[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, 116 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
deleted file mode 100644
index 4ece796..0000000
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ /dev/null
@@ -1,116 +0,0 @@
-package uk.ac.ox.cs.pagoda.tracking;
-
-import org.semanticweb.HermiT.model.*;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLOntology;
-import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.query.GapTupleIterator;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
-import uk.ac.ox.cs.pagoda.util.Namespace;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Set;
-
-public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
-
-        public TrackingRuleEncoderWithGap(UpperDatalogProgram program, BasicQueryEngine store) {
-                super(program, store);
-        }
-
-        @Override
-        protected String getEqualityRelatedRuleText() {
-                if (equalityRelatedRuleText != null) return equalityRelatedRuleText.replace("_tn", getTrackingPredicate("")); 
-                
-                Collection<DLClause> equalityRelatedClauses = new LinkedList<DLClause>(); 
-                Variable X = Variable.create("X"); 
-                AtomicRole trackingSameAs = AtomicRole.create(Namespace.EQUALITY + "_tn");  
-                OWLOntology onto = program.getOntology();
-                Atom[] headAtom = new Atom[]{Atom.create(trackingSameAs, X, X)}, bodyAtom;
-                for(OWLOntology o : onto.getImportsClosure())
-                        for(OWLClass cls : o.getClassesInSignature()) {
-                        String clsIRI = cls.getIRI().toString();
-                        unaryPredicates.add(clsIRI); 
-                        bodyAtom = new Atom[] {
-                                        Atom.create(AtomicConcept.create(clsIRI + "_tn"), X),
-                                        Atom.create(AtomicConcept.create(GapTupleIterator.getGapPredicate(clsIRI)), X)}; 
-                        equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 
-                }
-
-                Variable Y = Variable.create("Y");
-                Set<OWLObjectProperty> setOfProperties = new HashSet<OWLObjectProperty>();
-                for(OWLOntology o : onto.getImportsClosure())
-                        for(OWLObjectProperty prop : o.getObjectPropertiesInSignature())
-                                setOfProperties.add(prop);
-                setOfProperties.add(onto.getOWLOntologyManager()
-                                                                .getOWLDataFactory()
-                                                                .getOWLObjectProperty(IRI.create(Namespace.INEQUALITY)));
-                for(OWLObjectProperty prop : setOfProperties) {
-                        String propIRI = prop.getIRI().toString();
-                        binaryPredicates.add(propIRI); 
-                        AtomicRole trackingRole = AtomicRole.create(propIRI + "_tn"); 
-                        AtomicRole gapRole = AtomicRole.create(GapTupleIterator.getGapPredicate(propIRI)); 
-//                      AtomicRole role = AtomicRole.create(propIRI); 
-                        bodyAtom = new Atom[] {
-                                        Atom.create(trackingRole, X, Y), 
-                                        Atom.create(gapRole, X, Y)}; 
-                        equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom));
-                        
-                        bodyAtom = new Atom[] {
-                                        Atom.create(trackingRole, Y, X), 
-                                        Atom.create(gapRole, Y, X)}; 
-                        equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 
-                }
-                
-                equalityRelatedClauses.add(
-                                DLClause.create(
-                                                new Atom[] {Atom.create(trackingSameAs, Y, X)}, 
-                                                new Atom[] {Atom.create(trackingSameAs, X, Y)}));
-                
-                equalityRelatedRuleText = DLClauseHelper.toString(equalityRelatedClauses).toString();
-                return equalityRelatedRuleText.replace("_tn", getTrackingPredicate("")); 
-        }
-
-        @Override
-        protected void encodingRule(DLClause clause) {
-                LinkedList<Atom> newHeadAtoms = new LinkedList<Atom>();
-                newHeadAtoms.add(Atom.create(selected, getIndividual4GeneralRule(clause)));
-                
-                Atom headAtom;
-                for (Atom atom: clause.getBodyAtoms()) {
-                        headAtom = Atom.create(
-                                        getTrackingDLPredicate(atom.getDLPredicate()), 
-                                        DLClauseHelper.getArguments(atom));
-                        newHeadAtoms.add(headAtom);
-                }
-
-                DLClause newClause;
-                headAtom = clause.getHeadAtom(0);
-                
-                boolean equalityHead = headAtom.getDLPredicate() instanceof Equality || headAtom.getDLPredicate() instanceof AnnotatedEquality; 
-                int offset = (equalityHead || (clause.getBodyLength() == 1 && clause.getBodyAtom(0).getDLPredicate().toString().contains("owl:Nothing"))) ? 1 : 2;
-                
-                Atom[] newBodyAtoms = new Atom[clause.getBodyLength() + offset];
-                newBodyAtoms[0] = Atom.create(
-                                getTrackingDLPredicate(headAtom.getDLPredicate()), 
-                                DLClauseHelper.getArguments(headAtom));
-                
-                if (offset == 2)
-                newBodyAtoms[1] = Atom.create(
-                                getGapDLPredicate(headAtom.getDLPredicate()), 
-                                DLClauseHelper.getArguments(headAtom));
-
-                for (int i = 0; i < clause.getBodyLength(); ++i)
-                        newBodyAtoms[i + offset] = clause.getBodyAtom(i); 
-                
-                for (Atom atom: newHeadAtoms) {
-                        newClause = DLClause.create(new Atom[] {atom}, newBodyAtoms); 
-                        trackingClauses.add(newClause);
-                }
-                
-        }
-}