public void visit(OWLOntology ontology) {
checkOccurrence(ontology.getAnnotations());
for (AxiomType<?> t : AxiomType.AXIOM_TYPES) {
for (OWLAxiom ax : ontology.getAxioms(t)) {
checkOccurrence(ax.getAnnotations());
ax.accept(this);
}
}
singleAppearance.clear();
}
public ArrayList<OWLAxiom> rebuild(OWLAxiom axiom) throws TranscriptionException {
this.rebuiltAxioms = new ArrayList<OWLAxiom>();
this.rebuiltObjects = new ArrayList<OWLObject>();
if (axiom instanceof OWLSubClassAxiom || axiom instanceof OWLSubClassAxiomImpl) {
this.rebuild((OWLSubClassAxiom) axiom);
} else if (axiom instanceof OWLEquivalentClassesAxiom) {
this.rebuild((OWLEquivalentClassesAxiom) axiom);
} else if (axiom instanceof OWLDisjointUnionAxiom) {
this.rebuild((OWLDisjointUnionAxiom) axiom);
} else if (axiom instanceof OWLDisjointClassesAxiom) {
this.rebuild((OWLDisjointClassesAxiom) axiom);
} else if (axiom instanceof OWLDataPropertyDomainAxiom) {
this.rebuild((OWLDataPropertyDomainAxiom) axiom);
} else if (axiom instanceof OWLDataPropertyRangeAxiom) {
this.rebuild((OWLDataPropertyRangeAxiom) axiom);
} else if (axiom instanceof OWLObjectPropertyDomainAxiom) {
this.rebuild((OWLObjectPropertyDomainAxiom) axiom);
} else if (axiom instanceof OWLObjectPropertyRangeAxiom) {
this.rebuild((OWLObjectPropertyRangeAxiom) axiom);
} else {
throw new TranscriptionException(
"could not rewrite ontology to get rid of nominals ("
+ axiom
+ " is "
+ axiom.getClass()
+ ")");
}
return this.rebuiltAxioms;
}
private Set<OWLAnnotation> duplicateAxiomAnnotations(OWLAxiom axiom) {
Set<OWLAnnotation> duplicatedAnnos = new HashSet<OWLAnnotation>();
for (OWLAnnotation anno : axiom.getAnnotations()) {
anno.accept(this);
duplicatedAnnos.add((OWLAnnotation) obj);
}
return duplicatedAnnos;
}
public Object getRelationshipType(Object parentObject, Object childObject) {
AxiomEdge edge = new AxiomEdge(childObject, parentObject);
OWLObject edgeObject = edgeMap.get(edge);
if (edgeObject != null) {
edgeNameGenerator.reset();
if (edgeObject instanceof OWLClassExpression) {
((OWLClassExpression) edgeObject).accept(edgeNameGenerator);
} else {
((OWLAxiom) edgeObject).accept(edgeNameGenerator);
}
return edgeNameGenerator.edgeName;
} else {
return null;
}
}
public int getRelationshipDirection(Object parentObject, Object childObject) {
AxiomEdge edge = new AxiomEdge(childObject, parentObject);
OWLObject edgeObject = edgeMap.get(edge);
if (edgeObject != null) {
edgeNameGenerator.reset();
if (edgeObject instanceof OWLAxiom) {
((OWLAxiom) edgeObject).accept(edgeNameGenerator);
} else {
((OWLClassExpression) edgeObject).accept(edgeNameGenerator);
}
return edgeNameGenerator.direction;
}
return -1; // if no edge found, negative direction for handling in
// DefaultEdgeFactory
}
private boolean isOBOAxiom(OWLAxiom axiom) {
return axiom.accept(checker);
}
// ////////////////////////////////////////////////////////////////////////////////////////////
//
// Axiom Visitor stuff
//
// ////////////////////////////////////////////////////////////////////////////////////////////
protected void processAxiomAnnotations(OWLAxiom ax) {
// default behavior: iterate over the annotations outside the axiom
for (OWLAnnotation anno : ax.getAnnotations()) {
anno.accept(this);
}
}
/**
* This method clears all the map (invokes the clearMaps-method) at first. Then it iterates over
* all axioms and invokes their accept-Method with "this" as parameter.
*
* @param axioms The axioms to visualize
*/
public void addAndClearAxioms(Set<OWLAxiom> axioms) {
this.clearMaps();
for (OWLAxiom ax : axioms) {
ax.accept(this);
}
}
