Class QuercusMappingCore
- java.lang.Object
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- de.julielab.genemapper.mappingcores.QuercusMappingCore
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- All Implemented Interfaces:
MappingCore
public class QuercusMappingCore extends Object implements MappingCore
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Constructor Summary
Constructors Constructor Description QuercusMappingCore(GeneCompositeNameResolver geneCompositeNameResolver, QuercusCandidateSetter candidateSetter, QuercusDisambiguation disambiguation, de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner, de.julielab.speciesassignment.spi.SpeciesAssignmentFilter speciesAssignmentFilter)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description voidclear()CandidateRetrievalgetCandidateRetrieval()ContextRankergetContextualRanking()de.julielab.geneexpbase.TermNormalizergetTermNormalizer()de.julielab.geneexpbase.genemodel.DocumentMappingResultmap(de.julielab.geneexpbase.genemodel.GeneDocument document)de.julielab.geneexpbase.genemodel.DocumentMappingResultmap(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)de.julielab.geneexpbase.genemodel.MentionMappingResultmap(de.julielab.geneexpbase.genemodel.GeneMention geneMention)voidshutdown()Indicates that the mapping process has finished and all held resources should be freed.
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Constructor Detail
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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
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Method Detail
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map
public de.julielab.geneexpbase.genemodel.MentionMappingResult map(de.julielab.geneexpbase.genemodel.GeneMention geneMention) throws GeneMapperException- Specified by:
mapin interfaceMappingCore- Throws:
GeneMapperException
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getContextualRanking
public ContextRanker getContextualRanking()
- Specified by:
getContextualRankingin interfaceMappingCore
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getCandidateRetrieval
public CandidateRetrieval getCandidateRetrieval()
- Specified by:
getCandidateRetrievalin interfaceMappingCore
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getTermNormalizer
public de.julielab.geneexpbase.TermNormalizer getTermNormalizer()
- Specified by:
getTermNormalizerin interfaceMappingCore
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map
public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document) throws GeneMapperException- Specified by:
mapin interfaceMappingCore- Throws:
GeneMapperException
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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:
mapin interfaceMappingCore- Throws:
GeneMapperException
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shutdown
public void shutdown() throws GeneMapperExceptionDescription copied from interface:MappingCoreIndicates that the mapping process has finished and all held resources should be freed.- Specified by:
shutdownin interfaceMappingCore- Throws:
GeneMapperException
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clear
public void clear()
- Specified by:
clearin interfaceMappingCore
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