MakePrimitiveSubClassesMutuallyDisjoint doesn't work

I wanted to use MakePrimitiveSubClassesMutuallyDisjoint to make all the subclasses of a class disjoint. But with my code this doesn't happen:

OWLClass owlClass = createClass(concept.getId());

// Here I recursively create the subclasses 
processByLevel(skos, owlClass, concept.getNarrowerConcepts());

// But at this point all the subclass should have been created and set as subclasses  
MakePrimitiveSubClassesMutuallyDisjoint primitive = new MakePrimitiveSubClassesMutuallyDisjoint(dataFactory, owlClass, ontology);

manager.saveOntology(ontology);

I haven't been able to find an example of how it is used, and I'm not sure if I'm missing a step with the manager maybe (something like addAxiom but for this).

I can't debug inside the method, but I checked if the subclasses where set after the recursion by calling this:

ontology.getSubClassAxiomsForSuperClass(owlClass).size();

And the result is the expected one.

But still, I don't see anything on the resulting ontology stating that the classes are disjoint.

Solution

OWLClass owlClass = createClass(concept.getId());

// Here I recursively create the subclasses 
processByLevel(skos, owlClass, concept.getNarrowerConcepts());

// But at this point all the subclass should have been created and set as subclasses  
MakePrimitiveSubClassesMutuallyDisjoint primitive = new MakePrimitiveSubClassesMutuallyDisjoint(dataFactory, owlClass, ontology);

// this line is necessary, it actually changes the content of the ontology
manager.applyChanges(primitive.getChanges());

manager.saveOntology(ontology);