Solve inconsistencies in an OWL ontology

Question

(Thanks of the comments, I am updating my code and question. Maybe it will be useful for others.)
Update
I am doing several edit processes in one ontology, at the end, I realized my ontology is inconsistent. Now I should get rid of all the unsatisfiable classes. I searched a lot, but there is no code to solve the inconsistencies.

Follow the approach of this paper and the library of Matthew Horridge and this, still I am struggling with this issue. I update my code and question, this is my solution. Is there any more suggestion for it?

What I am doing to solve the inconsistencies:

1. Run a reasoner to find unsatisfiable classes
2. From the all unsatisfiable classes, only find the root-unsatisfiable-classes
3. Find explanation axioms for them
4. Rank them and select the axioms which should be deleted (or rewrite) by the user

In my below code (using other existing solutions), I only need to implement rank function (the left open issue in inconsistency resolver).

For example, for my ontology, it has 25 unsatisfiable classes, which only 2 of them are the root of inconsistencies. These 2 root-classes, has 11 axioms (which I get them by getExplanations)

import java.io.File;
import java.util.Iterator;
import java.util.Set;
import org.semanticweb.owl.explanation.impl.rootderived.CompleteRootDerivedReasoner;
import org.semanticweb.owl.explanation.impl.rootderived.StructuralRootDerivedReasoner;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import com.clarkparsia.owlapi.explanation.BlackBoxExplanation;
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;

public class InconsistencyTest {
 public static void main(String areg[]) throws Exception {

  File fileM = new File("address\\to\\my\\ontology\\myOnt.owl");
  OWLOntologyManager tempManager = OWLManager.createOWLOntologyManager();
  OWLOntology ont = tempManager.loadOntologyFromOntologyDocument(fileM);

  // run an reasoner
  OWLReasonerFactory reasonerFactory = new PelletReasonerFactory();
  OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ont);
  if (reasoner.isConsistent()) {
    // an ontology can be consistent, but have unsatisfiable classes.
    if (reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() > 0) {
    // means: an ontology is consistent but unsatisfiable!
        System.out.println("The ontology FAILED satisfiability test with Pellet reasoner. \n Unsatisfiable classes detected: "
                + reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size());

        // This line return all unsatisfibaleClasses, but I do not need it
        // Iterator<OWLClass> aList=reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().iterator();

        // get root of unstaisfiableClasses, and get their explanations 
        BlackBoxExplanation bb = new BlackBoxExplanation(ont, reasonerFactory, reasoner);
        HSTExplanationGenerator multExplanator = new HSTExplanationGenerator(bb);

        CompleteRootDerivedReasoner rdr = new CompleteRootDerivedReasoner(tempManager, reasoner, reasonerFactory);
        for (OWLClass cls : rdr.getRootUnsatisfiableClasses()) {
            System.out.println("**** ROOT! " + cls);
            int maxEntailment = 5;
            Set<Set<OWLAxiom>> exSet = multExplanator.getExplanations(cls, maxEntailment);
            OWLAxiom deletedAxiom = rankAxiom(exSet);
            //return these axioms to user to delete or rewrite them
        }
    } else {
        System.out.println("The ontology PASSED the consistency test.");
    }
} else {
    System.out.println("The ontology FAILED the consistency test, please review the Axioms or debug using Protege");
    }
reasoner.dispose();
  }

Do I follow everything correct? Is there any suggestion for rank the axioms?
Very Thanks