public class TaxonCommandRunner extends GafCommandRunner
CommandRunner.OptionException
bioentityDocument, eco, gafdoc
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
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TaxonCommandRunner() |
Modifier and Type | Method and Description |
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protected org.semanticweb.owlapi.model.OWLAxiom |
createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f,
org.semanticweb.owlapi.model.OWLClass sibling1,
org.semanticweb.owlapi.model.OWLClass sibling2) |
protected org.semanticweb.owlapi.model.OWLAxiom |
createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f,
org.semanticweb.owlapi.model.OWLClass sibling1,
org.semanticweb.owlapi.model.OWLClass sibling2,
org.semanticweb.owlapi.model.OWLObjectProperty property) |
protected org.semanticweb.owlapi.model.OWLAxiom |
createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f,
Set<org.semanticweb.owlapi.model.OWLClass> siblings,
org.semanticweb.owlapi.model.OWLObjectProperty inTaxon) |
void |
createTaxonDisjointOverInTaxon(Opts opts) |
void |
makeClassTaxonMatrix(Opts opts) |
void |
makeTaxonSet(Opts opts) |
createExperimentalPredictions, createRdfXml, extractOntologySubsetByGaf, fetchCandidateProcess, foldGafExtensions, gaCalculateSpecificity, gaf, gaf2Lego, gaf2LegoIndivduals, gaf2oa, gaf2Owl, gaf2OwlSimple, gafCompareBasic, gafFoldInferences, gafQuery, gafRemoveRedundant, gafTermCounts, gafTermICValues, gafXpPredict, generateJsonGafStatistics, generateMolecularModel, goMultiEnrichment, legoToAnnotations, loadGpadGpi, mapToSlim, preCheckOntology, runGAFChecks, runOntologyPreCheck, setExperimentalGAFPredictionFile, setExperimentalGAFPredictionReportFile, setGAFPredictionFile, setGAFPredictionReportFile, setGAFReportFile, setGAFReportSummaryFile, setGAFTaxonModule, unfoldGafExtensions, visualizeLego, writeGaf, writeGpad, writeGpi, writeLego, writeXgmml
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, exit, extractAnnotationValue, extractExtensionFile, filterExtensionFile, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, jsonLdToRdf, parseArgString, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeSubsetEntities, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runDAGCheck, runSingleIteration, runSingleIteration, summarizeOntology, verifyChanges
public void createTaxonDisjointOverInTaxon(Opts opts) throws Exception
Exception
protected org.semanticweb.owlapi.model.OWLAxiom createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f, Set<org.semanticweb.owlapi.model.OWLClass> siblings, org.semanticweb.owlapi.model.OWLObjectProperty inTaxon)
f
- siblings
- inTaxon
- protected org.semanticweb.owlapi.model.OWLAxiom createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f, org.semanticweb.owlapi.model.OWLClass sibling1, org.semanticweb.owlapi.model.OWLClass sibling2, org.semanticweb.owlapi.model.OWLObjectProperty property)
f
- sibling1
- sibling2
- property
- protected org.semanticweb.owlapi.model.OWLAxiom createDisjoint(org.semanticweb.owlapi.model.OWLDataFactory f, org.semanticweb.owlapi.model.OWLClass sibling1, org.semanticweb.owlapi.model.OWLClass sibling2)
f
- sibling1
- sibling2
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