Please check out and use the 0.8.x code
which is more statble.
Please see the code in the org.eclipse.eodm.examples.owl.LoadAndSaveOWLbyOWLFile
to find out how to obtain an OWLOntology instance from parsing an OWL file.
Then you can use the ontology.getResourceList(OWLClass.class) to get all
the OWL classes. The API will be majorly the aClass.getSubClass() method
to find all the sub-classes of a RDFS or an OWL Class, and also the aClass.getSubClassOf()
to find all the super-classes.