1. edu
   1. edu.arizona
      1. edu.arizona.sista
         1. edu.arizona.sista.coref
            1. (class)AntecedentSelector
            2. (class)ComposedCorefFlow
            3. (class)Coref
            4. (object)(trait)CorefFlow
            5. (object)
               CorefUtils
            6. (class)LinearSelector
            7. (class)Links
         2. edu.arizona.sista.reach
            1. (class)ComposedDarpaFlow
            2. (object)(class)DarpaActions
            3. (object)(trait)DarpaFlow
            4. (class)DarpaLinks
            5. (object)
               HypothesisHandler
            6. (object)
               MentionFilter
            7. (object)
               NegationHandler
            8. (object)(class)ReachCLI
            9. (object)
               ReachCSV
            10. (object)
                ReachShell
            11. (object)(class)ReachSystem
            12. (object)
                RuleReader
            1. edu.arizona.sista.reach.apis
               1. (object)
                  Api
               2. (object)
                  ApiRuler
               3. (object)
                  Ruler
               4. (class)RulerResults
               5. (class)Token
               1. edu.arizona.sista.reach.apis.open
                  1. (class)OpenActions
                  2. (class)OpenSystem
            2. edu.arizona.sista.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
            3. edu.arizona.sista.reach.context
               1. (trait)ContextEngine
               2. (trait)GlobalContext
            4. edu.arizona.sista.reach.extern
               1. edu.arizona.sista.reach.extern.export
                  1. (class)IncrementingCounter
                  2. (class)IncrementingId
                  3. (object)(trait)JsonOutputter
                  4. (class)MentionCacheValue
                  5. (object)(class)MentionManager
                  1. edu.arizona.sista.reach.extern.export.fries
                     1. (class)FriesOutput
                  2. edu.arizona.sista.reach.extern.export.indexcards
                     1. (object)(class)IndexCardOutput
               2. edu.arizona.sista.reach.extern.inward
                  1. (trait)ExternalKBAccessor
            5. edu.arizona.sista.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
            6. edu.arizona.sista.reach.grounding
               1. (class)AuxBioProcessKBAccessor
               2. (class)AuxMetaboliteKBAccessor
               3. (class)AuxProteinKBAccessor
               4. (class)AzFailsafeKBAccessor
               5. (object)
                  BroscoiDriver
               6. (object)
                  EntityChecker
               7. (class)GendCellLocationKBAccessor
               8. (class)GendChemicalKBAccessor
               9. (class)GendProteinFamilyKBAccessor
               10. (class)GendProteinKBAccessor
               11. (object)
                   GroundDriver
               12. (class)IdentityGrounder
               13. (class)IncrementingCounter
               14. (trait)KnowledgeBaseConstants
               15. (class)LocalGrounder
               16. (class)LocalKBAccessor
               17. (class)LocalKBLookup
               18. (object)
                   LocalKBUtils
               19. (object)
                   LocalKeyTransforms
               20. (class)LocalProteinFamilyKBAccessor
               21. (class)LocalProteinKBAccessor
               22. (class)ManualCellLocationKBAccessor
               23. (class)ManualChemicalKBAccessor
               24. (class)ManualProteinFamilyKBAccessor
               25. (class)ManualProteinKBAccessor
               26. (trait)SpeciatedKBAccessor
               27. (trait)SpeciatedKBLookup
               28. (class)StaticCellLocationKBAccessor
               29. (class)StaticCellLocationKBLookup
               30. (class)StaticChemicalKBAccessor
               31. (class)StaticChemicalKBLookup
               32. (class)StaticMetaboliteKBAccessor
               33. (class)StaticMetaboliteKBLookup
               34. (class)StaticProteinFamilyKBAccessor
               35. (class)StaticProteinFamilyKBLookup
               36. (class)StaticProteinKBAccessor
               37. (class)StaticProteinKBLookup
               38. (class)StaticTissueTypeKBAccessor
               39. (class)StaticTissueTypeKBLookup
            7. edu.arizona.sista.reach.mentions
               1. (trait)Anaphoric
               2. (class)BioEventMention
               3. (class)BioRelationMention
               4. (class)BioTextBoundMention
               5. (class)CorefEventMention
               6. (class)CorefRelationMention
               7. (class)CorefTextBoundMention
               8. (trait)Display
               9. (case class)EventSite
               10. (object)(trait)Grounding
               11. (case class)Hypothesis
               12. (class)MentionOps
               13. (trait)Modification
               14. (trait)Modifications
               15. (case class)Mutant
               16. (case class)Negation
               17. (case class)PTM
            8. edu.arizona.sista.reach.ner
               1. (object)
                  NERInputGenerator
               2. (object)
                  NERInputWriter
               3. (object)
                  RuleGenerator
               4. (object)
                  RuleWriter
               5. (case class)Syns
            9. edu.arizona.sista.reach.nxml
               1. (case class)FriesEntry
               2. (object)
                  MyXML
               3. (case class)NxmlDoc
               4. (case class)NxmlEntry
               5. (class)NxmlReader
               6. (object)
                  RunNxml2Fries
               1. edu.arizona.sista.reach.nxml.indexer
                  1. (object)(class)NxmlIndexer
                  2. (object)(class)NxmlSearcher
            10. edu.arizona.sista.reach.utils
                1. (object)
                   BratUtils
                2. (case class)BRI
                3. (object)(class)CSVParser
                4. (object)
                   DependencyUtils
                5. (object)
                   FileReader
                6. (class)PathFinder
         3. edu.arizona.sista.utils
            1. (class)DateUtils