Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

aabut() (in TEES.Utils.Libraries.pstat)	aduplicates() (in TEES.Utils.Libraries.pstat)	arctan (in TEES.Utils.STFormat.Scores)
abetacf() (in TEES.Utils.Libraries.stats)	aerfcc() (in TEES.Utils.Libraries.stats)	arctan2 (in TEES.Utils.STFormat.Scores)
abetai() (in TEES.Utils.Libraries.stats)	aF_oneway() (in TEES.Utils.Libraries.stats)	arctanh (in TEES.Utils.STFormat.Scores)
absolute (in TEES.Utils.STFormat.Scores)	aF_value() (in TEES.Utils.Libraries.stats)	arecode() (in TEES.Utils.Libraries.pstat)
abut() (in TEES.Utils.Libraries.pstat)	afindwithin() (in TEES.Utils.Libraries.stats)	arelfreq() (in TEES.Utils.Libraries.stats)
achisqprob() (in TEES.Utils.Libraries.stats)	afprob() (in TEES.Utils.Libraries.stats)	areplace() (in TEES.Utils.Libraries.pstat)
achisquare() (in TEES.Utils.Libraries.stats)	afriedmanchisquare() (in TEES.Utils.Libraries.stats)	argumentEntitiesExist() (in UnmergingExampleWriter)
acolex() (in TEES.Utils.Libraries.pstat)	agammln() (in TEES.Utils.Libraries.stats)	around() (in TEES.Utils.Libraries.stats)
acollapse() (in TEES.Utils.Libraries.pstat)	ageometricmean() (in TEES.Utils.Libraries.stats)	arowcompare() (in TEES.Utils.Libraries.pstat)
acorrelation() (in TEES.Utils.Libraries.stats)	aglm() (in TEES.Utils.Libraries.stats)	arowsame() (in TEES.Utils.Libraries.pstat)
acovariance() (in TEES.Utils.Libraries.stats)	aharmonicmean() (in TEES.Utils.Libraries.stats)	asamplestdev() (in TEES.Utils.Libraries.stats)
acumfreq() (in TEES.Utils.Libraries.stats)	ahistogram() (in TEES.Utils.Libraries.stats)	asamplevar() (in TEES.Utils.Libraries.stats)
acumsum() (in TEES.Utils.Libraries.stats)	aitemfreq() (in TEES.Utils.Libraries.stats)	ascoreatpercentile() (in TEES.Utils.Libraries.stats)
add (in TEES.Utils.STFormat.Scores)	akendalltau() (in TEES.Utils.Libraries.stats)	asem() (in TEES.Utils.Libraries.stats)
add() (in Model)	akruskalwallish() (in TEES.Utils.Libraries.stats)	ashellsort() (in TEES.Utils.Libraries.stats)
addAnalyses() (in TEES.Utils.Convert.convertBioNLP)	aks_2samp() (in TEES.Utils.Libraries.stats)	asign() (in TEES.Utils.Libraries.stats)
addBasicOptions() (in TEES.ExampleBuilders.ExampleBuilder)	aksprob() (in TEES.Utils.Libraries.stats)	asignaltonoise() (in TEES.Utils.Libraries.stats)
addClassifierModel() (in Detector)	akurtosis() (in TEES.Utils.Libraries.stats)	askew() (in TEES.Utils.Libraries.stats)
addCommand() (in PBSConnection)	akurtosistest() (in TEES.Utils.Libraries.stats)	askewtest() (in TEES.Utils.Libraries.stats)
addCommand() (in UnixConnection)	alignSentences() (in TEES.Tools.SentenceSplitter)	asortrows() (in TEES.Utils.Libraries.pstat)
addDependencies() (in TEES.Tools.StanfordParser)	alignText() (in Menu)	aspearmanr() (in TEES.Utils.Libraries.stats)
addEdge() (in Graph)	alinexand() (in TEES.Utils.Libraries.pstat)	asquare_of_sums() (in TEES.Utils.Libraries.stats)
addEdges() (in Graph)	alinexor() (in TEES.Utils.Libraries.pstat)	ass() (in TEES.Utils.Libraries.stats)
addEdgeTuple() (in Graph)	alinregress() (in TEES.Utils.Libraries.stats)	assertSameSentence() (in SentenceExampleWriter)
addElements() (in TEES.Utils.InteractionXML.ConvertPMC)	AllCorrectClassifier (in TEES.Classifiers)	assignNames() (in TEES.Classifiers.SVMMultiClassModelUtils)
addEntity() (in UnmergingExampleWriter)	AllCorrectClassifier (in TEES.Classifiers.AllCorrectClassifier)	astdev() (in TEES.Utils.Libraries.stats)
addEvent() (in UnmergingExampleWriter)	ALLOW_THREADS (in TEES.Utils.STFormat.Scores)	asterr() (in TEES.Utils.Libraries.stats)
addExample() (in ExampleStats)	AllTrueClassifier (in TEES.Classifiers)	asum() (in TEES.Utils.Libraries.stats)
addFN() (in EvaluationData)	AllTrueClassifier (in TEES.Classifiers.AllTrueClassifier)	asumdiffsquared() (in TEES.Utils.Libraries.stats)
addFP() (in EvaluationData)	allValidate() (in TEES.Utils.STFormat.Validate)	asummult() (in TEES.Utils.Libraries.stats)
addInstance() (in EvaluationData)	amannwhitneyu() (in TEES.Utils.Libraries.stats)	athreshold() (in TEES.Utils.Libraries.stats)
addInteraction() (in UnmergingExampleWriter)	amean() (in TEES.Utils.Libraries.stats)	atiecorrect() (in TEES.Utils.Libraries.stats)
addKnownPositives() (in ExampleStats)	amedian() (in TEES.Utils.Libraries.stats)	atmax() (in TEES.Utils.Libraries.stats)
addLog() (in StreamModifier)	amedianscore() (in TEES.Utils.Libraries.stats)	atmean() (in TEES.Utils.Libraries.stats)
addMTMX() (in TEES.Utils.Convert.DDITools)	aminoAcids (in TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder)	atmin() (in TEES.Utils.Libraries.stats)
addName() (in NameGazetteer)	amode() (in TEES.Utils.Libraries.stats)	atrim1() (in TEES.Utils.Libraries.stats)
addNode() (in Graph)	amoment() (in TEES.Utils.Libraries.stats)	atrimboth() (in TEES.Utils.Libraries.stats)
addNodes() (in Graph)	Analyze (in TEES.Utils.STFormat)	atsem() (in TEES.Utils.Libraries.stats)
addParse() (in TEES.Utils.ProteinNameSplitter)	analyzeNesting() (in TEES.Utils.STFormat.Analyze)	atstdev() (in TEES.Utils.Libraries.stats)
addStep() (in ToolChain)	Annotation (in TEES.Utils.STFormat.STTools)	attest_1samp() (in TEES.Utils.Libraries.stats)
addStr() (in Model)	anormaltest() (in TEES.Utils.Libraries.stats)	attest_ind() (in TEES.Utils.Libraries.stats)
addStrings() (in Model)	aobrientransform() (in TEES.Utils.Libraries.stats)	attest_rel() (in TEES.Utils.Libraries.stats)
addTN() (in EvaluationData)	apaired() (in TEES.Utils.Libraries.stats)	atvar() (in TEES.Utils.Libraries.stats)
addToCSV() (in TEES.Utils.TableUtils)	apearsonr() (in TEES.Utils.Libraries.stats)	aunique() (in TEES.Utils.Libraries.pstat)
addTokenization() (in TEES.Utils.ProteinNameSplitter)	apercentileofscore() (in TEES.Utils.Libraries.stats)	avar() (in TEES.Utils.Libraries.stats)
addTokensToTree() (in TEES.Utils.ProteinNameSplitter)	apointbiserialr() (in TEES.Utils.Libraries.stats)	avariation() (in TEES.Utils.Libraries.stats)
addToPattern() (in GiulianoFeatureBuilder)	appendExamples() (in TEES.Core.ExampleUtils)	average() (in BinaryEvaluator)
addTP() (in EvaluationData)	appendExamplesBinary() (in TEES.Core.ExampleUtils)	average() (in Evaluator)
addType() (in MultiEdgeFeatureBuilder)	applyParameters() (in ToolChain)	AveragingMultiClassEvaluator (in TEES.Evaluators)
addValue() (in ExampleStats)	arankdata() (in TEES.Utils.Libraries.stats)	AveragingMultiClassEvaluator (in TEES.Evaluators.AveragingMultiClassEvaluator)
addVariable() (in ExampleStats)	aranksums() (in TEES.Utils.Libraries.stats)	awilcoxont() (in TEES.Utils.Libraries.stats)
adescribe() (in TEES.Utils.Libraries.stats)	arccos (in TEES.Utils.STFormat.Scores)	az() (in TEES.Utils.Libraries.stats)
adjacencyMatrixToHtml() (in TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder)	arccosh (in TEES.Utils.STFormat.Scores)	azmap() (in TEES.Utils.Libraries.stats)
adjustEntity() (in TEES.Core.RecallAdjust)	arcsin (in TEES.Utils.STFormat.Scores)	azprob() (in TEES.Utils.Libraries.stats)
adm() (in TEES.Utils.Libraries.pstat)	arcsinh (in TEES.Utils.STFormat.Scores)	azs() (in TEES.Utils.Libraries.stats)

B

BABELFISH (in TEES.Utils.Settings)	buildAttachedEdgeFeatures() (in EdgeFeatureBuilder)	buildLinearOrderFeatures() (in PhraseTriggerExampleBuilder)
BacteriaRenamingFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	buildAttachedEdgeFeatures() (in TriggerFeatureBuilder)	buildMenus() (in TEES.configure)
BacteriaRenamingFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder)	buildChains() (in EntityExampleBuilder)	buildModels() (in TEES.Utils.Release)
BANNER (in TEES.Tools)	buildChains() (in TriggerFeatureBuilder)	buildMTMXFeatures() (in DrugFeatureBuilder)
BANNER_DIR (in TEES.Utils.Settings)	buildChains() (in ModifierExampleBuilder)	buildNGrams() (in NodalidaFeatureBuilder)
Bar (in TEES.Utils.Libraries.progressbar)	buildContentFeatures() (in TokenFeatureBuilder)	buildNXGraph() (in ParseGraph)
batch (in TEES)	buildDNAFeatures() (in RELFeatureBuilder)	buildOntologyFeatures() (in BioInferOntologyFeatureBuilder)
batch() (in TEES.batch)	buildEdgeFeatures() (in EVEXFeatureBuilder)	buildOntologyFeaturesForPath() (in BioInferOntologyFeatureBuilder)
begin() (in ETWriter)	buildEdgeFeatures() (in EdgeFeatureBuilder)	buildPairFeatures() (in BacteriaRenamingFeatureBuilder)
beginExample() (in ExampleStats)	buildEdgeFeatures() (in GiulianoFeatureBuilder)	buildPairFeatures() (in DrugFeatureBuilder)
beginModel() (in SingleStageDetector)	buildEdgeFeatures() (in UnmergingExampleBuilder)	buildPairFeaturesDict() (in BacteriaRenamingFeatureBuilder)
beta() (in TEES.Utils.STFormat.Scores)	buildEdgeGramFeatures() (in NodalidaFeatureBuilder)	buildParseGraph() (in ParseGraph)
betacf (in TEES.Utils.Libraries.stats)	buildEntityFeatures() (in MultiEdgeFeatureBuilder)	buildPathEdgeFeatures() (in MultiEdgeFeatureBuilder)
betai (in TEES.Utils.Libraries.stats)	buildExample() (in EdgeExampleBuilder)	buildPathGrams() (in MultiEdgeFeatureBuilder)
BinaryEvaluator (in TEES.Evaluators)	buildExample() (in UnmergingExampleBuilder)	buildPathLengthFeatures() (in MultiEdgeFeatureBuilder)
BinaryEvaluator (in TEES.Evaluators.BinaryEvaluator)	buildExamples() (in Detector)	buildPOSPairs() (in EntityExampleBuilder)
binomial() (in TEES.Utils.STFormat.Scores)	buildExamplesFromGraph() (in EdgeExampleBuilder)	buildPredictedValueFeatures() (in MultiEdgeFeatureBuilder)
BioInferOntologyFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	buildExamplesFromGraph() (in EntityExampleBuilder)	buildRandomFeatures() (in RandomFeatureBuilder)
BioInferOntologyFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	buildExamplesFromGraph() (in ExampleBuilder)	buildRangeFeatures() (in RELFeatureBuilder)
BioNLP11GeniaTools (in TEES.Evaluators)	buildExamplesFromGraph() (in ModifierExampleBuilder)	buildSentenceFeatures() (in MultiEdgeFeatureBuilder)
BIONLP_EVALUATOR_DIR (in TEES.Utils.Settings)	buildExamplesFromGraph() (in PhraseTriggerExampleBuilder)	buildShortestPathNX() (in ParseGraph)
BIONLP_EVALUATOR_GOLD_DIR (in TEES.Utils.Settings)	buildExamplesFromGraph() (in UnmergingExampleBuilder)	buildShortestPaths() (in NodalidaFeatureBuilder)
BioTextExampleWriter (in TEES.ExampleWriters)	buildFeatures() (in TriggerFeatureBuilder)	buildSingleElementFeatures() (in MultiEdgeFeatureBuilder)
BioTextExampleWriter (in TEES.ExampleWriters.BioTextExampleWriter)	buildGraphKernelFeatures() (in GraphKernelFeatureBuilder)	buildSubstringFeatures() (in BacteriaRenamingFeatureBuilder)
bitwise_and (in TEES.Utils.STFormat.Scores)	buildInteractionId() (in TEES.Utils.InteractionXML.IDUtils)	buildSubstringFeatures() (in RELFeatureBuilder)
bitwise_not (in TEES.Utils.STFormat.Scores)	buildInteractionPairs() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	buildTerminusFeatures() (in EdgeFeatureBuilder)
bitwise_or (in TEES.Utils.STFormat.Scores)	buildInterArgumentBagOfWords() (in UnmergingExampleBuilder)	buildTerminusFeatures() (in MultiEdgeFeatureBuilder)
bitwise_xor (in TEES.Utils.STFormat.Scores)	buildKnownWordFeatures() (in RELFeatureBuilder)	buildTerminusTokenFeatures() (in MultiEdgeFeatureBuilder)
BLLIP_PARSER_DIR (in TEES.Utils.Settings)	buildLinearNGram() (in EntityExampleBuilder)	buildTokenGramFeatures() (in NodalidaFeatureBuilder)
BLLIPParser (in TEES.Tools)	buildLinearNGram() (in PhraseTriggerExampleBuilder)	buildTokenGrams() (in TokenFeatureBuilder)
BUFSIZE (in TEES.Utils.STFormat.Scores)	buildLinearOrderFeatures() (in EntityExampleBuilder)	buildTriggerFeatures() (in GiulianoFeatureBuilder)
build() (in NameGazetteer)	buildLinearOrderFeatures() (in EdgeFeatureBuilder)	buildWalkPaths() (in MultiEdgeFeatureBuilder)
buildAllFeatures() (in RELFeatureBuilder)	buildLinearOrderFeatures() (in TokenFeatureBuilder)	bytes() (in TEES.Utils.STFormat.Scores)
buildAminoAcidFeatures() (in RELFeatureBuilder)	buildLinearOrderFeatures() (in TriggerFeatureBuilder)
buildArgumentFeatures() (in UnmergingExampleBuilder)	buildLinearOrderFeatures() (in ModifierExampleBuilder)

