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

Packages that use EntityMapper

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

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

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

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

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

Subinterfaces of EntityMapper in ubic.gemma.core.loader.util.mapper

Modifier and Type	Interface	Description
interface	BioAssayMapper	Strategy used for comparing BioAssay to sample names from the data.
interface	DesignElementMapper	Maps gene identifiers to CompositeSequence.
interface	HintingEntityMapper<T extends Identifiable>	Interface for mappers that can provide hints of identifier candidates.

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

Modifier and Type	Class	Description
class	AbstractBioAssayMapper
class	AbstractGeneIdentifierBasedDesignElementMapper<K>	Base class for design element mapper that use gene identifiers.
class	CellIdOverlapBioAssayMapper	Strategy for mapping sample name to BioAssay that relies on overlapping cell IDs.
class	ChainedEntityMapper<T extends Identifiable>	Implementation of a chain of entity mappers.
class	EnsemblIdDesignElementMapper	Match design elements using Ensembl IDs.
class	GeneNameDesignElementMapper
class	MapBasedDesignElementMapper
class	MapBasedEntityMapper<T extends Identifiable>	A simple implementation of EntityMapper that uses a Map to store association between identifiers and entities.
class	NcbiIdDesignElementMapper	Match design elements using the NCBI ID.
class	OfficialSymbolDesignElementMapper	Match design elements using the official symbol of a gene.
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.
class	SimpleDesignElementMapper	A simple design element mapper that simply uses the name as identifier.

Methods in ubic.gemma.core.loader.util.mapper with parameters of type EntityMapper

Modifier and Type	Method	Description
static String	EntityMapperUtils.getPossibleIdentifiers(Collection<BioAssay> bioAssays, EntityMapper<BioAssay> mapper)	Render a breakdown of possible BioAssay -> sample identifier associations.

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

Constructor	Description
ChainedEntityMapper(EntityMapper<T>... chain)