20 files changed, 2949 insertions, 0 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
new file mode 100644
index 0000000..a222645
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -0,0 +1,269 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.util.LinkedList;
+
+import org.semanticweb.HermiT.model.Atom;
+import org.semanticweb.HermiT.model.AtomicConcept;
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryManager;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
+import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
+import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
+import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
+import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+
+public class ConsistencyManager {
+
+        protected MyQueryReasoner m_reasoner;
+        protected QueryManager m_queryManager;  
+        
+        Timer t = new Timer(); 
+        
+        public ConsistencyManager(MyQueryReasoner reasoner) {
+                m_reasoner = reasoner; 
+                m_queryManager = reasoner.getQueryManager(); 
+        }
+        
+        QueryRecord fullQueryRecord; 
+        QueryRecord[] botQueryRecords;
+        
+        LinkedList<DLClause> toAddClauses;
+        
+        boolean checkRLLowerBound() {
+                fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
+                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
+                if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
+                        Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 
+                        return unsatisfiability(t.duration());
+                }
+                return true; 
+        }
+        
+        boolean checkELLowerBound() {
+                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
+                if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
+                        Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 
+                        return unsatisfiability(t.duration());
+                }
+                return true; 
+        }
+        
+        boolean checkLazyUpper() {
+                if (m_reasoner.lazyUpperStore != null) {
+                        AnswerTuples tuples = null; 
+                        try {
+                                tuples = m_reasoner.lazyUpperStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
+                                if (!tuples.isValid()) {
+                                        Utility.logInfo("There are no contradictions derived in the lazy upper bound materialisation."); 
+                                        return satisfiability(t.duration()); 
+                                }
+                        }
+                        finally {
+                                if (tuples != null) tuples.dispose();
+                        }
+                }
+                return false; 
+        }
+        
+        boolean check() {
+//              if (!checkRLLowerBound()) return false; 
+//              if (!checkELLowerBound()) return false;  
+//              if (checkLazyUpper()) return true; 
+                
+                fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
+                if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
+                        return satisfiability(t.duration()); 
+                
+                extractBottomFragment();
+                
+                try {
+                        extractAxioms4Full();
+                } catch (OWLOntologyCreationException e) {
+                        e.printStackTrace();
+                }
+                fullQueryRecord.saveRelevantClause();
+                
+                boolean satisfiability; 
+                
+                Checker checker; 
+                for (QueryRecord r: getQueryRecords()) {
+                        // TODO to be removed ... 
+//                      r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl");
+                        checker = new HermitSummaryFilter(r); // m_reasoner.factory.getSummarisedReasoner(r);
+                        satisfiability = checker.isConsistent(); 
+                        checker.dispose();
+                        if (!satisfiability) return unsatisfiability(t.duration()); 
+                }
+                
+//              Checker checker = m_reasoner.factory.getSummarisedReasoner(fullQueryRecord); 
+//              boolean satisfiable = checker.isConsistent(); 
+//              checker.dispose();
+//              if (!satisfiable) return unsatisfiability(t.duration()); 
+                
+                return satisfiability(t.duration()); 
+        }
+
+        protected boolean unsatisfiability(double duration) {
+                fullQueryRecord.dispose();
+                Utility.logDebug("The ontology and dataset is unsatisfiable."); 
+                return false;
+        }
+
+        protected boolean satisfiability(double duration) {
+                fullQueryRecord.dispose();
+                Utility.logDebug("The ontology and dataset is satisfiable."); 
+                return true;
+        }
+        
+        boolean fragmentExtracted = false; 
+
+        public void extractBottomFragment() {
+                if (fragmentExtracted) return ;
+                fragmentExtracted = true;
+                
+                UpperDatalogProgram upperProgram = m_reasoner.program.getUpper(); 
+                int number = upperProgram.getBottomNumber();
+                
+                if (number <= 1) {
+                        botQueryRecords = new QueryRecord[] { fullQueryRecord }; 
+                }
+                else {
+                        QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
+                        QueryRecord record; 
+                        for (int i = 0; i < number - 1; ++i) {
+                                tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1); 
+                                record.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables())); 
+                        }
+                        
+                        int bottomNumber = 0; 
+                        int[] group = new int[number - 1]; 
+                        for (int i = 0; i < number - 1; ++i) group[i] = i; 
+                        for (int i = 0; i < number - 1; ++i)
+                                if (tempQueryRecords[i].processed()) tempQueryRecords[i].dispose();
+                                else if (group[i] == i) {
+                                        ++bottomNumber; 
+                                        record = tempQueryRecords[i]; 
+                                        for (int j = i + 1; j < number - 1; ++j)
+                                                if (record.hasSameGapAnswers(tempQueryRecords[j]))
+                                                        group[j] = i; 
+                                }
+                        
+                        Utility.logInfo("There are " + bottomNumber + " different bottom fragments."); 
+                        toAddClauses = new LinkedList<DLClause>(); 
+                        int bottomCounter = 0;
+                        botQueryRecords = new QueryRecord[bottomNumber];
+                        Variable X = Variable.create("X"); 
+                        for (int i = 0; i < number - 1; ++i) 
+                                if (!tempQueryRecords[i].processed()) 
+                                        if (group[i] == i) {
+                                                botQueryRecords[bottomCounter] = record = tempQueryRecords[i];
+                                                record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0, group[i] = bottomCounter);
+                                                toAddClauses.add(
+                                                                DLClause.create(
+                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + bottomCounter), X)}, 
+                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
+                                        }
+                                        else {
+                                                toAddClauses.add(
+                                                                DLClause.create(
+                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + group[group[i]]), X)}, 
+                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
+                                                tempQueryRecords[i].dispose();
+                                        }
+                        
+                        upperProgram.updateDependencyGraph(toAddClauses); 
+                }
+                
+                String[] programs = collectTrackingProgramAndImport();
+                if (programs.length == 0)
+                        return ; 
+                
+                DataStore store = m_reasoner.trackingStore.getDataStore(); 
+                long oldTripleCount, tripleCount;
+                try {
+                        Timer t1 = new Timer();
+                        oldTripleCount = store.getTriplesCount();
+                        for (String program: programs) 
+                                store.importRules(program);
+                        store.applyReasoning(true);
+                        tripleCount = store.getTriplesCount(); 
+                        
+                        Utility.logInfo("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)", 
+                                        "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds.");
+                        
+                        extractAxioms();
+                        store.clearRulesAndMakeFactsExplicit();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } catch (OWLOntologyCreationException e) {
+                        e.printStackTrace();
+                }
+        }
+        
+        private void extractAxioms4Full() throws OWLOntologyCreationException {
+                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
+                OWLOntology fullOntology = manager.createOntology();
+                for (QueryRecord record: botQueryRecords) {
+                        for (DLClause clause: record.getRelevantClauses()) {
+                                fullQueryRecord.addRelevantClauses(clause);
+                        }
+                        manager.addAxioms(fullOntology, record.getRelevantOntology().getAxioms()); 
+                }
+                fullQueryRecord.setRelevantOntology(fullOntology);
+        }
+
+        private void extractAxioms() throws OWLOntologyCreationException {
+                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
+                for (QueryRecord record: botQueryRecords) {
+                        record.setRelevantOntology(manager.createOntology());
+                        QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, record); 
+                        m_reasoner.encoder.setCurrentQuery(record);
+                        tracker.extractAxioms(m_reasoner.trackingStore);
+//                      record.saveRelevantClause();
+//                      record.saveRelevantOntology("bottom" + record.getQueryID() + ".owl");
+                        Utility.logInfo("finish extracting axioms for bottom " + record.getQueryID());
+                }                       
+        }
+
+        private String[] collectTrackingProgramAndImport() {
+                String[] programs = new String[botQueryRecords.length]; 
+                TrackingRuleEncoder encoder = m_reasoner.encoder;
+                
+                StringBuilder builder;
+                LinkedList<DLClause> currentClauses = new LinkedList<DLClause>(); 
+                
+                for (int i = 0; i < botQueryRecords.length; ++i) {
+                        encoder.setCurrentQuery(botQueryRecords[i]);
+                        builder = new StringBuilder(encoder.getTrackingProgram());
+//                      encoder.saveTrackingRules("tracking_bottom" + (i + 1) + ".dlog");
+                        
+                        for (DLClause clause: toAddClauses)
+                                if (clause.getHeadAtom(0).getDLPredicate().toString().contains("_final" + (i + 1)))
+                                        currentClauses.add(clause); 
+                        
+                        builder.append(DLClauseHelper.toString(currentClauses));
+                        programs[i] = builder.toString(); 
+                        
+                        currentClauses.clear();
+                }
+                
+                return programs; 
+        }
+
+        public QueryRecord[] getQueryRecords() {
+                return botQueryRecords; 
+        }
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
new file mode 100644
index 0000000..67dc4fc
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
@@ -0,0 +1,70 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
+import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
+import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+@Deprecated
+public class ConsistencyManager2 extends ConsistencyManager {
+
+        public ConsistencyManager2(MyQueryReasoner reasoner) {
+                super(reasoner);
+                fragmentExtracted = true; 
+        }
+        
+        protected boolean unsatisfiability(double duration) {
+                Utility.logDebug("The ontology and dataset is unsatisfiable."); 
