[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, 94 insertions, 0 deletions

diff --git a/src/main/java/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java b/src/main/java/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java
new file mode 100644
index 0000000..de2f87e
--- /dev/null
+++ b/src/main/java/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java
@@ -0,0 +1,94 @@
+package org.semanticweb.karma2.model;
+
+import java.util.LinkedHashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+
+import org.semanticweb.HermiT.model.Atom;
+import org.semanticweb.HermiT.model.Term;
+import org.semanticweb.HermiT.model.Variable;
+
+import uk.ac.ox.cs.JRDFox.Prefixes;
+
+
+public class ExtendedConjunctiveQuery extends ConjunctiveQuery {
+
+        private Term[] ansTerms;
+        private Term[] terms;
+
+        public ExtendedConjunctiveQuery(
+                        Atom[] queryAtoms, Term[] answerTerms, Prefixes pref) {
+                super(queryAtoms, getExtendedHead(queryAtoms, answerTerms), pref);
+                this.ansTerms = answerTerms.clone(); 
+                terms = getQueryTerms(queryAtoms);
+        }
+
+        public int getNumberOfRealAnswerTerms() {
+                return ansTerms.length;
+        }
+
+        public Term getRealAnswerTerm(int termIndex) {
+                return ansTerms[termIndex];
+        }
+
+        public int getNumberOfTerms() {
+                return terms.length;
+        }
+
+        public Term[] getTerms() {
+                return terms;
+        }
+        
+        
+        public Atom[] getAtoms() {
+                return m_queryAtoms;
+        }
+        
+        public Term[] getRealAnswerTerms() {
+                return ansTerms;
+        }
+
+        private static  Term[] getExtendedHead(Atom[] queryAtoms, Term[] answerTerms) {
+                List<Term> terms = new LinkedList<Term>();
+                for (Term t :answerTerms) {
+                        terms.add(t);
+                }
+                for (Atom a : queryAtoms) {
+                        if (a.getArgument(0) instanceof Variable && !terms.contains(a.getArgument(0)))
+                                terms.add(a.getArgument(0));
+                        if (a.getArity()> 1 && a.getArgument(1) instanceof Variable && !terms.contains(a.getArgument(1)))
+                                terms.add(a.getArgument(1));
+                }
+                return terms.toArray(new Term[terms.size()]);
+                
+        }
+        
+        private static  Term[] getQueryTerms(Atom[] queryAtoms) {
+                Set<Term> terms = new LinkedHashSet<Term>();
+                for (Atom a : queryAtoms) {
+                        terms.add(a.getArgument(0));
+                        if (a.getArity()> 1)
+                                terms.add(a.getArgument(1));
+                }
+                return terms.toArray(new Term[terms.size()]);
+        }
+        
+        
+        public static ExtendedConjunctiveQuery computeExtension(ConjunctiveQuery q) {
+                Term[] answerTerms = new Term[q.getNumberOfAnswerTerms()];
+                for (int i = 0; i < q.getNumberOfAnswerTerms(); i++)
+                        answerTerms[i] = q.getAnswerTerm(i);
+                Atom[] atoms = new Atom[q.getNumberOfQueryAtoms()];
+                for (int i = 0; i < q.getNumberOfQueryAtoms(); i++)
+                        atoms[i] = q.getQueryAtom(i);
+                return new ExtendedConjunctiveQuery(atoms, answerTerms,q.prefixes);
+                
+        }
+
+        public Term getTerm(int i) {
+                return terms[i];
+        }
+        
+
+}