[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, 100 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java b/src/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java
deleted file mode 100644
index 09915e2..0000000
--- a/src/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package uk.ac.ox.cs.pagoda.tracking;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
-import org.semanticweb.owlapi.model.OWLDataProperty;
-import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
-
-import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
-import uk.ac.ox.cs.pagoda.rules.ApproxProgram;
-import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-public class BottomFragmentManager {
-        
-        QueryRecord m_record;
-        GeneralProgram m_program; 
-        PredicateDependency m_graph;  
-
-        public BottomFragmentManager(QueryRecord record) {
-                m_record = record;
-                m_program = new GeneralProgram(record.getRelevantClauses(), record.getRelevantOntology());
-                m_graph = m_program.buildDependencyGraph();
-        }
-        
-        public Set<DLClause> relevantClauses(Set<DLClause> disjuntiveRules) {
-                Set<DLClause> relevant = new HashSet<DLClause>(); 
-                Set<DLClause> now = new HashSet<DLClause>();
-                Set<DLClause> last = new HashSet<DLClause>();
-                
-                for (DLClause rule: disjuntiveRules) 
-                        for (DLPredicate p: m_graph.collectPredicate(rule.getHeadAtoms()))
-                                now.addAll(m_graph.pathToBottom(p)); 
-
-                while (!relevant.containsAll(now)) {
-                        relevant.addAll(now); 
-                        last.clear();
-                        last = now; 
-                        now = new HashSet<DLClause>();
-                        
-                        for (DLClause rule: last) {
-                                for (DLPredicate p: m_graph.collectPredicate(rule.getHeadAtoms()))
-                                        now.addAll(m_graph.pathToBottom(p)); 
-                                for (DLPredicate p: m_graph.collectPredicate(rule.getBodyAtoms()))
-                                        now.addAll(m_graph.pathTo(p)); 
-                        }
-                }
-                
-                Utility.logDebug("There are " + relevant.size() + " clauses in the bottom fragment related to this query."); 
-                return relevant; 
-        }
-        
-        public Set<OWLAxiom> relevantOntology(Set<DLClause> clauses, ApproxProgram upperProgram) {
-                Set<OWLAxiom> axioms = new HashSet<OWLAxiom>(); 
-                Set<DLPredicate> predicates = new HashSet<DLPredicate>();
-                for (DLClause clause: clauses) {
-                        OWLAxiom axiom = upperProgram.getEquivalentAxiom(clause); 
-                        axioms.add(axiom);
-                        predicates.addAll(m_graph.collectPredicate(clause.getHeadAtoms())); 
-                        predicates.addAll(m_graph.collectPredicate(clause.getBodyAtoms()));
-                }
-                
-                int tboxCounter = axioms.size(); 
-                Utility.logDebug("There are " + tboxCounter + " TBox axioms in the bottom fragment related to this query."); 
-                String name; 
-                for (OWLAxiom axiom: m_record.getRelevantOntology().getABoxAxioms(true)) {
-                        if (axiom instanceof OWLClassAssertionAxiom) {
-                                OWLClass cls = (OWLClass) ((OWLClassAssertionAxiom) axiom).getClassExpression();
-                                name = cls.getIRI().toString();
-                                if (predicates.contains(AtomicConcept.create(name)))
-                                        axioms.add(axiom); 
-                        }
-                        else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
-                                OWLObjectProperty prop = (OWLObjectProperty) ((OWLObjectPropertyAssertionAxiom) axiom).getProperty(); 
-                                name = prop.getIRI().toString(); 
-                                if (predicates.contains(AtomicRole.create(name)))
-                                        axioms.add(axiom); 
-                        }
-                        else if (axiom instanceof OWLDataPropertyAssertionAxiom) {
-                                OWLDataProperty prop = (OWLDataProperty) ((OWLDataPropertyAssertionAxiom) axiom).getProperty(); 
-                                name = prop.getIRI().toString();
-                                if (predicates.contains(AtomicRole.create(name)))
-                                        axioms.add(axiom);
-                        }
-                }
-                
-                Utility.logDebug("There are " + (axioms.size() - tboxCounter) + " ABox axioms in the bottom fragment related to this query."); 
-                return axioms; 
-        }
-}