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

Interface EntityMapper<T extends Identifiable>

Type Parameters:

T - the type of entity being mapped

All Known Subinterfaces:

BioAssayMapper, DesignElementMapper, HintingEntityMapper<T>

All Known Implementing Classes:

AbstractBioAssayMapper, AbstractGeneIdentifierBasedDesignElementMapper, CellIdOverlapBioAssayMapper, ChainedEntityMapper, EnsemblIdDesignElementMapper, GeneNameDesignElementMapper, GeoBioAssayMapper, MapBasedDesignElementMapper, MapBasedEntityMapper, NcbiIdDesignElementMapper, OfficialSymbolDesignElementMapper, RenamingBioAssayMapper, SimpleBioAssayMapper, SimpleDesignElementMapper

public interface EntityMapper<T extends Identifiable>

Map external identifiers to Gemma entities.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	EntityMapper.MappingStatistics	Mapping statistics computed from a given set of entities and identifiers.
static interface	EntityMapper.StatefulEntityMapper<T extends Identifiable>	A stateful entity mapper keeps an internal state for a set of candidates to optimize the mapping process.

Method Summary

Modifier and Type	Method	Description
default boolean	contains(Collection<T> candidates, String identifier)	Check if any of the candidates can be mapped to the identifier.
default boolean	containsAny(Collection<T> candidates, Collection<String> identifiers)	Check if any of the candidates can be mapped to any of the identifiers.
EntityMapper.StatefulEntityMapper<T>	forCandidates(Collection<T> candidates)	Create a stateful mapper for a set of candidates.
default EntityMapper.MappingStatistics	getMappingStatistics(Collection<T> candidates, Collection<String> identifiers)	Calculate mapping statistics for a set of gene identifiers and candidates.
String	getName()	Obtain the name of the mapping strategy.
default Set<T>	matchAll(Collection<T> candidates, String identifier)	Match the identifier to all the candidates.
default Map<String,Set<T>>	matchAll(Collection<T> candidates, Collection<String> identifiers)	Match each identifier to all the candidates.
default Optional<T>	matchOne(Collection<T> candidates, String identifier)	Map the identifier to a single candidate.
default Map<String,T>	matchOne(Collection<T> candidates, Collection<String> identifiers)	Match each identifier to a single candidate.

Method Detail

getName

String getName()

Obtain the name of the mapping strategy.

forCandidates

EntityMapper.StatefulEntityMapper<T> forCandidates(Collection<T> candidates)

Create a stateful mapper for a set of candidates.

contains

default boolean contains(Collection<T> candidates,
                         String identifier)

Check if any of the candidates can be mapped to the identifier.

containsAny

default boolean containsAny(Collection<T> candidates,
                            Collection<String> identifiers)

Check if any of the candidates can be mapped to any of the identifiers.

matchOne

default Optional<T> matchOne(Collection<T> candidates,
                             String identifier)

Map the identifier to a single candidate.

If more than one candidate matches the identifier, Optional.empty() is returned.

matchOne

default Map<String,T> matchOne(Collection<T> candidates,
                                     Collection<String> identifiers)

Match each identifier to a single candidate.

matchAll

default Set<T> matchAll(Collection<T> candidates,
                        String identifier)

Match the identifier to all the candidates.

matchAll

default Map<String,Set<T>> matchAll(Collection<T> candidates,
                                          Collection<String> identifiers)

Match each identifier to all the candidates.

getMappingStatistics

default EntityMapper.MappingStatistics getMappingStatistics(Collection<T> candidates,
                                                            Collection<String> identifiers)

Calculate mapping statistics for a set of gene identifiers and candidates.