[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 0 insertions, 607 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
deleted file mode 100644
index 638a151..0000000
--- a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
+++ /dev/null
@@ -1,607 +0,0 @@
-package uk.ac.ox.cs.pagoda.approx;
-
-import org.apache.commons.io.FilenameUtils;
-import org.semanticweb.HermiT.Configuration;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLOntology;
-import org.semanticweb.HermiT.structural.OWLClausification;
-import org.semanticweb.owlapi.model.*;
-import org.semanticweb.owlapi.profiles.OWL2RLProfile;
-import org.semanticweb.owlapi.profiles.OWLProfileReport;
-import org.semanticweb.owlapi.profiles.OWLProfileViolation;
-import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
-import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.util.Namespace;
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-import java.io.*;
-import java.nio.file.Paths;
-import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class RLPlusOntology implements KnowledgeBase {
-
-    private static final String DEFAULT_ONTOLOGY_FILE_EXTENSION = "owl";
-    private static final Pattern ONTOLOGY_ID_REGEX = Pattern.compile("ontologyid\\((?<id>[a-z0-9\\-]+)\\)");
-    OWLOntologyManager manager;
-    OWLDataFactory factory;
-    String ontologyIRI;
-    String corrFileName = null;
-    String outputPath, aBoxPath;
-    OWLOntology inputOntology = null;
-    OWLOntology tBox = null;
-    OWLOntology aBox = null;
-    OWLOntology restOntology = null;
-    OWLOntology outputOntology = null; //RL ontology
-    DLOntology dlOntology = null;
-    int rlCounter = 0;
-    LinkedList<Clause> clauses;
-    Map<OWLAxiom, OWLAxiom> correspondence;
-    BottomStrategy botStrategy;
-    Random random = new Random(19900114);
-    private Map<OWLClassExpression, Integer> subCounter = null;
-    private Map<OWLClass, OWLClass> atomic2negation = new HashMap<OWLClass, OWLClass>();
-
-    // TODO don't know if it is correct
-    @Override
-    public void load(OWLOntology ontology, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
-        if(bottomStrategy instanceof UnaryBottom)
-            botStrategy = BottomStrategy.UNARY;
-        else if(bottomStrategy instanceof NullaryBottom)
-            botStrategy = BottomStrategy.NULLARY;
-        else
-            botStrategy = BottomStrategy.TOREMOVE;
-
-        if(corrFileName == null)
-            corrFileName = "rlplus.crr";
-        manager = ontology.getOWLOntologyManager();
-//              manager = OWLManager.createOWLOntologyManager();
-        factory = manager.getOWLDataFactory();
-        inputOntology = ontology;
-
-        try {
-            IRI ontologyIri;
-            if(ontology.isAnonymous()) {
-                Matcher matcher = ONTOLOGY_ID_REGEX.matcher(ontology.getOntologyID().toString().toLowerCase());
-                if(!matcher.matches()) throw new Error("Anonymous ontology without internal id");
-                ontologyIri =
-                        IRI.create("http://www.example.org/", matcher.group("id") + "." + DEFAULT_ONTOLOGY_FILE_EXTENSION);
-            }
-            else
-                ontologyIri = inputOntology.getOntologyID().getOntologyIRI();
-
-            String ontologyIriPrefix = ontologyIri.getNamespace();
-            ontologyIRI = ontologyIri.toString();
-            String ontologyIriFragment = ontologyIri.getFragment();
-            String originalFileName = FilenameUtils.removeExtension(ontologyIriFragment);
-            String originalExtension = FilenameUtils.getExtension(ontologyIriFragment);
-            if(originalExtension.isEmpty()) originalExtension = DEFAULT_ONTOLOGY_FILE_EXTENSION;
-
-
-            IRI rlOntologyIRI = IRI.create(ontologyIriPrefix, originalFileName + "-RL." + originalExtension);
