[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, 112 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java
deleted file mode 100644
index 8d79090..0000000
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java
+++ /dev/null
@@ -1,112 +0,0 @@
-package uk.ac.ox.cs.pagoda.tracking;
-
-import org.semanticweb.HermiT.model.*;
-import uk.ac.ox.cs.pagoda.MyPrefixes;
-import uk.ac.ox.cs.pagoda.multistage.Normalisation;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
-import uk.ac.ox.cs.pagoda.rules.approximators.OverApproxExist;
-
-public class TrackingRuleEncoderDisj2 extends TrackingRuleEncoderDisj {
-
-        public TrackingRuleEncoderDisj2(UpperDatalogProgram program, BasicQueryEngine store) {
-                super(program, store);
-        }
-
-        @Override
-        public boolean encodingRules() {
-                if (ruleEncoded) return false;
-                ruleEncoded = true; 
-                
-                for (DLClause clause: program.getClauses()) {
-                        encodingRule(clause);
-                }
-                
-                if (disjunctiveRules.isEmpty())
-                        return true;
-                
-                processDisjunctiveRules(); 
-                return false; 
-        }
-        
-        @Override
-        protected DLPredicate generateAuxiliaryRule(AtomicConcept p) {
-                return getTrackingDLPredicate(p); 
-        }
-        
-        @Override
-        protected DLPredicate generateAuxiliaryRule(AtomicRole p) {
-                return getTrackingDLPredicate(p); 
-        }
-
-        private Variable X = Variable.create("X"); 
-        
-        @Override
-        protected DLPredicate generateAuxiliaryRule(AtLeastConcept p, DLClause original, Individual[] individuals) {
-                DLPredicate ret = AtomicConcept.create(getTrackingPredicate(Normalisation.getAuxiliaryConcept4Disjunct(p, individuals)));
-                Atom[] headAtom = new Atom[] {Atom.create(ret, X)};
-                
-                AtomicRole role = p.getOnRole() instanceof AtomicRole ? 
-                                (AtomicRole) p.getOnRole(): 
-                                        ((InverseRole) p.getOnRole()).getInverseOf(); 
-                        
-                AtomicConcept concept = p.getToConcept() instanceof AtomicConcept ? 
-                                (AtomicConcept) p.getToConcept() : 
-                                        OverApproxExist.getNegationConcept(((AtomicNegationConcept) p.getToConcept()).getNegatedAtomicConcept());
-                                                
-                Term[] roleArgs, conceptArg;
-                for (Individual i: individuals) {
-//              Variable i = Variable.create("Y"); 
-                        if (p.getOnRole() instanceof AtomicRole) {
-                                roleArgs = new Term[] {X, i};
-                                conceptArg = new Term[] {i}; 
-                        }
-                        else {
-                                roleArgs = new Term[] {i, X};
-                                conceptArg = new Term[] {i}; 
-                        }
-                                
-                        addTrackingClause(
-                                        DLClause.create(headAtom, 
-                                                        new Atom[] {Atom.create(getTrackingDLPredicate(role), roleArgs)}));
-                        
-                        Atom guard = Atom.create(role, roleArgs);  
-                                        
-                        if (!concept.equals(AtomicConcept.THING)) {
-                                addTrackingClause(
-                                                DLClause.create(headAtom, 
-                                                                new Atom[] {guard, Atom.create(getTrackingDLPredicate(concept), conceptArg)}));
-                        }
-                }
-                
-                return ret;  
-        }
-        
-        @Override
-        protected void encodingRule(DLClause clause) {
-                DLClause original = program.getCorrespondingClause(clause);
-                if (original.getHeadLength() <= 1) {
-                        super.encodingRule(clause);
-                }
-                else addDisjunctiveRule(original, clause);
-        }
-        
-        @Override
-        public String getTrackingProgram() {
-                StringBuilder sb = getTrackingProgramBody();
-                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText()); 
-                return sb.toString(); 
-        }
-
-        @Override
-        protected void encodingAtomicQuery(QueryRecord[] botQuerRecords) {
-                super.encodingAtomicQuery(botQuerRecords, true);
-        }
-
-        @Override
-        protected DLPredicate generateAuxiliaryRule(Inequality instance) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-}