C

c_ (in TEES.Utils.STFormat.Scores)	clearCommands() (in UnixConnection)	conjugate (in TEES.Utils.STFormat.Scores)
calculateFromCSV() (in TEES.Evaluators.Evaluator)	clearWorkDir() (in UnixConnection)	Connection (in TEES.Utils)
calculateFScore() (in EvaluationData)	CLIP (in TEES.Utils.STFormat.Scores)	Connection (in TEES.Utils.Connection)
calculateKernel() (in GiulianoFeatureBuilder)	close() (in Model)	coNPPhraseFirstToken (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)
calculatePredictedRange() (in ExampleBuilder)	close() (in ETWriter)	cons() (in PorterStemmer)
cast (in TEES.Utils.STFormat.Scores)	closeLog() (in TEES.Utils.Stream)	contains() (in TEES.Utils.Range)
Catenate (in TEES.Utils.InteractionXML)	ClusterConnection (in TEES.Utils.Connection)	Convert (in TEES.Utils)
catenate() (in TEES.Utils.InteractionXML.Catenate)	ClusterConnection (in TEES.Utils.Connection.ClusterConnection)	convert() (in Preprocessor)
catenateElements() (in TEES.Utils.InteractionXML.Catenate)	CODetector (in TEES.Detectors)	convert() (in TEES.Utils.Convert.convertBioNLP)
catenateFiles() (in TEES.Utils.InteractionXML.Catenate)	CODetector (in TEES.Detectors.CODetector)	convert() (in TEES.Utils.InteractionXML.ConvertPMC)
ceil (in TEES.Utils.STFormat.Scores)	colex() (in TEES.Utils.Libraries.pstat)	convertBioNLP (in TEES.Utils.Convert)
charOffsetToSingleTuple() (in TEES.Utils.Range)	collapse() (in TEES.Utils.Libraries.pstat)	convertDDI (in TEES.Utils.Convert)
charOffsetToTuples() (in TEES.Utils.Range)	combinations() (in TEES.ExampleBuilders.UnmergingExampleBuilder)	convertDDI() (in TEES.Utils.Convert.convertDDI)
check() (in StepSelector)	combine (in TEES.Utils.Libraries)	convertDownloaded() (in TEES.Utils.Convert.convertBioNLP)
checkCorpusInstall() (in TEES.configure)	combine() (in TEES.Utils.Libraries.combine)	ConvertPMC (in TEES.Utils.InteractionXML)
checkEvaluator() (in TEES.Evaluators.BioNLP11GeniaTools)	Compare (in TEES.Utils.STFormat)	convertToInteractions() (in TEES.Utils.Convert.convertDDI)
checkInstallPath() (in TEES.configure)	compare() (in AveragingMultiClassEvaluator)	ConvertXML (in TEES.Utils.STFormat)
checkPrograms() (in TEES.Tools.Tool)	compare() (in BinaryEvaluator)	convertXML() (in TEES.Tools.StanfordParser)
checkReturnCode() (in TEES.Tools.Tool)	compare() (in Evaluator)	copyExamples() (in TEES.Core.ExampleUtils)
checkReturnCode() (in TEES.Utils.Download)	compare() (in TEES.Evaluators.Evaluator)	CopyParse (in TEES.Utils.InteractionXML)
checkStep() (in Detector)	compare() (in TEES.Utils.STFormat.Compare)	copyParse() (in TEES.Utils.InteractionXML.CopyParse)
chisqprob (in TEES.Utils.Libraries.stats)	compareEntities() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	Core (in TEES)
chisquare (in TEES.Utils.Libraries.stats)	compareEntitiesByGENIARelaxedOffsetMethod() (in TEES.Evaluators.EvaluateInteractionXML)	CORPUS_DIR (in TEES.Utils.Settings)
chisquare() (in TEES.Utils.STFormat.Scores)	compareEntitiesSimple() (in TEES.Evaluators.EvaluateInteractionXML)	CorpusElements (in TEES.Utils.InteractionXML)
Classifier (in TEES.Classifiers)	compareEntitiesStrict() (in TEES.Evaluators.EvaluateInteractionXML)	CorpusElements (in TEES.Utils.InteractionXML.CorpusElements)
Classifier (in TEES.Classifiers.Classifier)	compareEvents() (in TEES.Utils.STFormat.Validate)	corpusMenuInitializer() (in TEES.configure)
Classifiers (in TEES)	CompareExamples (in TEES.Utils)	corpusRENtoASCII() (in TEES.Utils.Convert.convertBioNLP)
classify (in TEES)	compareExamples() (in TEES.Utils.CompareExamples)	cos (in TEES.Utils.STFormat.Scores)
classify() (in Classifier)	CompareFeatures (in TEES.Utils)	cosh (in TEES.Utils.STFormat.Scores)
classify() (in ExternalClassifier)	compareInteractionPrecedence() (in TEES.ExampleBuilders.UnmergingExampleBuilder)	count (in TEES.Utils.Convert.processLPSN)
classify() (in Detector)	compareInteractions() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	cumfreq (in TEES.Utils.Libraries.stats)
classify() (in EventDetector)	CompareParse (in TEES.Utils.InteractionXML)	cumsum (in TEES.Utils.Libraries.stats)
classify() (in SingleStageDetector)	configure (in TEES)	cutPoints() (in TEES.Utils.ProteinNameSplitter)
classify() (in TEES.classify)	configure() (in TEES.configure)	cvc() (in PorterStemmer)
classifyToXML() (in SingleStageDetector)	conj (in TEES.Utils.STFormat.Scores)

D

data (in DrugFeatureBuilder)	describe (in TEES.Utils.Libraries.stats)	Document (in TEES.Utils.STFormat.STTools)
DATAPATH (in TEES.Utils.DefaultSettings)	DetectHeads (in TEES.Utils)	doGrid() (in EventDetector)
DATAPATH (in TEES.Utils.Settings)	Detector (in TEES.Detectors)	doublec() (in PorterStemmer)
DDITools (in TEES.Utils.Convert)	Detector (in TEES.Detectors.Detector)	Download (in TEES.Utils)
decimals (in TEES.Utils.TableUtils)	Detectors (in TEES)	download() (in UnixConnection)
default_widgets (in TEES.Utils.Download)	determineNewType() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)	download() (in TEES.Utils.Download)
default_widgets (in TEES.Utils.Libraries.progressbar)	Dispatch (in TEES.Utils.Libraries.stats)	downloadAndExtract() (in TEES.Utils.Download)
DefaultSettings (in TEES.Utils)	divide (in TEES.Utils.STFormat.Scores)	downloadCorpus() (in TEES.Utils.Convert.convertBioNLP)
defineId() (in IdSet)	DivideCorpus (in TEES.Core)	downloadModel() (in ExternalClassifier)
definePredictedValueRange() (in EdgeExampleBuilder)	divideExampleFile() (in TEES.Core.ExampleUtils)	downloadPredictions() (in ExternalClassifier)
definePredictedValueRange() (in ExampleBuilder)	DivideExamples (in TEES.Core)	downloadProgress() (in TEES.Utils.Download)
definePredictedValueRange() (in MultiEdgeFeatureBuilder)	divideExamples() (in TEES.Core.DivideExamples)	DRUG_BANK_XML (in TEES.Utils.Settings)
deg2rad (in TEES.Utils.STFormat.Scores)	divideExamples() (in TEES.Core.ExampleUtils)	DrugFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
degrees (in TEES.Utils.STFormat.Scores)	DivideSets (in TEES.Utils.InteractionXML)	DrugFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)
DeleteAttributes (in TEES.Utils.InteractionXML)	divideSets() (in Preprocessor)	duplicateEquiv() (in TEES.Utils.STFormat.Equiv)
DeleteElements (in TEES.Utils.InteractionXML)	dm() (in TEES.Utils.Libraries.pstat)	duplicates() (in TEES.Utils.Libraries.pstat)
deleteTempWorkDir() (in Detector)	do() (in Option)