-            outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(),
-                                   originalFileName + "-RL." + originalExtension).toString();
-            IRI rlDocumentIRI = IRI.create("file://" + outputPath);
-            outputOntology = manager.createOntology(rlOntologyIRI);
-            manager.setOntologyDocumentIRI(outputOntology, rlDocumentIRI);
-
-            String tBoxOntologyFragment = originalFileName + "-TBox." + originalExtension;
-            IRI tBoxOntologyIRI = IRI.create(ontologyIriPrefix, tBoxOntologyFragment);
-            IRI tBoxDocumentIRI =
-                    IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), tBoxOntologyFragment));
-
-            String aBoxOntologyFragment = originalFileName + "-ABox." + originalExtension;
-            IRI aBoxOntologyIRI = IRI.create(ontologyIriPrefix, aBoxOntologyFragment);
-            aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment).toString();
-            IRI aBoxDocumentIRI =
-                    IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment));
-
-            tBox = manager.createOntology(tBoxOntologyIRI);
-            aBox = manager.createOntology(aBoxOntologyIRI);
-            manager.setOntologyDocumentIRI(tBox, tBoxDocumentIRI);
-            manager.setOntologyDocumentIRI(aBox, aBoxDocumentIRI);
-
-            FileOutputStream aBoxOut = new FileOutputStream(aBoxPath);
-            manager.saveOntology(aBox, aBoxOut);
-            aBoxOut.close();
-
-            restOntology = manager.createOntology();
-        } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
-            e.printStackTrace();
-            System.exit(1);
-        }
-    }
-
-    public OWLOntology getTBox() {
-        return tBox;
-    }
-
-    public String getABoxPath() {
-        return aBoxPath;
-    }
-
-    public void simplify() {
-        if(simplifyABox()) {
-            save(aBox);
-//                      save(tBox);
-        }
-        else
-            tBox = inputOntology;
-    }
-
-    @Override
-    public void transform() {
-        simplify();
-        filter();
-        clausify();
-
-        subCounter = new HashMap<OWLClassExpression, Integer>();
-        clauses = new LinkedList<Clause>();
-        Clausifier clausifier = Clausifier.getInstance(restOntology);
-
-        for(DLClause c : dlOntology.getDLClauses()) {
-            Clause clause = new Clause(clausifier, c);
-            clauses.add(clause);
-
-                        /*
-             * count the expressions in the left
-                         */
-            for(OWLClassExpression exp : clause.getSubClasses()) {
-                if(exp instanceof OWLClass)
-                    add2SubCounter(exp);
-                else if(exp instanceof OWLObjectSomeValuesFrom) {
-                    OWLObjectSomeValuesFrom someValue = (OWLObjectSomeValuesFrom) exp;
-                    add2SubCounter(factory.getOWLObjectSomeValuesFrom(someValue.getProperty(), factory.getOWLThing()));
-                    add2SubCounter(someValue.getFiller());
-                }
-                else if(exp instanceof OWLObjectMinCardinality) {
-                    OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
-                    add2SubCounter(factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing()));
-                    add2SubCounter(minCard.getFiller());
-                }
-                else
-                    Utility.logError("strange class expression: " + exp);
-
-            }
-        }
-
-        correspondence = new HashMap<OWLAxiom, OWLAxiom>();
-        Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
-        OWLClassExpression subExp;
-        for(Clause clause : clauses) {
