1. org
   1. org.clulab
      1. (class)TypesafeConfigPropertyDefiner
      1. org.clulab.coref
         1. (object)
            Alias
         2. (class)AntecedentSelector
         3. (class)ComposedCorefFlow
         4. (class)Coref
         5. (object)(trait)CorefFlow
         6. (object)
            CorefUtils
         7. (object)(class)InstanceFinder
         8. (class)LinearSelector
         9. (class)Links
      2. org.clulab.polarity
         1. (class)HybridLinguisticDeepLearningPolarityEngine
         2. (class)HybridPolarityEngine
         3. (object)
            LinguisticPolarityEngine
         4. (object)
            NegativePolarity
         5. (object)
            NeutralPolarity
         6. (class)Polarity
         7. (object)(trait)PolarityEngine
         8. (object)
            PositivePolarity
         1. org.clulab.polarity.ml
            1. (object)(class)DeepLearningPolarityClassifier
            2. (object)
               ManualCheckModel
            3. (class)MLPolarityEngine
            4. (trait)PolarityClassifier
            5. (object)
               TrainDeepLearningModel
            1. org.clulab.polarity.ml.data
               1. (object)
                  PolarityDatasetPreprocessor
               2. (class)RRNInput
      3. org.clulab.reach
         1. (object)(case class)FriesEntry
         2. (object)
            PaperReader
         3. (object)
            ReachConstants
         4. (object)
            ReachShell
         5. (object)(class)ReachSystem
         6. (object)
            ReadPapers
         7. (object)
            RuleReader
         1. org.clulab.reach.brat
            1. (trait)Annotation
            2. (case class)BinaryAttribute
            3. (object)
               Brat
            4. (case class)Equivalence
            5. (case class)Event
            6. (object)(class)IdTracker
            7. (case class)MultiValueAttribute
            8. (case class)Normalization
            9. (case class)Relation
            10. (case class)TextBound
         2. org.clulab.reach.context
            1. (class)BidirectionalPaddingContext
            2. (class)BoundedPaddingContext
            3. (trait)Context
            4. (object)(trait)ContextEngine
            5. (object)
               ContextEngineFactory
            6. (class)DummyContextEngine
            7. (class)FillingContext
            8. (class)PaddingContext
            9. (class)RuleBasedContextEngine
         3. org.clulab.reach.darpa
            1. (object)(class)DarpaActions
            2. (class)DarpaLinks
            3. (object)
               HyphenHandle
            4. (object)
               HypothesisHandler
            5. (object)
               MentionFilter
            6. (object)
               NegationHandler
            7. (object)
               RegulationHandler
            8. (object)
               reguTestZ
         4. org.clulab.reach.fragmenter
            1. (class)BioPAXElementUtils
            2. (class)CatalysisUtils
            3. (class)ComplexUtils
            4. (class)ControlUtils
            5. (class)ConversionUtils
            6. (class)EntityReferenceUtils
            7. (class)EntityUtils
            8. (object)(class)Fragmenter
            9. (object)
               FragmenterApp
            10. (object)
                Labeler
            11. (class)NamedUtils
            12. (class)PathwayUtils
            13. (class)PhysicalEntityUtils
            14. (class)ProcessUtils
            15. (class)SimplePhysicalEntityUtils
            16. (class)XReferrableUtils
            17. (class)XrefUtils
         5. org.clulab.reach.grounding
            1. (class)AdHocIMKBFactory
            2. (object)(class)AzFailsafeKBML
            3. (object)
               EntityChecker
            4. (trait)ExternalKBAccessor
            5. (class)IMKBLookup
            6. (class)IMKBMentionLookup
            7. (class)IMKBMetaInfo
            8. (class)IncrementingCounter
            9. (object)(class)InMemoryKB
            10. (object)(trait)KBKeyTransforms
            11. (case class)KBKeyTransformsGroup
            12. (trait)KBLookup
            13. (object)(class)KBLookupSet
            14. (trait)KBMentionLookup
            15. (class)KBMetaInfo
            16. (class)KBResolution
            17. (object)
                ReachContextKBLister
            18. (object)(class)ReachEntityLookup
            19. (class)ReachGrounder
            20. (object)
                ReachIMKBLookups
            21. (object)
                ReachIMKBMentionLookups
            22. (object)
                ReachKBConstants
            23. (object)(trait)ReachKBKeyTransforms
            24. (object)
                ReachKBUtils
            25. (object)(trait)Speciated
            26. (class)TsvIMKBFactory
         6. org.clulab.reach.indexer
            1. (object)
               DocListOverlap
            2. (object)(class)NxmlIndexer
            3. (object)(class)NxmlSearcher
            4. (case class)PMCMetaData
         7. org.clulab.reach.mentions
            1. (trait)Anaphoric
            2. (class)BioEventMention
            3. (object)
               BioMention
            4. (class)BioRelationMention
            5. (class)BioTextBoundMention
            6. (case class)CHEMtrigger
            7. (class)CorefEventMention
            8. (object)
               CorefMention
            9. (class)CorefRelationMention
            10. (class)CorefTextBoundMention
            11. (trait)Display
            12. (case class)DNtrigger
            13. (case class)EventSite
            14. (trait)Grounding
            15. (case class)Hypothesis
            16. (case class)KDtrigger
            17. (case class)KOtrigger
            18. (class)MentionOps
            19. (trait)Modification
            20. (trait)Modifications
            21. (case class)Mutant
            22. (case class)Negation
            23. (case class)OEtrigger
            24. (case class)PTM
            25. (case class)UnassignedTrigger
            1. org.clulab.reach.mentions.serialization
               1. org.clulab.reach.mentions.serialization.json
                  1. (class)AnaphoricOps
                  2. (object)
                     BioEventMention
                  3. (class)BioEventMentionOps
                  4. (class)BioMentionOps
                  5. (object)
                     BioRelationMention
                  6. (class)BioRelationMentionOps
                  7. (object)
                     BioTextBoundMention
                  8. (class)BioTextBoundMentionOps
                  9. (class)ContextOps
                  10. (object)
                      CorefEventMention
                  11. (class)CorefEventMentionOps
                  12. (class)CorefMentionOps
                  13. (object)
                      CorefRelationMention
                  14. (class)CorefRelationMentionOps
                  15. (object)
                      CorefTextBoundMention
                  16. (class)CorefTextBoundMentionOps
                  17. (object)
                      JSONSerializer
                  18. (class)KBResolutionOps
                  19. (class)MentionJSONOps
                  20. (class)ModificationOps
                  21. (class)ModificationsOps
                  22. (class)REACHMentionSeq
                  23. (class)StringSetOps
         8. org.clulab.reach.utils
            1. (object)
               BratUtils
            2. (case class)BRI
            3. (object)
               DependencyUtils
            4. (object)(class)DSVParser
            5. (object)
               FileReader
            6. (class)IncrementingCounter
            7. (class)IncrementingId
            8. (class)MentionCacheValue
            9. (object)(class)MentionManager
            10. (class)PathFinder
            11. (class)Preprocess
      4. org.clulab.utils
         1. (class)DateUtils