E

e (in TEES.Utils.STFormat.Scores)	ERR_RAISE (in TEES.Utils.STFormat.Scores)	EVEXFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
EdgeDetector (in TEES.Detectors)	ERR_WARN (in TEES.Utils.STFormat.Scores)	EVEXFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.EVEXFeatureBuilder)
EdgeDetector (in TEES.Detectors.EdgeDetector)	escDict (in TEES.Tools.BLLIPParser)	ExampleBuilder (in TEES.ExampleBuilders)
EdgeExampleBuilder (in TEES.ExampleBuilders)	escDict (in TEES.Tools.StanfordParser)	ExampleBuilder (in TEES.ExampleBuilders.ExampleBuilder)
EdgeExampleBuilder (in TEES.ExampleBuilders.EdgeExampleBuilder)	ETA (in TEES.Utils.Libraries.progressbar)	ExampleBuilders (in TEES)
EdgeExampleWriter (in TEES.ExampleWriters)	ETFromObj() (in TEES.Utils.ElementTreeUtils)	ExampleStats (in TEES.ExampleBuilders)
EdgeExampleWriter (in TEES.ExampleWriters.EdgeExampleWriter)	ETIteratorFromObj() (in TEES.Utils.ElementTreeUtils)	ExampleStats (in TEES.ExampleBuilders.ExampleStats)
EdgeFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	ETWriter (in TEES.Utils.ElementTreeUtils)	ExampleUtils (in TEES.Core)
EdgeFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.EdgeFeatureBuilder)	evaluate() (in TEES.Core.SimpleGraph)	ExampleWriters (in TEES)
elapsedTimeToString() (in Timer)	evaluate() (in AveragingMultiClassEvaluator)	exceptionMenu (in Option)
ElementTreeUtils (in TEES.Utils)	evaluate() (in BinaryEvaluator)	exists() (in UnixConnection)
encodeNewlines() (in TEES.Utils.ElementTreeUtils)	evaluate() (in TEES.Evaluators.BioNLP11GeniaTools)	exitState() (in Detector)
end() (in ETWriter)	evaluate() (in TEES.Utils.STFormat.Scores)	exp (in TEES.Utils.STFormat.Scores)
endExample() (in ExampleStats)	evaluateBX() (in TEES.Evaluators.BioNLP11GeniaTools)	exp2 (in TEES.Utils.STFormat.Scores)
endModel() (in SingleStageDetector)	evaluateCO() (in TEES.Evaluators.BioNLP11GeniaTools)	expm1 (in TEES.Utils.STFormat.Scores)
ends() (in PorterStemmer)	evaluateCSV() (in TEES.Evaluators.Evaluator)	exponential() (in TEES.Utils.STFormat.Scores)
endUpdate() (in ProgressCounter)	evaluateEPIorID() (in TEES.Evaluators.BioNLP11GeniaTools)	export() (in TEES.Utils.InteractionXML.ExportParse)
enterState() (in Detector)	evaluateGE() (in TEES.Evaluators.BioNLP11GeniaTools)	ExportParse (in TEES.Utils.InteractionXML)
EntityDetector (in TEES.Detectors)	evaluateGE09 (in TEES.Evaluators.BioNLP11GeniaTools)	exportPennTreeBank() (in TEES.Utils.InteractionXML.ExportParse)
EntityDetector (in TEES.Detectors.EntityDetector)	evaluateGrid() (in EventDetector)	exportStanfordDependencies() (in TEES.Utils.InteractionXML.ExportParse)
EntityExampleBuilder (in TEES.ExampleBuilders)	EvaluateInteractionXML (in TEES.Evaluators)	exportTokenization() (in TEES.Utils.InteractionXML.ExportParse)
EntityExampleBuilder (in TEES.ExampleBuilders.EntityExampleBuilder)	evaluateREN() (in TEES.Evaluators.BioNLP11GeniaTools)	extend() (in TEES.Utils.InteractionXML.ExtendTriggers)
EntityExampleWriter (in TEES.ExampleWriters)	evaluateVariance() (in TEES.Evaluators.BioNLP11GeniaTools)	ExtendTriggers (in TEES.Utils.InteractionXML)
EntityExampleWriter (in TEES.ExampleWriters.EntityExampleWriter)	EvaluationData (in TEES.Evaluators.Evaluator)	ExternalClassifier (in TEES.Classifiers)
equal (in TEES.Utils.STFormat.Scores)	Evaluator (in TEES.Evaluators)	ExternalClassifier (in TEES.Classifiers.ExternalClassifier)
Equiv (in TEES.Utils.STFormat)	Evaluator (in TEES.Evaluators.Evaluator)	extractModels() (in TEES.Utils.Release)
erfcc (in TEES.Utils.Libraries.stats)	EVALUATOR (in TEES.Utils.DefaultSettings)	extractPackage() (in TEES.Utils.Download)
ERR_CALL (in TEES.Utils.STFormat.Scores)	EVALUATOR (in TEES.Utils.Settings)	extraPath (in TEES.Utils.InteractionXML.DeleteAttributes)
ERR_DEFAULT (in TEES.Utils.STFormat.Scores)	Evaluators (in TEES)	extraPath (in TEES.Utils.InteractionXML.ListInteractors)
ERR_DEFAULT2 (in TEES.Utils.STFormat.Scores)	EventDetector (in TEES.Detectors)	extraPath (in TEES.Utils.InteractionXML.MapPhrases)
ERR_IGNORE (in TEES.Utils.STFormat.Scores)	EventDetector (in TEES.Detectors.EventDetector)	extraPath (in TEES.Utils.InteractionXML.ResolveIdentityChains)
ERR_LOG (in TEES.Utils.STFormat.Scores)	EventFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	extraPath (in TEES.Utils.InteractionXML.SplitMergedElements)
ERR_PRINT (in TEES.Utils.STFormat.Scores)	eventIsGold() (in UnmergingExampleBuilder)

F

f (in TEES.Utils.Convert.processLPSN)	FindHeads (in TEES.Utils)	floatToString() (in TEES.Utils.TableUtils)
f() (in TEES.Utils.STFormat.Scores)	findHeads() (in TEES.Utils.DetectHeads)	floor (in TEES.Utils.STFormat.Scores)
F_oneway (in TEES.Utils.Libraries.stats)	findHeads() (in TEES.Utils.FindHeads)	floor_divide (in TEES.Utils.STFormat.Scores)
F_value (in TEES.Utils.Libraries.stats)	findHeadsDictionary() (in TEES.Utils.DetectHeads)	FloydWarshall() (in Graph)
F_value_multivariate() (in TEES.Utils.Libraries.stats)	findHeadsSyntactic() (in TEES.Utils.DetectHeads)	flush() (in StreamModifier)
fabs (in TEES.Utils.STFormat.Scores)	findHeadToken() (in SentenceGraph)	fmax (in TEES.Utils.STFormat.Scores)
False_ (in TEES.Utils.STFormat.Scores)	findHeadToken() (in TEES.Utils.DetectHeads)	fmin (in TEES.Utils.STFormat.Scores)
FeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	findSubstring() (in RELFeatureBuilder)	fmod (in TEES.Utils.STFormat.Scores)
FeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.FeatureBuilder)	findwithin (in TEES.Utils.Libraries.stats)	format_time() (in ETA)
FeatureBuilders (in TEES.ExampleBuilders)	finish() (in ProgressBar)	FPE_DIVIDEBYZERO (in TEES.Utils.STFormat.Scores)
FileTransferSpeed (in TEES.Utils.Libraries.progressbar)	FixAltOffsets (in TEES.Utils.InteractionXML)	FPE_INVALID (in TEES.Utils.STFormat.Scores)
filter() (in ExampleStats)	fixAltOffsets() (in TEES.Utils.InteractionXML.FixAltOffsets)	FPE_OVERFLOW (in TEES.Utils.STFormat.Scores)
filterEdge() (in EdgeExampleBuilder)	fixEntities() (in TEES.Utils.Convert.convertDDI)	FPE_UNDERFLOW (in TEES.Utils.STFormat.Scores)
filterEdgesByType() (in EdgeExampleBuilder)	fixIndices() (in TEES.Utils.InteractionXML.MapPhrases)	fprob (in TEES.Utils.Libraries.stats)
finalize() (in MenuSystem)	fixOffset() (in TEES.Tools.BANNER)	frexp (in TEES.Utils.STFormat.Scores)
finalizeInstall() (in TEES.Tools.Tool)	flat() (in TEES.Utils.Libraries.pstat)	friedmanchisquare (in TEES.Utils.Libraries.stats)
findAminoAcid() (in RELFeatureBuilder)	FLOATING_POINT_SUPPORT (in TEES.Utils.STFormat.Scores)	fromXML() (in NameGazetteer)

G

g_bioInferFileName (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	getFileStatus() (in UnixConnection)	getPhraseTypeCounts() (in TEES.Utils.InteractionXML.MapPhrases)
g_evaluatorFieldnames (in TEES.Evaluators.Evaluator)	getFN() (in EvaluationData)	getPOSSuperType() (in FeatureBuilder)
gamma() (in TEES.Utils.STFormat.Scores)	getFolds() (in TEES.Core.Split)	getPredictedValueRange() (in EdgeExampleBuilder)
gammln (in TEES.Utils.Libraries.stats)	getFolds() (in TEES.Evaluators.BioNLP11GeniaTools)	getPredictedValueRange() (in ExampleBuilder)
gen2iterable() (in TEES.Core.ExampleUtils)	getFP() (in EvaluationData)	getPredictionStrength() (in UnmergingExampleWriter)
GENIA_SENTENCE_SPLITTER_DIR (in TEES.Utils.Settings)	getFScore() (in TEES.Evaluators.BioNLP11GeniaTools)	getPredictionStrengthString() (in SentenceExampleWriter)
GeniaEventsToSharedTask (in TEES.Tools)	getGlobalContextKernel() (in GiulianoFeatureBuilder)	getPrevElementIndex() (in TEES.Tools.ProcessUtils)
GeniaSentenceSplitter (in TEES.Tools)	getGoldCategoryName() (in EdgeExampleBuilder)	getPubMed() (in TEES.classify)
geometric() (in TEES.Utils.STFormat.Scores)	getHeads() (in TEES.Utils.DetectHeads)	getRangeDicts() (in TEES.Utils.STFormat.Scores)
geometricmean (in TEES.Utils.Libraries.stats)	getHexColor() (in TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder)	getRelativePosition() (in GiulianoFeatureBuilder)
get() (in Model)	getHypernyms() (in WordNetFeatureBuilder)	getRemotePath() (in UnixConnection)
get() (in TEES.Utils.Parameters)	getId() (in IdSet)	getResults() (in TEES.Utils.STFormat.Scores)
get_state() (in TEES.Utils.STFormat.Scores)	getIdFromLine() (in TEES.Core.DivideExamples)	getRoots() (in TEES.Utils.STFormat.Equiv)
getArgs() (in TEES.Utils.STFormat.Equiv)	getIdNumberType() (in TEES.Utils.InteractionXML.IDUtils)	getSample() (in TEES.Core.Split)
getArgumentCombinations() (in UnmergingExampleBuilder)	getIds() (in IdSet)	getSample() (in TEES.Utils.InteractionXML.Subset)
getAttrString() (in Menu)	getIdSets() (in ExampleBuilder)	getScore() (in TEES.Utils.STFormat.Scores)
getBacteriaNames() (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	getIdsFromFile() (in TEES.Core.ExampleUtils)	getScoreDict() (in TEES.Utils.STFormat.Scores)
getBacteriaTokens() (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	getInEdges() (in Graph)	getSentenceId() (in SentenceGraph)
getBioNLPSharedTaskParams() (in Detector)	getInput() (in TEES.classify)	getSentences() (in ExampleBuilder)
getBISuperType() (in EdgeExampleBuilder)	getInteraction() (in DrugFeatureBuilder)	getSentences() (in TEES.Tools.BLLIPParser)
getBISuperType() (in TEES.Utils.STFormat.Validate)	getInteractionEdgeLengths() (in UnmergingExampleBuilder)	getSets() (in TEES.Utils.Convert.convertDDI)
getCategoryName() (in EdgeExampleBuilder)	getInteractionPredictions() (in TEES.Evaluators.EvaluateInteractionXML)	getSetting() (in UnixConnection)
getCategoryName() (in PhraseTriggerExampleBuilder)	getInteractions() (in SentenceGraph)	getStatistics() (in TEES.Utils.STFormat.STTools)
getCategoryNameFromTokens() (in EdgeExampleBuilder)	getIntermediateFilePath() (in ToolChain)	getStatus() (in ExternalClassifier)
getChoice() (in Menu)	getJob() (in ExternalClassifier)	getStatValues() (in TEES.Utils.STFormat.Scores)
getClassRanges() (in TEES.Core.RecallAdjust)	getJob() (in UnixConnection)	getSteps() (in TEES.train)
getClassRangesFromPredictions() (in TEES.Core.RecallAdjust)	getJobStatus() (in ClusterConnection)	getStepStatus() (in Detector)
getClassSet() (in TEES.Evaluators.Evaluator)	getJobStatus() (in SLURMConnection)	getStepStatus() (in StepSelector)
getCleared() (in SentenceGraph)	getJobStatus() (in UnixConnection)	getStr() (in Model)
getClue() (in TEES.Tools.GeniaEventsToSharedTask)	getJobStatusByName() (in UnixConnection)	getStr() (in Detector)
getColorFromBRGSpectrum() (in TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder)	getKeys() (in TEES.Utils.TableUtils)	getStreams() (in ClusterConnection)
getCombinations() (in TEES.Utils.Parameters)	getLatexString() (in TEES.Utils.TableUtils)	getSubsetEndPos() (in TEES.Tools.ProcessUtils)
getConnection() (in TEES.Utils.Connection.Connection)	getLines() (in TEES.Tools.ProcessUtils)	getSupportVectors() (in TEES.Classifiers.SVMMultiClassModelUtils)
getCorpusIterator() (in TEES.Core.SentenceGraph)	getLocalPath() (in UnixConnection)	getSupportVectorsTest() (in TEES.Classifiers.SVMMultiClassModelUtils)
getCorpusIterator() (in TEES.Utils.InteractionXML.SentenceElements)	getManualEvaluationPrecisions() (in TEES.Utils.STFormat.Scores)	getSynonyms() (in TEES.Utils.Convert.SubtiWiki)
getCounts() (in TEES.Utils.STFormat.Compare)	getMatchingPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	getSynset() (in WordNetFeatureBuilder)
getData() (in AveragingMultiClassEvaluator)	getMaxId() (in TEES.Utils.STFormat.STTools)	getTaskSettings() (in TEES.train)
getData() (in Evaluator)	getMaxJobs() (in TEES.batch)	getText() (in TEES.Tools.GeniaEventsToSharedTask)
getDataInput() (in Menu)	getMaxJobsFromFile() (in TEES.batch)	getText() (in TEES.Utils.InteractionXML.ConvertPMC)
getDefaultOption() (in Menu)	getMergedEntityType() (in EntityExampleBuilder)	getTN() (in EvaluationData)
getDefaultParameters() (in ToolChain)	getMergedEntityType() (in TriggerFeatureBuilder)	getTokenAnnotatedType() (in BioInferOntologyFeatureBuilder)
getDefaultSteps() (in Preprocessor)	getMergedEntityType() (in ModifierExampleBuilder)	getTokenAnnotatedType() (in FeatureBuilder)
getDefaultSteps() (in ToolChain)	getMergedEntityType() (in EntityExampleWriter)	getTokenFeatures() (in EntityExampleBuilder)
getDefinedBool() (in TEES.train)	getModel() (in Detector)	getTokenFeatures() (in FeatureBuilder)
getDefinedBoolOption() (in TEES.train)	getModel() (in TEES.classify)	getTokenFeatures() (in TriggerFeatureBuilder)
getDetector() (in TEES.train)	getMTMXAttrs() (in DrugFeatureBuilder)	getTokenFeatures() (in WordNetFeatureBuilder)
getDistribution() (in TEES.Utils.DetectHeads)	getName() (in IdSet)	getTokenFeatures() (in ModifierExampleBuilder)
getDocumentFolds() (in TEES.Core.DivideExamples)	getNamedEntityHeadTokens() (in EntityExampleBuilder)	getTokenHeadScores() (in SentenceGraph)
getDocumentId() (in TEES.Core.DivideExamples)	getNamedEntityTokenIds() (in ParseGraph)	getTokenHeadScores() (in TEES.Utils.DetectHeads)
getDocumentIds() (in TEES.Core.DivideExamples)	getNames() (in IdSet)	getTokenIdsByText() (in ParseGraph)
getDuplicatesMapping() (in TEES.Utils.STFormat.STTools)	getNECounts() (in TEES.Utils.InteractionXML.MapPhrases)	getTokenization() (in TEES.Utils.ProteinNameSplitter)
getEdges() (in Graph)	getNestedItems() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	getTokens() (in NameGazetteer)
getEdgeType() (in MultiEdgeFeatureBuilder)	getNestingChains() (in TEES.Utils.STFormat.Analyze)	getTokens() (in TEES.Utils.InteractionXML.ExportParse)
getElapsedTime() (in Timer)	getNewType() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)	getTokenText() (in SentenceGraph)
getElapsedTimeString() (in ProgressCounter)	getNextFreeId() (in TEES.Utils.InteractionXML.IDUtils)	getTokenText() (in TEES.Utils.InteractionXML.ExportParse)
getElementByAttrib() (in TEES.Tools.ProcessUtils)	getNumInstances() (in EvaluationData)	getTokenWeights() (in TEES.Classifiers.SVMMultiClassModelUtils)
getElementByAttrib() (in TEES.Utils.ElementTreeUtils)	getNumJobs() (in ClusterConnection)	getTopDir() (in TEES.Utils.Download)
getElementCounts() (in ExampleBuilder)	getNumJobs() (in UnixConnection)	getTP() (in EvaluationData)
getElementIndex() (in TEES.Tools.ProcessUtils)	getOutEdges() (in Graph)	getTriggers() (in TEES.Utils.DetectHeads)
getElementTypes() (in SentenceExampleWriter)	getOutInteractions() (in SentenceGraph)	getUnicode() (in TEES.Tools.StanfordParser)
getElementTypes() (in TEES.Utils.InteractionXML.SplitMergedElements)	getOutputDir() (in TEES.batch)	getUnzipped() (in ExternalClassifier)
getEmptyCorpus() (in TEES.Utils.InteractionXML.DeleteElements)	getOverlap() (in TEES.Utils.DetectHeads)	getUserName() (in UnixConnection)
getEntity() (in SentenceElements)	getParameters() (in ToolChain)	getValueSet() (in TEES.Utils.TableUtils)
getEntityHeadToken() (in TEES.Utils.DetectHeads)	getParameters() (in ExampleBuilder)	getWalks() (in Graph)
getEntityPredictions() (in TEES.Evaluators.EvaluateInteractionXML)	getParents() (in BioInferOntologyFeatureBuilder)	getWeights() (in TEES.Classifiers.SVMMultiClassModelUtils)
getEntityTokens() (in SentenceElements)	getParents() (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	getWeightsPosNeg() (in TEES.Classifiers.SVMMultiClassModelUtils)
getEntityType() (in FeatureBuilder)	getParse() (in TEES.Utils.ProteinNameSplitter)	getWorkFile() (in EventDetector)
getEPIBaseType() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)	getPathOldSinglePath() (in Graph)	GiulianoFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
getEventEVEXScore() (in TEES.Utils.STFormat.Scores)	getPaths() (in Graph)	GiulianoFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.GiulianoFeatureBuilder)
getEventPredictions() (in TEES.Evaluators.EvaluateInteractionXML)	getPatterns() (in GiulianoFeatureBuilder)	Graph (in TEES.Core.SimpleGraph)
getExampleCount() (in ExampleStats)	getPhraseDict() (in TEES.Utils.InteractionXML.MapPhrases)	GraphKernelFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
getExampleFile() (in ExternalClassifier)	getPhraseEntityMapping() (in TEES.Utils.InteractionXML.MapPhrases)	GraphKernelFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder)
getFeatureNames() (in TEES.Utils.CompareExamples)	getPhraseHeadToken() (in PhraseTriggerExampleBuilder)	greater (in TEES.Utils.STFormat.Scores)
getFeatureNames() (in TEES.Utils.CompareFeatures)	getPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	greater_equal (in TEES.Utils.STFormat.Scores)
getFileCounter() (in ExternalClassifier)	getPhraseTokens() (in PhraseTriggerExampleBuilder)	gumbel() (in TEES.Utils.STFormat.Scores)

