Uses of Class
de.julielab.genemapper.Configuration

Packages that use Configuration

Package	Description
de.julielab.genemapper
de.julielab.genemapper.composites
de.julielab.genemapper.disambig
de.julielab.genemapper.filtering.families
de.julielab.genemapper.hpo
de.julielab.genemapper.mappingcores

Uses of Configuration in de.julielab.genemapper

Methods in de.julielab.genemapper that return Configuration

Modifier and Type	Method	Description
Configuration	GeneMapper.getConfiguration()

Constructors in de.julielab.genemapper with parameters of type Configuration

Constructor	Description
GeneMapper(Configuration config, MappingCore mappingCore)

Uses of Configuration in de.julielab.genemapper.composites

Constructors in de.julielab.genemapper.composites with parameters of type Configuration

Constructor	Description
FlairCompositeMentionTagger(de.julielab.geneexpbase.services.CacheService cacheService, Configuration configuration)
GeneCompositeNameResolver(FlairCompositeMentionTagger compositeTagger, Configuration configuration)

Uses of Configuration in de.julielab.genemapper.disambig

Constructors in de.julielab.genemapper.disambig with parameters of type Configuration

Constructor	Description
ContextItemRecordsIndex(Configuration configuration)	Deprecated.
ContextItemsIndex(de.julielab.geneexpbase.services.CacheService cacheService, Configuration configuration)
DypsisContextRanker(Configuration config, CandidateRetrieval candidateRetrieval, ContextItemsIndex contextItemsIndex, de.julielab.geneexpbase.services.CacheService cacheService)

Uses of Configuration in de.julielab.genemapper.filtering.families

Methods in de.julielab.genemapper.filtering.families with parameters of type Configuration

Modifier and Type	Method	Description
cc.mallet.types.InstanceList	InstanceListCreator.createInstanceList(Stream<de.julielab.geneexpbase.genemodel.GeneDocument> documents, Configuration configuration)
List<cc.mallet.pipe.Pipe>	InstanceListCreator.createPipes(Configuration configuration)
void	GeneConfigurationDependentPipe.initialize(Configuration configuration)
void	SymbolPrefixPipe.initialize(Configuration configuration)

Constructors in de.julielab.genemapper.filtering.families with parameters of type Configuration

Constructor	Description
SymbolPrefixPipe(String prefix, Configuration configuration)

Uses of Configuration in de.julielab.genemapper.hpo

Constructors in de.julielab.genemapper.hpo with parameters of type Configuration

Constructor	Description
CandidateRetrievalOptimizationRoute(Configuration configuration)
GeneMappingOptimizationRoute(Configuration configuration)
GenesetsOptimizationRoute(Configuration configuration)
GNormPlusBC2TestRoute(Configuration configuration)

Uses of Configuration in de.julielab.genemapper.mappingcores

Methods in de.julielab.genemapper.mappingcores with parameters of type Configuration

Modifier and Type	Method	Description
void	DypsisCandidateSetter.loadLexicalCandidateRankingModel(Configuration config)

Constructors in de.julielab.genemapper.mappingcores with parameters of type Configuration

Constructor	Description
DypsisCandidateSetter(Configuration config, CandidateRetrieval candidateRetrieval, NameCentricRetrieval nameCentricRetrieval, DypsisCandidateRanker candidateRanker, de.julielab.geneexpbase.genemodel.GeneOrthologs geneOrthologs)