+                return false;
+        }
+
+        protected boolean satisfiability(double duration) {
+                Utility.logDebug("The ontology and dataset is satisfiable."); 
+                return true;
+        }
+        
+        @Override
+        boolean check() {
+//              if (!checkRLLowerBound()) return false; 
+//              if (!checkELLowerBound()) return false;  
+                if (checkLazyUpper()) return true; 
+                
+                fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
+                if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
+                        return satisfiability(t.duration());
+                
+                try {
+                        extractAxioms();
+                } catch (OWLOntologyCreationException e) {
+                        e.printStackTrace();
+                }
+                
+                Checker checker = new HermitSummaryFilter(fullQueryRecord);  // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
+//              fullQueryRecord.saveRelevantOntology("fragment_bottom.owl");
+                boolean satisfiable = checker.isConsistent(); 
+                checker.dispose();
+                if (!satisfiable) return unsatisfiability(t.duration()); 
+                
+                return satisfiability(t.duration()); 
+        }
+
+        private void extractAxioms() throws OWLOntologyCreationException {
+                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
+                fullQueryRecord.setRelevantOntology(manager.createOntology());
+                QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, fullQueryRecord); 
+                m_reasoner.encoder.setCurrentQuery(fullQueryRecord);
+                tracker.extract(m_reasoner.trackingStore, null, true); 
+        }
+
+        @Override
+        public QueryRecord[] getQueryRecords() {
+                if (botQueryRecords == null)
+                        botQueryRecords = new QueryRecord[] {fullQueryRecord}; 
+                return botQueryRecords; 
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
new file mode 100644
index 0000000..4ebe5f2
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -0,0 +1,96 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import org.semanticweb.karma2.profile.ELHOProfile;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
+import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class ELHOQueryReasoner extends QueryReasoner {
+
+        LowerDatalogProgram program; 
+        
+        OWLOntology elho_ontology; 
+        KarmaQueryEngine elLowerStore = null; 
+
+        private Timer t = new Timer(); 
+        
+        public ELHOQueryReasoner() {
+                elLowerStore = new KarmaQueryEngine("el");
+        }
+        
+        @Override
+        public void evaluate(QueryRecord queryRecord) {
+                AnswerTuples elAnswer = null;
+                t.reset(); 
+                try {
+                        elAnswer = elLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        queryRecord.updateLowerBoundAnswers(elAnswer); 
+                } finally {
+                        if (elAnswer != null) elAnswer.dispose();
+                }
+                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
+                
+                queryRecord.setDifficulty(Step.ELLowerBound);
+                queryRecord.markAsProcessed();
+        }
+
+        @Override
+        public void evaluateUpper(QueryRecord queryRecord) {
+                evaluate(queryRecord); 
+        }
+
+        @Override
+        public void dispose() {
+                if (elLowerStore != null) elLowerStore.dispose();
+                super.dispose();
+        }
+
+        @Override
+        public void loadOntology(OWLOntology ontology) {
+                program = new LowerDatalogProgram(!forSemFacet); 
+                program.load(ontology, new UnaryBottom());
+                program.transform();
+                
+                importData(program.getAdditionalDataFile());
+                
+                elho_ontology = new ELHOProfile().getFragment(ontology);
+                elLowerStore.processOntology(elho_ontology);
+        }
+
+        @Override
+        public boolean preprocess() {
+                elLowerStore.importRDFData("data", importedData.toString()); 
+                String rlLowerProgramText = program.toString();
+//              program.save();
+                elLowerStore.materialise("lower program", rlLowerProgramText);
+                elLowerStore.initialiseKarma(); 
+                
+                if (!isConsistent()) {
+                        Utility.logDebug("The dataset is not consistent with the ontology."); 
+                        return false; 
+                }
+                return true; 
+        }
+
+        @Override
+        public boolean isConsistent() {
+                String[] X = new String[] {"X"}; 
+                AnswerTuples ans = null;
+                try {
+                        ans = elLowerStore.evaluate(QueryRecord.botQueryText, X); 
+                        if (ans.isValid()) return false; 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+                
+                return true;
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
new file mode 100644
index 0000000..62d238b
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -0,0 +1,195 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import org.semanticweb.karma2.profile.ELHOProfile;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
+import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
+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.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class ELHOUQueryReasoner extends QueryReasoner {
+
+        DatalogProgram program; 
+        
+        BasicQueryEngine rlLowerStore; 
+        BasicQueryEngine rlUpperStore; 
+        
+        OWLOntology elho_ontology; 
+        KarmaQueryEngine elLowerStore = null; 
+        
+        boolean multiStageTag, equalityTag;
+        
+        public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+                this.multiStageTag = multiStageTag;
+                this.equalityTag = considerEqualities;
+                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+                elLowerStore = new KarmaQueryEngine("el-lower-bound");
+                
+                if (!multiStageTag) 
+                        rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
+                else  
+                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
+        }
+        
+        private Timer t = new Timer(); 
+
+        @Override
+        public void evaluate(QueryRecord queryRecord) {
+                AnswerTuples rlAnswer = null;
+                t.reset();
+                try {
+                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 
+                        queryRecord.updateLowerBoundAnswers(rlAnswer);
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose(); 
+                }
+                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                
+                String extendedQueryText = queryRecord.getExtendedQueryText()[0];
+                String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
+                                new String[] {queryRecord.getQueryText()} : 
+                                new String[] {queryRecord.getQueryText(), extendedQueryText};
+                                
+                for (String queryText: toQuery) {
+                        rlAnswer = null; 
+                        t.reset();
+                        try {
+                                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables()); 
+                                queryRecord.updateUpperBoundAnswers(rlAnswer);
+                        } finally {
+                                if (rlAnswer != null) rlAnswer.dispose(); 
+                        }
+                        queryRecord.addProcessingTime(Step.UpperBound, t.duration());
+                        
+                        if (queryRecord.processed()) {
+                                queryRecord.setDifficulty(Step.UpperBound);
+                                return ; 
+                        }
+                }
+                
+                AnswerTuples elAnswer = null;
+                t.reset(); 
+                try {
+                        elAnswer = elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers()); 
+                        queryRecord.updateLowerBoundAnswers(elAnswer);
+                } finally {
+                        if (elAnswer != null) elAnswer.dispose();
+                }
+                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
+        }
+
+        @Override
+        public void evaluateUpper(QueryRecord queryRecord) {
+                AnswerTuples rlAnswer = null; 
+                try {
+                        rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 
+                        queryRecord.updateUpperBoundAnswers(rlAnswer, true);
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose(); 
+                }
+        }
+
+        @Override
+        public void dispose() {
+                if (elLowerStore != null) elLowerStore.dispose();
+                if (rlUpperStore != null) rlUpperStore.dispose();               
+                super.dispose();
+        }
+
+        @Override
+        public void loadOntology(OWLOntology o) {
+                if (!equalityTag) {
+                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+                        o = eliminator.getOutputOntology();
+                        eliminator.save();
+                }                       
+
+                OWLOntology ontology = o; 
+                program = new DatalogProgram(ontology, !forSemFacet); 
+                
+                importData(program.getAdditionalDataFile());
+                
+                elho_ontology = new ELHOProfile().getFragment(ontology);
+                elLowerStore.processOntology(elho_ontology);
+                originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
+        }
+        
+        String originalMarkProgram;  
+
+        @Override
+        public boolean preprocess() {
+                String name = "data", datafile = importedData.toString(); 
+
+                String lowername = "lower program";
+                String rlLowerProgramText = program.getLower().toString();
+                
+                rlUpperStore.importRDFData(name, datafile);
+                rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
+                
+                int flag = rlUpperStore.materialiseRestrictedly(program, null); 
+                if (flag != 1) {
+                        if (flag == -1) return false;           
+                        rlUpperStore.dispose();
+                        
+                        if (!multiStageTag) 
+                                rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
+                        else  
+                                rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
+                        rlUpperStore.importRDFData(name, datafile);
+                        rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
+                        rlUpperStore.materialiseFoldedly(program, null); 
+                }
+                Utility.logInfo("upper store ready.");
+                
+                rlLowerStore.importRDFData(name, datafile);
+                rlLowerStore.materialise(lowername, rlLowerProgramText);
+                Utility.logInfo("lower store ready.");
+                
+                elLowerStore.importRDFData(name, datafile);
+                elLowerStore.materialise("saturate named individuals", originalMarkProgram);
+                elLowerStore.materialise(lowername, rlLowerProgramText);
+                
+                elLowerStore.initialiseKarma(); 
+                Utility.logInfo("EL lower store ready.");
+                
+                if (!isConsistent()) {
+                        Utility.logInfo("The dataset is not consistent with the ontology."); 
+                        return false;
+                }
+                Utility.logInfo("The dataset is consistent.");
+                return true; 
+        }
+
+        @Override
+        public boolean isConsistent() {
+                Utility.logInfo("Start checking consistency... ");
+                String[] X = new String[] {"X"}; 
+                AnswerTuples ans = null; 
+                try {
+                        ans = rlUpperStore.evaluate(QueryRecord.botQueryText, X);
+                        if (!ans.isValid()) return true; 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+
+                ans = null; 
+                try {
+                        ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
+                        if (ans.isValid()) return false; 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+                
+                Utility.logDebug("The consistency of the data has not been determined yet.");
+                return true; 
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
new file mode 100644
index 0000000..5511691
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -0,0 +1,133 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+