H

I

IdSet (in TEES.Core)	insertPhrases() (in TEES.Tools.BLLIPParser)	isIDTask() (in TEES.Utils.STFormat.Validate)
IdSet (in TEES.Core.IdSet)	insertTokens() (in TEES.Tools.BLLIPParser)	isinf (in TEES.Utils.STFormat.Scores)
IDUtils (in TEES.Utils.InteractionXML)	install() (in TEES.Classifiers.SVMMultiClassClassifier)	isIntersentence() (in UnmergingExampleWriter)
importFrom() (in Model)	install() (in TEES.Evaluators.BioNLP11GeniaTools)	isLocal() (in UnixConnection)
incr (in TEES.Utils.Libraries.stats)	install() (in TEES.Tools.BANNER)	isName() (in Annotation)
indent() (in TEES.Utils.ElementTreeUtils)	install() (in TEES.Tools.BLLIPParser)	isnan (in TEES.Utils.STFormat.Scores)
index_exp (in TEES.Utils.STFormat.Scores)	install() (in TEES.Tools.GeniaSentenceSplitter)	isNegatableEPITrigger() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)
Inf (in TEES.Utils.STFormat.Scores)	install() (in TEES.Tools.StanfordParser)	isNegated() (in Annotation)
inf (in TEES.Utils.STFormat.Scores)	installBBData() (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	isNegative() (in SentenceExampleWriter)
Infinity (in TEES.Utils.STFormat.Scores)	installDrugBank() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	isPotentialBBInteraction() (in EdgeExampleBuilder)
infty (in TEES.Utils.STFormat.Scores)	installEvaluators() (in TEES.Utils.Convert.convertBioNLP)	isPotentialBIInteraction() (in EdgeExampleBuilder)
initLocalSettings() (in TEES.configure)	installPreconverted() (in TEES.Utils.Convert.convertBioNLP)	isPotentialCOInteraction() (in EdgeExampleBuilder)
initModel() (in Detector)	installRENData() (in TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder)	isPotentialCOTrigger() (in PhraseTriggerExampleBuilder)
initProgramTestMenu() (in TEES.Tools.Tool)	instanceCountsToString() (in EvaluationData)	isPotentialEPIInteraction() (in EdgeExampleBuilder)
initSentence() (in EVEXFeatureBuilder)	InteractionXML (in TEES.Utils)	isPotentialGeniaInteraction() (in EdgeExampleBuilder)
initSentence() (in GiulianoFeatureBuilder)	interpret() (in TEES.Utils.TableUtils)	isPotentialIDInteraction() (in EdgeExampleBuilder)
initSentence() (in TriggerFeatureBuilder)	invert (in TEES.Utils.STFormat.Scores)	isPotentialRELInteraction() (in EdgeExampleBuilder)
initVariables() (in Detector)	isBacteriaToken() (in TEES.Utils.InteractionXML.ExtendTriggers)	isPunct() (in Token)
insert() (in Model)	isDirected() (in Graph)	isSpeculative() (in Annotation)
insertParse() (in TEES.Tools.BLLIPParser)	isDuplicate() (in TEES.Core.ExampleUtils)	isstring() (in TEES.Utils.Libraries.pstat)
insertParse() (in TEES.Tools.StanfordParser)	isExtraWord() (in TEES.Utils.InteractionXML.ExtendTriggers)	itemfreq (in TEES.Utils.Libraries.stats)
insertParses() (in TEES.Tools.BLLIPParser)	isfinite (in TEES.Utils.STFormat.Scores)	iterparse() (in TEES.Utils.ElementTreeUtils)
insertParses() (in TEES.Tools.StanfordParser)	isIDCore() (in TEES.Utils.STFormat.Validate)

K

k (in TEES.Utils.InteractionXML.ExportParse)	kill() (in ProcessWrapper)	ksprob (in TEES.Utils.Libraries.stats)
keepEvent() (in TEES.Tools.GeniaEventsToSharedTask)	kruskalwallish (in TEES.Utils.Libraries.stats)	kurtosis (in TEES.Utils.Libraries.stats)
kendalltau (in TEES.Utils.Libraries.stats)	ks_2samp (in TEES.Utils.Libraries.stats)	kurtosistest (in TEES.Utils.Libraries.stats)

L

LA (in TEES.Utils.Libraries.stats)	lkendalltau() (in TEES.Utils.Libraries.stats)	logistic() (in TEES.Utils.STFormat.Scores)
laplace() (in TEES.Utils.STFormat.Scores)	lkruskalwallish() (in TEES.Utils.Libraries.stats)	lognormal() (in TEES.Utils.STFormat.Scores)
layoutLatex() (in TEES.Utils.TableUtils)	lks_2samp() (in TEES.Utils.Libraries.stats)	logseries() (in TEES.Utils.STFormat.Scores)
lbetacf() (in TEES.Utils.Libraries.stats)	lksprob() (in TEES.Utils.Libraries.stats)	LOUHI (in TEES.Utils.Settings)
lbetai() (in TEES.Utils.Libraries.stats)	lkurtosis() (in TEES.Utils.Libraries.stats)	lpaired() (in TEES.Utils.Libraries.stats)
lchisqprob() (in TEES.Utils.Libraries.stats)	llinregress() (in TEES.Utils.Libraries.stats)	lpearsonr() (in TEES.Utils.Libraries.stats)
lchisquare() (in TEES.Utils.Libraries.stats)	lmannwhitneyu() (in TEES.Utils.Libraries.stats)	lpercentileofscore() (in TEES.Utils.Libraries.stats)
lcumfreq() (in TEES.Utils.Libraries.stats)	lmean() (in TEES.Utils.Libraries.stats)	lpointbiserialr() (in TEES.Utils.Libraries.stats)
lcumsum() (in TEES.Utils.Libraries.stats)	lmedian() (in TEES.Utils.Libraries.stats)	lrankdata() (in TEES.Utils.Libraries.stats)
ldescribe() (in TEES.Utils.Libraries.stats)	lmedianscore() (in TEES.Utils.Libraries.stats)	lranksums() (in TEES.Utils.Libraries.stats)
ldexp (in TEES.Utils.STFormat.Scores)	lmode() (in TEES.Utils.Libraries.stats)	lrelfreq() (in TEES.Utils.Libraries.stats)
left_shift (in TEES.Utils.STFormat.Scores)	lmoment() (in TEES.Utils.Libraries.stats)	lsamplestdev() (in TEES.Utils.Libraries.stats)
length() (in TEES.Utils.Range)	load() (in IdSet)	lsamplevar() (in TEES.Utils.Libraries.stats)
lerfcc() (in TEES.Utils.Libraries.stats)	load() (in TEES.Utils.STFormat.STTools)	lscoreatpercentile() (in TEES.Utils.Libraries.stats)
less (in TEES.Utils.STFormat.Scores)	loadA1() (in TEES.Utils.STFormat.STTools)	lsem() (in TEES.Utils.Libraries.stats)
less_equal (in TEES.Utils.STFormat.Scores)	loadCorpus() (in TEES.Core.SentenceGraph)	LSFConnection (in TEES.Utils.Connection)
lF_oneway() (in TEES.Utils.Libraries.stats)	loadCorpus() (in SentenceExampleWriter)	LSFConnection (in TEES.Utils.Connection.LSFConnection)
lF_value() (in TEES.Utils.Libraries.stats)	loadCorpus() (in TEES.Utils.InteractionXML.CorpusElements)	LSFJobTemplate (in TEES.Utils.Connection.LSFConnection)
lfindwithin() (in TEES.Utils.Libraries.stats)	loadDocs() (in TEES.Utils.Convert.convertDDI)	lshellsort() (in TEES.Utils.Libraries.stats)
lfprob() (in TEES.Utils.Libraries.stats)	loadDrugBank() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	lskew() (in TEES.Utils.Libraries.stats)
lfriedmanchisquare() (in TEES.Utils.Libraries.stats)	loadEventXML() (in TEES.Tools.GeniaEventsToSharedTask)	lspearmanr() (in TEES.Utils.Libraries.stats)
lgammln() (in TEES.Utils.Libraries.stats)	loadExamples() (in SentenceExampleWriter)	lsquare_of_sums() (in TEES.Utils.Libraries.stats)
lgeometricmean() (in TEES.Utils.Libraries.stats)	loadOntologies() (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	lss() (in TEES.Utils.Libraries.stats)
lharmonicmean() (in TEES.Utils.Libraries.stats)	loadPages() (in TEES.Utils.Convert.SubtiWiki)	lstdev() (in TEES.Utils.Libraries.stats)
lhistogram() (in TEES.Utils.Libraries.stats)	loadPredictions() (in TEES.Core.ExampleUtils)	lsterr() (in TEES.Utils.Libraries.stats)
Libraries (in TEES.Utils)	loadRelOrA2() (in TEES.Utils.STFormat.STTools)	lsum() (in TEES.Utils.Libraries.stats)
lincr() (in TEES.Utils.Libraries.stats)	loadSet() (in TEES.Utils.STFormat.STTools)	lsumdiffsquared() (in TEES.Utils.Libraries.stats)
line (in TEES.Utils.Convert.processLPSN)	loadText() (in TEES.Utils.STFormat.STTools)	lsummult() (in TEES.Utils.Libraries.stats)
linedelimited() (in TEES.Utils.Libraries.pstat)	lobrientransform() (in TEES.Utils.Libraries.stats)	ltiecorrect() (in TEES.Utils.Libraries.stats)
lineincols() (in TEES.Utils.Libraries.pstat)	LOCAL (in TEES.Utils.Settings)	ltrim1() (in TEES.Utils.Libraries.stats)
lineincustcols() (in TEES.Utils.Libraries.pstat)	LOCAL_REMOTE (in TEES.Utils.Settings)	ltrimboth() (in TEES.Utils.Libraries.stats)
linexand() (in TEES.Utils.Libraries.pstat)	log (in TEES.Utils.STFormat.Scores)	lttest_1samp() (in TEES.Utils.Libraries.stats)
linexor() (in TEES.Utils.Libraries.pstat)	log10 (in TEES.Utils.STFormat.Scores)	lttest_ind() (in TEES.Utils.Libraries.stats)
linkDuplicates() (in TEES.Utils.Release)	log1p (in TEES.Utils.STFormat.Scores)	lttest_rel() (in TEES.Utils.Libraries.stats)
linregress (in TEES.Utils.Libraries.stats)	logaddexp (in TEES.Utils.STFormat.Scores)	lvar() (in TEES.Utils.Libraries.stats)
list2string() (in TEES.Utils.Libraries.pstat)	logaddexp2 (in TEES.Utils.STFormat.Scores)	lvariation() (in TEES.Utils.Libraries.stats)
listExecutables() (in TEES.Utils.Release)	logical_and (in TEES.Utils.STFormat.Scores)	lwilcoxont() (in TEES.Utils.Libraries.stats)
ListInteractors (in TEES.Utils.InteractionXML)	logical_not (in TEES.Utils.STFormat.Scores)	lz() (in TEES.Utils.Libraries.stats)
litemfreq() (in TEES.Utils.Libraries.stats)	logical_or (in TEES.Utils.STFormat.Scores)	lzprob() (in TEES.Utils.Libraries.stats)
little_endian (in TEES.Utils.STFormat.Scores)	logical_xor (in TEES.Utils.STFormat.Scores)	lzs() (in TEES.Utils.Libraries.stats)

