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. (class)BoundedPaddingContext
               2. (trait)Context
               3. (object)(trait)ContextEngine
               4. (class)DummyContextEngine
               5. (class)FillingContext
               6. (class)PaddingContext
               1. edu.arizona.sista.reach.context.rulebased
                  1. (class)RuleBasedContextEngine
            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.context
                     1. (class)PandasOutput
                  2. edu.arizona.sista.reach.extern.export.fries
                     1. (class)FriesOutput
                  3. 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)AuxBioProcessKBML
               2. (class)AuxCellLocationKBML
               3. (class)AuxChemicalKBML
               4. (class)AuxMetaboliteKBML
               5. (class)AuxProteinFamilyKBML
               6. (class)AuxProteinKBML
               7. (class)AuxTissueTypeKBML
               8. (class)AzFailsafeKBML
               9. (class)ContextCellLineKBML
               10. (class)ContextCellTypeKBML
               11. (class)ContextOrganKBML
               12. (class)ContextSpeciesKBML
               13. (object)
                   EntityChecker
               14. (class)GendCellLocationKBML
               15. (class)GendChemicalKBML
               16. (class)GendProteinFamilyKBML
               17. (class)GendProteinKBML
               18. (trait)IMKBFamilyLookup
               19. (trait)IMKBFamilyMentionLookup
               20. (trait)IMKBLookup
               21. (trait)IMKBMentionLookup
               22. (trait)IMKBOrganCellTypeLookup
               23. (trait)IMKBOrganCellTypeMentionLookup
               24. (trait)IMKBProteinLookup
               25. (trait)IMKBProteinMentionLookup
               26. (class)IncrementingCounter
               27. (class)InMemoryKB
               28. (trait)KBAltLookup
               29. (trait)KBAltMentionLookup
               30. (object)(class)KBEntry
               31. (trait)KBKeyTransforms
               32. (trait)KBLookup
               33. (trait)KBMentionLookup
               34. (class)KBMetaInfo
               35. (class)KBResolution
               36. (class)ManualCellLocationKBML
               37. (class)ManualChemicalKBML
               38. (class)ManualProteinFamilyKBML
               39. (class)ManualProteinKBML
               40. (class)ReachGrounder
               41. (object)
                   ReachKBConstants
               42. (object)(trait)ReachKBKeyTransforms
               43. (object)
                   ReachKBUtils
               44. (object)(trait)Speciated
               45. (class)StaticCellLocationKBLookup
               46. (class)StaticCellLocationKBML
               47. (class)StaticCellLocationKBML2
               48. (class)StaticChemicalKBLookup
               49. (class)StaticChemicalKBML
               50. (class)StaticMetaboliteKBLookup
               51. (class)StaticMetaboliteKBML
               52. (class)StaticProteinFamilyKBLookup
               53. (class)StaticProteinFamilyKBML
               54. (class)StaticProteinKBLookup
               55. (class)StaticProteinKBML
               56. (class)StaticTissueTypeKBLookup
               57. (class)StaticTissueTypeKBML
            7. edu.arizona.sista.reach.mentions
               1. (trait)Anaphoric
               2. (class)BioEventMention
               3. (object)
                  BioMention
               4. (class)BioRelationMention
               5. (class)BioTextBoundMention
               6. (class)CorefEventMention
               7. (class)CorefRelationMention
               8. (class)CorefTextBoundMention
               9. (trait)Display
               10. (case class)EventSite
               11. (object)(trait)Grounding
               12. (case class)Hypothesis
               13. (class)MentionOps
               14. (trait)Modification
               15. (trait)Modifications
               16. (case class)Mutant
               17. (case class)Negation
               18. (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