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diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
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+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
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+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.util.Collection;
+
+import org.semanticweb.karma2.profile.ELHOProfile;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.multistage.*; 
+import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.query.*;
+import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
+import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
+import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
+import uk.ac.ox.cs.pagoda.tracking.*;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class MyQueryReasoner extends QueryReasoner {
+
+        OWLOntology ontology; 
+
+//      String additonalDataFile; 
+        
+        DatalogProgram program; 
+
+        BasicQueryEngine rlLowerStore = null;
+        BasicQueryEngine lazyUpperStore = null;  
+//      boolean[] namedIndividuals_lazyUpper; 
+        
+        OWLOntology elho_ontology; 
+        KarmaQueryEngine elLowerStore = null; 
+        
+        BasicQueryEngine trackingStore = null;
+//      boolean[] namedIndividuals_tracking; 
+        
+        boolean equalityTag; 
+        boolean multiStageTag;
+        
+        public MyQueryReasoner() {
+                setup(true, true); 
+        }
+        
+        public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+                setup(multiStageTag, considerEqualities); 
+        }
+        
+        private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
+                if (multiStageTag)
+                        return new MultiStageQueryEngine(name, checkValidity); 
+//                      return new TwoStageQueryEngine(name, checkValidity);
+                else 
+                        return new BasicQueryEngine(name); 
+        }
+        
+        public void setup(boolean multiStageTag, boolean considerEqualities) {
+                satisfiable = null; 
+                this.multiStageTag = multiStageTag; 
+                this.equalityTag = considerEqualities;
+
+                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+                elLowerStore = new KarmaQueryEngine("elho-lower-bound");
+                
+                trackingStore = getUpperStore("tracking", false);
+        }
+        
+        protected void internal_importDataFile(String name, String datafile) {
+//              addDataFile(datafile);
+                rlLowerStore.importRDFData(name, datafile);
+                if (lazyUpperStore != null)
+                        lazyUpperStore.importRDFData(name, datafile);
+                elLowerStore.importRDFData(name, datafile);
+                trackingStore.importRDFData(name, datafile);
+        }
+        
+        @Override
+        public void loadOntology(OWLOntology o) {
+                if (!equalityTag) {
+                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+                        o = eliminator.getOutputOntology();
+                        eliminator.save();
+                }                       
+
+                ontology = o; 
+                program = new DatalogProgram(ontology, !forSemFacet);
+//              program.getLower().save();
+//              program.getUpper().save();
+//              program.getGeneral().save();
+                
+                if (multiStageTag && !program.getGeneral().isHorn()) { 
+                        lazyUpperStore =  getUpperStore("lazy-upper-bound", true); // new MultiStageQueryEngine("lazy-upper-bound", true); //
+                }
+                
+                importData(program.getAdditionalDataFile());
+        
+                elho_ontology = new ELHOProfile().getFragment(ontology);
+                elLowerStore.processOntology(elho_ontology);
+        }
+
+        private Collection<String> predicatesWithGap = null; 
+        
+        public Collection<String> getPredicatesWithGap() {
+                return predicatesWithGap; 
+        }       
+        
+        @Override
+        public boolean preprocess() {
+                t.reset(); 
+                Utility.logInfo("Preprocessing ... checking satisfiability ... ");
+
+                String name = "data", datafile = importedData.toString(); 
+                rlLowerStore.importRDFData(name, datafile);
+                rlLowerStore.materialise("lower program", program.getLower().toString());
+//              program.getLower().save();
+                if (!consistency.checkRLLowerBound()) return false;
+                Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
+                
+                String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
+                
+                elLowerStore.importRDFData(name, datafile);
+                elLowerStore.materialise("saturate named individuals", originalMarkProgram);
+                elLowerStore.materialise("lower program", program.getLower().toString());
+                elLowerStore.initialiseKarma();
+                if (!consistency.checkELLowerBound()) return false;                     
+
+                if (lazyUpperStore != null) {
+                        lazyUpperStore.importRDFData(name, datafile);
+                        lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
+                        int tag = lazyUpperStore.materialiseRestrictedly(program, null);  
+                        if (tag != 1) {
+                                lazyUpperStore.dispose();
+                                lazyUpperStore = null;
+                        }
+                        if (tag == -1) return false; 
+                }
+                if (consistency.checkLazyUpper()) {
+                        satisfiable = true; 
+                        Utility.logInfo("time for satisfiability checking: " + t.duration()); 
+                }
+                        
+                trackingStore.importRDFData(name, datafile);
+                trackingStore.materialise("saturate named individuals", originalMarkProgram);
+                
+//              materialiseFullUpper();
+                GapByStore4ID gap = new GapByStore4ID(trackingStore); 
+                trackingStore.materialiseFoldedly(program, gap);
+                predicatesWithGap = gap.getPredicatesWithGap(); 
+                gap.clear();
+                
+                if (program.getGeneral().isHorn())
+                        encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
+                else 
+                        encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore); 
+//                      encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore); 
+//                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore); 
+//                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore); 
+                
+                program.deleteABoxTurtleFile(); 
+
+                if (!isConsistent())
+                        return false; 
+                
+                consistency.extractBottomFragment();
+                return true; 
+        }
+        