M

m() (in PorterStemmer)	mannwhitneyu (in TEES.Utils.Libraries.stats)	mergeOutput() (in TEES.Tools.ProcessUtils)
mainFunc() (in TEES.Utils.ProteinNameSplitter)	mapEntities() (in TEES.Evaluators.EvaluateInteractionXML)	MergeParse (in TEES.Utils.InteractionXML)
mainTEESDir (in TEES.Utils.Release)	mapEntity() (in SentenceGraph)	mgrid (in TEES.Utils.STFormat.Scores)
makeConfigXML() (in TEES.Tools.BANNER)	mapIds() (in TEES.Classifiers.SVMMultiClassModelUtils)	minimum (in TEES.Utils.STFormat.Scores)
makeCorpusDivision() (in TEES.Core.ExampleUtils)	mapInteractions() (in SentenceGraph)	mismatch() (in TEES.Utils.Range)
makeCorpusFolds() (in TEES.Core.ExampleUtils)	mapNamesToIds() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	MixSets (in TEES.Utils.InteractionXML)
makeDDISubmissionFile() (in TEES.Utils.Convert.DDITools)	MapPhrases (in TEES.Utils.InteractionXML)	mixSets() (in TEES.Utils.InteractionXML.MixSets)
makeDETSubPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	mapSplits() (in TEES.Utils.DetectHeads)	mkdir() (in UnixConnection)
makeDivision() (in TEES.Core.ExampleUtils)	markFinished() (in ProgressCounter)	mod (in TEES.Utils.STFormat.Scores)
makeEntityElements() (in TEES.Tools.BANNER)	markForRemoval() (in TEES.Utils.STFormat.Scores)	mode (in TEES.Utils.Libraries.stats)
makeEntityGraph() (in SentenceGraph)	markNamedEntities() (in ParseGraph)	Model (in TEES.Core)
makeEvent() (in TEES.Utils.STFormat.Equiv)	markOmitSteps() (in StepSelector)	Model (in TEES.Core.Model)
makeExampleDivision() (in TEES.Core.ExampleUtils)	matchTokens() (in NameGazetteer)	MODEL_DIR (in TEES.Utils.Settings)
makeExampleFolds() (in TEES.Core.ExampleUtils)	MAXDIMS (in TEES.Utils.STFormat.Scores)	modelsMenuInitializer() (in TEES.configure)
makeFolds() (in TEES.Core.ExampleUtils)	maximum (in TEES.Utils.STFormat.Scores)	modf (in TEES.Utils.STFormat.Scores)
makeINSubPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	MCCLOSKY_BIOPARSINGMODEL_DIR (in TEES.Utils.Settings)	ModifierDetector (in TEES.Detectors)
makeJobScript() (in ClusterConnection)	mean (in TEES.Utils.Libraries.stats)	ModifierDetector (in TEES.Detectors.ModifierDetector)
makelol() (in TEES.Utils.Libraries.pstat)	median (in TEES.Utils.Libraries.stats)	ModifierExampleBuilder (in TEES.ExampleBuilders)
makePath() (in TEES.Utils.ElementTreeUtils)	medianscore (in TEES.Utils.Libraries.stats)	ModifierExampleBuilder (in TEES.ExampleBuilders.ModifierExampleBuilder)
makePhrase() (in TEES.Utils.InteractionXML.MapPhrases)	Menu (in TEES.Utils)	ModifierExampleWriter (in TEES.ExampleWriters)
makePhrases() (in TEES.Utils.InteractionXML.MapPhrases)	Menu (in TEES.Utils.Menu)	ModifierExampleWriter (in TEES.ExampleWriters.ModifierExampleWriter)
makeSentence() (in TEES.Tools.GeniaSentenceSplitter)	MenuSystem (in TEES.Utils.Menu)	moment (in TEES.Utils.Libraries.stats)
makeSentences() (in TEES.Tools.GeniaSentenceSplitter)	merge() (in TEES.Utils.Range)	moveBI (in TEES.Utils.Convert.convertBioNLP)
makeSentences() (in TEES.Tools.SentenceSplitter)	mergeAll() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	moveElements() (in TEES.Tools.GeniaSentenceSplitter)
makestr() (in TEES.Utils.Libraries.pstat)	MergeDuplicateEntities (in TEES.Utils.InteractionXML)	MultiEdgeFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
MakeSubset (in TEES.Utils.InteractionXML)	mergeDuplicateEntities() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	MultiEdgeFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.MultiEdgeFeatureBuilder)
makeSubset() (in TEES.Tools.ProcessUtils)	mergeDuplicateInteractions() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	multinomial() (in TEES.Utils.STFormat.Scores)
makeSubset() (in TEES.Utils.InteractionXML.MakeSubset)	mergeInteractionGraph() (in SentenceGraph)	multiply (in TEES.Utils.STFormat.Scores)
makeTokenSubPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	MergeNamedEntityTypes (in TEES.Utils.InteractionXML)	multivariate_normal() (in TEES.Utils.STFormat.Scores)

N

NameGazetteer (in TEES.ExampleBuilders.FeatureBuilders)	newaxis (in TEES.Utils.STFormat.Scores)	normalizeFeatureVector() (in FeatureBuilder)
NameGazetteer (in TEES.ExampleBuilders.FeatureBuilders.NameGazetteer)	newParseName (in TEES.Utils.ProteinNameSplitter)	normalizeFeatureVectors() (in TEES.Core.ExampleUtils)
NAN (in TEES.Utils.STFormat.Scores)	NINF (in TEES.Utils.STFormat.Scores)	normalizeScore() (in TEES.Utils.STFormat.Scores)
NaN (in TEES.Utils.STFormat.Scores)	NodalidaFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	normalizeText() (in NameGazetteer)
nan (in TEES.Utils.STFormat.Scores)	NodalidaFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.NodalidaFeatureBuilder)	normaltest (in TEES.Utils.Libraries.stats)
nbytes (in TEES.Utils.STFormat.Scores)	noncentral_chisquare() (in TEES.Utils.STFormat.Scores)	not_equal (in TEES.Utils.STFormat.Scores)
negateEvents() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)	noncentral_f() (in TEES.Utils.STFormat.Scores)	NOTHING (in TEES.Core.Model)
negateType() (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)	nonrepeats() (in TEES.Utils.Libraries.pstat)	NOTHING (in TEES.Detectors.ToolChain)
negative (in TEES.Utils.STFormat.Scores)	normal() (in TEES.Utils.STFormat.Scores)	numpyAvailable (in TEES.Classifiers.SVMMultiClassModelUtils)
negative_binomial() (in TEES.Utils.STFormat.Scores)	normalizeDrugName() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	NZERO (in TEES.Utils.STFormat.Scores)

O

P

package() (in TEES.Utils.STFormat.STTools)	pi (in TEES.Utils.STFormat.Scores)	printStepTime() (in StepSelector)
paired (in TEES.Utils.Libraries.stats)	PINF (in TEES.Utils.STFormat.Scores)	printText() (in Menu)
Parameters (in TEES.Utils)	pl() (in TEES.Utils.Libraries.pstat)	process() (in Preprocessor)
pareto() (in TEES.Utils.STFormat.Scores)	plotManualEvaluationPrecisions() (in TEES.Utils.STFormat.Scores)	process() (in ToolChain)
parse() (in TEES.Tools.BLLIPParser)	pnToString() (in EvaluationData)	process() (in TEES.Utils.STFormat.Equiv)
parse__version__ (in TEES.Tools.BANNER)	pointbiserialr (in TEES.Utils.Libraries.stats)	processCorpora() (in TEES.Evaluators.EvaluateInteractionXML)
parse__version__ (in TEES.Tools.GeniaEventsToSharedTask)	poisson() (in TEES.Utils.STFormat.Scores)	processCorpus() (in ExampleBuilder)
ParseGraph (in TEES.Utils.InteractionXML)	poll() (in ProcessWrapper)	processCorpus() (in TEES.Utils.InteractionXML.DeleteAttributes)
ParseGraph (in TEES.Utils.InteractionXML.ParseGraph)	pool() (in BinaryEvaluator)	processCorpus() (in TEES.Utils.InteractionXML.DeleteElements)
ParseGraphNode (in TEES.Utils.InteractionXML.ParseGraph)	pool() (in Evaluator)	processCorpus() (in TEES.Utils.InteractionXML.DivideSets)
parseModel() (in TEES.Classifiers.SVMMultiClassModelUtils)	PorterStemmer (in TEES.Utils.Libraries)	processCorpus() (in TEES.Utils.InteractionXML.ListInteractors)
parseNodes() (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	PorterStemmer (in TEES.Utils.Libraries.PorterStemmer)	processCorpus() (in TEES.Utils.InteractionXML.MapPhrases)
parseResults() (in TEES.Evaluators.BioNLP11GeniaTools)	porterStemmerSingleton (in TEES.Utils.Libraries.PorterStemmer)	processDocument() (in TEES.Evaluators.EvaluateInteractionXML)
ParseStats (in TEES.Utils.InteractionXML)	posSuperTypes (in TEES.ExampleBuilders.FeatureBuilders.FeatureBuilder)	processDocument() (in ExampleBuilder)
parseStats() (in TEES.Utils.InteractionXML.ParseStats)	power() (in TEES.Utils.STFormat.Scores)	processLPSN (in TEES.Utils.Convert)
pathMenuInitializer() (in TEES.configure)	prepareCommand() (in TEES.batch)	processParses() (in TEES.Utils.Convert.convertBioNLP)
pathname (in TEES.Utils.Settings)	prepareDrugBank() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	processScores() (in TEES.Utils.STFormat.Scores)
pbar (in TEES.Utils.Download)	prepareTokens() (in NameGazetteer)	processSentence() (in ExampleBuilder)
PBSConnection (in TEES.Utils.Connection)	Preprocessor (in TEES.Detectors)	processSentence() (in TEES.Utils.InteractionXML.DeleteElements)
PBSConnection (in TEES.Utils.Connection.PBSConnection)	Preprocessor (in TEES.Detectors.Preprocessor)	processSentence() (in TEES.Utils.InteractionXML.SplitMergedElements)
PBSJobTemplate (in TEES.Utils.Connection.PBSConnection)	prfToString() (in EvaluationData)	ProcessUtils (in TEES.Tools)
pearsonr (in TEES.Utils.Libraries.stats)	printBorder() (in Menu)	ProcessWrapper (in TEES.Tools.ProcessUtils)
pennPOSToWordNet() (in WordNetFeatureBuilder)	printcc() (in TEES.Utils.Libraries.pstat)	progressbar (in TEES.Utils.Libraries)
Percentage (in TEES.Utils.Libraries.progressbar)	printincols() (in TEES.Utils.Libraries.pstat)	ProgressBar (in TEES.Utils.Libraries.progressbar)
percentage() (in ProgressBar)	printl() (in TEES.Utils.Libraries.pstat)	ProgressBarWidget (in TEES.Utils.Libraries.progressbar)
percentileofscore (in TEES.Utils.Libraries.stats)	printLines() (in TEES.Evaluators.BioNLP11GeniaTools)	ProgressBarWidgetHFill (in TEES.Utils.Libraries.progressbar)
permutation() (in TEES.Utils.STFormat.Scores)	printLinesBX() (in TEES.Evaluators.BioNLP11GeniaTools)	ProgressCounter (in TEES.Utils)
PhraseTriggerExampleBuilder (in TEES.ExampleBuilders)	printNode() (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	ProgressCounter (in TEES.Utils.ProgressCounter)
PhraseTriggerExampleBuilder (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	printOptions() (in Menu)	ProteinNameSplitter (in TEES.Utils)
PhraseTriggerExampleWriter (in TEES.ExampleWriters)	printStats() (in ExampleStats)	pstat (in TEES.Utils.Libraries)
PhraseTriggerExampleWriter (in TEES.ExampleWriters.PhraseTriggerExampleWriter)	printStats() (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	PZERO (in TEES.Utils.STFormat.Scores)

