code: private Set<Inclusion> transformAxiom(final Set<? extends Axiom> axioms) {
          Set<Inclusion> res = new HashSet<Inclusion>();
          
          for(Axiom aa : axioms) {
              if(aa instanceof ConceptInclusion) {
                  ConceptInclusion ci = (ConceptInclusion)aa;
                  Concept lhs = ci.getLhs();
                  Concept rhs = ci.getRhs();
                  res.add(new GCI(transformConcept(lhs), transformConcept(rhs)));
              } else if(aa instanceof RoleInclusion) {
                  RoleInclusion ri = (RoleInclusion)aa;
                  Role[] lh = ri.getLhs();
                  NamedRole[] lhs = new NamedRole[lh.length];
                  for(int i = 0; i < lh.length; i++) {
                      lhs[i] = (NamedRole) lh[i];
                  }
                  NamedRole rhs = (NamedRole) ri.getRhs();
                  int[] lhsInt = new int[lhs.length];
                  for(int i = 0; i < lhsInt.length; i++) {
                      lhsInt[i] = factory.getRole(lhs[i].getId());
                  }
                  res.add(new RI(lhsInt, factory.getRole(rhs.getId())));
              } else if (aa instanceof FunctionalFeature) {
              	FunctionalFeature ff = (FunctionalFeature) aa;
              	int featureInt = factory.getFeature(((NamedFeature) ff.getFeature()).getId());
              	functionalFeatures.add(featureInt);
              } else {
              	throw new InternalError("Unknown Axiom type discovered: " + aa);
              }
          }
          
          return res;
      }
docs: Transforms a {@link Set} of {@link AbstractAxiom}s into a {@link Set} of {@link Inclusion}s.
  
  @param axioms The axioms in the ontology model format.
  @return The axioms in the internal model format.