Merge branch 'upstream' into Query-dependent-skolemisation

Conflicts:
	src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
	src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
	src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
	src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
	src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
	src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
	src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
	src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
	src/uk/ac/ox/cs/pagoda/util/Utility.java
	test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
	test/uk/ac/ox/cs/pagoda/junit/TestGapMappedToLower.java

1 files changed, 61 insertions, 52 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/junit/TestGapMappedToLower.java b/test/uk/ac/ox/cs/pagoda/junit/TestGapMappedToLower.java
index 8fae16c..3e385e5 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/TestGapMappedToLower.java
+++ b/test/uk/ac/ox/cs/pagoda/junit/TestGapMappedToLower.java
@@ -1,9 +1,18 @@
 package uk.ac.ox.cs.pagoda.junit;
 
 import junit.framework.Assert;
+
 import org.junit.Test;
 import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
 import uk.ac.ox.cs.pagoda.query.AnswerTuple;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
@@ -11,58 +20,58 @@ import uk.ac.ox.cs.pagoda.util.Namespace;
 
 public class TestGapMappedToLower {
 
-    public static final String ns = "http://example.org/test#%s";
-
-    public IRI getEntityIRI(String name) {
-        return IRI.create(String.format(ns, name));
-    }
-
-    @Test
-    public void test() throws OWLOntologyCreationException {
-        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
-        OWLDataFactory factory = manager.getOWLDataFactory();
-        OWLOntology ontology = manager.createOntology();
-        OWLClass A = factory.getOWLClass(getEntityIRI("A"));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A));
-        OWLClass B = factory.getOWLClass(getEntityIRI("B"));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(B));
-        OWLClass C = factory.getOWLClass(getEntityIRI("C"));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(C));
-        OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1));
-        OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2));
-        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
-        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
-        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
-        OWLObjectProperty r = factory.getOWLObjectProperty(IRI.create(String.format(ns, "r")));
-        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(r));
+        public static final String ns = "http://example.org/test#%s";
+        
+        public IRI getEntityIRI(String name) {
+                return IRI.create(String.format(ns, name)); 
+        }
+        
+        @Test
+        public void test() throws OWLOntologyCreationException {
+                OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 
+                OWLDataFactory factory = manager.getOWLDataFactory(); 
+                OWLOntology ontology = manager.createOntology(); 
+                OWLClass A = factory.getOWLClass(getEntityIRI("A"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A)); 
+                OWLClass B = factory.getOWLClass(getEntityIRI("B"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(B)); 
+                OWLClass C = factory.getOWLClass(getEntityIRI("C"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(C)); 
+                OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1)); 
+                OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2)); 
+                OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a")); 
+                OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+                OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c")); 
+                OWLObjectProperty r = factory.getOWLObjectProperty(IRI.create(String.format(ns, "r")));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(r));
 
-        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A, a));    // A(a)
-        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(B, b));    // B(b)
-        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(C, c));    // C(c)
-        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, b));    // r(a,b)
-        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, c));    // r(a,c)
-        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A, factory.getOWLObjectUnionOf(A1, A2)));    // A \sqsubseteq A1 \sqcup A2
-        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectMaxCardinality(1, r)));    // A1 \sqsubseteq \leq 1 r.\top
-        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectMaxCardinality(1, r)));    // A2 \sqsubseteq \leq 1 r.\top
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A, a));    // A(a)
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(B, b));    // B(b)
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(C, c));    // C(c)
+                manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, b));        // r(a,b)
+                manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, c));        // r(a,c)
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A, factory.getOWLObjectUnionOf(A1, A2)));      // A \sqsubseteq A1 \sqcup A2
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectMaxCardinality(1, r)));        // A1 \sqsubseteq \leq 1 r.\top 
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectMaxCardinality(1, r)));        // A2 \sqsubseteq \leq 1 r.\top 
 
-        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
-        pagoda.loadOntology(ontology);
-        if(pagoda.preprocess()) {
-            String sparql = "select ?x where { "
-                    + "?x <" + r.toStringID() + "> ?y . "
-                    + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + B.toStringID() + "> . "
-                    + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + C.toStringID() + "> . } ";
-            AnswerTuples rs = pagoda.evaluate(sparql);
-            int count = 0;
-            for(AnswerTuple ans; rs.isValid(); rs.moveNext()) {
-                ans = rs.getTuple();
-                System.out.println(ans.getGroundTerm(0));
-                ++count;
-            }
-            Assert.assertEquals(1, count);
-        }
-    }
+                QueryReasoner pagoda = QueryReasoner.getInstance(ontology); 
+                pagoda.loadOntology(ontology);
+                if (pagoda.preprocess()) {
+                        String sparql = "select ?x where { "
+                                        + "?x <" + r.toStringID() + "> ?y . "
+                                        + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + B.toStringID() + "> . "
+                                        + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + C.toStringID() + "> . } ";
+                        AnswerTuples rs = pagoda.evaluate(sparql);
+                        int count = 0; 
+                        for (AnswerTuple ans; rs.isValid(); rs.moveNext()) {
+                                ans = rs.getTuple(); 
+                                System.out.println(ans.getGroundTerm(0)); 
+                                ++count; 
+                        }
+                        Assert.assertEquals(1, count);
+                }
+        }
 
 }