+        private Boolean satisfiable;
+        private ConsistencyManager consistency = new ConsistencyManager(this); 
+        
+        TrackingRuleEncoder encoder;
+
+        @Override
+        public boolean isConsistent() {
+                if (satisfiable == null) {
+                        satisfiable = consistency.check();              
+                        Utility.logInfo("time for satisfiability checking: " + t.duration());
+                }
+                return satisfiable; 
+        }
+        
+        Timer t = new Timer();
+
+        private OWLOntology relevantPart(QueryRecord queryRecord) {
+                AnswerTuples rlAnswer = null, elAnswer = null;
+                
+                t.reset(); 
+                try {
+                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateLowerBoundAnswers(rlAnswer);
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose();
+                }
+                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                rlAnswer = null;
+                
+                t.reset();
+                BasicQueryEngine upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;  
+                        
+                String[] extendedQuery = queryRecord.getExtendedQueryText(); 
+                
+                queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                if (!queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery[0]))
+                        queryUpperBound(upperStore, queryRecord, extendedQuery[0], queryRecord.getAnswerVariables());
+                if (!queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables()) 
+                        queryUpperBound(upperStore, queryRecord, extendedQuery[1], queryRecord.getDistinguishedVariables());
+                        
+                queryRecord.addProcessingTime(Step.UpperBound, t.duration());
+                if (queryRecord.processed()) {
+                        queryRecord.setDifficulty(Step.UpperBound); 
+                        return null;
+                }
+                
+                t.reset();
+                try {
+                        elAnswer = elLowerStore.evaluate(extendedQuery[0], queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateLowerBoundAnswers(elAnswer);
+                } finally {
+                        if (elAnswer != null) elAnswer.dispose();
+                }
+                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
+
+                if (queryRecord.processed()) {
+                        queryRecord.setDifficulty(Step.ELLowerBound); 
+                        return null; 
+                }
+                
+                t.reset(); 
+                
+                QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
+                
+                OWLOntology knowledgebase; 
+                t.reset(); 
+//              if (program.getGeneral().isHorn()) {
+//                      knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
+//                      queryRecord.addProcessingTime(Step.Fragment, t.duration());
+//                      return knowledgebase; 
+//              }
+//              else { 
+                        knowledgebase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
+                        queryRecord.addProcessingTime(Step.Fragment, t.duration());
+//              }
+                
+                        if (knowledgebase.isEmpty() || queryRecord.isBottom()) 
+                                return knowledgebase; 
+                        
+                if (program.getGeneral().isHorn()) return knowledgebase; 
+
+//              t.reset(); 
+//              if (queryRecord.isHorn() && lazyUpperStore != null) { 
+////                    knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true); 
+//              } else if (queryRecord.getArity() < 3) {
+//                      IterativeRefinement iterativeRefinement = new IterativeRefinement(queryRecord, tracker, trackingStore, consistency.getQueryRecords());
+//                      knowledgebase = iterativeRefinement.extractWithFullABox(importedData.toString(), program.getUpperBottomStrategy());
+//              }
+//              
+//              queryRecord.addProcessingTime(Step.FragmentRefinement, t.duration());
+//              
+//              if (knowledgebase == null)
+//                      queryRecord.setDifficulty(Step.FragmentRefinement);
+                
+                return knowledgebase; 
+        }
+
+//      int counter = 0; 
+
+        private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
+                AnswerTuples rlAnswer = null; 
+                try {
+                        Utility.logDebug(queryText);
+                        rlAnswer = upperStore.evaluate(queryText, answerVariables);
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateUpperBoundAnswers(rlAnswer); 
+                        rlAnswer.dispose();
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose();
+                }
+                rlAnswer = null;
+        }
+
+        @Override
+        public void evaluate(QueryRecord queryRecord) {
+                OWLOntology knowledgebase = relevantPart(queryRecord);
+                
+                if (knowledgebase == null) {
+                        Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
+                        return ; 
+                }
+                
+                int aboxcount = knowledgebase.getABoxAxioms(true).size(); 
+                Utility.logDebug("ABox axioms: " + aboxcount + " TBox axioms: " + (knowledgebase.getAxiomCount() - aboxcount)); 
+//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 
+                
+                Timer t = new Timer(); 
+                Checker summarisedChecker = new HermitSummaryFilter(queryRecord); 
+                int validNumber = summarisedChecker.check(queryRecord.getGapAnswers()); 
+                summarisedChecker.dispose();
+                Utility.logDebug("Total time for full reasoner: " + t.duration());
+                if (!forSemFacet || validNumber == 0) { 
+                        queryRecord.markAsProcessed(); 
+                        Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
+                }
+        }
+        
+        @Override
+        public void evaluateUpper(QueryRecord queryRecord) {
+                AnswerTuples rlAnswer = null; 
+                boolean useFull = queryRecord.isBottom() || lazyUpperStore == null; 
+                try {
+                        rlAnswer = (useFull ? trackingStore: lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        queryRecord.updateUpperBoundAnswers(rlAnswer, true); 
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose();
+                }
+        }
+        
+        @Override
+        public void dispose() {
+                if (encoder != null) encoder.dispose();
+                if (rlLowerStore != null) rlLowerStore.dispose();
+                if (lazyUpperStore != null) lazyUpperStore.dispose();
+                if (elLowerStore != null) elLowerStore.dispose();
+                if (trackingStore != null) trackingStore.dispose();
+                super.dispose();
+        }
+
+}