+import uk.ac.ox.cs.JRDFox.model.Individual;
+import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.owl.QueryRoller;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.AnswerTuplesImp;
+import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class HermiTReasoner extends QueryReasoner {
+        
+        Reasoner hermit;
+        
+        BasicQueryEngine upperStore = null;
+        
+        OWLOntology onto;
+        OWLDataFactory factory; 
+        
+        String importedOntologyPath = null;
+
+        QueryRoller roller;
+        boolean toCheckSatisfiability;  
+        
+        public HermiTReasoner(boolean toCheckSatisfiability) {
+                this.toCheckSatisfiability = toCheckSatisfiability;  
+        }
+
+        @Override
+        public void loadOntology(OWLOntology ontology) {
+                onto = ontology; 
+        }
+
+        @Override
+        public boolean preprocess() {
+                OWLOntology tbox = onto;
+                try {
+                        onto = OWLHelper.getImportedOntology(tbox, importedData.toString().split(ImportDataFileSeparator));
+                        importedOntologyPath = OWLHelper.getOntologyPath(onto); 
+                } catch (OWLOntologyCreationException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } catch (OWLOntologyStorageException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } catch (IOException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                }
+                
+                DatalogProgram datalogProgram = new DatalogProgram(tbox, false);
+                importData(datalogProgram.getAdditionalDataFile()); 
+                upperStore = new MultiStageQueryEngine("rl-upper", false);
+                upperStore.importRDFData("data", importedData.toString());
+                GapByStore4ID gap = new GapByStore4ID(upperStore); 
+                upperStore.materialiseFoldedly(datalogProgram, gap);
+                gap.clear();
+
+                factory = onto.getOWLOntologyManager().getOWLDataFactory();
+                roller = new QueryRoller(factory);
+                
+                hermit = new Reasoner(onto);
+                return isConsistent();
+        }
+
+        @Override
+        public boolean isConsistent() {
+                if (toCheckSatisfiability)
+                        return hermit.isConsistent(); 
+                return true; 
+        }
+
+        @Override
+        public void evaluate(QueryRecord record) {
+                String[] disVars = record.getDistinguishedVariables();
+                Set<OWLNamedIndividual> individuals = onto.getIndividualsInSignature(true); 
+                if (disVars.length == 1) {
+                        OWLClassExpression clsExp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]);
+                        Set<AnswerTuple> answers = new HashSet<AnswerTuple>(); 
+                        for (OWLNamedIndividual individual: individuals) {
+                                Utility.logDebug("checking ... " + individual);
+                                if (hermit.isEntailed(factory.getOWLClassAssertionAxiom(clsExp, individual))) {
+                                        answers.add(new AnswerTuple(new Individual[] {Individual.create(individual.toStringID())})); 
+                                }
+                        }
+                        record.updateLowerBoundAnswers(new AnswerTuplesImp(record.getAnswerVariables(), answers));              
+                        record.markAsProcessed();
+                }
+                else {
+                        // FIXME join here
+                        record.markAsProcessed(); 
+                }
+        }
+
+        @Override
+        public void evaluateUpper(QueryRecord record) {
+                AnswerTuples rlAnswer = null; 
+                try {
+                        rlAnswer = upperStore.evaluate(record.getQueryText(), record.getAnswerVariables());
+                        record.updateUpperBoundAnswers(rlAnswer, true); 
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose();
+                }
+        }
+
+        @Override
+        public void dispose() {
+                if (importedOntologyPath != null) {
+                        File tmp = new File(importedOntologyPath);
+                        if (tmp.exists()) tmp.delete(); 
+                }
+                super.dispose();
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
new file mode 100644
index 0000000..ba6a4d4
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
@@ -0,0 +1,106 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.io.File;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
+import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
+import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
+import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class IterativeRefinement {
+        
+        private static final int depthLimit = 1; 
+        
+        QueryRecord m_record;
+        QueryTracker m_tracker; 
+        BasicQueryEngine m_trackingStore;
+        QueryRecord[] botQueryRecords;  
+        
+        int m_depth = 0; 
+
+        public IterativeRefinement(QueryRecord queryRecord, QueryTracker tracker, BasicQueryEngine trackingStore, QueryRecord[] botQueryRecords) {
+                m_record = queryRecord;                 
+                m_tracker = tracker; 
+                m_trackingStore = trackingStore;
+                this.botQueryRecords = botQueryRecords; 
+        }
+        
+        String tempDataFile = "temp.ttl"; 
+
+        public OWLOntology extractWithFullABox(String dataset, BottomStrategy upperBottom) {
+                GeneralProgram program; 
+                boolean update; 
+                while (m_depth < depthLimit) {
+                        ++m_depth;
+                        program = new GeneralProgram(m_record.getRelevantClauses(), m_record.getRelevantOntology());
+                        
+                        MultiStageQueryEngine tEngine = new MultiStageQueryEngine("query-tracking", true);
+                        try {
+                                tEngine.importRDFData("data", dataset);
+                                if (tEngine.materialise4SpecificQuery(program, m_record, upperBottom) != 1) {
+                                        return m_record.getRelevantOntology(); 
+                                }
+                                
+                                update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText()));
+                        } finally {
+                                tEngine.dispose();
+                        }
+                        
+                        if (m_record.processed())
+                                return null;
+                        
+                        if (!update) break; 
+                        
+                        m_record.updateSubID();
+                        m_tracker.extract(m_trackingStore, botQueryRecords, true); 
+                }
+                
+                return m_record.getRelevantOntology(); 
+        }
+        
+        public OWLOntology extract(UpperUnaryBottom upperBottom) {
+                GeneralProgram program; 
+                boolean update; 
+                while (m_depth < depthLimit) {
+                        m_record.saveABoxInTurtle(tempDataFile); 
+                        program = new GeneralProgram(m_record.getRelevantClauses(), m_record.getRelevantOntology());
+                        
+                        MultiStageQueryEngine tEngine = new MultiStageQueryEngine("query-tracking", true);
+                        try {
+                                tEngine.importRDFData("fragment abox", tempDataFile);
+                                if (tEngine.materialise4SpecificQuery(program, m_record, upperBottom) != 1) {
+                                        return m_record.getRelevantOntology(); 
+                                }
+                                
+                                update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText()));
+                        } finally {
+                                tEngine.dispose();
+                        }
+                        
+                        if (m_record.processed())
+                                return null;
+                        
+                        if (!update) break; 
+                        
+                        m_record.updateSubID();
+                        m_tracker.extract(m_trackingStore, botQueryRecords, true); 
+                }
+                
+                return m_record.getRelevantOntology(); 
+        }
+        
+        public void dispose() {
+                File file = new File(tempDataFile);  
+                if (file.exists()) {
+                        file.delete(); 
+                        Utility.logDebug(file.getAbsolutePath() + " is deleted.");
+                }
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
new file mode 100644
index 0000000..2c2feae
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -0,0 +1,331 @@
+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();
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
new file mode 100644
index 0000000..b9abf07
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
@@ -0,0 +1,17 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.util.Collection;
+
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+
+public interface QueryEngine {
+
+        public void evaluate(Collection<String> queryTexts, String answerFile);
+        
+        public AnswerTuples evaluate(String queryText);
+        
+        public AnswerTuples evaluate(String queryText, String[] answerVariables);
+        
+        public void dispose(); 
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
new file mode 100644
index 0000000..0c009a2
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -0,0 +1,221 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.Collection;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryManager;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public abstract class QueryReasoner {
+        
+        protected boolean forSemFacet = false;
+        
+        public static enum Type { Full, RLU, ELHOU };  
+        
+        public static QueryReasoner getInstanceForSemFacet(OWLOntology o) {
+                QueryReasoner reasoner = getInstance(Type.Full, o, true, true); 
+                reasoner.forSemFacet = true;            
+                return reasoner; 
+        }
+        
+        
+        public static QueryReasoner getInstance(OWLOntology o) {
+                return getInstance(Type.Full, o, true, true); 
+        }
+        
+        public static QueryReasoner getInstance(Type type, OWLOntology o, boolean performMultiStages, boolean considerEqualities) {
+                Utility.initialise(); 
+                QueryReasoner reasoner; 
+                if (OWLHelper.isInOWL2RL(o)) reasoner = new RLQueryReasoner();
+                else if (OWLHelper.isInELHO(o)) reasoner = new ELHOQueryReasoner();
+                else 
+                switch (type) {
+                        case RLU: 
+                                reasoner = new RLUQueryReasoner(performMultiStages, considerEqualities); break;   
+                        case ELHOU: 
+                                reasoner = new ELHOUQueryReasoner(performMultiStages, considerEqualities); break;  
+                        default: 
+                                reasoner = new MyQueryReasoner(performMultiStages, considerEqualities); 
+                        }
+                return reasoner; 
+        }
+        
+        public static final String ImportDataFileSeparator = ";"; 
+        protected StringBuilder importedData = new StringBuilder(); 
+        
+        public void importData(String datafile) {
+                if (datafile != null && !datafile.equalsIgnoreCase("null"))
+                        importData(datafile.split(ImportDataFileSeparator)); 
+        }
+
+        public void importData(String[] datafiles) {
+                if (datafiles != null) {
+                        for (String datafile: datafiles) {
+                                File file = new File(datafile); 
+                                if (file.exists()) {
+                                        if (file.isFile()) importDataFile(file);
+                                        else importDataDirectory(file);
+                                }
+                                else {
+                                        Utility.logError("warning: file " + datafile + " doesn't exists."); 
+                                }
+                        }
+                }
+        }
+        
+        private void importDataDirectory(File file) {
+                for (File child: file.listFiles())
+                        if (child.isFile()) importDataFile(child);
+                        else importDataDirectory(child);
+        }
+        
+        private void importDataFile(File file) {
+                String datafile;
+                try {
+                        datafile = file.getCanonicalPath();
+                } catch (IOException e) {
+                        e.printStackTrace();
+                        return ; 
+                } 
+                importDataFile(datafile); 
+        }
+        
+        protected final void importDataFile(String datafile) {
+                if (importedData.length() == 0)