-            subExp = uk.ac.ox.cs.pagoda.owl.OWLHelper.getSimplifiedConjunction(factory, clause.getSubClasses());
-            addedAxioms.clear();
-            for(OWLClassExpression exp : getDisjunctionApprox0(clause.getSuperClasses())) {
-                addedAxioms.add(factory.getOWLSubClassOfAxiom(subExp, transform(exp, addedAxioms)));
-                for(OWLAxiom a : addedAxioms)
-                    addAxiom2output(a, factory.getOWLSubClassOfAxiom(subExp,
-                                                                     OWLHelper.getSimplifiedDisjunction(factory, clause.getSuperClasses())));
-            }
-        }
-
-        subCounter.clear();
-    }
-
-    @Override
-    public void save() {
-        if(corrFileName != null)
-            save(correspondence, corrFileName);
-        save(outputOntology);
-    }
-
-    public OWLOntologyManager getOWLOntologyManager() {
-        return inputOntology.getOWLOntologyManager();
-    }
-
-    public String getOntologyIRI() {
-        return ontologyIRI;
-    }
-
-    public OWLOntology getOutputOntology() {
-        return outputOntology;
-    }
-
-    @Override
-    public String getOutputPath() {
-        return outputPath;
-    }
-
-    @Override
-    public String getDirectory() {
-        return outputPath.substring(0, outputPath.lastIndexOf(Utility.FILE_SEPARATOR));
-    }
-
-    public void setCorrespondenceFileLoc(String path) {
-        corrFileName = path;
-    }
-
-    private void add2SubCounter(OWLClassExpression exp) {
-        Integer count = subCounter.get(exp);
-        if(count == null) count = 0;
-        ++count;
-        subCounter.put(exp, count);
-    }
-
-    private void save(Map<OWLAxiom, OWLAxiom> map, String corrFileName) {
-        if(corrFileName == null) return;
-        ObjectOutput output;
-        try {
-            output = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(corrFileName)));
-            output.writeObject(map);
-            output.close();
-        } catch(IOException e) {
-            e.printStackTrace();
-        }
-    }
-
-    protected void save(OWLOntology onto) {
-        try {
-            onto.getOWLOntologyManager().saveOntology(onto);
-        } catch(OWLOntologyStorageException e) {
-            e.printStackTrace();
-        }
-    }
-
-    /*
-     * treat disjunction as conjunction
-     */
-    private Set<OWLClassExpression> getDisjunctionApprox0(Set<OWLClassExpression> superClasses) {
-        return superClasses;
-    }
-
-    /*
-     * choose one simple class disjunct
-     */
-    @SuppressWarnings("unused")
-    private Set<OWLClassExpression> getDisjunctionApprox1(Set<OWLClassExpression> superClasses) {
-        if(superClasses.isEmpty() || superClasses.size() == 1)
-            return superClasses;
-
-        OWLClassExpression rep = null;
-        int min = Integer.MAX_VALUE, o;
-        for(OWLClassExpression exp : superClasses)
-            if(exp instanceof OWLClass && (o = getOccurrence(exp)) < min) {
-                min = o;
-                rep = exp;
-            }
-
-        if(rep == null) rep = superClasses.iterator().next();
-
-        return Collections.singleton(rep);
-    }
-
-    /*
-     * randomly choose a class expression to represent this disjunction
-     */
-    @SuppressWarnings("unused")
-    private Set<OWLClassExpression> getDisjunctionApprox2(Set<OWLClassExpression> superClasses) {
-        if(superClasses.isEmpty() || superClasses.size() == 1)
-            return superClasses;
-
-        int index = random.nextInt() % superClasses.size();
-        if(index < 0) index += superClasses.size();
-
-        int i = 0;
-        for(OWLClassExpression exp : superClasses)
-            if(i++ == index)
-                return Collections.singleton(exp);
-        return null;
-    }
-
-    /*
-     * choose the one that appears least in the l.h.s.
