Package ubic.gemma.core.loader.expression.geo.singleCell

Class GeoBioAssayMapper

java.lang.Object

ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper

ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper

All Implemented Interfaces:

BioAssayMapper, EntityMapper<BioAssay>, HintingEntityMapper<BioAssay>

public class GeoBioAssayMapper
extends AbstractBioAssayMapper
implements HintingEntityMapper<BioAssay>

Strategy to match a BioAssay against a sample name provided by GEO.

Ideally, the provided sample name is a GSM accession, but in some cases it might originate from a supplementary file, so this has some fallback on other metadata.

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

EntityMapper.MappingStatistics, EntityMapper.StatefulEntityMapper<T extends Identifiable>

Constructor Summary

Constructors

Constructor	Description
GeoBioAssayMapper()

Method Summary

Modifier and Type	Method	Description
List<String>	getCandidateIdentifiers(BioAssay entity)	Obtain a list of possible identifiers for the given entity from higher to lower confidence.
String	getName()	Obtain the name of the mapping strategy.
protected Set<BioAssay>	matchAllInternal(Collection<BioAssay> bas, String sampleName)

Methods inherited from class ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper

contains, containsAny, forCandidates, matchAll, matchAll, matchDescriptionIgnoreCase, matchId, matchName, matchNameIgnoreCase, matchOne, matchOne, matchWithFunction, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.gemma.core.loader.util.mapper.BioAssayMapper

forCandidates

Methods inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper

contains, containsAny, forCandidates, getMappingStatistics, matchAll, matchAll, matchOne, matchOne

Constructor Details

GeoBioAssayMapper

public GeoBioAssayMapper()

Method Details

getName

public String getName()

Description copied from interface: EntityMapper

Obtain the name of the mapping strategy.

Specified by:

getName in interface EntityMapper<BioAssay>

matchAllInternal

protected Set<BioAssay> matchAllInternal(Collection<BioAssay> bas,
 String sampleName)

Specified by:

matchAllInternal in class AbstractBioAssayMapper

getCandidateIdentifiers

public List<String> getCandidateIdentifiers(BioAssay entity)

Description copied from interface: HintingEntityMapper

Obtain a list of possible identifiers for the given entity from higher to lower confidence.

Specified by:

getCandidateIdentifiers in interface HintingEntityMapper<BioAssay>