public class JsCommandRunner extends Sim2CommandRunner
OWLGraphWrapper
with dynamic scripts.CommandRunnerBase.OptionException
resultOutStream
bioentityDocument, eco, gafdoc
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
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JsCommandRunner() |
Modifier and Type | Method and Description |
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void |
runJavaScript(Opts opts)
Run the given js with the current graph (and reasoner).
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attributeAllByAll, attributeAllByAllOld, attributeSimilarityAllByAllPairwise, attributeSimilarityByPair, classICPairs, fsimAttTopSimJ, fsimBasic, fsimCompareAtts, fsimCompareAttsLCS, fsimCompareAttsLite, fsimCompareAttsSimJ, fsimFindMatches, fsimSearchAll, fsimTest, getOwlSimFactory, getProperty, instanceICValues, instanceStats, learnClassDifferentia, loadProperties, mergeSim, OLDinstanceICValues, owlsimEnrichmentAnalysis, owlsimEnrichmentAnalysisAllByAll, removeDangningAnnotations, runOwlSim, runOwlSim, saveSim, setOwlSimFactory, setSimProperty, showAttributeGroupings, showAttributeGroupingsAsList, showAttributeGroupingsInTable, showSimProperties, simAttMatchOld, simBasic, simBasicStats, simDlQuery, simLCS, simLoadICCache, simLoadLCSCache, simPairwiseAttMatch, simSaveICCache, simSaveLCSCache, simSavePhenodigmClassScores, simSaveState, simTest, startSimServer, useFastOwlSim, useSimpleOwlSim
allClassIC, getAncestorsWithIC, getIC, lcsx, lcsxAll, phenoSim, setSimMethod, sim, simAll, simResume
configRead, dumpShuntGraphs, experimentalLoadComplexAnnotationSolr, flexDumpOntologySolr, flexLoadOntologySolr, generalLoadOntologySolr, loadComplexAnnotationSolr, loadGAFsSolr, loadGPADsSolr, loadModelAnnotations, loadPANTHERGeneralSolr, loadPANTHERSolr, optimizeSolr, processCAFiles, processLegoCatalogs, processLegoFiles, processModelFolder, processModelUrlPrefix, processPantherTrees, purgeSolr, setSolrLogFile, setSolrUrl, solrSchemaDump
createDisjoint, createDisjoint, createDisjoint, createTaxonDisjointOverInTaxon, makeClassTaxonMatrix, makeTaxonSet
createExperimentalPredictions, createRdfXml, extractOntologySubsetByGaf, foldGafExtensions, gaCalculateSpecificity, gaf, gaf2oa, gaf2Owl, gaf2OwlSimple, gafCompareBasic, gafFoldInferences, gafQuery, gafRemoveRedundant, gafTermCounts, gafTermICValues, gafXpPredict, generateJsonGafStatistics, loadGpadGpi, mapToSlim, preCheckOntology, runGAFChecks, runOntologyPreCheck, setExperimentalGAFPredictionFile, setExperimentalGAFPredictionReportFile, setGAFPredictionFile, setGAFPredictionReportFile, setGAFReportFile, setGAFReportSummaryFile, setGAFTaxonModule, unfoldGafExtensions, writeGaf, writeGpad, writeGpi, writeXgmml
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, extractAnnotationValue, extractExtensionFile, filterExtensionFile, removeRedundantInferredSuperClassAxioms, removeRedundantInferredSVFs, removeRedundantSubclasses, removeRedundantSVFs, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
exit, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, printVersion, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runSingleIteration, summarizeOntology
public void runJavaScript(Opts opts)
opts
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