-     */
-    @SuppressWarnings("unused")
-    private Set<OWLClassExpression> getDisjunctionApprox3(Set<OWLClassExpression> superClasses) {
-        if(superClasses.isEmpty() || superClasses.size() == 1)
-            return superClasses;
-
-        OWLClassExpression rep = null, exp1;
-        int occurrence = Integer.MAX_VALUE, o;
-        for(OWLClassExpression exp : superClasses) {
-            o = 0;
-            exp1 = exp;
-            if(exp instanceof OWLObjectMinCardinality) {
-                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
-                if(minCard.getCardinality() == 1)
-                    exp1 = factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), minCard.getFiller());
-            }
-
-            if(!subCounter.containsKey(exp1) || (o = subCounter.get(exp1)) < occurrence) {
-                rep = exp;
-                occurrence = o;
-            }
-        }
-
-        return Collections.singleton(rep);
-    }
-
-    private int getOccurrence(OWLClassExpression exp) {
-        if(!subCounter.containsKey(exp))
-            return 0;
-        return subCounter.get(exp);
-    }
-
-    @SuppressWarnings("unused")
-    private Set<OWLClassExpression> getDisjunctionApprox4(Set<OWLClassExpression> superClasses) {
-        if(superClasses.isEmpty() || superClasses.size() == 1)
-            return superClasses;
-
-        OWLClassExpression rep = null;
-        int occurrence = Integer.MAX_VALUE, o;
-        for(OWLClassExpression exp : superClasses) {
-            o = 0;
-            if(exp instanceof OWLObjectMinCardinality) {
-                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
-                if(minCard.getCardinality() == 1) {
-                    o =
-                            getOccurrence((factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing())));
-                    o += getOccurrence(minCard.getFiller());
-//                                      if (o < o1) o = o1;
-                }
-            }
-            else
-                o = getOccurrence(exp);
-
-            if(o < occurrence || o == occurrence && !(rep instanceof OWLClass)) {
-                rep = exp;
-                occurrence = o;
-            }
-        }
-
-        return Collections.singleton(rep);
-    }
-
-    private boolean simplifyABox() {
-        boolean flag = false;
-        Map<OWLClassExpression, OWLClass> complex2atomic = new HashMap<OWLClassExpression, OWLClass>();
-
-        OWLDatatype anyURI = factory.getOWLDatatype(IRI.create(Namespace.XSD_NS + "anyURI"));
-        OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY));
-        OWLObjectProperty differentFrom = factory.getOWLObjectProperty(IRI.create(Namespace.INEQUALITY));
-
-        for(OWLOntology imported : inputOntology.getImportsClosure())
-            for(OWLAxiom axiom : imported.getAxioms()) {
-                if(axiom instanceof OWLClassAssertionAxiom) {
-                    flag = true;
-                    OWLClassAssertionAxiom assertion = (OWLClassAssertionAxiom) axiom;
-                    OWLClassExpression clsExp = assertion.getClassExpression();
-                    OWLClass cls;
-                    if(clsExp instanceof OWLClass) {
-                        if(((OWLClass) clsExp).toStringID().startsWith("owl:"))
-                            manager.addAxiom(tBox, axiom);
-                        else manager.addAxiom(aBox, axiom);
-                    }
-                    else {
-                        if((cls = complex2atomic.get(clsExp)) == null) {
-                            complex2atomic.put(clsExp, cls = getNewConcept(tBox, rlCounter++));
-                            manager.addAxiom(tBox, factory.getOWLSubClassOfAxiom(cls, clsExp));
-                        }
-                        manager.addAxiom(aBox, factory.getOWLClassAssertionAxiom(cls, assertion.getIndividual()));
-                    }
-                }
-                else if(axiom instanceof OWLObjectPropertyAssertionAxiom || axiom instanceof OWLDataPropertyAssertionAxiom || axiom instanceof OWLAnnotationAssertionAxiom) {
-                    if(axiom.getDataPropertiesInSignature().contains(anyURI)) continue;
-                    flag = true;
-                    manager.addAxiom(aBox, axiom);
-                }
-                else if(axiom instanceof OWLSameIndividualAxiom) {
-                    OWLIndividual firstIndividual = null, previousIndividual = null, lastIndividual = null;
-                    for(OWLIndividual next : ((OWLSameIndividualAxiom) axiom).getIndividuals()) {