+                        importedData.append(datafile); 
+                else 
+                        importedData.append(ImportDataFileSeparator).append(datafile);
+
+        }
+        
+        public abstract void loadOntology(OWLOntology ontology);
+        
+        public abstract boolean preprocess(); 
+
+        public abstract boolean isConsistent(); 
+
+        public boolean fullReasoner = this instanceof MyQueryReasoner; 
+
+        public abstract void evaluate(QueryRecord record);
+        
+        public abstract void evaluateUpper(QueryRecord record); 
+        
+        public AnswerTuples evaluate(String queryText, boolean forFacetGeneration) {
+                if (forFacetGeneration) {
+                        QueryRecord record = m_queryManager.create(queryText);
+                        Utility.logInfo("---------- start evaluating upper bound for Query " + record.getQueryID() + " ----------", queryText);
+                        if (!record.processed()) 
+                                evaluateUpper(record);
+//                      AnswerTuples tuples = record.getUpperBoundAnswers();
+//                      for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
+//                              tuple = tuples.getTuple(); 
+//                              if (tuple.toString().contains("NC"))
+//                                      System.out.println(tuple.toString()); 
+//                      }
+                        return record.getUpperBoundAnswers(); 
+                }
+                else 
+                        return evaluate(queryText); 
+        }
+        
+        public AnswerTuples evaluate(String queryText) {
+                QueryRecord record = m_queryManager.create(queryText); 
+                Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
+                if (!record.processed())
+                        evaluate(record);
+                AnswerTuples answer = record.getAnswers(); 
+                record.dispose();
+                return answer;
+  
+        }
+        
+        public void evaluate_shell(String queryText) {
+                QueryRecord record = m_queryManager.create(queryText); 
+                Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
+                if (!record.processed())
+                        evaluate(record);
+                Utility.logInfo("Answers to this query: ", record.outputSoundAnswerTuple());
+                record.dispose();
+  
+        }
+        
+        public void evaluate(Collection<QueryRecord> queryRecords) {
+                evaluate(queryRecords, null); 
+        }
+        
+        BufferedWriter answerWriter = null; 
+        
+        public void evaluate(Collection<QueryRecord> queryRecords, String answerFile) {
+                if (!isConsistent()) {
+                        Utility.logDebug("The ontology and dataset is inconsistent."); 
+                        return ; 
+                }
+                
+                if (answerWriter == null && answerFile != null) {
+                        try {
+                                answerWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(answerFile)));
+                        } catch (FileNotFoundException e) {
+                                Utility.logInfo("The answer file not found! " + answerFile);
+                                return ; 
+                        } 
+                }
+                
+                Timer t = new Timer(); 
+                for (QueryRecord record: queryRecords) {
+//                      if (Integer.parseInt(record.getQueryID()) != 218) continue; 
+                        Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", 
+                                        record.getQueryText());
+                        if (!record.processed()) {
+                                t.reset();
+                                if (!record.processed())
+                                        evaluate(record); 
+                                Utility.logInfo("Total time to answer this query: " + t.duration()); 
+                                if (!fullReasoner && !record.processed()) {
+                                        Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds."); 
+                                        continue; 
+                                }
+                        }
+                        // FIXME: change the argument below
+                        try {
+                                record.outputAnswers(answerWriter);
+                        } catch (IOException e) {
+                                Utility.logInfo("Error in outputing answers " + answerFile);
+                        }
+                        record.outputTimes();
+                        record.dispose();
+                }
+        }
+        
+        public void dispose() {
+                if (answerWriter != null)
+                        try {
+                                answerWriter.close();
+                        } catch (IOException e) {
+                                e.printStackTrace();
+                        }
+                Utility.cleanup();
+        }  
+
+        private QueryManager m_queryManager = new QueryManager(); 
+        
+        public QueryManager getQueryManager() {
+                return m_queryManager; 
+        }
+
+
+        public static QueryReasoner getHermiTReasoner(boolean toCheckSatisfiability) {
+                return new HermiTReasoner(toCheckSatisfiability);
+        }
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
new file mode 100644
index 0000000..3894874
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
@@ -0,0 +1,83 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
+import uk.ac.ox.cs.pagoda.util.Timer;
+
+public class RLQueryReasoner extends QueryReasoner {
+        
+        RDFoxQueryEngine rlLowerStore = null;
+
+        LowerDatalogProgram program; 
+        
+        public RLQueryReasoner() {
+                rlLowerStore = new BasicQueryEngine("rl"); 
+        }
+        
+        Timer t = new Timer(); 
+        
+        @Override
+        public void evaluate(QueryRecord queryRecord) {
+                AnswerTuples rlAnswer = null; 
+                t.reset();
+                try {
+                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        queryRecord.updateLowerBoundAnswers(rlAnswer);
+                } finally {
+                        if (rlAnswer != null) rlAnswer.dispose();
+                }
+                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                queryRecord.setDifficulty(Step.LowerBound);
+                queryRecord.markAsProcessed();
+        }
+
+        @Override
+        public void dispose() {
+                if (rlLowerStore != null) rlLowerStore.dispose();
+                super.dispose();
+        }
+
+        @Override
+        public void loadOntology(OWLOntology ontology) {
+                program = new LowerDatalogProgram(); 
+                program.load(ontology, new UnaryBottom());
+                program.transform();
+                
+                importData(program.getAdditionalDataFile());
+        }
+
+        @Override
+        public boolean preprocess() {
+                rlLowerStore.importRDFData("data", importedData.toString());
+                rlLowerStore.materialise("lower program", program.toString());
+                
+                if (!isConsistent())  
+                        return false; 
+                return true; 
+        }
+
+        @Override
+        public boolean isConsistent() {
+                AnswerTuples ans = null; 
+                try {
+                        ans = rlLowerStore.evaluate(QueryRecord.botQueryText, new String[] {"X"});
+                        return !ans.isValid(); 
+                } finally {
+                        if (ans != null) ans.dispose();
+                                
+                }
+                
+        }
+
+        @Override
+        public void evaluateUpper(QueryRecord record) {
+                evaluate(record); 
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
new file mode 100644
index 0000000..fe4022d
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
@@ -0,0 +1,134 @@
+package uk.ac.ox.cs.pagoda.reasoner;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
+import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class RLUQueryReasoner extends QueryReasoner {
+
+        DatalogProgram program; 
+        
+        BasicQueryEngine rlLowerStore, rlUpperStore;
+        
+        boolean multiStageTag, equalityTag; 
+        
+        public RLUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+                this.multiStageTag = multiStageTag;
+                this.equalityTag = considerEqualities; 
+                rlLowerStore = new BasicQueryEngine("rl-lower-bound"); 
+                if (!multiStageTag) 
+                        rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
+                else  
+                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
+        }
+        
+        Timer t = new Timer();
+        
+        @Override
+        public void evaluate(QueryRecord queryRecord) {
+                AnswerTuples ans = null;
+                t.reset(); 
+                try {
+                        ans = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateLowerBoundAnswers(ans); 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                
+                ans = null; 
+                t.reset(); 
+                try {
+                        ans = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateUpperBoundAnswers(ans); 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+                queryRecord.addProcessingTime(Step.UpperBound, t.duration());
+                
+                if (queryRecord.processed())
+                        queryRecord.setDifficulty(Step.UpperBound);
+        }
+        
+        @Override
+        public void evaluateUpper(QueryRecord queryRecord) {
+                AnswerTuples ans = null; 
+                try {
+                        ans = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        Utility.logDebug(t.duration());
+                        queryRecord.updateUpperBoundAnswers(ans, true); 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+        }
+
+        @Override
+        public void dispose() {
+                if (rlLowerStore != null) rlLowerStore.dispose();
+                if (rlUpperStore != null) rlUpperStore.dispose();
+                super.dispose();
+        }
+
+        @Override
+        public void loadOntology(OWLOntology o) {
+                if (!equalityTag) {
+                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+                        o = eliminator.getOutputOntology();
+                        eliminator.save();
+                }                       
+
+                OWLOntology ontology = o; 
+                program = new DatalogProgram(ontology);
+                importData(program.getAdditionalDataFile());
+        }
+
+        @Override
+        public boolean preprocess() {
+                String datafile = importedData.toString(); 
+                rlLowerStore.importRDFData("data", datafile);
+                rlLowerStore.materialise("lower program", program.getLower().toString());
+                
+                rlUpperStore.importRDFData("data", datafile);
+                rlUpperStore.materialiseRestrictedly(program, null);
+                
+                if (!isConsistent()) 
+                        return false; 
+
+                return true; 
+        }
+
+        @Override
+        public boolean isConsistent() {
+                String[] X = new String[] { "X" }; 
+                AnswerTuples ans = null; 
+                try {
+                        ans = rlLowerStore.evaluate(QueryRecord.botQueryText, X);
+                        if (ans.isValid()) return false; 
+                } finally {
+                        if (ans != null) ans.dispose();
+                }
+
+                ans = null; 
+                try {
+                        ans = rlUpperStore.evaluate(QueryRecord.botQueryText, X);
+                        if (!ans.isValid()) return true; 
+                } finally { 
+                        if (ans != null) ans.dispose();
+                }
+                
+                Utility.logDebug("The consistency of the data has not been determined yet.");
+                return true; 
+        }
+        
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java b/src/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java
new file mode 100644
index 0000000..849b971
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java
@@ -0,0 +1,15 @@
+package uk.ac.ox.cs.pagoda.reasoner.full;
+
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+
+public interface Checker {
+
+        public int check(AnswerTuples answers);
+        
+        public boolean check(AnswerTuple answer);
+
+        public boolean isConsistent();
+
+        public void dispose(); 
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
new file mode 100644
index 0000000..6f5d363
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -0,0 +1,237 @@
+package uk.ac.ox.cs.pagoda.reasoner.full;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.HermiT.model.Term;
+import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+
+import uk.ac.ox.cs.pagoda.endomorph.Clique;
