Hierarchy For All Packages

Package Hierarchies:

• 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.evaluation,
• de.julielab.genemapper.evaluation.tools,
• de.julielab.genemapper.filtering,
• de.julielab.genemapper.filtering.families,
• de.julielab.genemapper.genemodel,
• de.julielab.genemapper.hpo,
• de.julielab.genemapper.index,
• de.julielab.genemapper.ioc,
• de.julielab.genemapper.mappingcores,
• de.julielab.genemapper.mappingcores.quercus,
• de.julielab.genemapper.uima,
• de.julielab.genemapper.utils,
• de.julielab.genemapper.utils.dict,
• de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction,
• de.julielab.jcore.ae.genemapper.desc.FamilyResolution,
• de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer,
• de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration,
• de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion,
• de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • de.julielab.genemapper.composites.ResolvedCompositeGeneName
        • de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputList
        • de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
        • de.julielab.genemapper.SynHitSet
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResult
  • com.google.inject.AbstractModule (implements com.google.inject.Module)
    • de.julielab.genemapper.ioc.GeneMappingModule
    • de.julielab.genemapper.ioc.WikipediaModule
  • de.julielab.genemapper.utils.dict.ACCollector
  • de.julielab.genemapper.evaluation.tools.AcronymTextCoverWriter
  • org.apache.uima.analysis_component.AnalysisComponent_ImplBase (implements org.apache.uima.analysis_component.AnalysisComponent)
    • org.apache.uima.analysis_component.Annotator_ImplBase
      • org.apache.uima.analysis_component.JCasAnnotator_ImplBase
        • de.julielab.genemapper.uima.EGSummaryStructureAnnotator
        • de.julielab.genemapper.uima.EmbeddingsWithTokensConnectionAnnotator
        • de.julielab.genemapper.uima.ExtendedProteinsMerger
        • de.julielab.genemapper.uima.GeneMapperAnnotator
        • de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
        • de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
        • de.julielab.genemapper.uima.GeneToProteinConverter
        • de.julielab.genemapper.uima.ProteinConsistencyTagger
        • de.julielab.genemapper.uima.ProteinFamilyRulesApplier
        • de.julielab.genemapper.uima.ProteinToGeneConverter
        • de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
        • de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
  • de.julielab.genemapper.mappingcores.quercus.AnchorDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.apps.AppUtils
  • de.julielab.genemapper.mappingcores.quercus.BioThesaurusFilterDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.utils.dict.BioThesaurusIproClassMerger
  • de.julielab.genemapper.utils.dict.BTMatcher
  • de.julielab.genemapper.utils.dict.Column
  • de.julielab.genemapper.composites.CompositeMentionTokenizer
  • de.julielab.genemapper.composites.CompositePatternResolver
    • de.julielab.genemapper.composites.EmbeddedAcronymPatternResolver
    • de.julielab.genemapper.composites.EnumerationResolver
    • de.julielab.genemapper.composites.NumberElipseEnumerationPatternResolver
    • de.julielab.genemapper.composites.PatternResolutionChain
    • de.julielab.genemapper.composites.SlashDashAlternativePatternResolver
    • de.julielab.genemapper.composites.TwoPartedRangePatternResolver
  • de.julielab.genemapper.composites.CompositeToken (implements java.io.Serializable)
  • de.julielab.genemapper.index.ContextGenerator
  • de.julielab.genemapper.index.ContextIndexFieldNames
  • de.julielab.genemapper.disambig.ContextItemRecordsIndex (implements de.julielab.genemapper.disambig.SemanticIndex)
  • de.julielab.genemapper.ContextItemsCacheKey
  • de.julielab.genemapper.disambig.ContextItemsIndex (implements de.julielab.genemapper.disambig.SemanticIndex)
