Uses of Class
de.julielab.genemapper.utils.GeneMapperException

Packages that use GeneMapperException

Package	Description
de.julielab.genemapper
de.julielab.genemapper.apps
de.julielab.genemapper.classification
de.julielab.genemapper.composites
de.julielab.genemapper.disambig
de.julielab.genemapper.disambig.wikipedia
de.julielab.genemapper.filtering.families
de.julielab.genemapper.mappingcores
de.julielab.genemapper.mappingcores.quercus

Uses of GeneMapperException in de.julielab.genemapper

Methods in de.julielab.genemapper that throw GeneMapperException

Modifier and Type	Method	Description
static void	WikipediaCategoryManager.main(String[] args)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	GeneMapper.map(de.julielab.geneexpbase.genemodel.GeneDocument document)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	GeneMapper.map(de.julielab.geneexpbase.genemodel.GeneDocument doc, de.julielab.geneexpbase.configuration.Parameters parameterMap)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	GeneMapper.map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	GeneMapper.map(de.julielab.geneexpbase.genemodel.GeneDocument document, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	GeneMapper.map(de.julielab.geneexpbase.genemodel.GeneMention searchTerm, org.apache.lucene.search.BooleanQuery contextQuery, String documentContext)	Actual mapping method.
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	GeneMapper.map(String searchTerm, org.apache.lucene.search.BooleanQuery contextQuery)	A wrapper to the main mapping function.
de.julielab.geneexpbase.genemodel.MentionMappingResult	GeneMapper.map(String term, org.apache.lucene.search.BooleanQuery contextQuery, String documentContext)	Convenience method mostly used for tests.

Uses of GeneMapperException in de.julielab.genemapper.apps

Methods in de.julielab.genemapper.apps that throw GeneMapperException

Modifier and Type	Method	Description
static void	GeneNameToAmbiguousIdsMapper.main(String[] args)
static void	InteractiveCandidateFinder.main(String[] args)
static void	InteractiveNameCentricCandidateFinder.main(String[] args)

Uses of GeneMapperException in de.julielab.genemapper.classification

Methods in de.julielab.genemapper.classification that throw GeneMapperException

Modifier and Type	Method	Description
static void	TransformerDisambiguationDataUtils.writeData(GeneMapper mapper, File outputFile, Stream<de.julielab.geneexpbase.genemodel.GeneDocument> geneDocumentStream)
static void	TransformerDisambiguationDataUtils.writeData(BufferedWriter bw, GeneMapper mapper, de.julielab.geneexpbase.genemodel.GeneDocument doc)

Uses of GeneMapperException in de.julielab.genemapper.composites

Methods in de.julielab.genemapper.composites that throw GeneMapperException

Modifier and Type	Method	Description
List<de.julielab.geneexpbase.genemodel.GeneMention>	GeneCompositeNameResolver.resolve(de.julielab.geneexpbase.genemodel.GeneMention gm, boolean... print)
void	GeneCompositeNameResolver.shutdown()

Constructors in de.julielab.genemapper.composites that throw GeneMapperException

Constructor	Description
GeneCompositeNameResolver(FlairCompositeMentionTagger compositeTagger, Configuration configuration)

Uses of GeneMapperException in de.julielab.genemapper.disambig

Methods in de.julielab.genemapper.disambig that throw GeneMapperException

Modifier and Type	Method	Description
de.julielab.geneexpbase.genemodel.MentionMappingResult	ContextRanker.assignContextScore(MentionDisambiguationData disambiguationData)
cc.mallet.types.InstanceList	ContextRanker.doContextRanking(DocumentDisambiguationData disambiguationData, de.julielab.geneexpbase.configuration.Parameters parameters)

Constructors in de.julielab.genemapper.disambig that throw GeneMapperException

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 GeneMapperException in de.julielab.genemapper.disambig.wikipedia

Methods in de.julielab.genemapper.disambig.wikipedia that throw GeneMapperException

Modifier and Type	Method	Description
static void	WikipediaIndexReader.main(String[] args)

Constructors in de.julielab.genemapper.disambig.wikipedia that throw GeneMapperException

Constructor	Description
WikipediaEntityClassDecisionBear(WikipediaIndexReader wikipediaIndexReader, de.julielab.geneexpbase.TermNormalizer normalizer)
WikipediaIndexReader(String wikipediaIndexPath, de.julielab.geneexpbase.TermNormalizer normalizer)

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

Methods in de.julielab.genemapper.filtering.families that throw GeneMapperException

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	RuleBasedFamilyAssigner.doit(de.julielab.geneexpbase.genemodel.GeneDocument document)
void	RuleBasedFamilyAssigner.doit(Collection<de.julielab.geneexpbase.genemodel.GeneDocument> docs)
void	GeneConfigurationDependentPipe.initialize(Configuration configuration)
void	SymbolPrefixPipe.initialize(Configuration configuration)

Constructors in de.julielab.genemapper.filtering.families that throw GeneMapperException

Constructor	Description
MentionPrefixPipe(String prefix)
NoDbHitsPipe(String featureName)
SymbolPrefixPipe(String prefix, Configuration configuration)

Uses of GeneMapperException in de.julielab.genemapper.mappingcores

Methods in de.julielab.genemapper.mappingcores that throw GeneMapperException

Modifier and Type	Method	Description
de.julielab.geneexpbase.genemodel.DocumentMappingResult	DypsisMappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document)	Maps the gene mentions in the passed document to database IDs.
de.julielab.geneexpbase.genemodel.DocumentMappingResult	DypsisMappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	DypsisMappingCore.map(de.julielab.geneexpbase.genemodel.GeneMention predictedMention)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	MappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	MappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	MappingCore.map(de.julielab.geneexpbase.genemodel.GeneMention geneMention)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	QuercusMappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	QuercusMappingCore.map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	QuercusMappingCore.map(de.julielab.geneexpbase.genemodel.GeneMention geneMention)
void	DypsisCandidateSetter.setCandidates(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
void	DypsisCandidateSetter.setCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm, AtomicInteger gmidCounter, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
void	DypsisCandidateSetter.shutdown()
void	DypsisMappingCore.shutdown()
void	MappingCore.shutdown()	Indicates that the mapping process has finished and all held resources should be freed.
void	QuercusMappingCore.shutdown()

Constructors in de.julielab.genemapper.mappingcores that throw GeneMapperException

Constructor	Description
DypsisMappingCore(de.julielab.geneexpbase.TermNormalizer normalizer, CandidateRetrieval candidateRetrieval, DypsisCandidateSetter candidateSetter, WikipediaEntityClassDecisionBear decisionBear, GeneCompositeNameResolver geneCompositeNameResolver, de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner, de.julielab.speciesassignment.spi.SpeciesAssignmentFilter assignmentFilter)

Uses of GeneMapperException in de.julielab.genemapper.mappingcores.quercus

Constructors in de.julielab.genemapper.mappingcores.quercus that throw GeneMapperException

Constructor	Description
SemanticIndexDisambiguationStep(de.julielab.geneexpbase.configuration.Configuration config)