COMPONENT
JsonOutputter
CSVParser
utils
CatalysisUtils
fragmenter
CharInterval
BratUtils
Closeable
brat
Complex
assembly
ComplexEvent
assembly
ComplexUtils
fragmenter
ComposedCorefFlow
coref
ComposedDarpaFlow
reach
Constraints
assembly
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
ControlUtils
fragmenter
ConversionUtils
fragmenter
Coref
coref
CorefEventMention
mentions
CorefFlow
coref
CorefMention
mentions
CorefRelationMention
mentions
CorefTextBoundMention
mentions
CorefUtils
coref
cachedRules
OpenSystem
canEqual
KBEntry
KBResolution
candidates
Grounding
catalysis
Fragmenter
catalysisDirection
CatalysisUtils
cellComponentSeq
ReachEntityLookup
cellLineSeq
ReachEntityLookup
cellLocationSearcher
EntityChecker
cellTypeSeq
ReachEntityLookup
cellularLocation
PhysicalEntityUtils
charInterval
IdTracker
chemSearcher
EntityChecker
chemicalSeq
ReachEntityLookup
chunkId
FriesEntry
chunkIdColumn
ReachCSV
citationArtifact
NxmlReader
cleanupEvents
DarpaActions
cli
ReachCLI
close
NxmlSearcher
cntr
IncrementingCounter
IncrementingId
IncrementingCounter
cofactors
CatalysisUtils
combination
Coref
combineArgs
Coref
commands
ReachShell
compatibleContext
CorefUtils
compatibleGrounding
CorefUtils
compatibleMutants
CorefUtils
complexAssemblies
Fragmenter
components
ComplexUtils
config
AssembleFromDataset
RunAssembly
PaperReader
ReachCLI
ReachCSV
ReadPapers
Api
ApiRuler
ReachEntityLookup
RunNxml2Fries
consecutivePreps
DarpaActions
contains
Complex
containsFamily
AssemblyExporter
containsHumanNsId
Speciated
containsHumanSpecies
Speciated
containsID
Complex
ComplexEvent
EntityEventRepresentation
SimpleEntity
SimpleEvent
context
Rules
reach
Context
export
contextCellLineKBML
ReachIMKBMentionLookups
contextCellTypeKBML
ReachIMKBMentionLookups
contextConfig
PaperReader
ReachCLI
contextEngineParams
PaperReader
ReachCLI
contextEngineType
PaperReader
ReachCLI
contextMatching
ContextEngine
contextOrganKBML
ReachIMKBMentionLookups
contextRelationsFile
RuleReader
contextRules
ReachSystem
contextSpeciesKBML
ReachIMKBMentionLookups
contextTypes
BoundedPaddingContext
controlType
ControlUtils
controlled
ComplexEvent
ControlUtils
controlledArgs
MentionOps
controlledOf
ProcessUtils
controlledPointers
Activation
ComplexEvent
Regulation
controller
ComplexEvent
Row
ControlUtils
controllerArgs
MentionOps
controllerPointers
Activation
ComplexEvent
Regulation
controls
Fragmenter
conversionDirection
ConversionUtils
conversionLabels
ConversionUtils
Labeler
conversions
Fragmenter
convertEventToEntity
DarpaActions
copyAttachments
BioMention
CorefMention
copyGroundingFrom
Grounding
coref
EntityEventRepresentation
sista
corefDistinct
CorefUtils
count
ReachCSV
countDocsContaining
NxmlSearcher
countSemanticNegatives
DarpaActions
covalentBindingFeatures
PhysicalEntityUtils
createComplexWithID
AssemblyManager
createContextEngineParams
context
createController
AssemblyExporter
createInput
AssemblyExporter
createOutput
AssemblyExporter
createSimpleEntity
AssemblyManager
createSimpleEntityText
AssemblyExporter
createSimpleEntityWithID
AssemblyManager
csvFile
ReachCSV
csvParser
ReachCSV
csvReader
PaperReader
ctxType
ContextGrounding
currEvent
FriesOutput
current
IncrementingCounter
IncrementingCounter
currentId
IncrementingId