  • de.julielab.genemapper.disambig.ContextScoreCacheKey (implements java.io.Serializable)
  • de.julielab.genemapper.utils.ContextUtils
  • java.util.Dictionary<K,V>
    • java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.Properties
        • de.julielab.geneexpbase.configuration.Configuration
          • de.julielab.genemapper.Configuration
  • de.julielab.genemapper.utils.dict.DictionaryClusterCleaner
  • de.julielab.genemapper.evaluation.tools.DocResult
  • de.julielab.genemapper.mappingcores.DypsisCandidateRanker
  • de.julielab.genemapper.disambig.DypsisCandidateRejector
  • de.julielab.genemapper.mappingcores.DypsisCandidateSetter
  • de.julielab.genemapper.disambig.DypsisContextRanker (implements de.julielab.genemapper.disambig.ContextRanker)
  • de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData (implements de.julielab.genemapper.disambig.DocumentDisambiguationData)
  • de.julielab.genemapper.mappingcores.DypsisGeneSelector
  • de.julielab.genemapper.disambig.DypsisGeneSetHomogenizator
  • de.julielab.genemapper.disambig.DypsisMapLocationDisambiguator
  • de.julielab.genemapper.mappingcores.DypsisMappingCore (implements de.julielab.genemapper.mappingcores.MappingCore)
  • de.julielab.genemapper.disambig.DypsisRankingMerger
  • de.julielab.genemapper.utils.dict.EntrezGeneUniProtLexcionCreator
  • de.julielab.genemapper.utils.ExtensionFileFilter (implements java.io.FilenameFilter)
  • de.julielab.genemapper.filtering.families.FamilyUtils
  • org.apache.uima.cas.impl.FeatureStructureImpl (implements java.lang.Cloneable, org.apache.uima.cas.FeatureStructure)
    • org.apache.uima.jcas.cas.TOP
      • org.apache.uima.jcas.cas.AnnotationBase (implements org.apache.uima.cas.AnnotationBaseFS)
        • org.apache.uima.jcas.tcas.Annotation (implements org.apache.uima.cas.text.AnnotationFS)
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
          • de.julielab.jcore.types.Annotation
            • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
          • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
            • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
            • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
          • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
          • de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
          • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
          • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
          • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
  • de.julielab.genemapper.composites.FlairCompositeMentionTagger (implements de.julielab.geneexpbase.services.ShutdownRequiring)
  • de.julielab.genemapper.composites.GeneCompositeNameResolver
  • de.julielab.genemapper.genemodel.GeneDocumentFactory
  • de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
  • de.julielab.genemapper.evaluation.tools.GenelistByTaxonomyFilter
  • de.julielab.genemapper.evaluation.tools.GenelistIdUpdater
  • de.julielab.genemapper.evaluation.tools.GenelistTaxonomyPredictor
  • de.julielab.genemapper.evaluation.tools.GenelistToTaxonomyListConverter
  • de.julielab.genemapper.GeneMapper
  • de.julielab.genemapper.filtering.families.GeneMentionFamilyFeatureSetter
  • de.julielab.genemapper.GeneMentionFilter
  • de.julielab.genemapper.apps.GeneNameToAmbiguousIdsMapper
  • de.julielab.genemapper.mappingcores.quercus.GeneRecordQueryDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.evaluation.GNormPlusBC2GNTrainEntityFiltering
  • de.julielab.geneexpbase.hpo.HpoRoute (implements spark.Route, java.io.Serializable)
    • de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
      • de.julielab.genemapper.hpo.GNormPlusBC2TestRoute
    • de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
    • de.julielab.genemapper.hpo.GenesetsOptimizationRoute
  • de.julielab.geneexpbase.hpo.HttpParamOptClient
    • de.julielab.genemapper.hpo.BC2Evaluation
    • de.julielab.genemapper.hpo.BC3CorpusEvaluation