-                        if(firstIndividual == null) firstIndividual = previousIndividual = next;
-                        else
-                            manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, previousIndividual, next));
-                        previousIndividual = lastIndividual = next;
-                    }
-                    manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, lastIndividual, firstIndividual));
-                }
-                else if(axiom instanceof OWLDifferentIndividualsAxiom) {
-                    int index1 = 0, index2;
-                    for(OWLIndividual individual1 : ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
-                        ++index1;
-                        index2 = 0;
-                        for(OWLIndividual individual2 : ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
-                            if(index2++ < index1) {
-                                manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(differentFrom, individual1, individual2));
-                            }
-                            else break;
-                        }
-                    }
-                }
-                else
-                    manager.addAxiom(tBox, axiom);
-            }
-
-        return flag;
-    }
-
-    private void filter() {
-        OWL2RLProfile profile = new OWL2RLProfile();
-        OWLProfileReport report = profile.checkOntology(tBox);
-        Set<OWLAxiom> rlAxioms = tBox.getAxioms();
-        OWLAxiom axiom;
-
-        for(OWLProfileViolation violation : report.getViolations()) {
-            manager.addAxiom(restOntology, axiom = violation.getAxiom());
-            rlAxioms.remove(axiom);
-        }
-
-        for(Iterator<OWLAxiom> iter = rlAxioms.iterator(); iter.hasNext(); )
-            addAxiom2output(iter.next(), null);
-    }
-
-    private void clausify() {
-        Configuration conf = new Configuration();
-        OWLClausification clausifier = new OWLClausification(conf);
-        dlOntology = (DLOntology) clausifier.preprocessAndClausify(restOntology, null)[1];
-        clausifier = null;
-    }
-
-    protected void addAxiom2output(OWLAxiom axiom, OWLAxiom correspondingAxiom) {
-        manager.addAxiom(outputOntology, axiom);
-        if(correspondingAxiom != null)
-            correspondence.put(axiom, correspondingAxiom);
-    }
-
-    private OWLClassExpression transform(OWLClassExpression exp, Set<OWLAxiom> addedAxioms) {
-        if(exp instanceof OWLClass)
-            return exp;
-
-        if(exp instanceof OWLObjectHasValue)
-            return exp;
-
-        if(exp instanceof OWLObjectSomeValuesFrom) {
-            OWLObjectSomeValuesFrom someValueExp = (OWLObjectSomeValuesFrom) exp;
-
-            OWLClassExpression tExp = someValueExp.getFiller();
-            if(tExp.equals(factory.getOWLThing()))
-                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty());
-            else
-                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty(), someValueExp.getFiller());
-        }
-
-        if(exp instanceof OWLObjectMinCardinality) {
-            OWLObjectMinCardinality minExp = (OWLObjectMinCardinality) exp;
-            OWLObjectPropertyExpression r;
-
-            if(minExp.getFiller().equals(factory.getOWLThing())) {
-                r = minExp.getProperty();
-            }
-            //TODO to be restored ...
-            //else if ((r = exists2role.get(someValueExp)) == null) {
-            // deal with r' \subseteq r & range(r') \subseteq C
-            else {
-                r = getNewRole(outputOntology, rlCounter);
-                addedAxioms.add(factory.getOWLSubObjectPropertyOfAxiom(r, minExp.getProperty()));
-                OWLClassExpression tExp = minExp.getFiller();
-                if(!(tExp instanceof OWLObjectComplementOf)) {
-                    if(tExp.equals(factory.getOWLThing())) ;
-                    else
-                        addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, tExp));
-                }
-                else if(botStrategy != BottomStrategy.TOREMOVE) {
-                    OWLClass cls = (OWLClass) tExp.getComplementNNF();
-                    OWLClass neg;
-                    if((neg = atomic2negation.get(cls)) == null) {
-                        neg = getNewConcept(outputOntology, rlCounter);
-                        addedAxioms.add(factory.getOWLDisjointClassesAxiom(neg, cls));
-                        atomic2negation.put(cls, neg);
-                    }
-                    addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, neg));
