1. edu
   1. edu.arizona
      1. edu.arizona.sista
         1. edu.arizona.sista.assembly
            1. (class)Activation
            2. (object)
               AssembleFromDataset
            3. (object)(class)AssemblyExporter
            4. (object)(class)AssemblyManager
            5. (trait)AssemblyModification
            6. (object)
               AssemblyRunner
            7. (object)(trait)AssemblySieve
            8. (class)Complex
            9. (trait)ComplexEvent
            10. (object)
                Constraints
            11. (trait)Entity
            12. (trait)EntityEventRepresentation
            13. (case class)EntityLabel
            14. (trait)Event
            15. (case class)MutantEntity
            16. (case class)PrecedenceRelation
            17. (case class)PTM
            18. (class)Regulation
            19. (case class)Row
            20. (object)
                RunAssembly
            21. (class)SieveMixture
            22. (class)Sieves
            23. (object)
                SieveUtils
            24. (class)SimpleEntity
            25. (class)SimpleEvent
         2. 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
         3. 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)
               PaperReader
            9. (object)(class)ReachCLI
            10. (object)
                ReachCSV
            11. (object)
                ReachShell
            12. (object)(class)ReachSystem
            13. (object)
                ReadPapers
            14. (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)BidirectionalPaddingContext
               2. (class)BoundedPaddingContext
               3. (trait)Context
               4. (object)(trait)ContextEngine
               5. (object)
                  ContextEngineFactory
               6. (class)DummyContextEngine
               7. (class)FillingContext
               8. (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)AdHocIMKBFactory
               2. (object)(class)AzFailsafeKBML
               3. (object)
                  EntityChecker
               4. (class)IMKBFamilyLookup
               5. (class)IMKBFamilyMentionLookup
               6. (class)IMKBLookup
               7. (class)IMKBMentionLookup
               8. (class)IMKBMetaInfo
               9. (class)IMKBOrganCellTypeLookup
               10. (class)IMKBOrganCellTypeMentionLookup
               11. (class)IMKBProteinLookup
               12. (class)IMKBProteinMentionLookup
               13. (class)IncrementingCounter
               14. (class)InMemoryKB
               15. (trait)KBAltLookup
               16. (trait)KBAltMentionLookup
               17. (object)(class)KBEntry
               18. (trait)KBKeyTransforms
               19. (trait)KBLookup
               20. (trait)KBMentionLookup
               21. (class)KBResolution
               22. (object)
                   ReachContextKBLister
               23. (object)(class)ReachEntityLookup
               24. (class)ReachGrounder
               25. (object)
                   ReachIMKBLookups
               26. (object)
                   ReachIMKBMentionLookups
               27. (object)
                   ReachKBConstants
               28. (object)(trait)ReachKBKeyTransforms
               29. (object)
                   ReachKBUtils
               30. (object)
                   ReachRLKBLookups
               31. (class)ReverseLookupKB
               32. (class)RLKBFactory
               33. (object)(trait)Speciated
               34. (class)TsvIMKBFactory
            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. (object)
                  CorefMention
               8. (class)CorefRelationMention
               9. (class)CorefTextBoundMention
               10. (trait)Display
               11. (case class)EventSite
               12. (trait)Grounding
               13. (case class)Hypothesis
               14. (class)MentionOps
               15. (trait)Modification
               16. (trait)Modifications
               17. (case class)Mutant
               18. (case class)Negation
               19. (case class)PTM
            8. 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)
                  PreprocessNxml
               7. (object)
                  RunNxml2Fries
               1. edu.arizona.sista.reach.nxml.indexer
                  1. (object)(class)NxmlIndexer
                  2. (object)(class)NxmlSearcher
            9. 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
         4. edu.arizona.sista.utils
            1. (class)DateUtils