public class JsCommandRunner extends Sim2CommandRunner
OWLGraphWrapper
with dynamic scripts.Modifier and Type | Field and Description |
---|---|
boolean |
exitOnException |
OWLGraphWrapper |
g |
boolean |
isDisposeReasonerOnExit |
Set<org.semanticweb.owlapi.model.OWLObject> |
owlObjectCachedSet |
protected ParserWrapper |
pw |
org.semanticweb.owlapi.model.OWLOntology |
queryOntology |
org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
String |
reasonerName |
resultOutStream
bioentityDocument, eco, gafdoc
Constructor and Description |
---|
JsCommandRunner() |
Modifier and Type | Method and Description |
---|---|
protected void |
exit(int code) |
protected OWLPrettyPrinter |
getPrettyPrinter() |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
org.semanticweb.owlapi.model.OWLClass |
resolveClass(String id) |
List<org.semanticweb.owlapi.model.OWLClass> |
resolveClassList(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(String id) |
Set<org.semanticweb.owlapi.model.OWLObject> |
resolveEntityList(Opts opts) |
org.semanticweb.owlapi.model.OWLObjectProperty |
resolveObjectProperty(String id) |
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyList(Opts opts) |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyListAsList(Opts opts) |
void |
run(Opts opts) |
void |
run(String[] args) |
void |
runJavaScript(Opts opts)
Run the given js with the current graph (and reasoner).
|
void |
runSingleIteration(String[] args) |
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
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, loadPANTHERGeneralSolr, loadPANTHERSolr, optimizeSolr, processCAFiles, processLegoCatalogs, processLegoFiles, 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, jsonLdToRdf, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeRedundantSubclasses, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
public OWLGraphWrapper g
public org.semanticweb.owlapi.model.OWLOntology queryOntology
public boolean exitOnException
public boolean isDisposeReasonerOnExit
public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
public String reasonerName
public Set<org.semanticweb.owlapi.model.OWLObject> owlObjectCachedSet
protected ParserWrapper pw
public void runJavaScript(Opts opts)
opts
- protected void exit(int code)
protected OWLPrettyPrinter getPrettyPrinter()
public void summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyList(Opts opts)
public List<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyListAsList(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(String id)
public org.semanticweb.owlapi.model.OWLObjectProperty resolveObjectProperty(String id)
public org.semanticweb.owlapi.model.OWLClass resolveClass(String id)
public void help()
public void helpFooter()
Copyright © 2010–2015. All rights reserved.