.geo.singleCell that implement BioAssayMapper

Modifier and Type	Class	Description
class	GeoBioAssayMapper	Strategy to match a BioAssay against a sample name provided by GEO.

Uses of BioAssayMapper in ubic.gemma.core.loader.expression.sequencing

Constructors in ubic.gemma.core.loader.expression.sequencing with parameters of type BioAssayMapper

Modifier	Constructor	Description
	SequencingMetadataFileDataLoader(SequencingDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)

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

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

Modifier and Type	Method	Description
void	AnnDataSingleCellDataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)
void	MexSingleCellDataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)
void	NullSingleCellDataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)

Constructors in ubic.gemma.core.loader.expression.singleCell with parameters of type BioAssayMapper

Modifier	Constructor	Description
	AnnDataSingleCellDataLoaderConfigurer(Path annDataFile, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper)
	GenericMetadataSingleCellDataLoaderConfigurer(SingleCellDataLoaderConfigurer<?> delegate, BioAssayMapper bioAssayMapper)
	MexSingleCellDataLoaderConfigurer(Path mexDir, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper, Path cellRangerPrefix, GeoSeries geoSeries)
	SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)
	SequencingMetadataFileSingleCellDataLoaderConfigurer(SingleCellDataLoaderConfigurer<?> delegate, BioAssayMapper bioAssayMapper)

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

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

Modifier and Type	Method	Description
void	GenericMetadataSingleCellDataLoader.setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)

Uses of BioAssayMapper in ubic.gemma.core.loader.util.mapper

Classes in ubic.gemma.core.loader.util.mapper that implement BioAssayMapper

Modifier and Type	Class	Description
class	AbstractBioAssayMapper
class	CellIdOverlapBioAssayMapper	Strategy for mapping sample name to BioAssay that relies on overlapping cell IDs.
class	RenamingBioAssayMapper	A BioAssay-to-sample-name matcher that renames samples before matching them.
class	SimpleBioAssayMapper	A simple strategy for matching BioAssay to sample name.

Methods in ubic.gemma.core.loader.util.mapper that return BioAssayMapper

Modifier and Type	Method	Description
BioAssayMapper	RenamingBioAssayMapperParser.parse(Path file)

Constructors in ubic.gemma.core.loader.util.mapper with parameters of type BioAssayMapper

Modifier	Constructor	Description
	RenamingBioAssayMapper(BioAssayMapper delegate, String[] bioAssayNames, String[] sampleNames)
	RenamingBioAssayMapperParser(BioAssayMapper delegate)