Merged updates from upstream.

1 files changed, 21 insertions, 17 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
index 67d07a8..c3694ad 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
@@ -1,25 +1,21 @@
 package uk.ac.ox.cs.pagoda.tracking;
 
-import java.util.Collection;
-import java.util.LinkedList;
-
-import org.semanticweb.HermiT.model.AnnotatedEquality;
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.Equality;
-import org.semanticweb.HermiT.model.Variable;
+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.*; 
+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) {
@@ -34,8 +30,9 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
                 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 (OWLClass cls: onto.getClassesInSignature(true)) {
+                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[] {
@@ -43,9 +40,16 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
                                         Atom.create(AtomicConcept.create(GapTupleIterator.getGapPredicate(clsIRI)), X)}; 
                         equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 
                 }
-                
-                Variable Y = Variable.create("Y"); 
-                for (OWLObjectProperty prop: onto.getObjectPropertiesInSignature(true)) {
+
+                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");