Q

QUIT (in Option)

R

r() (in PorterStemmer)	RecallAdjust (in TEES.Core)	removeUnconnectedEntities() (in TEES.Utils.InteractionXML.RemoveUnconnectedEntities)
r_ (in TEES.Utils.STFormat.Scores)	RecallAdjust (in TEES.Core.RecallAdjust)	removeUnusedTriggers() (in TEES.Utils.STFormat.Validate)
rad2deg (in TEES.Utils.STFormat.Scores)	reciprocal (in TEES.Utils.STFormat.Scores)	replace() (in TEES.Utils.Libraries.pstat)
radians (in TEES.Utils.STFormat.Scores)	recode() (in TEES.Utils.Libraries.pstat)	resetAnalyses() (in Graph)
RAISE (in TEES.Utils.STFormat.Scores)	Release (in TEES.Utils)	resetStats() (in EvaluationData)
rand() (in TEES.Utils.STFormat.Scores)	RELFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	ResolveEPITriggerTypes (in TEES.Utils.InteractionXML)
randint() (in TEES.Utils.STFormat.Scores)	RELFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder)	resolveHeads() (in TEES.Utils.ProteinNameSplitter)
randn() (in TEES.Utils.STFormat.Scores)	relfreq (in TEES.Utils.Libraries.stats)	ResolveIdentityChains (in TEES.Utils.InteractionXML)
random_integers() (in TEES.Utils.STFormat.Scores)	remainder (in TEES.Utils.STFormat.Scores)	resolveInteractions() (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)
random_sample() (in TEES.Utils.STFormat.Scores)	remap() (in TEES.Utils.Libraries.pstat)	resultsToGraph() (in TEES.Utils.STFormat.Scores)
RandomFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	remapKeys() (in TEES.Utils.TableUtils)	ReverseBar (in TEES.Utils.Libraries.progressbar)
RandomFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.RandomFeatureBuilder)	removeAll() (in TEES.Utils.ElementTreeUtils)	right_shift (in TEES.Utils.STFormat.Scores)
Range (in TEES.Utils)	removeArguments() (in TEES.Utils.STFormat.Validate)	rint (in TEES.Utils.STFormat.Scores)
rankdata (in TEES.Utils.Libraries.stats)	removeAttributes() (in TEES.Utils.InteractionXML.DeleteAttributes)	RotatingMarker (in TEES.Utils.Libraries.progressbar)
ranksums (in TEES.Utils.Libraries.stats)	removeChildren() (in SentenceExampleWriter)	roundlist() (in TEES.Utils.Libraries.pstat)
rayleigh() (in TEES.Utils.STFormat.Scores)	removeDocuments() (in TEES.Evaluators.BioNLP11GeniaTools)	RoundTrip (in TEES.Utils.STFormat)
readBacsu() (in TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder)	RemoveDuplicateDependencies (in TEES.Utils.InteractionXML)	roundTrip() (in TEES.Utils.STFormat.RoundTrip)
readCSV() (in TEES.Utils.TableUtils)	removeDuplicates() (in TEES.Core.ExampleUtils)	RUBY_PATH (in TEES.Utils.DefaultSettings)
readDependencyAnnotation() (in TEES.Utils.STFormat.STTools)	removeDuplicates() (in TEES.Tools.GeniaEventsToSharedTask)	RUBY_PATH (in TEES.Utils.Settings)
readEvent() (in TEES.Utils.STFormat.STTools)	removeDuplicates() (in TEES.Utils.STFormat.Validate)	run() (in RecallAdjust)
readExamples() (in TEES.Core.ExampleUtils)	removeElements() (in TEES.Utils.InteractionXML.DeleteElements)	run() (in TEES.Evaluators.EvaluateInteractionXML)
readPenn() (in TEES.Tools.BLLIPParser)	removeEntities() (in TEES.Utils.STFormat.Validate)	run() (in ExampleBuilder)
readProteinNames() (in TEES.Utils.Convert.SubtiWiki)	removeFeatures() (in TEES.Utils.CompareExamples)	run() (in TEES.Tools.BANNER)
readRAnnotation() (in TEES.Utils.STFormat.STTools)	removeHeads() (in TEES.Utils.DetectHeads)	run() (in TEES.Tools.GeniaEventsToSharedTask)
readStarAnnotation() (in TEES.Utils.STFormat.STTools)	removeInstance() (in EvaluationData)	run() (in UnixConnection)
readSubtiwiki() (in TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder)	removeKeys() (in TEES.Utils.TableUtils)	run() (in MenuSystem)
readTAnnotation() (in TEES.Utils.STFormat.STTools)	removeLog() (in StreamModifier)	runBLLIPParser() (in TEES.Tools.BLLIPParser)
readWords() (in TEES.ExampleBuilders.ModifierExampleBuilder)	removeNamedEntityPhrases() (in TEES.Utils.InteractionXML.MapPhrases)	runSentenceProcess() (in TEES.Tools.ProcessUtils)
rebuildEventList() (in TEES.Utils.STFormat.Equiv)	removeNonNameEntities() (in SentenceExampleWriter)	runStanford() (in TEES.Tools.StanfordParser)
RecalculateIds (in TEES.Utils.InteractionXML)	removeTempUnzipped() (in TEES.Classifiers.ExternalClassifier)
recalculateIds() (in TEES.Utils.InteractionXML.RecalculateIds)	RemoveUnconnectedEntities (in TEES.Utils.InteractionXML)

S

s_ (in TEES.Utils.STFormat.Scores)	setState() (in ExternalClassifier)	splitTokenizationName (in TEES.Utils.ProteinNameSplitter)
samplestdev (in TEES.Utils.Libraries.stats)	setTag() (in FeatureBuilder)	splitTokens() (in TEES.Utils.ProteinNameSplitter)
samplevar (in TEES.Utils.Libraries.stats)	setTempWorkDir() (in Detector)	sqrt (in TEES.Utils.STFormat.Scores)
save() (in Model)	setTimeStamp() (in StreamModifier)	square (in TEES.Utils.STFormat.Scores)
save() (in NameGazetteer)	setTimeStamp() (in TEES.Utils.Stream)	square_of_sums (in TEES.Utils.Libraries.stats)
saveAs() (in Model)	Settings (in TEES.Utils)	ss (in TEES.Utils.Libraries.stats)
saveCSV() (in EvaluationData)	setto() (in PorterStemmer)	standard_cauchy() (in TEES.Utils.STFormat.Scores)
saveCSV() (in Evaluator)	setup (in TEES)	standard_exponential() (in TEES.Utils.STFormat.Scores)
saveIds() (in ExampleBuilder)	setWorkDir() (in Detector)	standard_gamma() (in TEES.Utils.STFormat.Scores)
saveStr() (in Detector)	setWorkDir() (in EventDetector)	standard_normal() (in TEES.Utils.STFormat.Scores)
saveStrings() (in Detector)	shellsort (in TEES.Utils.Libraries.stats)	standard_t() (in TEES.Utils.STFormat.Scores)
ScalarType (in TEES.Utils.STFormat.Scores)	SHIFT_DIVIDEBYZERO (in TEES.Utils.STFormat.Scores)	standardize() (in TEES.Utils.STFormat.Scores)
scaleRange() (in TEES.Core.RecallAdjust)	SHIFT_INVALID (in TEES.Utils.STFormat.Scores)	STANFORD_PARSER_DIR (in TEES.Utils.Settings)
scaleVal() (in TEES.Core.RecallAdjust)	SHIFT_OVERFLOW (in TEES.Utils.STFormat.Scores)	StanfordParser (in TEES.Tools)
scoreatpercentile (in TEES.Utils.Libraries.stats)	SHIFT_UNDERFLOW (in TEES.Utils.STFormat.Scores)	start() (in ProgressBar)
Scores (in TEES.Utils.STFormat)	show() (in Menu)	start() (in Timer)
scp() (in UnixConnection)	show() (in Option)	startTimeToString() (in Timer)
sctypeDict (in TEES.Utils.STFormat.Scores)	showAnalyses() (in Graph)	stats (in TEES.Utils.Libraries)
sctypeNA (in TEES.Utils.STFormat.Scores)	showLastUpdate() (in ProgressCounter)	stdev (in TEES.Utils.Libraries.stats)
sctypes (in TEES.Utils.STFormat.Scores)	shuffle() (in TEES.Utils.STFormat.Scores)	stem() (in PorterStemmer)
seed() (in TEES.Utils.STFormat.Scores)	sign (in TEES.Utils.STFormat.Scores)	stem() (in TEES.Utils.Libraries.PorterStemmer)
selectBestMatch() (in TEES.Utils.InteractionXML.MapPhrases)	signaltonoise (in TEES.Utils.Libraries.stats)	stemTokens() (in ParseGraph)
selectRowsCSV() (in TEES.Utils.TableUtils)	signbit (in TEES.Utils.STFormat.Scores)	step1ab() (in PorterStemmer)
sem (in TEES.Utils.Libraries.stats)	simpleabut() (in TEES.Utils.Libraries.pstat)	step1c() (in PorterStemmer)
SentenceElements (in TEES.Utils.InteractionXML)	SimpleGraph (in TEES.Core)	step2() (in PorterStemmer)
SentenceElements (in TEES.Utils.InteractionXML.SentenceElements)	sin (in TEES.Utils.STFormat.Scores)	step3() (in PorterStemmer)
SentenceExampleWriter (in TEES.ExampleWriters)	SingleStageDetector (in TEES.Detectors)	step4() (in PorterStemmer)
SentenceExampleWriter (in TEES.ExampleWriters.SentenceExampleWriter)	SingleStageDetector (in TEES.Detectors.SingleStageDetector)	step5() (in PorterStemmer)
SentenceGraph (in TEES.Core)	sinh (in TEES.Utils.STFormat.Scores)	stepArgs() (in ToolChain)
SentenceGraph (in TEES.Core.SentenceGraph)	skew (in TEES.Utils.Libraries.stats)	StepSelector (in TEES.Detectors)
SentenceSplitter (in TEES.Tools)	skewtest (in TEES.Utils.Libraries.stats)	StepSelector (in TEES.Detectors.StepSelector)
set_state() (in TEES.Utils.STFormat.Scores)	SLURMConnection (in TEES.Utils.Connection)	sterr (in TEES.Utils.Libraries.stats)
setArgForAllSteps() (in ToolChain)	SLURMConnection (in TEES.Utils.Connection.SLURMConnection)	STFormat (in TEES.Utils)
setAttr() (in Menu)	SLURMJobTemplate (in TEES.Utils.Connection.SLURMConnection)	stop() (in Timer)
setAttr() (in MenuSystem)	sortby() (in TEES.Utils.Libraries.pstat)	Stream (in TEES.Utils)
setClosingMessage() (in TEES.configure)	sortByScore() (in TEES.Utils.STFormat.Scores)	StreamModifier (in TEES.Utils.Stream)
setConnection() (in Detector)	sortInteractionIds() (in TEES.Utils.InteractionXML.IDUtils)	STTools (in TEES.Utils.STFormat)
setConnection() (in EventDetector)	sortInteractionsById() (in UnmergingExampleBuilder)	subcomponent (in TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder)
setDefault() (in Menu)	SPACE (in Option)	submit() (in ClusterConnection)
setDefaultElement() (in TEES.Tools.ProcessUtils)	spearmanr (in TEES.Utils.Libraries.stats)	submit() (in SLURMConnection)
setDefaultElement() (in TEES.Utils.ElementTreeUtils)	speculationWords (in TEES.ExampleBuilders.ModifierExampleBuilder)	submit() (in UnixConnection)
setElementType() (in SentenceExampleWriter)	speedNX() (in TEES.Core.SimpleGraph)	submitJob() (in TEES.batch)
setFeature() (in ExampleBuilder)	speedSimple() (in TEES.Core.SimpleGraph)	Subset (in TEES.Utils.InteractionXML)
setFeature() (in FeatureBuilder)	Split (in TEES.Core)	SubtiWiki (in TEES.Utils.Convert)
setFeatureVector() (in FeatureBuilder)	split (in TEES.Utils.Convert.processLPSN)	subtract (in TEES.Utils.STFormat.Scores)
setFeatureVector() (in MultiEdgeFeatureBuilder)	split2 (in TEES.Utils.Convert.processLPSN)	sum (in TEES.Utils.Libraries.stats)
setIndent() (in StreamModifier)	splitDefaultDepName (in TEES.Utils.ProteinNameSplitter)	sumdiffsquared (in TEES.Utils.Libraries.stats)
setIndent() (in TEES.Utils.Stream)	splitHyphenDepName (in TEES.Utils.ProteinNameSplitter)	summult (in TEES.Utils.Libraries.stats)
setIntermediateFile() (in ToolChain)	splitInteractionId() (in TEES.Utils.InteractionXML.IDUtils)	supergroup (in TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder)
setIntermediateFiles() (in ToolChain)	splitMerged() (in TEES.Utils.InteractionXML.SplitMergedElements)	SVM_MULTICLASS_DIR (in TEES.Utils.Settings)
setLimits() (in StepSelector)	SplitMergedElements (in TEES.Utils.InteractionXML)	svmMenuInitializer() (in TEES.configure)
setLocal() (in TEES.Utils.Settings)	splitMergedElements() (in TEES.Utils.InteractionXML.SplitMergedElements)	SVMMultiClassClassifier (in TEES.Classifiers)
setLog() (in StreamModifier)	splitParensDepName (in TEES.Utils.ProteinNameSplitter)	SVMMultiClassClassifier (in TEES.Classifiers.SVMMultiClassClassifier)
setLog() (in TEES.Utils.Stream)	splits (in TEES.Utils.Convert.processLPSN)	SVMMultiClassModelUtils (in TEES.Classifiers)
setNoIntermediateFiles() (in ToolChain)	splitSlashDepName (in TEES.Utils.ProteinNameSplitter)	system (in Menu)

