@ParametersAreNonnullByDefault

Package ubic.gemma.core.loader.util.mapper

Utilities for mapping Identifiable entities to external identifiers.

Author:

poirigui

Interface Summary

Interface	Description
BioAssayMapper	Strategy used for comparing BioAssay to sample names from the data.
DesignElementMapper	Maps gene identifiers to CompositeSequence.
EntityMapper<T extends Identifiable>	Map external identifiers to Gemma entities.
EntityMapper.StatefulEntityMapper<T extends Identifiable>	A stateful entity mapper keeps an internal state for a set of candidates to optimize the mapping process.
HintingEntityMapper<T extends Identifiable>	Interface for mappers that can provide hints of identifier candidates.

Class Summary

Class	Description
AbstractBioAssayMapper
AbstractGeneIdentifierBasedDesignElementMapper<K>	Base class for design element mapper that use gene identifiers.
CellIdOverlapBioAssayMapper	Strategy for mapping sample name to BioAssay that relies on overlapping cell IDs.
ChainedEntityMapper<T extends Identifiable>	Implementation of a chain of entity mappers.
EnsemblIdDesignElementMapper	Match design elements using Ensembl IDs.
EntityMapper.MappingStatistics	Mapping statistics computed from a given set of entities and identifiers.
EntityMapperUtils
GeneNameDesignElementMapper
MapBasedDesignElementMapper
MapBasedEntityMapper<T extends Identifiable>	A simple implementation of EntityMapper that uses a Map to store association between identifiers and entities.
NcbiIdDesignElementMapper	Match design elements using the NCBI ID.
OfficialSymbolDesignElementMapper	Match design elements using the official symbol of a gene.
RenamingBioAssayMapper	A BioAssay-to-sample-name matcher that renames samples before matching them.
RenamingBioAssayMapperParser	Parses a file that contains a mapping between old and new bioassay names.
SimpleBioAssayMapper	A simple strategy for matching BioAssay to sample name.
SimpleDesignElementMapper	A simple design element mapper that simply uses the name as identifier.