COMPLEX_EVENTS
ReachConstants
COMPONENT
JsonOutputter
CatalysisUtils
fragmenter
CausalPrecedence
export
CharInterval
BratUtils
ClassifyAssemblyRelations
classifier
Closeable
brat
Complex
representations
ComplexEvent
representations
ComplexUtils
fragmenter
ComposedCorefFlow
coref
ComposedDarpaFlow
reach
Constraints
sieves
Context
context
ContextCellLine
ReachIMKBMentionLookups
ContextCellLineFilename
ReachKBConstants
ContextCellType
ReachIMKBMentionLookups
ContextCellTypeFilename
ReachKBConstants
ContextEngine
context
ContextEngineFactory
context
ContextGrounding
ReachContextKBLister
ContextKBs
ReachContextKBLister
ContextMap
context
ContextOrgan
ReachIMKBMentionLookups
ContextOrganFilename
ReachKBConstants
ContextSpecies
ReachIMKBMentionLookups
ContextSpeciesFilename
ReachKBConstants
ContextTissueType
ReachIMKBMentionLookups
ContextTissueTypeFilename
ReachKBConstants
ControlUtils
fragmenter
ConversionUtils
fragmenter
Coref
coref
CorefEventMention
mentions
CorefFlow
coref
CorefMention
mentions
CorefRelationMention
mentions
CorefTextBoundMention
mentions
CorefUtils
coref
Corpus
corpus
CorpusBuilder
corpus
CorpusReader
corpus
CrossValidateAssemblyRelationClassifier
classifier
CtxIDed
FriesOutput
cachedRules
OpenSystem
calculateAccuracy
Evaluator
calculatePerformance
Evaluator
canEqual
KBEntry
KBResolution
candidates
Grounding
catalysis
Fragmenter
catalysisDirection
CatalysisUtils
causalPredecessors
Assembler
cellComponentSeq
ReachEntityLookup
cellLineSeq
ReachEntityLookup
cellLocationSearcher
EntityChecker
cellTypeSeq
ReachEntityLookup
cellularLocation
PhysicalEntityUtils
charInterval
IdTracker
checkArgumentsForResolutions
FeatureExtractor
chemSearcher
EntityChecker
chemicalSeq
ReachEntityLookup
chunkId
FriesEntry
chunkIdColumn
ReachCSV
chunkedDependencyPaths
PathFinder
citationArtifact
NxmlReader
classifier
relations
AssemblyRelationClassifier
classifierPath
CrossValidateAssemblyRelationClassifier
TrainAssemblyRelationClassifier
SieveUtils
classifierType
AssemblyRelationClassifier
TrainAssemblyRelationClassifier
classify
AssemblyRelationClassifier
cleanupEvents
DarpaActions
clf
SieveUtils
cli
AssemblyCLI
ReachCLI
close
NxmlSearcher
cntr
IncrementingCounter
IncrementingId
IncrementingCounter
cofactors
CatalysisUtils
combination
Coref
combineArgs
Coref
commands
AssemblyShell
ReachShell
compatibleContext
CorefUtils
compatibleGrounding
CorefUtils
compatibleMutants
CorefUtils
complexAssemblies
Fragmenter
components
ComplexUtils
config
AssembleFromDataset
AssemblyShell
RunAnnotationEval
RunAssembly
ClassifyAssemblyRelations
CrossValidateAssemblyRelationClassifier
TrainAssemblyRelationClassifier
BuildCorpus
SieveUtils
AssemblyCLI
PaperReader
ReachCLI
ReachCSV
ReachShell
ReadPapers
Api
ApiRuler
ReachEntityLookup
ReachGrounder
RunNxml2Fries
consecutivePreps
DarpaActions
contains
Complex
containsFamily
AssemblyExporter
containsHumanNsId
Speciated
containsHumanSpecies
Speciated
containsID
Complex
ComplexEvent
EntityEventRepresentation
SimpleEntity
SimpleEvent
content
BuildCorpus
context
Rules
reach
Context
export
contextCellLineKBML
ReachIMKBMentionLookups
contextCellTypeKBML
ReachIMKBMentionLookups
contextConfig
AssemblyShell
PaperReader
ReachCLI
ReachShell
contextEngineParams
AssemblyShell
PaperReader
ReachCLI
ReachShell
contextEngineType
AssemblyShell
PaperReader
ReachCLI
ReachShell
contextIdCntr
FriesOutput
contextMatching
ContextEngine
contextNameMap
FriesOutput
contextOrganKBML
ReachIMKBMentionLookups
contextRelationsFile
RuleReader
contextRules
ReachSystem
contextSpeciesKBML
ReachIMKBMentionLookups
contextTissueTypeKBML
ReachIMKBMentionLookups
contextTypes
BoundedPaddingContext
controlType
ControlUtils
controlled
ComplexEvent
ControlUtils
controlledArgs
MentionOps
controlledHash
ComplexEvent
controlledOf
ProcessUtils
controlledPointers
Activation
ComplexEvent
Regulation
controller
Row
ComplexEvent
ControlUtils
controllerArgs
MentionOps
controllerHash
ComplexEvent
controllerPointers
Activation
ComplexEvent
Regulation
controls
Fragmenter
conversionDirection
ConversionUtils
conversionLabels
ConversionUtils
Labeler
conversions
Fragmenter
convertEventToEntity
DarpaActions
copy
AssemblyAnnotation
copyAttachments
BioMention
CorefMention
copyGroundingFrom
Grounding
coref
AssemblyAnnotation
TrainingInstance
EntityEventRepresentation
sista
corefDistinct
CorefUtils
corpus
relations
BuildCorpus
count
ReachCSV
countDocsContaining
NxmlSearcher
countSemanticNegatives
DarpaActions
covalentBindingFeatures
PhysicalEntityUtils
createComplexWithID
AssemblyManager
createContextEngineParams
context
createController
AssemblyExporter
createEvidenceForCPR
SieveUtils
createInput
AssemblyExporter
createOutput
AssemblyExporter
createSimpleEntity
AssemblyManager
createSimpleEntityText
AssemblyExporter
createSimpleEntityWithID
AssemblyManager
cross-sentence
AssemblyAnnotation
crossValidate
Evaluator
csvFile
ReachCSV
csvParser
ReachCSV
ctxType
ContextGrounding
currEvent
FriesOutput
current
IncrementingCounter
IncrementingCounter
currentId
IncrementingId