Package de.julielab.genemapper.mappingcores

Class QuercusMappingCore

java.lang.Object

de.julielab.genemapper.mappingcores.QuercusMappingCore

All Implemented Interfaces:

MappingCore

public class QuercusMappingCore
extends Object
implements MappingCore

Constructor Summary

Constructors

Constructor	Description
QuercusMappingCore(GeneCompositeNameResolver geneCompositeNameResolver, QuercusCandidateSetter candidateSetter, QuercusDisambiguation disambiguation, de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner, de.julielab.speciesassignment.spi.SpeciesAssignmentFilter speciesAssignmentFilter)

Method Summary

Modifier and Type	Method	Description
void	clear()
CandidateRetrieval	getCandidateRetrieval()
ContextRanker	getContextualRanking()
de.julielab.geneexpbase.TermNormalizer	getTermNormalizer()
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	map(de.julielab.geneexpbase.genemodel.GeneMention geneMention)
void	shutdown()	Indicates that the mapping process has finished and all held resources should be freed.

Methods inherited from class java.lang.Object

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

Constructor Detail

QuercusMappingCore

@Inject
public QuercusMappingCore(GeneCompositeNameResolver geneCompositeNameResolver,
                          QuercusCandidateSetter candidateSetter,
                          QuercusDisambiguation disambiguation,
                          de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner,
                          de.julielab.speciesassignment.spi.SpeciesAssignmentFilter speciesAssignmentFilter)
                   throws IOException

Throws:

IOException

Method Detail

map

public de.julielab.geneexpbase.genemodel.MentionMappingResult map(de.julielab.geneexpbase.genemodel.GeneMention geneMention)
                                                           throws GeneMapperException

Specified by:

map in interface MappingCore

Throws:

GeneMapperException

getContextualRanking

public ContextRanker getContextualRanking()

Specified by:

getContextualRanking in interface MappingCore

getCandidateRetrieval

public CandidateRetrieval getCandidateRetrieval()

Specified by:

getCandidateRetrieval in interface MappingCore

getTermNormalizer

public de.julielab.geneexpbase.TermNormalizer getTermNormalizer()

Specified by:

getTermNormalizer in interface MappingCore

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document)
                                                            throws GeneMapperException

Specified by:

map in interface MappingCore

Throws:

GeneMapperException

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document,
                                                                   de.julielab.geneexpbase.configuration.Parameters parameterMap,
                                                                   Stats stats)
                                                            throws GeneMapperException

Specified by:

map in interface MappingCore

Throws:

GeneMapperException

shutdown

public void shutdown()
              throws GeneMapperException

Description copied from interface: MappingCore

Indicates that the mapping process has finished and all held resources should be freed.

Specified by:

shutdown in interface MappingCore

Throws:

GeneMapperException

clear

public void clear()

Specified by:

clear in interface MappingCore