AbstractGeneIdentifierBasedDesignElementMapper (Gemma 1.32.0 API)

java.lang.Object
- ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper<K>

All Implemented Interfaces:

DesignElementMapper, EntityMapper<CompositeSequence>

Direct Known Subclasses:

EnsemblIdDesignElementMapper, GeneNameDesignElementMapper, NcbiIdDesignElementMapper, OfficialSymbolDesignElementMapper
```
public abstract class AbstractGeneIdentifierBasedDesignElementMapper<K>
extends Object
implements DesignElementMapper
```
Base class for design element mapper that use gene identifiers.

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
Modifier Constructor Description

protected AbstractGeneIdentifierBasedDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`EntityMapper.StatefulEntityMapper<CompositeSequence>`	`forCandidates(Collection<CompositeSequence> candidates)`	Create a stateful mapper for a set of candidates.
`protected abstract K`	`getIdentifier(Gene gene)`	Extract an identifier from the gene.
`protected abstract K`	`processIdentifier(String identifier)`	Extract an identifier from an externally supplied string.
`String`	`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.DesignElementMapper
forCandidates

Methods inherited from interface ubic.gemma.core.loader.util.mapper.EntityMapper
contains, containsAny, getMappingStatistics, getName, matchAll, matchAll, matchOne, matchOne

- Constructor Detail
  - AbstractGeneIdentifierBasedDesignElementMapper
```
protected AbstractGeneIdentifierBasedDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
```
- Method Detail
  - forCandidates
```
public EntityMapper.StatefulEntityMapper<CompositeSequence> forCandidates(Collection<CompositeSequence> candidates)
```
    Description copied from interface: EntityMapper
    
    Create a stateful mapper for a set of candidates.
    
    Specified by:
    
    forCandidates in interface EntityMapper<K>
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getIdentifier
```
@Nullable
protected abstract K getIdentifier(Gene gene)
```
    Extract an identifier from the gene.
  - processIdentifier
```
@Nullable
protected abstract K processIdentifier(String identifier)
```
    Extract an identifier from an externally supplied string.
    This may return null if the identifier cannot be parsed.