+import uk.ac.ox.cs.pagoda.endomorph.DependencyGraph;
+import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.rollup.QueryGraph;
+import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class HermitChecker implements Checker {
+        
+        protected OWLDataFactory factory;
+
+        private String queryText; 
+        private DLClause queryClause; 
+        
+        private Reasoner hermit;
+        protected String[][] answerVariable;
+        protected OWLOntology ontology;
+        protected QueryRecord record; 
+        protected QueryGraph qGraph = null; 
+        
+        public HermitChecker(Checker checker) {
+                if (checker instanceof HermitChecker) {
+                        HermitChecker other = (HermitChecker) checker;
+                        factory = other.factory; 
+                        queryText = other.queryText;
+                        queryClause = other.queryClause; 
+                        answerVariable = other.answerVariable;
+                        ontology = other.ontology;
+//                      record = other.record; 
+                }
+                
+                hermit = new Reasoner(ontology);
+        }
+        
+        public HermitChecker(OWLOntology ontology, QueryRecord record) {
+                this.ontology = ontology;
+                queryText = record.getQueryText(); 
+                answerVariable = record.getVariables();
+                queryClause = record.getClause(); 
+//              this.record = record;  
+        }
+        
+        public HermitChecker(OWLOntology ontology, String queryText) {
+                this.ontology = ontology;
+                this.queryText = queryText; 
+                answerVariable = queryText == null ? null : ConjunctiveQueryHelper.getAnswerVariables(queryText);
+                queryClause = DLClauseHelper.getQuery(queryText, null); 
+//              this.record = null; 
+        }
+        
+        private int tag = 0;
+        AnswerTuple topAnswerTuple = null, botAnswerTuple = null; 
+        
+        private void initialiseReasoner() {
+                qGraph = new QueryGraph(queryClause.getBodyAtoms(), answerVariable[1], ontology); 
+                OWLOntologyManager manager = ontology.getOWLOntologyManager(); 
+                factory = manager.getOWLDataFactory();
+                
+                if (hermit != null)     hermit.dispose();
+                
+                if (dGraph != null && answerVariable[1].length == 1 && (dGraph.getExits().size() > 1 || dGraph.getEntrances().size() > 1)) {
+                        Set<OWLAxiom> axioms = new HashSet<OWLAxiom>(); 
+                        addTopAndBotTuple(axioms);
+                        manager.addAxioms(ontology, axioms); 
+                        hermit = new Reasoner(ontology);
+                        if (!hermit.isConsistent()) {
+                                hermit.dispose();
+                                manager.removeAxioms(ontology, axioms); 
+                                hermit = new Reasoner(ontology); 
+                        } else {
+                                if (topAnswerTuple != null && !check(topAnswerTuple)) tag = -1; 
+                                else if (botAnswerTuple != null && check(botAnswerTuple)) tag = 1; 
+                        }
+                }
+                else 
+                        hermit = new Reasoner(ontology);
+        }
+        
+        private void addTopAndBotTuple(Set<OWLAxiom> axioms) {
+                String top_str = Namespace.PAGODA_ANONY + "top", bot_str = Namespace.PAGODA_ANONY + "bot";
+                topAnswerTuple = new AnswerTuple(new uk.ac.ox.cs.JRDFox.model.Individual[] { uk.ac.ox.cs.JRDFox.model.Individual.create(top_str) } ); 
+                botAnswerTuple = new AnswerTuple(new uk.ac.ox.cs.JRDFox.model.Individual[] { uk.ac.ox.cs.JRDFox.model.Individual.create(bot_str) } );  
+                OWLIndividual top_ind = factory.getOWLNamedIndividual(IRI.create(top_str)), bot_ind = factory.getOWLNamedIndividual(IRI.create(bot_str));
+                Map<OWLAxiom, Integer> counter = new HashMap<OWLAxiom, Integer>(); 
+                
+                Set<String> topAnswers = new HashSet<String>(), botAnswers = new HashSet<String>();
+                OWLIndividual sub, obj; 
+                if (dGraph.getExits().size() > 1) {
+                        for (Clique answerClique: dGraph.getExits())  
+                                topAnswers.add(((uk.ac.ox.cs.JRDFox.model.Individual) answerClique.getRepresentative().getAnswerTuple().getGroundTerm(0)).getIRI());
+                }
+                else topAnswerTuple = null; 
+                
+                if (dGraph.getEntrances().size() > 1) {
+                        for (Clique answerClique: dGraph.getEntrances()) 
+                                botAnswers.add(((uk.ac.ox.cs.JRDFox.model.Individual) answerClique.getRepresentative().getAnswerTuple().getGroundTerm(0)).getIRI()); 
+                }
+                else botAnswerTuple = null; 
+                
+                for (OWLAxiom axiom: ontology.getABoxAxioms(true)) 
+                        if (axiom instanceof OWLClassAssertionAxiom) {
+                                OWLClassAssertionAxiom ca = (OWLClassAssertionAxiom) axiom;
+                                sub = ca.getIndividual();
+                                if (topAnswers.contains(sub.toStringID())) 
+                                        axioms.add(factory.getOWLClassAssertionAxiom(ca.getClassExpression(), top_ind));
+                                if (botAnswers.contains(sub.toStringID())) 
+                                        inc(counter, factory.getOWLClassAssertionAxiom(ca.getClassExpression(), bot_ind));
+                        }
+                        else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
+                                OWLObjectPropertyAssertionAxiom oa = (OWLObjectPropertyAssertionAxiom) axiom; 
+                                sub = oa.getSubject(); obj = oa.getObject(); 
+                                if (topAnswers.contains(sub.toStringID()))
+                                        if (topAnswers.contains(obj.toStringID()))
+                                                axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, top_ind));
+                                        else 
+                                                axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, obj));
+                                else {
+                                        if (topAnswers.contains(obj.toStringID()))
+                                                axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), sub, top_ind));
+                                }
+                                
+                                if (botAnswers.contains(sub.toStringID()))
+                                        if (botAnswers.contains(obj.toStringID()))
+                                                inc(counter, factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), bot_ind, bot_ind));
+                                        else 
+                                                inc(counter, factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), bot_ind, obj));
+                                else {
+                                        if (botAnswers.contains(obj.toStringID()))
+                                                inc(counter, factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), sub, bot_ind));
+                                }
+                                
+                        }
+                        else if (axiom instanceof OWLDataPropertyAssertionAxiom) {
+                                OWLDataPropertyAssertionAxiom da = (OWLDataPropertyAssertionAxiom) axiom; 
+                                sub = da.getSubject(); 
+                                if (topAnswers.contains(sub.toStringID())) 
+                                        axioms.add(factory.getOWLDataPropertyAssertionAxiom(da.getProperty(), top_ind, da.getObject()));
+                                
+                                if (botAnswers.contains(sub.toStringID())) 
+                                        inc(counter, factory.getOWLDataPropertyAssertionAxiom(da.getProperty(), bot_ind, da.getObject()));
+                        }
+                
+                int number = botAnswers.size(); 
+                for (Map.Entry<OWLAxiom, Integer> entry: counter.entrySet()) {
+                        if (entry.getValue() == number) 
+                                axioms.add(entry.getKey());
+                }
+        }
+
+        private void inc(Map<OWLAxiom, Integer> counter, OWLAxiom newAxiom) {
+                Integer number = counter.get(newAxiom);  
+                if (number == null) counter.put(newAxiom, 1);
+                else counter.put(newAxiom, number + 1); 
+        }
+
+        @Override
+        public int check(AnswerTuples answers) {
+                if (hermit == null) initialiseReasoner();
+                int answerCounter = 0, counter = 0; 
+                for (; answers.isValid(); answers.moveNext()) {
+                        ++counter; 
+                        if (check(answers.getTuple())) ++answerCounter;
+                }
+                answers.dispose();
+                
+                Utility.logDebug("The number of individuals to be checked by HermiT: " + counter, 
+                                "The number of correct answers: " + answerCounter);
+                return answerCounter; 
+        }
+        
+        private int counter = 0;
+        
+        @Override
+        public boolean check(AnswerTuple answerTuple) {
+                if (hermit == null) initialiseReasoner();
+                if (tag != 0) return tag == 1; 
+                ++counter; 
+                Timer t = new Timer(); 
+                Map<Variable, Term> sub = answerTuple.getAssignment(answerVariable[1]); 
+                Set<OWLAxiom> toCheckAxioms = qGraph.getAssertions(sub);
+                
+//              for (OWLAxiom axiom: toCheckAxioms)     System.out.println(axiom.toString());
+                
+                if (hermit.isEntailed(toCheckAxioms)) {
+                        Utility.logDebug("@TIME to check one tuple: " + t.duration()); 
+                        return true; 
+                }
+                Utility.logDebug("@TIME to check one tuple: " + t.duration()); 
+                return false; 
+        }
+
+        @Override
+        public boolean isConsistent() {
+                if (hermit == null) initialiseReasoner();                       
+                return hermit.isConsistent();
+        }
+        
+
+        public void dispose() {
+                Utility.logInfo("Hermit was called " + counter + " times.");
+                if (hermit != null) hermit.dispose(); 
+                hermit = null; 
+        }
+
+        private DependencyGraph dGraph = null; 
+        
+        public void setDependencyGraph(DependencyGraph dGraph) {
+                this.dGraph = dGraph; 
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
new file mode 100644
index 0000000..3207ff1
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -0,0 +1,366 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.semanticweb.HermiT.model.DLClause;
+
+import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
+import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
+import uk.ac.ox.cs.pagoda.rules.Program;
+import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.UFS;
+import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+
+public class BasicQueryEngine extends RDFoxQueryEngine {
+
+        protected DataStore store; 
+        protected Parameters parameters = new Parameters(); 
+        
+        public BasicQueryEngine(String name) {
+                super(name); 
+                store = RDFoxQueryEngine.createDataStore();
+                parameters.m_allAnswersInRoot = true; 
+                parameters.m_useBushy = true; 
+        }
+        
+        public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
+                if (gap != null) {
+                        materialise("lower program", dProgram.getLower().toString());
+                        String program = dProgram.getUpper().toString();
+                        try {
+                                gap.compile(program);
+                                gap.addBackTo();
+                                getDataStore().clearRulesAndMakeFactsExplicit();
+                        } catch (JRDFStoreException e) {
+                                e.printStackTrace();
+                                gap.clear(); 
+                        } finally {
+                        }
+                }
+                else 
+                        materialise("upper program", dProgram.getUpper().toString());
+        }
+        
+        public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
+                if (gap != null) {
+                        materialise("lower program", dProgram.getLower().toString());
+                        String program = dProgram.getUpper().toString();
+                        try {
+                                gap.compile(program);
+                                gap.addBackTo();
+                                getDataStore().clearRulesAndMakeFactsExplicit();
+                        } catch (JRDFStoreException e) {
