public String getIdentifier(OWLObject obj) { try { return getIdentifierFromObject(obj, owlOntology); } catch (UntranslatableAxiomException e) { error(e.getMessage()); } return null; }
/** * Check the annotations for cardinality violations. Try to resolve * conflicts with the default handler. * * @param ontology the target ontology * @throws AnnotationCardinalityException throws exception in case a conflict cannot be resolved * by the handler * @see #DEFAULT_HANDLER */ public static void checkAnnotationCardinality(OWLOntology ontology) { checkAnnotationCardinality(ontology, null, DEFAULT_HANDLER); }
@Override public IRI load(String key) { return loadOboToIRI(key); } });
/** * Convert. * * @param ont the ont * @return the oBO doc */ public OBODoc convert(OWLOntology ont) { owlOntology = ont; ontologyId = getOntologyId(ont); init(); return tr(); }
@Override public void visit(OWLDisjointClassesAxiom ax) { tr(ax); }
/** * Tr class. * * @param v the v * @return the oWL class expression */ protected OWLClassExpression trClass(Object v) { return trClass((String) v); }
@Override public void doDefault(Object o) { if (!(o instanceof OWLAnnotationAssertionAxiom)) { error((OWLAxiom) o, false); } } }
public OBODoc convert(OWLOntology ont) throws OWLOntologyCreationException { owlOntology = ont; if (ont != null) { ontologyId = getOntologyId(ont); } else { ontologyId = "TODO"; } init(); return tr(); }
/** * See table 5.9.2. Translation of identifiers * * @param iriId * @return obo identifier or null */ public static String getIdentifier(IRI iriId) { return getIdentifier(iriId, null); }
/** * Converts an OBO document to an OWL ontology * * @param obodoc * @return ontology * @throws OWLOntologyCreationException */ public OWLOntology convert(OBODoc obodoc) throws OWLOntologyCreationException { // always create a new manager, when loading a new obo document - TODO - why? // creates problems for sharing ontologies return convert(obodoc, false); }
/** * Convert. * * @param ont the ont * @return the oBO doc */ public OBODoc convert(OWLOntology ont) { owlOntology = ont; ontologyId = getOntologyId(ont); init(); return tr(); }
/** * Check the annotations for cardinality violations. Try to resolve * conflicts with the default handler. * * @param ontology the target ontology * @throws AnnotationCardinalityException throws exception in case a conflict cannot be resolved * by the handler * @see #DEFAULT_HANDLER */ public static void checkAnnotationCardinality(OWLOntology ontology) { checkAnnotationCardinality(ontology, null, DEFAULT_HANDLER); }
@Override public void visit(OWLSubAnnotationPropertyOfAxiom ax) { tr(ax); }
/** * Tr class. * * @param v the v * @return the oWL class expression */ protected OWLClassExpression trClass(Object v) { return trClass((String) v); }
@Override public IRI load(String key) { return loadOboToIRI(key); } });
/** * Check the annotations for cardinality violations. Try to resolve * conflicts with the default handler. * * @param ontology the target ontology * @throws AnnotationCardinalityException throws exception in case a conflict cannot be resolved * by the handler * @see #DEFAULT_HANDLER */ public static void checkAnnotationCardinality(OWLOntology ontology) { checkAnnotationCardinality(ontology, null, DEFAULT_HANDLER); }
@Override public void visit(OWLObjectPropertyRangeAxiom ax) { tr(ax); }
/** * Tr class. * * @param v the v * @return the oWL class expression */ protected OWLClassExpression trClass(Object v) { return trClass((String) v); }
@Override public void visit(OWLAsymmetricObjectPropertyAxiom ax) { tr(ax); }
@Override public void visit(OWLDisjointObjectPropertiesAxiom ax) { tr(ax); }