1 files changed, 361 insertions, 359 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
index 79be8aa..fe43e09 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -1,375 +1,377 @@
 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.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+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.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.*;
 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;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
+
+import java.util.*;
 
 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();
-                        } finally {
-                                gap.clear(); 
-                        }
-                }
-                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(); 
-                                }
-                        }
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {                     
-                        if (predicateTuples != null) predicateTuples.dispose();
-                        predicateTuples = null; 
-                }
-                        
-                try {
-                        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();
-                        predicateTuples = null;
-                }
-                
-                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);
+    protected DataStore store;
+    protected Parameters parameters = new Parameters();
+    Set<DLClause> materialisedRules = new HashSet<DLClause>();
+    private UFS<String> equalityGroups = null;
+
+    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(isDisposed()) throw new DisposedException();
+        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());
+    }
+
+    public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+        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) {
+        if(isDisposed()) throw new DisposedException();
+        return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]);
+    }
+
+    @Override
+    public AnswerTuples evaluate(String queryText, String[] answerVars) {
+        if(isDisposed()) throw new DisposedException();
+        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() {
+        if(isDisposed()) throw new DisposedException();
+        return store;
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        store.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();
+                }
+            }
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(predicateTuples != null) predicateTuples.dispose();
+            predicateTuples = null;
+        }
+
+        try {
+            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();
+            predicateTuples = null;
+        }
+
+        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();
-                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(boolean reuse) {
-                if (reuse && 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);
-                        
-                        try {
-                                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);
-                                }
-                        } finally {
-                                if (iter != null) iter.dispose();
-                                iter = null; 
-                        }
-                        store.applyReasoning(true);
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } 
-                Utility.logInfo("Time for deletion: " + timer.duration()); 
-        }
+        parameters.m_expandEquality = true;
+        return iter;
+    }
+
+    public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException {
+        return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText);
+    }
+
+    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;
+    }
+
+    public UFS<String> getEqualityGroups(boolean reuse) {
+        if(reuse && 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();
+        }
+    }
+
+    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();
+        }
+    }
+
+    @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);
+
+            try {
+                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);
+                }
+            } finally {
+                if(iter != null) iter.dispose();
+                iter = null;
+            }
+            store.applyReasoning(true);
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        Utility.logInfo("Time for deletion: " + timer.duration());
+    }
 
 
 }