GeoBioAssayMapper (Gemma 1.32.1 API)

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

All Methods Instance Methods Concrete Methods
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 Detail
  - GeoBioAssayMapper
```
public GeoBioAssayMapper()
```
- Method Detail
  - 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>