+                                e.printStackTrace();
+                        } finally {
+                                gap.clear(); 
+                        }
+                }
+                else 
+                        materialise("upper program", dProgram.getUpper().toString());
+                
+                return 1; 
+        }
+        
+        @Override
+        public AnswerTuples evaluate(String queryText) {
+                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]); 
+        }
+        
+        @Override
+        public AnswerTuples evaluate(String queryText, String[] answerVars) {
+                TupleIterator tupleIterator;
+                try {
+                        tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                        return null; 
+                }
+                return new RDFoxAnswerTuples(answerVars, tupleIterator); 
+        }
+
+        @Override
+        public DataStore getDataStore() {
+                return store;
+        }
+
+        @Override
+        public void dispose() {
+                store.dispose();                
+        }
+
+        protected void outputClassAssertions(String filename) {
+                TupleIterator allTuples = null;
+                boolean redirect = false; 
+                try {
+                        allTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Z }", prefixes, parameters);
+                        redirect = Utility.redirectCurrentOut(filename);
+                        for (long multi = allTuples.open(); multi != 0; multi = allTuples.getNext()) 
+                                System.out.println(RDFoxTripleManager.getQuotedTerm(allTuples.getResource(0)) + " " + RDFoxTripleManager.getQuotedTerm(allTuples.getResource(1))); 
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (redirect) Utility.closeCurrentOut();
+                        if (allTuples != null) allTuples.dispose();
+                }
+        }
+        
+        public void outputInstance4BinaryPredicate(String iri, String filename) {
+                Utility.redirectCurrentOut(filename);
+                outputInstance4BinaryPredicate(iri);
+                Utility.closeCurrentOut();
+        }
+        
+        public void outputInstance4BinaryPredicate(String iri) {
+                outputAnswers("select ?x ?y where { ?x <" + iri + "> ?y . }");
+        }
+        
+        public void outputInstanceNumbers(String filename) {
+                TupleIterator predicateTuples = null;
+                TupleIterator instanceTuples; 
+                Set<String> number = new HashSet<String>(); 
+                String predicate; 
+                try {
+                        predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Y }", prefixes, parameters);
+                        for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
+                                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
+                                instanceTuples = null; 
+                                try {
+                                        instanceTuples = getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters);
+                                        long totalCount = 0; 
+                                        for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) {
+                                                totalCount += instanceTuples.getMultiplicity();
+                                        }
+                                        number.add(predicate + " * " + totalCount);
+                                } finally {
+                                        if (instanceTuples != null) instanceTuples.dispose(); 
+                                }
+                        }
+                        
+                        predicateTuples.dispose();
+                        
+                        predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
+                        for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
+                                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 
+                                instanceTuples = null; 
+                                try {
+                                        instanceTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters);
+                                        ;
+                                        long totalCount = 0; 
+                                        for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext())
+                                                totalCount += instanceTuples.getMultiplicity();
+                                        number.add(predicate + " * " + totalCount); 
+                                } finally {
+                                        if (instanceTuples != null) instanceTuples.dispose(); 
+                                }
+                        }
+                        
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (predicateTuples != null) predicateTuples.dispose();
+                }
+                
+                Utility.redirectCurrentOut(filename);
+                String[] ordered = number.toArray(new String[0]);
+                Arrays.sort(ordered, new DLPredicateComparator());
+                for (String line: ordered) System.out.println(line); 
+                Utility.closeCurrentOut();
+                
+        }
+        
+        public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
+                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+                iter.open();
+                return iter; 
+        }
+
+        public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
+                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
+                iter.open(); 
+                return iter; 
+        }
+        
+        public void setExpandEquality(boolean flag) {
+                parameters.m_expandEquality = flag; 
+        }
+        
+        public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
+                parameters.m_expandEquality = false; 
+                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 
+                iter.open(); 
+                parameters.m_expandEquality = true; 
+                return iter;
+        }
+
+        
+        public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException {
+                return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText);
+        }
+
+        Set<DLClause> materialisedRules = new HashSet<DLClause>(); 
+        
+        public String getUnusedRules(Collection<DLClause> clauses, boolean toUpdate) {
+                DLClause clause;
+                for (Iterator<DLClause> iter = clauses.iterator(); iter.hasNext(); ) {
+                        if (materialisedRules.contains(clause = iter.next()))
+                                iter.remove();
+                        else if (toUpdate) materialisedRules.add(clause); 
+                }
+                
+                if (clauses.isEmpty()) return null;
+                
+                return Program.toString(clauses);
+        }
+
+        public void outputMaterialisedRules() {
+                System.out.println(DLClauseHelper.toString(materialisedRules));         
+        }
+
+        public void outputAnswers(String query) {
+                TupleIterator iter = null;
+                try {
+                        iter = internal_evaluate(query);
+                        System.out.println(query); 
+                        int arity = iter.getArity(); 
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext())  {
+                                for (int i = 0; i < arity; ++i)
+                                        System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
+                                System.out.println(); 
+                        }
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (iter != null) iter.dispose(); 
+                }
+        }
+
+        public void outputInstance4UnaryPredicate(String iri) {
+                outputAnswers("select ?x where { ?x "
+                                        + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <"
+                                        + iri 
+                                        + "> .}"); 
+        }
+
+        public void outputSubjects(String p, String o) {
+                outputAnswers("select x where { ?x <" + p + "> <" + o + "> . }");
+        }
+
+        public void outputObjects(String s, String p) {
+                outputAnswers("select ?x where { <" + s + "> <" + p + "> ?x . }");
+        }
+
+        public void outputIDBFacts() {
+                TupleIterator iter = null; 
+                try {
+                        iter = internal_evaluateAgainstIDBs("select distict ?x ?y ?z where { ?x ?y ?z }");
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                                for (int i = 0; i < 3; ++i)
+                                        System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t"); 
+                                System.out.println(); 
+                        }
+                } catch (JRDFStoreException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                
+        }
+        
+        public void outputType4Individual(String iri) {
+                outputAnswers("select ?z where { <" + iri + "> " + Namespace.RDF_TYPE_QUOTED + " ?z }");
+        }
+        
+        public int getSameAsNumber() {
+                TupleIterator iter = null; 
+                int counter = 0; 
+                try {
+                        iter = internal_evaluate("select ?x ?y where {?x " + Namespace.EQUALITY_QUOTED + " ?y . }");
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                if (iter.getResourceID(0) != iter.getResourceID(1))
+                                        ++counter;
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace(); 
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                return counter; 
+        }
+        
+        private UFS<String> equalityGroups = null; 
+        
+        public UFS<String> getEqualityGroups() {
+                if (equalityGroups != null) return equalityGroups; 
+
+                equalityGroups = new UFS<String>(); 
+                
+                TupleIterator answers = null; 
+                try {
+                        Timer t = new Timer(); 
+                        answers = internal_evaluate("select ?x ?z  where {?x " + Namespace.EQUALITY_QUOTED + "?z . }");
+                        for (long multi = answers.open(); multi != 0; multi = answers.getNext()) {
+                                if (answers.getResourceID(0) != answers.getResourceID(1))
+                                        equalityGroups.merge(answers.getResource(0).m_lexicalForm, answers.getResource(1).m_lexicalForm); 
+                        }
+                        Utility.logInfo("@Time to group individuals by equality: " + t.duration());
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (answers != null) answers.dispose(); 
+                }
+
+                return equalityGroups; 
+        }
+
+        public void clearRulesAndIDBFacts(Collection<int[]> collection) {
+//              performDeletion(collection); 
+                collection.clear();
+                try {
+                        store.clearRulesAndMakeFactsExplicit();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+        }
+
+        @SuppressWarnings("unused")
+        private void performDeletion(Collection<int[]> collection) {
+                Utility.logInfo("Remove all rules, idb facts and added staff...");
+                Timer timer = new Timer();  
+                TupleIterator iter = null;
+                try {
+                        UpdateType ut = UpdateType.ScheduleForDeletion; 
+                        for (int[] t: collection) 
+                                store.addTriplesByResourceIDs(t, ut);
+                        
+                        iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                                int[] triple = new int[3];
+                                for (int i = 0; i < 3; ++i)
+                                        triple[i] = iter.getResourceID(i); 
+                                store.addTriplesByResourceIDs(triple, ut);
+                        }
+                        store.applyReasoning(true);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                Utility.logInfo("Time for deletion: " + timer.duration()); 
+        }
+
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java
new file mode 100644
index 0000000..c22902c
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java
@@ -0,0 +1,24 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import java.util.Comparator;
+
+import uk.ac.ox.cs.pagoda.multistage.Normalisation;
+import uk.ac.ox.cs.pagoda.rules.OverApproxExist;
+
+public class DLPredicateComparator implements Comparator<String> {
+
+        @Override
+        public int compare(String arg0, String arg1) {
+                int ret = type(arg0) - type(arg1);
+                if (ret != 0) return ret;
+                
+                return arg0.compareTo(arg1); 
+        }
+
+        private int type(String p) {
+                if (p.contains(OverApproxExist.negativeSuffix)) return 1; 
+                if (p.contains(Normalisation.auxiliaryConceptPrefix)) return 2; 
+                else return 0; 