    • de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
    • de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
  • de.julielab.geneexpbase.hpo.HttpParamOptServer
    • de.julielab.genemapper.hpo.GnHpoServer
  • de.julielab.genemapper.evaluation.tools.IndexIdWriter
  • java.io.InputStream (implements java.io.Closeable)
    • de.julielab.genemapper.utils.ReaderInputStream
  • de.julielab.genemapper.filtering.families.InstanceListCreator
  • de.julielab.genemapper.filtering.InstanceListCreator
  • de.julielab.genemapper.apps.InteractiveCandidateFinder
  • de.julielab.genemapper.apps.InteractiveNameCentricCandidateFinder
  • de.julielab.genemapper.evaluation.tools.InteractiveSpellingChecker
  • de.julielab.genemapper.apps.InteractiveWikipediaPageRetrieval
  • de.julielab.genemapper.utils.IOUtils
  • de.julielab.genemapper.evaluation.tools.JCasConverter
  • de.julielab.genemapper.evaluation.tools.MentionAndDocResult
  • de.julielab.genemapper.filtering.MLGeneFilter
  • de.julielab.genemapper.utils.NDCG
  • de.julielab.genemapper.mappingcores.quercus.OfficialSymbolPromotionDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • cc.mallet.pipe.Pipe (implements cc.mallet.types.AlphabetCarrying, java.io.Serializable)
    • de.julielab.genemapper.filtering.families.AcronymPipe
    • de.julielab.genemapper.filtering.families.ChemicalSuffix
    • de.julielab.genemapper.filtering.ChunkTypePipe
    • de.julielab.genemapper.filtering.families.ContextEmbeddingPipe
    • de.julielab.genemapper.filtering.ContextPosPipe
    • de.julielab.genemapper.filtering.families.ContextPosPipe
    • de.julielab.genemapper.filtering.ExperimentsPipe
    • de.julielab.genemapper.filtering.families.FamilyConfidencePipe
    • de.julielab.genemapper.filtering.families.FamilyGenegroupProbabilityPipe
    • de.julielab.genemapper.filtering.families.FamilyMatchPipe
    • de.julielab.genemapper.filtering.families.GeneMention2Token
    • de.julielab.genemapper.filtering.GeneSequence2SingleGene
    • de.julielab.genemapper.filtering.GeneSet2GeneSequence
    • de.julielab.genemapper.filtering.families.GeneSet2Token
    • de.julielab.genemapper.filtering.families.IsAPipe
    • de.julielab.genemapper.filtering.families.IsFamilyPipe
    • de.julielab.genemapper.filtering.families.LastWordPipe
    • de.julielab.genemapper.filtering.families.LowerCaseBoWPipe
    • de.julielab.genemapper.filtering.LowerCasePipe
    • de.julielab.genemapper.filtering.families.MentionEnvironmentPipe
    • de.julielab.genemapper.filtering.families.MentionPrefixPipe
    • de.julielab.genemapper.filtering.families.MentionTypeHint
    • de.julielab.genemapper.filtering.NextCharPipe
    • de.julielab.genemapper.filtering.families.NoDbHitsPipe
    • de.julielab.genemapper.filtering.families.NonDescriptivePipe
    • de.julielab.genemapper.filtering.families.NormalizeFeaturesForGeneSetSize
    • de.julielab.genemapper.filtering.NounPipe
    • de.julielab.genemapper.filtering.NumberClassPipe
    • de.julielab.genemapper.filtering.families.PluralPipe
    • de.julielab.genemapper.filtering.families.PoSBoWPipe
    • de.julielab.genemapper.filtering.PrevCharPipe
    • de.julielab.genemapper.filtering.families.ProteinSymbols
    • de.julielab.genemapper.filtering.RegExPipe
    • de.julielab.genemapper.filtering.families.SetFeatureVectorToGeneSetPipe
    • de.julielab.genemapper.filtering.families.SetInstanceSourceToGeneSetPipe
    • de.julielab.genemapper.filtering.families.SpecifierDetectionPipe
    • de.julielab.genemapper.filtering.families.SymbolPrefixPipe (implements de.julielab.genemapper.filtering.families.GeneConfigurationDependentPipe)
    • de.julielab.genemapper.filtering.TokenPrefixPipe
    • de.julielab.genemapper.filtering.families.UnspecifiedPipe
    • de.julielab.genemapper.filtering.WordClassPipe
    • de.julielab.genemapper.filtering.families.WordEmbeddingPipe
  • de.julielab.genemapper.hpo.PrintBestSmacConfiguration