T

TableUtils (in TEES.Utils)	thisPath (in TEES.Utils.STFormat.ConvertXML)	toStringConcise() (in BinaryEvaluator)
tan (in TEES.Utils.STFormat.Scores)	thisPath (in TEES.Utils.STFormat.Equiv)	toStringConcise() (in EvaluationData)
tanh (in TEES.Utils.STFormat.Scores)	thisPath (in TEES.Utils.STFormat.RoundTrip)	toStringConcise() (in Evaluator)
TEES	thisPath (in TEES.Utils.STFormat.Scores)	toUndirected() (in Graph)
TEES_RESOURCES (in TEES.Utils.Settings)	threshold (in TEES.Utils.Libraries.stats)	train (in TEES)
tempEVALUATOR (in TEES.Utils.Settings)	threshold() (in AveragingMultiClassEvaluator)	train() (in AllCorrectClassifier)
tempURL (in TEES.Utils.Settings)	tiecorrect (in TEES.Utils.Libraries.stats)	train() (in AllTrueClassifier)
test() (in AllCorrectClassifier)	Timer (in TEES.Utils)	train() (in Classifier)
test() (in AllTrueClassifier)	Timer (in TEES.Utils.Timer)	train() (in ExternalClassifier)
test() (in TEES.Tools.BANNER)	tmean (in TEES.Utils.Libraries.stats)	train() (in Detector)
testPrograms() (in TEES.Tools.Tool)	toDict() (in AveragingMultiClassEvaluator)	train() (in EventDetector)
thisPath (in TEES.Core.RecallAdjust)	toDict() (in BinaryEvaluator)	train() (in SingleStageDetector)
thisPath (in TEES.Detectors.Preprocessor)	toDict() (in EvaluationData)	train() (in TEES.train)
thisPath (in TEES.Evaluators.BioNLP11GeniaTools)	toDict() (in Evaluator)	trainUnmergingDetector() (in EventDetector)
thisPath (in TEES.ExampleBuilders.EdgeExampleBuilder)	toDict() (in TEES.Utils.Parameters)	transferClassifications() (in TEES.Utils.Convert.DDITools)
thisPath (in TEES.ExampleBuilders.EntityExampleBuilder)	toGraphviz() (in Graph)	triangular() (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.ExampleBuilders.FeatureBuilders.GiulianoFeatureBuilder)	toInteractionXML() (in TEES.Utils.STFormat.ConvertXML)	TriggerFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)
thisPath (in TEES.ExampleBuilders.FeatureBuilders.NameGazetteer)	Token (in TEES.Utils.ProteinNameSplitter)	TriggerFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.TriggerFeatureBuilder)
thisPath (in TEES.ExampleBuilders.ModifierExampleBuilder)	TokenFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	trim1 (in TEES.Utils.Libraries.stats)
thisPath (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	TokenFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.TokenFeatureBuilder)	trimboth (in TEES.Utils.Libraries.stats)
thisPath (in TEES.ExampleBuilders.UnmergingExampleBuilder)	tokenIdPrefix (in TEES.Utils.ProteinNameSplitter)	True_ (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.ExampleWriters.BioTextExampleWriter)	tokenize() (in TEES.Utils.InteractionXML.ExtendTriggers)	true_divide (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.ExampleWriters.SentenceExampleWriter)	tokenizeModel() (in TEES.Classifiers.SVMMultiClassModelUtils)	trunc (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.Tools.GeniaSentenceSplitter)	tokens (in TEES.Utils.Convert.processLPSN)	tsem (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.Convert.DDITools)	tokenString (in TEES.Utils.Convert.processLPSN)	tstdev (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.Convert.convertBioNLP)	Tool (in TEES.Tools)	ttest_1samp (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.Convert.convertDDI)	ToolChain (in TEES.Detectors)	ttest_ind (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.FindHeads)	ToolChain (in TEES.Detectors.ToolChain)	ttest_rel (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.InteractionXML.Catenate)	Tools (in TEES)	tuplesToCharOffset() (in TEES.Utils.Range)
thisPath (in TEES.Utils.InteractionXML.CorpusElements)	toolsMenuInitializer() (in TEES.configure)	tvar (in TEES.Utils.Libraries.stats)
thisPath (in TEES.Utils.InteractionXML.DeleteElements)	toSTFormat() (in TEES.Utils.STFormat.ConvertXML)	type (in AveragingMultiClassEvaluator)
thisPath (in TEES.Utils.InteractionXML.DivideSets)	toStr() (in TEES.Utils.ElementTreeUtils)	typecodes (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.Utils.InteractionXML.MergeDuplicateEntities)	toString() (in ParseGraphNode)	typeDict (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.Utils.InteractionXML.MixSets)	toString() (in TEES.Utils.Parameters)	typeNA (in TEES.Utils.STFormat.Scores)
thisPath (in TEES.Utils.InteractionXML.RemoveUnconnectedEntities)	toString() (in Timer)
thisPath (in TEES.Utils.InteractionXML.Subset)	toStringConcise() (in AveragingMultiClassEvaluator)

U

UFUNC_BUFSIZE_DEFAULT (in TEES.Utils.STFormat.Scores)	UnmergingExampleWriter (in TEES.ExampleWriters)	update() (in ProgressCounter)
UFUNC_PYVALS_NAME (in TEES.Utils.STFormat.Scores)	UnmergingExampleWriter (in TEES.ExampleWriters.UnmergingExampleWriter)	updateIds() (in TEES.Utils.STFormat.STTools)
unEscDict (in TEES.Utils.InteractionXML.ExportParse)	update() (in Bar)	updateRange() (in TEES.Utils.STFormat.Scores)
uniform() (in TEES.Utils.STFormat.Scores)	update() (in ETA)	upload() (in UnixConnection)
unique() (in TEES.Utils.Libraries.pstat)	update() (in FileTransferSpeed)	URL (in TEES.Utils.DefaultSettings)
UnixConnection (in TEES.Utils.Connection)	update() (in Percentage)	URL (in TEES.Utils.Settings)
UnixConnection (in TEES.Utils.Connection.UnixConnection)	update() (in ProgressBar)	urlBase (in TEES.Utils.DefaultSettings)
UnmergingDetector (in TEES.Detectors)	update() (in ProgressBarWidget)	urlBase (in TEES.Utils.Settings)
UnmergingDetector (in TEES.Detectors.UnmergingDetector)	update() (in ProgressBarWidgetHFill)	Utils (in TEES)
UnmergingExampleBuilder (in TEES.ExampleBuilders)	update() (in ReverseBar)
UnmergingExampleBuilder (in TEES.ExampleBuilders.UnmergingExampleBuilder)	update() (in RotatingMarker)

V

v (in TEES.Utils.InteractionXML.ExportParse)	validateREL() (in TEES.Utils.STFormat.Validate)	vonmises() (in TEES.Utils.STFormat.Scores)
Validate (in TEES.Utils.STFormat)	var (in TEES.Utils.Libraries.stats)	vowelinstem() (in PorterStemmer)
validate() (in TEES.Utils.STFormat.Validate)	variation (in TEES.Utils.Libraries.stats)	VUORI (in TEES.Utils.Settings)

W

waitForJob() (in UnixConnection)	write() (in BioTextExampleWriter)	writeSet() (in TEES.Utils.STFormat.STTools)
waitForJobCount() (in UnixConnection)	write() (in SentenceExampleWriter)	writeTAnnotation() (in TEES.Utils.STFormat.STTools)
waitForJobs() (in UnixConnection)	write() (in ETWriter)	writeToLog() (in StreamModifier)
waitForJobs() (in TEES.batch)	write() (in TEES.Utils.ElementTreeUtils)	writeToLog() (in TEES.Utils.Stream)
waitForProcess() (in TEES.Tools.ProcessUtils)	write() (in TEES.Utils.STFormat.STTools)	writeToScreen() (in TEES.Utils.Stream)
wald() (in TEES.Utils.STFormat.Scores)	write() (in StreamModifier)	writeToStream() (in StreamModifier)
weibull() (in TEES.Utils.STFormat.Scores)	writecc() (in TEES.Utils.Libraries.stats)	writeXML() (in ModifierExampleWriter)
wilcoxont (in TEES.Utils.Libraries.stats)	writeCSV() (in TEES.Utils.TableUtils)	writeXML() (in SentenceExampleWriter)
WordNetFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders)	writeEvents() (in TEES.Utils.STFormat.STTools)	writeXMLSentence() (in EdgeExampleWriter)
WordNetFeatureBuilder (in TEES.ExampleBuilders.FeatureBuilders.WordNetFeatureBuilder)	writeExamples() (in TEES.Core.ExampleUtils)	writeXMLSentence() (in EntityExampleWriter)
workdir() (in TEES.train)	writeLatex() (in TEES.Utils.TableUtils)	writeXMLSentence() (in PhraseTriggerExampleWriter)
WRAP (in TEES.Utils.STFormat.Scores)	writeModel() (in TEES.Classifiers.SVMMultiClassModelUtils)	writeXMLSentence() (in SentenceExampleWriter)
write() (in IdSet)	writePredictions() (in TEES.Core.ExampleUtils)	writeXMLSentence() (in UnmergingExampleWriter)

X

xcombine() (in TEES.Utils.Libraries.combine)

Z

z (in TEES.Utils.Libraries.stats)	zprob (in TEES.Utils.Libraries.stats)
zipf() (in TEES.Utils.STFormat.Scores)	zs (in TEES.Utils.Libraries.stats)

