private static Set<OWLAnnotationProperty> getProperties(OWLDataFactory factory, OboFormatTag... tags) { Set<OWLAnnotationProperty> set = new HashSet<>(); for (OboFormatTag tag : tags) { set.add(factory.getOWLAnnotationProperty(OWLAPIObo2Owl.trTagToIRI(tag.getTag()))); } return set; }
private static Set<OWLAnnotationProperty> getProperties(OWLDataFactory factory, OboFormatTag... tags) { Set<OWLAnnotationProperty> set = new HashSet<>(); for (OboFormatTag tag : tags) { set.add(factory.getOWLAnnotationProperty(OWLAPIObo2Owl.trTagToIRI(tag.getTag()))); } return set; }
private OWLAnnotationProperty trSynonymType(String type) { if (type.equals(OboFormatTag.TAG_RELATED.getTag()) || type.equals(OboFormatTag.TAG_EXACT.getTag()) || type.equals(OboFormatTag.TAG_NARROW.getTag()) || type.equals(OboFormatTag.TAG_BROAD.getTag())) { return trTagToAnnotationProp(type); } return trAnnotationProp(type); }
private void tr(OWLSymmetricObjectPropertyAxiom ax){ OWLObjectPropertyExpression prop = ax.getProperty(); if(prop instanceof OWLObjectProperty){ if( trObjectProperty((OWLObjectProperty)prop, OboFormatTag.TAG_IS_SYMMETRIC.getTag(), Boolean.TRUE, ax.getAnnotations()) ) { return; } } error(ax); }
/** * @param <T> the generic type * @param tag the tag * @param cls the cls * @return the tag value for tag and class */ @Nullable public <T> T getTagValue(OboFormatTag tag, Class<T> cls) { return getTagValue(tag.getTag(), cls); }
private boolean isMetadataTag(OWLAnnotationProperty p) { final IRI metadataTagIRI = IRI .create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, OboFormatTag.TAG_IS_METADATA_TAG .getTag()); return owlOntology.annotationAssertionAxioms(p.getIRI()) .anyMatch(ax -> metadataTagIRI.equals(ax.getProperty() .getIRI())); }
private void tr(OWLAsymmetricObjectPropertyAxiom ax){ OWLObjectPropertyExpression prop = ax.getProperty(); if(prop instanceof OWLObjectProperty){ if( trObjectProperty((OWLObjectProperty)prop, OboFormatTag.TAG_IS_ASYMMETRIC.getTag(), Boolean.TRUE, ax.getAnnotations()) ){ return; } } error(ax); }
private static void addVersion(OWLOntology ontology, String version, OWLOntologyManager manager){ OWLDataFactory fac = manager.getOWLDataFactory(); OWLAnnotationProperty ap = fac.getOWLAnnotationProperty( Obo2Owl.trTagToIRI(OboFormatTag.TAG_REMARK.getTag())); OWLAnnotation ann = fac.getOWLAnnotation(ap, fac.getOWLLiteral(version)); OWLAxiom ax = fac.getOWLAnnotationAssertionAxiom(ontology.getOntologyID().getOntologyIRI(), ann); manager.applyChange(new AddAxiom(ontology, ax)); } }
/** * @param tag the tag * @return the tag value for tag */ @Nullable public Object getTagValue(OboFormatTag tag) { return getTagValue(tag.getTag()); }
/** * @param tag the tag * @return the tag values for tag */ public Collection<Object> getTagValues(OboFormatTag tag) { return getTagValues(tag.getTag()); }
/** * @param tag the tag * @return the clause for tag */ @Nullable public Clause getClause(OboFormatTag tag) { return getClause(tag.getTag()); }
/** * @param tag tag * @param value value */ public Clause(OboFormatTag tag, String value) { this(tag.getTag(), value); }
/** * @param tag the tag * @return the tag values for tag */ public Collection<Object> getTagValues(OboFormatTag tag) { return getTagValues(tag.getTag()); }
/** * @param tag tag */ public Clause(OboFormatTag tag) { this(tag.getTag()); }
private boolean isMetadataTag(OWLAnnotationProperty p) { final IRI metadataTagIRI = IRI .create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, OboFormatTag.TAG_IS_METADATA_TAG .getTag()); return owlOntology.annotationAssertionAxioms(p.getIRI()) .anyMatch(ax -> metadataTagIRI.equals(ax.getProperty() .getIRI())); }
/** * @param tag the tag * @return the clause for tag */ @Nullable public Clause getClause(OboFormatTag tag) { return getClause(tag.getTag()); }
/** * @param tag the tag * @return the clauses for tag */ public List<Clause> getClauses(OboFormatTag tag) { return getClauses(tag.getTag()); }
/** * @param tag the tag * @return the tag value for tag */ @Nullable public Object getTagValue(OboFormatTag tag) { return getTagValue(tag.getTag()); }
/** * @param tag the tag * @return the clause for tag */ @Nullable public Clause getClause(OboFormatTag tag) { return getClause(tag.getTag()); }
/** * @param tag tag * @param value value */ public Clause(OboFormatTag tag, String value) { this(tag.getTag(), value); }