-                }
-//                              exists2role.put(someValueExp, (OWLObjectProperty) r);
-            }
-
-            // deal with r'(x,c)
-            Set<OWLClassExpression> ret = new HashSet<OWLClassExpression>();
-            int num = minExp.getCardinality();
-
-            Set<OWLNamedIndividual> cs = new HashSet<OWLNamedIndividual>();
-            OWLNamedIndividual c;
-            for(int i = 0; i < num; ++i) {
-                c = getNewIndividual(outputOntology, rlCounter++);
-                ret.add(factory.getOWLObjectHasValue(r, c));
-                cs.add(c);
-            }
-
-            if(botStrategy != BottomStrategy.TOREMOVE && cs.size() > 1) {
-                addedAxioms.add(factory.getOWLDifferentIndividualsAxiom(cs));
-            }
-
-            return OWLHelper.getSimplifiedConjunction(factory, ret);
-        }
-
-        if(exp instanceof OWLObjectMaxCardinality) {
-            OWLObjectMaxCardinality maxExp = (OWLObjectMaxCardinality) exp;
-            OWLClassExpression tExp = maxExp.getFiller();
-            int card = maxExp.getCardinality() >= 1 ? 1 : 0;
-            if(!(tExp instanceof OWLObjectComplementOf))
-                return factory.getOWLObjectMaxCardinality(card, maxExp.getProperty(), tExp);
-            else {
-                Utility.logDebug("oh, to be tested ... ");
-                OWLClassExpression tExp1 =
-                        factory.getOWLObjectAllValuesFrom(maxExp.getProperty(), tExp.getComplementNNF());
-                if(card == 0)
-                    return tExp1;
-                else {
-                    OWLClassExpression tExp2 = factory.getOWLObjectMaxCardinality(1, maxExp.getProperty());
-                    return factory.getOWLObjectIntersectionOf(tExp1, tExp2);
-                }
-            }
-        }
-
-        if(exp instanceof OWLObjectAllValuesFrom)
-            return exp;
-
-        if(exp instanceof OWLObjectOneOf)
-            if(((OWLObjectOneOf) exp).getIndividuals().size() == 1)
-                return exp;
-            else
-                return null;
-
-        if(exp instanceof OWLDataHasValue)
-            return exp;
-
-        //TODO overapproximation - dealing with OWLDataMinCardinality
-
-        if(exp instanceof OWLDataSomeValuesFrom) {
-            return exp;
-        }
-
-        if(exp instanceof OWLDataMinCardinality) {
-            return exp;
-        }
-
-        if(exp instanceof OWLDataMaxCardinality) {
-            return exp;
-        }
-
-
-        Set<OWLClassExpression> exps = exp.asConjunctSet();
-        if(exps.size() == 1 && exps.iterator().next() == exp) {
-            Utility.logError(exp, "error in transform of Ontology~~~~");
-        }
-        Set<OWLClassExpression> nexps = new HashSet<OWLClassExpression>();
-        OWLClassExpression ne;
-        boolean changes = false;
-        for(OWLClassExpression e : exps) {
-            ne = transform(e, addedAxioms);
-            if(ne != e) changes = true;
-            nexps.add(ne);
-        }
-        if(changes)
-            return OWLHelper.getSimplifiedConjunction(factory, nexps);
-        else
-            return exp;
-    }
-
-    protected OWLNamedIndividual getNewIndividual(OWLOntology onto, int number) {
-        OWLOntologyManager manager = onto.getOWLOntologyManager();
-        OWLDataFactory factory = manager.getOWLDataFactory();
-        OWLNamedIndividual newIndividual =
-                factory.getOWLNamedIndividual(IRI.create(Namespace.PAGODA_ANONY + "NI" + number));
-        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newIndividual));
-        return newIndividual;
-    }
-
-    protected OWLObjectProperty getNewRole(OWLOntology onto, int number) {
-        OWLOntologyManager manager = onto.getOWLOntologyManager();
-        OWLDataFactory factory = manager.getOWLDataFactory();
-        OWLObjectProperty newProperty = factory.getOWLObjectProperty(IRI.create(Namespace.PAGODA_AUX + "NR" + number));
-        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newProperty));
-        return newProperty;
-    }
-
-    private OWLClass getNewConcept(OWLOntology onto, int number) {
-        OWLOntologyManager manager = onto.getOWLOntologyManager();
-        OWLDataFactory factory = manager.getOWLDataFactory();
-        OWLClass newClass = factory.getOWLClass(IRI.create(Namespace.PAGODA_AUX + "NC" + number));
-        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newClass));
-        return newClass;
-    }
-
-    private enum BottomStrategy {TOREMOVE, NULLARY, UNARY}
-}
-