3 files changed, 21 insertions, 30 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index d179d14..b7a3667 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -73,6 +73,9 @@ public class ConsistencyManager {
                         AnswerTuples tuples = null; 
                         try {
                                 tuples = m_reasoner.lazyUpperStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
+
+                                Utility.logDebug("CheckLazyUpperBound: answerVars=" + fullQueryRecord.getAnswerVariables());
+
                                 if (!tuples.isValid()) {
                                         Utility.logInfo("There are no contradictions derived in the lazy upper bound materialisation."); 
                                         return satisfiability(t.duration()); 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 233963e..36ea7de 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -33,7 +33,8 @@ public class MyQueryReasoner extends QueryReasoner {
         DatalogProgram program; 
 
         BasicQueryEngine rlLowerStore = null;
-        BasicQueryEngine lazyUpperStore = null;  
+        BasicQueryEngine lazyUpperStore = null;
+        BasicQueryEngine limitedSkolemUpperStore;
 //      boolean[] namedIndividuals_lazyUpper; 
         
         OWLOntology elho_ontology; 
@@ -49,7 +50,6 @@ public class MyQueryReasoner extends QueryReasoner {
         private Collection<String> predicatesWithGap = null;
         private Boolean satisfiable;
         private ConsistencyManager consistency = new ConsistencyManager(this);
-        BasicQueryEngine limitedSkolemUpperStore;
 
         public MyQueryReasoner() {
                 setup(true, true);
@@ -163,10 +163,11 @@ public class MyQueryReasoner extends QueryReasoner {
                         }
                         if (tag == -1) return false;
                 }
-                if (consistency.checkSkolemUpper()) {
-                        satisfiable = true;
-                        Utility.logInfo("time for satisfiability checking: " + t.duration());
-                }
+                // FIXME nullPointerException
+//              if (consistency.checkSkolemUpper()) {
+//                      satisfiable = true;
+//                      Utility.logInfo("time for satisfiability checking: " + t.duration());
+//              }
 
                 trackingStore.importRDFData(name, datafile);
                 trackingStore.materialise("saturate named individuals", originalMarkProgram);
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
index c2065dc..232bc31 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
@@ -1,31 +1,17 @@
 package uk.ac.ox.cs.pagoda.reasoner.light;
 
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.Queue;
-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.Constant;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.Equality;
-import org.semanticweb.HermiT.model.Individual;
-import org.semanticweb.HermiT.model.Inequality;
-import org.semanticweb.HermiT.model.Term;
-import org.semanticweb.HermiT.model.Variable;
-
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.util.Namespace;
+import org.semanticweb.HermiT.model.*;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.model.Datatype;
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.store.DataStore;
-import uk.ac.ox.cs.JRDFox.model.Datatype;
-import uk.ac.ox.cs.JRDFox.store.Dictionary;
 import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.JRDFox.store.Dictionary;
 import uk.ac.ox.cs.JRDFox.store.Resource;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+
+import java.util.*;
 
 public class RDFoxTripleManager {
         
@@ -183,10 +169,11 @@ public class RDFoxTripleManager {
         int sizeLimit = 10000; 
 
         private int getResourceID(Term arg, Map<Variable, Integer> assignment) {
-                while (termCache.size() > sizeLimit) 
-                        termCache.remove(termList.poll()); 
+                // FIXME infinite loop
+//              while (termCache.size() > sizeLimit)
+//                      termCache.remove(termList.poll());
                 
-                if (arg instanceof Variable) return assignment.get((Variable) arg); 
+                if (arg instanceof Variable) return assignment.get(arg);
                 Integer id = null; 
                 if ((id = termCache.get(arg)) != null)
                         return id;