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

Class AbstractGeneIdentifierBasedDesignElementMapper<K>

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

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 Details

AbstractGeneIdentifierBasedDesignElementMapper

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

Method Details

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.