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java
new file mode 100644
index 0000000..03d2b67
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java
@@ -0,0 +1,95 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.LinkedList;
+import java.util.Map.Entry;
+
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.karma2.exception.IllegalInputQueryException;
+import org.semanticweb.karma2.model.ConjunctiveQuery;
+import org.semanticweb.karma2.model.cqparser.ConjunctiveQueryParser;
+import uk.ac.ox.cs.pagoda.MyPrefixes;
+import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
+import uk.ac.ox.cs.pagoda.hermit.RuleHelper;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class KarmaQuery {
+        
+        StringBuffer queryBuffer; 
+
+        public KarmaQuery(String queryText) {
+                LinkedList<String> answerVariables = new LinkedList<String>(); 
+                DLClause clause = DLClauseHelper.getQuery(queryText, answerVariables);
+                String clauseText = RuleHelper.getText(clause); 
+//              clauseText = RuleHelper.abbreviateIRI(clauseText).replace(":-", "<-");
+                clauseText = clauseText.replace(":-", "<-");
+                queryBuffer = new StringBuffer();
+                
+                clauseText = expandIRI4Arguments(clauseText); 
+                
+                for (Entry<String, String> entry : MyPrefixes.PAGOdAPrefixes.getPrefixIRIsByPrefixName().entrySet()) 
+                        if (clauseText.contains(entry.getKey())) {
+                                if (queryBuffer.length() > 0) queryBuffer.append(',').append(Utility.LINE_SEPARATOR);
+                                queryBuffer.append("prefix ").append(entry.getKey()).append(" <").append(entry.getValue()).append(">"); 
+                        }
+                if (queryBuffer.length() > 0) queryBuffer.append(Utility.LINE_SEPARATOR); 
+                
+                queryBuffer.append("p(");
+                boolean first = true; 
+                for (String var: answerVariables) { 
+                        if (first) first = false; 
+                        else queryBuffer.append(","); 
+                                
+                        queryBuffer.append("?").append(var); 
+                }
+                queryBuffer.append(")").append(clauseText.substring(0, clauseText.length() - 1));
+        }
+        
+        private String expandIRI4Arguments(String clauseText) {
+                int leftIndex = clauseText.indexOf('('), rightIndex = clauseText.indexOf(')', leftIndex + 1);
+                String argsText, newArgsText; 
+                while (leftIndex != -1) {
+                        argsText = clauseText.substring(leftIndex + 1, rightIndex);
+                        newArgsText = MyPrefixes.PAGOdAPrefixes.expandText(argsText); 
+                        clauseText = clauseText.replace(argsText, newArgsText); 
+                        
+                        rightIndex += newArgsText.length() - argsText.length();
+                        leftIndex = clauseText.indexOf('(', rightIndex + 1); 
+                        rightIndex = clauseText.indexOf(')', leftIndex + 1); 
+                }
+                
+                return clauseText; 
+        }
+
+        public ConjunctiveQuery getConjunctiveQuery() {
+                ConjunctiveQuery cq = null;
+                try {
+                        cq = new ConjunctiveQueryParser(toString()).parse();
+                } catch (FileNotFoundException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } catch (IllegalInputQueryException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } catch (IOException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                } catch (Exception e) {
+                        Utility.logDebug("The query cannot be properly handled by KARMA."); 
+                        return null; 
+                }
+                return cq; 
+        }
+        
+        @Override
+        public String toString() {
+                return queryBuffer.toString(); 
+        }
+
+        static String sample = "prefix P0: <http://swat.cse.lehigh.edu/onto/univ-bench.owl#>, " +
+                        "prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>, " +
+                        "prefix owl: <http://www.w3.org/2002/07/owl#>" +
+                        "q(?0) <- owl:Thing(?0), P0:Person(?0)";
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
new file mode 100644
index 0000000..f70dde9
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
@@ -0,0 +1,98 @@
+package uk.ac.ox.cs.pagoda.reasoner.light; 
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+
+import org.semanticweb.karma2.*; 
+import org.semanticweb.karma2.clausifier.OntologyProcesser;
+import org.semanticweb.karma2.exception.IllegalInputOntologyException;
+import org.semanticweb.karma2.model.ConjunctiveQuery;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.query.*; 
+import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
+import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+
+public class KarmaQueryEngine extends RDFoxQueryEngine {
+        
+        private MyKarma reasoner = null;
+        
+        String karmaDataFile = null, karmaRuleFile = null; 
+        
+        public KarmaQueryEngine(String name) {
+                super(name);
+                
+//              int Base = 1 << 6; 
+//              int index = (new Random().nextInt() % Base + Base) % Base;
+//              karmaDataFile = "karma_data" + index + ".ttl"; 
+//              karmaRuleFile = "karma_rule" + index + ".dlog";
+                karmaDataFile = Utility.TempDirectory + "karma_data.ttl"; 
+                karmaRuleFile = Utility.TempDirectory + "karma_rule.dlog";
+                
+                reasoner = new MyKarma(); 
+        }
+        
+        public MyKarma getReasoner() {
+                return reasoner; 
+        }
+        
+        public void processOntology(OWLOntology elhoOntology) {
+                try {
+                        OntologyProcesser.transformOntology(elhoOntology, new File(karmaDataFile), new File(karmaRuleFile));
+                } catch (IllegalInputOntologyException e) {
+                        e.printStackTrace();
+                }
+        }
+
+        @Override
+        public void dispose() {
+                reasoner.dispose(); 
+        }
+        
+        @Override
+        public AnswerTuples evaluate(String queryText) {
+                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], null); 
+        }
+        
+        @Override
+        public AnswerTuples evaluate(String queryText, String[] answerVars) {
+                return evaluate(queryText, answerVars, null); 
+        }
+        
+        public AnswerTuples evaluate(String queryText, AnswerTuples soundAnswerTuples) {
+                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], soundAnswerTuples); 
+        }
+        
+        public AnswerTuples evaluate(String queryText, String[] answerVars, AnswerTuples soundAnswerTuples) {
+                KarmaQuery karmaQuery = new KarmaQuery(queryText.replace("_:", "?"));
+                reasoner.setConcurrence(false);
+                ConjunctiveQuery cq = karmaQuery.getConjunctiveQuery(); 
+                if (cq == null) return null; 
+                Set<AnswerTuple> answers = reasoner.answerCQ(cq, soundAnswerTuples, !queryText.contains("_:"));
+                return new AnswerTuplesImp(answerVars, answers); 
+        }
+
+        @Override
+        public DataStore getDataStore() {
+                return reasoner.getStore();
+        }
+        
+        public void initialiseKarma() {
+                try {
+                        reasoner.initializeData(new File(karmaDataFile));
+                        reasoner.materialise(new File(karmaRuleFile));
+                        
+                        File tmp; 
+                        if (karmaDataFile != null && ((tmp = new File(karmaDataFile)).exists())) tmp.delete(); 
+                        if (karmaRuleFile != null && ((tmp = new File(karmaRuleFile)).exists())) tmp.delete(); 
+                } catch (FileNotFoundException e) {
+                        e.printStackTrace();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
new file mode 100644
index 0000000..dd71809
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
@@ -0,0 +1,100 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import org.semanticweb.HermiT.model.Constant;
+import org.semanticweb.HermiT.model.Individual;
+import org.semanticweb.HermiT.model.Term;
+
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.model.GroundTerm;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+
+public class RDFoxAnswerTuples implements AnswerTuples {
+
+        long multi; 
+        TupleIterator m_iter; 
+        String[] m_answerVars; 
+        
+        public RDFoxAnswerTuples(String[] answerVars, TupleIterator iter) {
+                m_answerVars = answerVars;
+                m_iter = iter; 
+                reset(); 
+        }
+        
+        @Override
+        public boolean isValid() {
+                return multi != 0;
+        }
+
+        @Override
+        public int getArity() {
+                try {
+                        return m_iter.getArity();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                        return -1; 
+                }
+        }
+
+        @Override
+        public void moveNext() {
+                try {
+                        multi = m_iter.getNext();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }  
+        }
+
+        @Override
+        public void dispose() {
+                m_iter.dispose();
+        }
+        
+        protected void finalize() {
+                m_iter.dispose();
+        }
+        
+        @Override
+        public AnswerTuple getTuple() {
+                return new AnswerTuple(m_iter, m_answerVars.length); 
+        }
+
+        @Override
+        public void reset() {
+                try {
+                        multi = m_iter.open();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }               
+        }
+
+        @Override
+        public boolean contains(AnswerTuple t) {
+                Utility.logError("Unsupported operation in RDFoxAnswerTuples"); 
+                return false;
+        }
+
+        @Override
+        public void remove() {
+                Utility.logError("Unsupported operation in RDFoxAnswerTuples"); 
+        }
+
+        @Override
+        public String[] getAnswerVariables() {
+                return m_answerVars;
+        }
+        
+        public static Term getHermitTerm(GroundTerm t) {
+                if (t instanceof uk.ac.ox.cs.JRDFox.model.Individual) {
+                        uk.ac.ox.cs.JRDFox.model.Individual individual = (uk.ac.ox.cs.JRDFox.model.Individual) t; 
+                        return Individual.create(individual.getIRI());
+                }
+                else {
+                        uk.ac.ox.cs.JRDFox.model.Literal literal = ((uk.ac.ox.cs.JRDFox.model.Literal) t); 
+                        return Constant.create(literal.getLexicalForm(), literal.getDatatype().getIRI());
+                }
+        }
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
new file mode 100644
index 0000000..30771ab
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -0,0 +1,110 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import java.io.File;
+import java.util.Collection;
+
+import uk.ac.ox.cs.pagoda.MyPrefixes;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.reasoner.QueryEngine;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.tracking.AnswerTuplesWriter;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.Prefixes;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.StoreType;
+
+public abstract class RDFoxQueryEngine implements QueryEngine {
+        
+        public static final int matNoOfThreads = Runtime.getRuntime().availableProcessors() * 2;
+        
+        protected String name; 
+        protected Prefixes prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes();
+
+        public RDFoxQueryEngine(String name) {
+                this.name = name; 
+        } 
+        
+        public abstract DataStore getDataStore();
+        
+        public abstract void dispose(); 
+        
+        public void importRDFData(String fileName, String importedFile) {
+                if (importedFile == null || importedFile.isEmpty()) return ; 
+                Timer t = new Timer(); 
+                DataStore store = getDataStore(); 
+                try {
+                        long oldTripleCount = store.getTriplesCount(), tripleCount;
+                        for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator))
+                                store.importTurtleFile(new File(file), prefixes);
+                        tripleCount = store.getTriplesCount(); 
+                        Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
+                        store.clearRulesAndMakeFactsExplicit();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                Utility.logDebug(name + " store finished importing " + fileName + " in " + t.duration() + " seconds.");
+        }
+        
+        public void materialise(String programName, String programText) {
+                if (programText == null) return ; 
+                Timer t = new Timer();
+                DataStore store = getDataStore(); 
+                try {
