public class TaxonCommandRunner extends GafCommandRunner
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 |
bioentityDocument, eco, gafdoc
Constructor and Description |
---|
TaxonCommandRunner() |
Modifier and Type | Method and Description |
---|---|
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) |
protected void |
exit(int code) |
protected OWLPrettyPrinter |
getPrettyPrinter() |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
void |
makeClassTaxonMatrix(Opts opts) |
void |
makeTaxonSet(Opts opts) |
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 |
runSingleIteration(String[] args) |
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
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 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
- 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()
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