_

__author_email__ (in TEES.Utils.Libraries.progressbar)	__package__ (in TEES.Classifiers)	__package__ (in TEES.Utils.InteractionXML.CopyParse)
__calculateAUC() (in BinaryEvaluator)	__package__ (in TEES.Core.DivideCorpus)	__package__ (in TEES.Utils.InteractionXML.CorpusElements)
__call__() (in Dispatch)	__package__ (in TEES.Core.DivideExamples)	__package__ (in TEES.Utils.InteractionXML.DeleteAttributes)
__del__() (in AllCorrectClassifier)	__package__ (in TEES.Core.ExampleUtils)	__package__ (in TEES.Utils.InteractionXML.DeleteElements)
__del__() (in AllTrueClassifier)	__package__ (in TEES.Core.IdSet)	__package__ (in TEES.Utils.InteractionXML.DivideSets)
__del__() (in Model)	__package__ (in TEES.Core.Model)	__package__ (in TEES.Utils.InteractionXML.ExportParse)
__del__() (in Detector)	__package__ (in TEES.Core.RecallAdjust)	__package__ (in TEES.Utils.InteractionXML.ExtendTriggers)
__del__() (in ProgressCounter)	__package__ (in TEES.Core.SentenceGraph)	__package__ (in TEES.Utils.InteractionXML.FixAltOffsets)
__getitem__() (in IdSet)	__package__ (in TEES.Core.SimpleGraph)	__package__ (in TEES.Utils.InteractionXML.IDUtils)
__getWalks() (in Graph)	__package__ (in TEES.Core.Split)	__package__ (in TEES.Utils.InteractionXML.ListInteractors)
__init__() (in AllCorrectClassifier)	__package__ (in TEES.Core)	__package__ (in TEES.Utils.InteractionXML.MakeSubset)
__init__() (in AllTrueClassifier)	__package__ (in TEES.Detectors.CODetector)	__package__ (in TEES.Utils.InteractionXML.MapPhrases)
__init__() (in ExternalClassifier)	__package__ (in TEES.Detectors.Detector)	__package__ (in TEES.Utils.InteractionXML.MergeDuplicateEntities)
__init__() (in SVMMultiClassClassifier)	__package__ (in TEES.Detectors.EdgeDetector)	__package__ (in TEES.Utils.InteractionXML.MergeNamedEntityTypes)
__init__() (in IdSet)	__package__ (in TEES.Detectors.EntityDetector)	__package__ (in TEES.Utils.InteractionXML.MergeParse)
__init__() (in Model)	__package__ (in TEES.Detectors.EventDetector)	__package__ (in TEES.Utils.InteractionXML.MixSets)
__init__() (in SentenceGraph)	__package__ (in TEES.Detectors.ModifierDetector)	__package__ (in TEES.Utils.InteractionXML.ParseGraph)
__init__() (in Graph)	__package__ (in TEES.Detectors.Preprocessor)	__package__ (in TEES.Utils.InteractionXML.ParseStats)
__init__() (in CODetector)	__package__ (in TEES.Detectors.SingleStageDetector)	__package__ (in TEES.Utils.InteractionXML.RecalculateIds)
__init__() (in Detector)	__package__ (in TEES.Detectors.StepSelector)	__package__ (in TEES.Utils.InteractionXML.RemoveDuplicateDependencies)
__init__() (in EdgeDetector)	__package__ (in TEES.Detectors.ToolChain)	__package__ (in TEES.Utils.InteractionXML.RemoveUnconnectedEntities)
__init__() (in EntityDetector)	__package__ (in TEES.Detectors.UnmergingDetector)	__package__ (in TEES.Utils.InteractionXML.ResolveEPITriggerTypes)
__init__() (in EventDetector)	__package__ (in TEES.Detectors)	__package__ (in TEES.Utils.InteractionXML.ResolveIdentityChains)
__init__() (in ModifierDetector)	__package__ (in TEES.Evaluators.AveragingMultiClassEvaluator)	__package__ (in TEES.Utils.InteractionXML.SentenceElements)
__init__() (in Preprocessor)	__package__ (in TEES.Evaluators.BinaryEvaluator)	__package__ (in TEES.Utils.InteractionXML.SplitMergedElements)
__init__() (in SingleStageDetector)	__package__ (in TEES.Evaluators.BioNLP11GeniaTools)	__package__ (in TEES.Utils.InteractionXML.Subset)
__init__() (in StepSelector)	__package__ (in TEES.Evaluators.EvaluateInteractionXML)	__package__ (in TEES.Utils.InteractionXML)
__init__() (in ToolChain)	__package__ (in TEES.Evaluators.Evaluator)	__package__ (in TEES.Utils.Libraries.PorterStemmer)
__init__() (in UnmergingDetector)	__package__ (in TEES.Evaluators)	__package__ (in TEES.Utils.Libraries)
__init__() (in AveragingMultiClassEvaluator)	__package__ (in TEES.ExampleBuilders.EdgeExampleBuilder)	__package__ (in TEES.Utils.Libraries.combine)
__init__() (in BinaryEvaluator)	__package__ (in TEES.ExampleBuilders.EntityExampleBuilder)	__package__ (in TEES.Utils.Libraries.progressbar)
__init__() (in EvaluationData)	__package__ (in TEES.ExampleBuilders.ExampleBuilder)	__package__ (in TEES.Utils.Libraries.pstat)
__init__() (in EdgeExampleBuilder)	__package__ (in TEES.ExampleBuilders.ExampleStats)	__package__ (in TEES.Utils.Libraries.stats)
__init__() (in EntityExampleBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder)	__package__ (in TEES.Utils.Menu)
__init__() (in ExampleBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder)	__package__ (in TEES.Utils.Parameters)
__init__() (in ExampleStats)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder)	__package__ (in TEES.Utils.ProgressCounter)
__init__() (in BacteriaRenamingFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.EVEXFeatureBuilder)	__package__ (in TEES.Utils.ProteinNameSplitter)
__init__() (in BioInferOntologyFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.EdgeFeatureBuilder)	__package__ (in TEES.Utils.Range)
__init__() (in DrugFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.EventFeatureBuilder)	__package__ (in TEES.Utils.Release)
__init__() (in EVEXFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.FeatureBuilder)	__package__ (in TEES.Utils.STFormat.Analyze)
__init__() (in EdgeFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.GiulianoFeatureBuilder)	__package__ (in TEES.Utils.STFormat.Compare)
__init__() (in FeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder)	__package__ (in TEES.Utils.STFormat.ConvertXML)
__init__() (in GiulianoFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.MultiEdgeFeatureBuilder)	__package__ (in TEES.Utils.STFormat.Equiv)
__init__() (in GraphKernelFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.NameGazetteer)	__package__ (in TEES.Utils.STFormat.RoundTrip)
__init__() (in MultiEdgeFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.NodalidaFeatureBuilder)	__package__ (in TEES.Utils.STFormat.STTools)
__init__() (in NameGazetteer)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder)	__package__ (in TEES.Utils.STFormat.Scores)
__init__() (in NodalidaFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.RandomFeatureBuilder)	__package__ (in TEES.Utils.STFormat.Validate)
__init__() (in RELFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.TokenFeatureBuilder)	__package__ (in TEES.Utils.STFormat)
__init__() (in RandomFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.TriggerFeatureBuilder)	__package__ (in TEES.Utils.Settings)
__init__() (in TokenFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders.WordNetFeatureBuilder)	__package__ (in TEES.Utils.Stream)
__init__() (in TriggerFeatureBuilder)	__package__ (in TEES.ExampleBuilders.FeatureBuilders)	__package__ (in TEES.Utils.TableUtils)
__init__() (in WordNetFeatureBuilder)	__package__ (in TEES.ExampleBuilders.ModifierExampleBuilder)	__package__ (in TEES.Utils.Timer)
__init__() (in ModifierExampleBuilder)	__package__ (in TEES.ExampleBuilders.PhraseTriggerExampleBuilder)	__package__ (in TEES.Utils)
__init__() (in PhraseTriggerExampleBuilder)	__package__ (in TEES.ExampleBuilders.UnmergingExampleBuilder)	__package__ (in TEES)
__init__() (in UnmergingExampleBuilder)	__package__ (in TEES.ExampleBuilders)	__package__ (in TEES.batch)
__init__() (in EdgeExampleWriter)	__package__ (in TEES.ExampleWriters.BioTextExampleWriter)	__package__ (in TEES.classify)
__init__() (in EntityExampleWriter)	__package__ (in TEES.ExampleWriters.EdgeExampleWriter)	__package__ (in TEES.configure)
__init__() (in ModifierExampleWriter)	__package__ (in TEES.ExampleWriters.EntityExampleWriter)	__package__ (in TEES.train)
__init__() (in PhraseTriggerExampleWriter)	__package__ (in TEES.ExampleWriters.ModifierExampleWriter)	__repr__() (in Annotation)
__init__() (in SentenceExampleWriter)	__package__ (in TEES.ExampleWriters.PhraseTriggerExampleWriter)	__resetAnalyses() (in Graph)
__init__() (in UnmergingExampleWriter)	__package__ (in TEES.ExampleWriters.SentenceExampleWriter)	__warningregistry__ (in TEES.Utils.InteractionXML.ExportParse)
__init__() (in ProcessWrapper)	__package__ (in TEES.ExampleWriters.UnmergingExampleWriter)	_addPositionTags() (in GraphKernelFeatureBuilder)
__init__() (in ClusterConnection)	__package__ (in TEES.ExampleWriters)	_buildAdjacencyMatrix() (in GraphKernelFeatureBuilder)
__init__() (in LSFConnection)	__package__ (in TEES.Tools.BANNER)	_calculate() (in AveragingMultiClassEvaluator)
__init__() (in PBSConnection)	__package__ (in TEES.Tools.BLLIPParser)	_calculate() (in BinaryEvaluator)
__init__() (in SLURMConnection)	__package__ (in TEES.Tools.GeniaEventsToSharedTask)	_calculate() (in Evaluator)
__init__() (in UnixConnection)	__package__ (in TEES.Tools.GeniaSentenceSplitter)	_closeLogs() (in UnixConnection)
__init__() (in ETWriter)	__package__ (in TEES.Tools.ProcessUtils)	_closeModels() (in Detector)
__init__() (in CorpusElements)	__package__ (in TEES.Tools.SentenceSplitter)	_flush() (in ETWriter)
__init__() (in ParseGraph)	__package__ (in TEES.Tools.StanfordParser)	_format_line() (in ProgressBar)
__init__() (in ParseGraphNode)	__package__ (in TEES.Tools.Tool)	_format_marker() (in Bar)
__init__() (in SentenceElements)	__package__ (in TEES.Tools)	_format_widgets() (in ProgressBar)
__init__() (in PorterStemmer)	__package__ (in TEES.Utils.CompareExamples)	_getEdgeList() (in GraphKernelFeatureBuilder)
__init__() (in Bar)	__package__ (in TEES.Utils.CompareFeatures)	_getJobPath() (in UnixConnection)
__init__() (in FileTransferSpeed)	__package__ (in TEES.Utils.Connection.ClusterConnection)	_getScript() (in UnixConnection)
__init__() (in ProgressBar)	__package__ (in TEES.Utils.Connection.Connection)	_getTokenId() (in GraphKernelFeatureBuilder)
__init__() (in RotatingMarker)	__package__ (in TEES.Utils.Connection.LSFConnection)	_getTokenText() (in GraphKernelFeatureBuilder)
__init__() (in Dispatch)	__package__ (in TEES.Utils.Connection.PBSConnection)	_getValues() (in Model)
__init__() (in Menu)	__package__ (in TEES.Utils.Connection.SLURMConnection)	_markNamedEntities() (in SentenceGraph)
__init__() (in MenuSystem)	__package__ (in TEES.Utils.Connection.UnixConnection)	_matrixToFeatures() (in GraphKernelFeatureBuilder)
__init__() (in Option)	__package__ (in TEES.Utils.Connection)	_need_update() (in ProgressBar)
__init__() (in ProgressCounter)	__package__ (in TEES.Utils.Convert.DDITools)	_openDir() (in Model)
__init__() (in Token)	__package__ (in TEES.Utils.Convert)	_openPackage() (in Model)
__init__() (in Annotation)	__package__ (in TEES.Utils.Convert.convertBioNLP)	_prepareMatrix() (in GraphKernelFeatureBuilder)
__init__() (in Document)	__package__ (in TEES.Utils.Convert.convertDDI)	_processUntypedUndirectedQueue() (in AveragingMultiClassEvaluator)
__init__() (in StreamModifier)	__package__ (in TEES.Utils.Convert.processLPSN)	_queueUntypedUndirected() (in AveragingMultiClassEvaluator)
__init__() (in Timer)	__package__ (in TEES.Utils.DefaultSettings)	_readJobFile() (in UnixConnection)
__insertEdge() (in Graph)	__package__ (in TEES.Utils.DetectHeads)	_reduceWeightByDistance() (in GraphKernelFeatureBuilder)
__package__ (in TEES.Classifiers.AllCorrectClassifier)	__package__ (in TEES.Utils.Download)	_runHandler() (in Option)
__package__ (in TEES.Classifiers.AllTrueClassifier)	__package__ (in TEES.Utils.ElementTreeUtils)	_setAllDependencyWeights() (in GraphKernelFeatureBuilder)
__package__ (in TEES.Classifiers.Classifier)	__package__ (in TEES.Utils.FindHeads)	_setDefaultParameters() (in ExampleBuilder)
__package__ (in TEES.Classifiers.ExternalClassifier)	__package__ (in TEES.Utils.InteractionXML.Catenate)	_setDependencyWeightsByPath() (in GraphKernelFeatureBuilder)
__package__ (in TEES.Classifiers.SVMMultiClassClassifier)	__package__ (in TEES.Utils.InteractionXML.CompareParse)	_setValues() (in Model)
__package__ (in TEES.Classifiers.SVMMultiClassModelUtils)	__package__ (in TEES.Utils.InteractionXML.ConvertPMC)	_writeJobFile() (in UnixConnection)