Merged updates from upstream.

1 files changed, 75 insertions, 79 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 5d2e411..9aa6235 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -19,16 +19,18 @@ import java.util.*;
 
 public class BasicQueryEngine extends RDFoxQueryEngine {
 
-        protected DataStore store; 
-        protected Parameters parameters = new Parameters(); 
+        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); 
+                super(name);
                 store = RDFoxQueryEngine.createDataStore();
-                parameters.m_allAnswersInRoot = true; 
-                parameters.m_useBushy = true; 
+                parameters.m_allAnswersInRoot = true;
+                parameters.m_useBushy = true;
         }
-        
+
         public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
                 if (gap != null) {
                         materialise("lower program", dProgram.getLower().toString());
@@ -40,10 +42,9 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                         } catch (JRDFStoreException e) {
                                 e.printStackTrace();
                         } finally {
-                                gap.clear(); 
+                                gap.clear();
                         }
-                }
-                else 
+                } else
                         materialise("upper program", dProgram.getUpper().toString());
         }
         
@@ -58,24 +59,23 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                         } catch (JRDFStoreException e) {
                                 e.printStackTrace();
                         } finally {
-                                gap.clear(); 
+                                gap.clear();
                         }
-                }
-                else 
+                } else
                         materialise("upper program", dProgram.getUpper().toString());
-                
-                return 1; 
-        }
 
+                return 1;
+        }
+        
         public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
                 throw new UnsupportedOperationException();
         }
-        
+
         @Override
         public AnswerTuples evaluate(String queryText) {
-                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]); 
+                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]);
         }
-        
+
         @Override
         public AnswerTuples evaluate(String queryText, String[] answerVars) {
                 TupleIterator tupleIterator;
@@ -83,9 +83,9 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                         tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters);
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                        return null; 
+                        return null;
                 }
-                return new RDFoxAnswerTuples(answerVars, tupleIterator); 
+                return new RDFoxAnswerTuples(answerVars, tupleIterator);
         }
 
         @Override
@@ -95,17 +95,18 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
 
         @Override
         public void dispose() {
-                store.dispose();                
+                store.dispose();
         }
 
         protected void outputClassAssertions(String filename) {
                 TupleIterator allTuples = null;
-                boolean redirect = false; 
+                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))); 
+                        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 {
@@ -123,137 +124,134 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
         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; 
+                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; 
+                                instanceTuples = null;
                                 try {
                                         instanceTuples = getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters);
-                                        long totalCount = 0; 
+                                        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(); 
+                                        if(instanceTuples != null) instanceTuples.dispose();
                                 }
                         }
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                } finally {                     
+                } finally {
                         if (predicateTuples != null) predicateTuples.dispose();
-                        predicateTuples = null; 
+                        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; 
+                                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); 
+                                        number.add(predicate + " * " + totalCount);
                                 } finally {
-                                        if (instanceTuples != null) instanceTuples.dispose(); 
+                                        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); 
+                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; 
+                return iter;
         }
 
         public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
                 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
-//              iter.open(); 
-                return iter; 
+//              iter.open();
+                return iter;
         }
-        
+
         public void setExpandEquality(boolean flag) {
-                parameters.m_expandEquality = 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; 
+                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); 
+                        else if(toUpdate) materialisedRules.add(clause);
                 }
-                
+
                 if (clauses.isEmpty()) return null;
-                
+
                 return Program.toString(clauses);
         }
 
         public void outputMaterialisedRules() {
-                System.out.println(DLClauseHelper.toString(materialisedRules));         
+                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(); 
+                        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(); 
+                                System.out.println();
                         }
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
                 } finally {
-                        if (iter != null) iter.dispose(); 
+                        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 
-                                        + "> .}"); 
+                                                          + iri
+                                                          + "> .}");
         }
 
         public void outputSubjects(String p, String o) {
@@ -265,13 +263,13 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
         }
 
         public void outputIDBFacts() {
-                TupleIterator iter = null; 
+                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(); 
+                                        System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
+                                System.out.println();
                         }
                 } catch (JRDFStoreException e) {
                         // TODO Auto-generated catch block
@@ -279,7 +277,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                 } finally {
                         if (iter != null) iter.dispose();
                 }
-                
+
         }
         
         public void outputType4Individual(String iri) {
@@ -287,25 +285,23 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
         }
         
         public int getSameAsNumber() {
-                TupleIterator iter = null; 
-                int counter = 0; 
+                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()) 
+                        for(long multi = iter.open(); multi != 0; multi = iter.getNext())
                                 if (iter.getResourceID(0) != iter.getResourceID(1))
                                         ++counter;
                 } catch (JRDFStoreException e) {
-                        e.printStackTrace(); 
+                        e.printStackTrace();
                 } finally {
                         if (iter != null) iter.dispose();
                 }
-                return counter; 
+                return counter;
         }
-        
-        private UFS<String> equalityGroups = null; 
-        
-        public UFS<String> getEqualityGroups() {
-                if (equalityGroups != null) return equalityGroups; 
+
+        public UFS<String> getEqualityGroups(boolean reuse) {
+                if(reuse && equalityGroups != null) return equalityGroups;
 
                 equalityGroups = new UFS<String>();