+                        long oldTripleCount = store.getTriplesCount(), tripleCount;
+//                      store.addRules(new String[] {programText});
+                        store.importRules(programText);
+                        store.applyReasoning();
+                        tripleCount = store.getTriplesCount(); 
+                        Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
+                        store.clearRulesAndMakeFactsExplicit();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                Utility.logDebug(name + " store finished the materialisation of " + programName + " in " + t.duration() + " seconds.");
+        }
+
+        @Override
+        public void evaluate(Collection<String> queryTexts, String answerFile) {
+                if (queryTexts == null)
+                        return ;
+                
+                int queryID = 0; 
+                AnswerTuplesWriter answerWriter = new AnswerTuplesWriter(answerFile); 
+                AnswerTuples answerTuples;
+                Timer t = new Timer(); 
+                try {
+                        for (String query: queryTexts) {
+                                t.reset();
+                                answerTuples = null; 
+                                try {
+                                        answerTuples = evaluate(query); 
+                                        Utility.logDebug("time to answer Query " + ++queryID + ": " + t.duration());
+                                        answerWriter.write(answerTuples.getAnswerVariables(), answerTuples);
+                                } finally {
+                                        if (answerTuples != null) answerTuples.dispose();
+                                }
+                        }
+                } finally {
+                        answerWriter.close();
+                }
+                
+                Utility.logDebug("done computing query answers by RDFox.");
+                
+        }
+        
+        public static DataStore createDataStore() {
+                DataStore instance = null; 
+                try {
+//                      instance = new DataStore("par-head-n");
+                        instance = new DataStore(StoreType.NarrowParallelHead);
+                        instance.setNumberOfThreads(matNoOfThreads);
+                        instance.initialize();
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                return instance;
+        }
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
new file mode 100644
index 0000000..2280b12
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
@@ -0,0 +1,249 @@
+package uk.ac.ox.cs.pagoda.reasoner.light;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+
+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 uk.ac.ox.cs.JRDFox.JRDFStoreException;
+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.Resource;
+
+public class RDFoxTripleManager {
+        
+        UpdateType m_incrementally; 
+//      boolean m_incrementally; 
+
+        DataStore m_store;
+        Dictionary m_dict; 
+        Set<Atom> triplesByTerm = new HashSet<Atom>();
+        
+        public RDFoxTripleManager(DataStore store, boolean incrementally) {
+                m_store = store;
+//              m_incrementally = incrementally; 
+                if (incrementally)
+                        m_incrementally = UpdateType.ScheduleForAddition;
+                else 
+                        m_incrementally = UpdateType.Add; 
+                
+                try {
+                        m_dict = store.getDictionary();
+                        resourceID = m_dict.resolveResources(
+                                        new String[] {Namespace.RDF_TYPE,  Namespace.EQUALITY, Namespace.INEQUALITY},
+                                        new int[] {Datatype.IRI_REFERENCE.value(), Datatype.IRI_REFERENCE.value(), Datatype.IRI_REFERENCE.value()} 
+                                        ); 
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+        }
+        
+        public boolean isRdfTypeID(int id) {
+                return id == resourceID[0]; 
+        }
+        
+        public void addTripleByID(int[] tuple) {
+                try {
+                        m_store.addTriplesByResourceIDs(tuple, m_incrementally);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+        }
+        
+        public void addTripleByTerm(Atom atom) {
+                try {
+                        m_store.addTriples(getRDFoxTriple(atom), m_incrementally);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } 
+        }
+        
+        public static GroundTerm[] getRDFoxTriple(Atom instance) {
+                if (instance.getArity() == 1) 
+                        return new GroundTerm[] {
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(0)).getIRI()), 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.RDF_TYPE, 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((AtomicConcept) instance.getDLPredicate()).getIRI()) };
+                else if (instance.getDLPredicate() instanceof Equality || instance.getDLPredicate() instanceof AnnotatedEquality) 
+                        return new GroundTerm[] {
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(0)).getIRI()), 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.SAME_AS, 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(1)).getIRI()) };
+                else if (instance.getDLPredicate() instanceof Inequality) 
+                        return new GroundTerm[] {
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(0)).getIRI()), 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.DIFFERENT_FROM, 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(1)).getIRI()) }; 
+                else 
+                        return new GroundTerm[] {
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(0)).getIRI()), 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((AtomicRole) instance.getDLPredicate()).getIRI()), 
+                                        uk.ac.ox.cs.JRDFox.model.Individual.create(((Individual) instance.getArgument(1)).getIRI()) };
+        }
+        
+        int[] resourceID; // rdf:type, owl:sameAs, owl:differentFrom 
+
+        public int[] getInstance(Atom atom, Map<Variable, Integer> assignment) {
+                DLPredicate p = atom.getDLPredicate(); 
+                if (p instanceof Equality || p instanceof AnnotatedEquality) 
+                        return new int[] {
+                                        getResourceID(atom.getArgument(0), assignment),
+                                        resourceID[1],
+                                        getResourceID(atom.getArgument(1), assignment)
+                        }; 
+                else if (p instanceof Inequality) 
+                        return new int[] {
+                                        getResourceID(atom.getArgument(0), assignment), 
+                                        resourceID[2], 
+                                        getResourceID(atom.getArgument(1), assignment)
+                        }; 
+                else if (atom.getArity() == 1) 
+                        return new int[] {
+                                        getResourceID(atom.getArgument(0), assignment), 
+                                        resourceID[0], 
+                                        getResourceID(p)
+                        }; 
+                else 
+                        return new int[] {
+                                        getResourceID(atom.getArgument(0), assignment), 
+                                        getResourceID(p), 
+                                        getResourceID(atom.getArgument(1), assignment)
+                        }; 
+        }
+        
+        public String getRawTerm(int id) {
+                Resource[] res = new Resource[1]; 
+                try {
+                        m_dict.getResources(new int[] {id}, 0, 1, res);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                return getQuotedTerm(res[0]); 
+        }
+
+        Map<String, Integer> predicateCache = new HashMap<String, Integer>(); 
+        
+        public int getResourceID(DLPredicate p) {
+                Integer id; 
+                String name = p instanceof AtomicConcept ? ((AtomicConcept) p).getIRI() : ((AtomicRole) p).getIRI();
+                if ((id = predicateCache.get(name)) != null) return id;
+                try {
+                        predicateCache.put(name, id = resolveResource(name, Datatype.IRI_REFERENCE.value()));
+                        
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } 
+                return id;
+        }
+        
+        public int getResourceID(String name) {
+                Integer id = null; 
+                try {
+                        id =  resolveResource(name, Datatype.IRI_REFERENCE.value()); 
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                return id; 
+        }
+        
+        private int resolveResource(String name, int type) throws JRDFStoreException {
+                String[] lexicalForms = new String[] {name}; 
+                int[] types = new int[] {type};
+                return m_dict.resolveResources(lexicalForms, types)[0]; 
+        }
+        
+        Map<Term, Integer> termCache = new HashMap<Term, Integer>(); 
+        Queue<Term> termList = new LinkedList<Term>();
+        int sizeLimit = 10000; 
+
+        private int getResourceID(Term arg, Map<Variable, Integer> assignment) {
+                while (termCache.size() > sizeLimit) 
+                        termCache.remove(termList.poll()); 
+                
+                if (arg instanceof Variable) return assignment.get((Variable) arg); 
+                Integer id = null; 
+                if ((id = termCache.get(arg)) != null)
+                        return id; 
+                
+//              if (arg instanceof Individual) {
+                        try {
+                                if (arg instanceof Individual)
+                                        termCache.put(arg, id = resolveResource(((Individual) arg).getIRI(), Datatype.IRI_REFERENCE.value())); 
+                                else if (arg instanceof Constant)
+                                        termCache.put(arg, id = resolveResource(((Constant) arg).getLexicalForm(), getDatatypeID(((Constant) arg).getDatatypeURI()))); 
+                                
+                        } catch (JRDFStoreException e) {
+                                e.printStackTrace();
+                        } 
+//              }
+                        
+                return id;
+        }
+        
+        private static int getDatatypeID(String uri) {
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#string")) return Datatype.XSD_STRING.value(); 
+                if (uri.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral")) return Datatype.RDF_PLAIN_LITERAL.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#integer")) return Datatype.XSD_INTEGER.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#float")) return Datatype.XSD_FLOAT.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#double")) return Datatype.XSD_DOUBLE.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#boolean")) return Datatype.XSD_BOOLEAN.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#dateTime")) return Datatype.XSD_DATE_TIME.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#time")) return Datatype.XSD_TIME.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#date")) return Datatype.XSD_DATE.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#gYearMonth")) return Datatype.XSD_G_YEAR_MONTH.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#gYear")) return Datatype.XSD_G_YEAR.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#gMonthDay")) return Datatype.XSD_G_MONTH_DAY.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#gDay")) return Datatype.XSD_G_DAY.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#gMonth")) return Datatype.XSD_G_MONTH.value(); 
+                if (uri.equals("http://www.w3.org/2001/XMLSchema#duration")) return Datatype.XSD_DURATION.value(); 
+                
+                return -1;
+        }
+
+        public int[] getResourceIDs(Collection<uk.ac.ox.cs.JRDFox.model.Individual> individuals) {
+                String[] str = new String[individuals.size()]; 
+                int[] types = new int[individuals.size()]; 
+                int index = 0; 
+                for (uk.ac.ox.cs.JRDFox.model.Individual individual : individuals) {
+                        types[index] = Datatype.IRI_REFERENCE.value(); 
+                        str[index++] = individual.getIRI(); 
+                }
+                        
+                try {
+                        return m_dict.resolveResources(str, types);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                        return null; 
+                } 
+        }
+        
+        public static String getQuotedTerm(Resource r) {
+                if (r.m_datatype.equals(Datatype.IRI_REFERENCE))
+                        return OWLHelper.addAngles(r.m_lexicalForm); 
+                if (r.m_datatype.equals(Datatype.XSD_STRING) || r.m_datatype.equals(Datatype.RDF_PLAIN_LITERAL))
+                        return "\"" + r.m_lexicalForm + "\"";
+                else 
+                        return "\"" + r.m_lexicalForm + "\"^^<" + r.m_datatype.getIRI() + ">"; 
+        }
+        
+}