  • de.julielab.genemapper.mappingcores.QuercusCandidateSetter
  • de.julielab.genemapper.mappingcores.QuercusDisambiguation
  • de.julielab.genemapper.mappingcores.QuercusMappingCore (implements de.julielab.genemapper.mappingcores.MappingCore)
  • de.julielab.genemapper.utils.dict.RefCounter
  • de.julielab.genemapper.RejectionConstants
  • de.julielab.genemapper.disambig.RRFSynHitListFusion (implements de.julielab.genemapper.disambig.SynHitListFusion)
  • de.julielab.genemapper.filtering.families.RuleBasedFamilyAssigner
  • de.julielab.genemapper.disambig.SemanticContextIndex (implements de.julielab.genemapper.disambig.SemanticIndex)
  • de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.apps.SmacRunRepeater
  • de.julielab.genemapper.utils.SpeciesMultiPatternSearcher
  • de.julielab.genemapper.evaluation.tools.Stats
  • de.julielab.genemapper.filtering.StringHelper
  • de.julielab.genemapper.utils.SynHitUtils
  • de.julielab.genemapper.evaluation.tools.TAPEvaluator
  • de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputLine
  • de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
  • de.julielab.genemapper.mappingcores.quercus.TestDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.utils.dict.ThesaurusCleaner
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • de.julielab.geneexpbase.GeneExpException
        • de.julielab.genemapper.utils.GeneMapperException
      • de.julielab.genemapper.utils.GeneMapperInitializationException
      • java.lang.RuntimeException
        • de.julielab.geneexpbase.GeneExpRuntimeException
          • de.julielab.genemapper.utils.GeneMapperRuntimeException
            • de.julielab.genemapper.utils.MissingConfigurationException
  • org.apache.uima.jcas.cas.TOP_Type
    • org.apache.uima.jcas.cas.AnnotationBase_Type
      • org.apache.uima.jcas.tcas.Annotation_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A_Type
        • de.julielab.jcore.types.Annotation_Type
          • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase_Type
        • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity_Type
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type
          • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator_Type
        • de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of_Type
        • de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword_Type
        • de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord_Type
        • de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer_Type
        • de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle_Type
  • de.julielab.genemapper.classification.TransformerClassifier (implements de.julielab.geneexpbase.services.ShutdownRequiring)
  • de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
  • de.julielab.genemapper.utils.UIMAUtils
  • de.julielab.genemapper.mappingcores.quercus.UnderspecifiedNameDisambiguationStep (implements de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep)
  • de.julielab.genemapper.filtering.UnspecificNameFilter
  • de.julielab.genemapper.WikipediaCategoryManager
  • de.julielab.genemapper.evaluation.WikipediaClassLookupDevelopment
  • de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
  • de.julielab.genemapper.disambig.wikipedia.WikipediaEntityClassDecisionBear
  • de.julielab.genemapper.index.WikipediaIndexFields
  • de.julielab.genemapper.disambig.wikipedia.WikipediaIndexReader

Interface Hierarchy

• de.julielab.genemapper.disambig.ContextRanker
• de.julielab.genemapper.disambig.DocumentDisambiguationData
• de.julielab.genemapper.filtering.families.GeneConfigurationDependentPipe
• de.julielab.genemapper.mappingcores.MappingCore
• de.julielab.genemapper.disambig.MentionDisambiguationData
• de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep
• de.julielab.genemapper.disambig.SemanticIndex
• de.julielab.genemapper.disambig.SynHitListFusion

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy