4 files changed, 11 insertions, 8 deletions

diff --git a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index ac62488..ebf1960 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.JRDFox.model.Individual;
@@ -63,7 +64,7 @@ class HermiTReasoner extends QueryReasoner {
         factory = onto.getOWLOntologyManager().getOWLDataFactory();
         roller = new QueryRoller(factory);
 
-        hermit = new Reasoner(onto);
+        hermit = new Reasoner(new Configuration(), onto);
         return isConsistent();
     }
 
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
index 3f3c22d..fb7e062 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.reasoner.full;
 
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.HermiT.model.Term;
@@ -57,7 +58,7 @@ public class HermitChecker extends Checker {
 //                      record = other.record;
         }
 
-        hermit = new Reasoner(ontology);
+        hermit = new Reasoner(new Configuration(), ontology);
     }
 
     public HermitChecker(OWLOntology ontology, QueryRecord record, boolean toCheck) {
@@ -174,12 +175,12 @@ public class HermitChecker extends Checker {
             addTopAndBotTuple(topAxioms, botAxioms);
             manager.addAxioms(ontology, topAxioms);
             manager.addAxioms(ontology, botAxioms);
-            hermit = new Reasoner(ontology);
+            hermit = new Reasoner(new Configuration(), ontology);
             boolean topValid = true;
             if(!hermit.isConsistent() || topAnswerTuple != null && (topValid = check(topAnswerTuple))) {
                 hermit.dispose();
                 manager.removeAxioms(ontology, topAxioms);
-                hermit = new Reasoner(ontology);
+                hermit = new Reasoner(new Configuration(), ontology);
             }
             else {
                 if(!topValid) tag = -1;
@@ -187,7 +188,7 @@ public class HermitChecker extends Checker {
             }
         }
         else
-            hermit = new Reasoner(ontology);
+            hermit = new Reasoner(new Configuration(), ontology);
     }
 
     private void addTopAndBotTuple(Set<OWLAxiom> topAxioms, Set<OWLAxiom> botAxioms) {
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index a2676e8..2610652 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.pagoda.rules;
 
 import org.apache.commons.io.FilenameUtils;
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
@@ -149,7 +150,7 @@ class ClassifyThread extends Thread {
         public void run() {
                 ontology = m_program.getOntology();
                 try {
-                        hermitReasoner = new Reasoner(ontology);
+                        hermitReasoner = new Reasoner(new Configuration(), ontology);
                         Timer t = new Timer(); 
                         hermitReasoner.classifyClasses();
                         Utility.logInfo("HermiT classification done: " + t.duration());
@@ -235,4 +236,4 @@ class ClassifyThread extends Thread {
         private Atom getAtom(OWLClass c) {
                 return Atom.create(AtomicConcept.create(c.toStringID()), X);
         }
-}
\ No newline at end of file
+}
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
index de06f52..22eb9ec 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -273,7 +273,7 @@ protected PredicateDependency dependencyGraph;
                 Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
 
         DLOntology dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
-        dlClauses = dlOntology.getDLClauses();
+        dlClauses = new HashSet<DLClause>(dlOntology.getDLClauses());
         positiveFacts = dlOntology.getPositiveFacts();
         }