1. edu
   1. edu.arizona
      1. edu.arizona.sista
         1. edu.arizona.sista.assembly
            1. (object)
               AssembleFromDataset
            2. (class)Assembler
            3. (object)(class)AssemblyManager
            4. (object)
               AssemblyRunner
            5. (object)
               AssemblyShell
            6. (case class)PrecedenceRelation
            7. (object)
               RunAnnotationEval
            8. (object)
               RunAssembly
            1. edu.arizona.sista.assembly.export
               1. (object)(class)AssemblyExporter
               2. (trait)AssemblyLink
               3. (case class)CausalPrecedence
               4. (case class)Equivalence
               5. (case class)Row
               6. (case class)Subsumption
            2. edu.arizona.sista.assembly.relations
               1. edu.arizona.sista.assembly.relations.classifier
                  1. (object)(class)AssemblyRelationClassifier
                  2. (object)
                     ClassifyAssemblyRelations
                  3. (object)
                     CrossValidateAssemblyRelationClassifier
                  4. (case class)DatasetStratifiedFold
                  5. (object)
                     Evaluator
                  6. (object)
                     FeatureExtractor
                  7. (class)PathFinder
                  8. (case class)Performance
                  9. (object)
                     TrainAssemblyRelationClassifier
               2. edu.arizona.sista.assembly.relations.corpus
                  1. (case class)AssemblyAnnotation
                  2. (object)
                     BuildCorpus
                  3. (case class)Corpus
                  4. (object)
                     CorpusBuilder
                  5. (object)
                     CorpusReader
                  6. (case class)E
                  7. (case class)TrainingInstance
            3. edu.arizona.sista.assembly.representations
               1. (class)Activation
               2. (trait)AssemblyModification
               3. (class)Complex
               4. (trait)ComplexEvent
               5. (trait)Entity
               6. (trait)EntityEventRepresentation
               7. (case class)EntityLabel
               8. (trait)Event
               9. (case class)Location
               10. (case class)MutantEntity
               11. (case class)PTM
               12. (class)Regulation
               13. (class)SimpleEntity
               14. (class)SimpleEvent
            4. edu.arizona.sista.assembly.sieves
               1. (object)(trait)AssemblySieve
               2. (object)
                  Constraints
               3. (class)DeduplicationSieves
               4. (class)PrecedenceSieves
               5. (class)SieveMixture
               6. (class)Sieves
               7. (object)
                  SieveUtils
         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. (object)(class)AssemblyCLI
            2. (class)ComposedDarpaFlow
            3. (object)(class)DarpaActions
            4. (object)(trait)DarpaFlow
            5. (class)DarpaLinks
            6. (object)
               HypothesisHandler
            7. (object)
               MentionFilter
            8. (object)
               NegationHandler
            9. (object)
               PaperReader
            10. (object)(class)ReachCLI
            11. (object)
                ReachConstants
            12. (object)
                ReachCSV
            13. (object)
                ReachShell
            14. (object)(class)ReachSystem
            15. (object)
                ReadPapers
            16. (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)
                  DependencyUtils
               4. (object)(class)DSVParser
               5. (object)
                  FileReader
               6. (class)PathFinder
         4. edu.arizona.sista.utils
            1. (class)DateUtils