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