Merged updates from upstream.

1 files changed, 59 insertions, 61 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
index 1c0eb48..02db18d 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
@@ -1,103 +1,106 @@
 package uk.ac.ox.cs.pagoda.query;
 
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.Map;
-
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 import uk.ac.ox.cs.pagoda.MyPrefixes;
-//import uk.ac.ox.cs.pagoda.multistage.AnswerTupleID;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
+import uk.ac.ox.cs.pagoda.util.Namespace;
 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;
-import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.Map;
+
+//import uk.ac.ox.cs.pagoda.multistage.AnswerTupleID;
 
 //public class GapByStore4ID extends GapTupleIterator<AnswerTupleID> {
 public class GapByStore4ID extends GapTupleIterator<int[]> {
 
-        private MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes; 
-        private TupleIterator iterator = null; 
+        protected MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes;
+        protected TupleIterator iterator = null; 
         
 //      AnswerTupleID tuple;
-        int[] tuple; 
-        private BasicQueryEngine m_engine; 
-        private DataStore m_store;
-        private RDFoxTripleManager tripleManager; 
+protected int[] tuple;
+        protected BasicQueryEngine m_engine;
+        protected DataStore m_store;
+        protected RDFoxTripleManager tripleManager;
+        protected long multi;
+        Map<Integer, Integer> original2gap = new HashMap<Integer, Integer>();
+        LinkedList<String> predicatesWithGap = new LinkedList<String>();
         
         public GapByStore4ID(BasicQueryEngine engine) {
-                m_engine = engine; 
-                m_store = engine.getDataStore(); 
-                tripleManager = new RDFoxTripleManager(m_store, false); 
+                m_engine = engine;
+                m_store = engine.getDataStore();
+                tripleManager = new RDFoxTripleManager(m_store, false);
         }
         
-        long multi; 
-        
         @Override
         public void compile(String program) throws JRDFStoreException {
-                clear(); 
+                clear();
 
-                boolean incrementally = true; 
+                boolean incrementally = true;
                 Timer t = new Timer();
                 long oldTripleCount = m_store.getTriplesCount();
-                
+
                 if (program != null) {
 //                      m_store.addRules(new String[] {program});
                         m_store.importRules(program);
-                        incrementally = false; 
+                        incrementally = false;
                 }
-                
+
                 m_store.applyReasoning(incrementally);
-                
+
                 long tripleCount = m_store.getTriplesCount();
-                        
-                Utility.logDebug("current store after materialising upper related rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)", 
+
+                Utility.logDebug("current store after materialising upper related rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)",
                                 "current store finished the materialisation of upper related rules in " + t.duration() + " seconds.");
-                
+
                 m_engine.setExpandEquality(false);
                 iterator = m_engine.internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
                 m_engine.setExpandEquality(true);
-                
+
                 multi = iterator.open();
-                Utility.logDebug("gap query evaluted ..."); 
+                Utility.logDebug("gap query evaluted ...");
         }
         
         @Override
         public boolean hasNext() {
-                if (iterator == null) return false; 
+                if(iterator == null) return false;
                 try {
 //                      tuple = new AnswerTupleID(3);
-                        tuple = new int[3]; 
-                        Integer predicate; 
+                        tuple = new int[3];
+                        Integer predicate;
                         for (; multi != 0; multi = iterator.getNext()) {
                                 for (int i = 0; i < 3; ++i)
 //                                      tuple.setTerm(i, (int) iterator.getResourceID(i));
-                                        tuple[i] = (int) iterator.getResourceID(i); 
-                                
+                                        tuple[i] = iterator.getResourceID(i);
+
                                 if (isRDF_TYPE()) {
 //                                      predicate = getGapPredicateID(tuple.getTerm(2));
-                                        predicate = getGapPredicateID(tuple[2]); 
-                                        if (predicate == null) continue; 
+                                        predicate = getGapPredicateID(tuple[2]);
+                                        if(predicate == null) continue;
 //                                      tuple.setTerm(2, predicate);
-                                        tuple[2] = predicate; 
+                                        tuple[2] = predicate;
                                 }
                                 else {
 //                                      predicate = getGapPredicateID(tuple.getTerm(1));
-                                        predicate = getGapPredicateID(tuple[1]); 
-                                        if (predicate == null) continue;  
+                                        predicate = getGapPredicateID(tuple[1]);
+                                        if(predicate == null) continue;
 //                                      tuple.setTerm(1, predicate);
-                                        tuple[1] = predicate; 
+                                        tuple[1] = predicate;
                                 }
-                                return true; 
+                                return true;
                         }
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                        return false; 
+                        return false;
                 }
-                return false; 
+                return false;
         }
-        
+
         @Override
 //      public AnswerTupleID next() {
         public int[] next() {
@@ -105,19 +108,16 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                         multi = iterator.getNext();
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                } 
-                
-                return tuple; 
+                }
+
+                return tuple;
         }
         
-        Map<Integer, Integer> original2gap = new HashMap<Integer, Integer>();
-        LinkedList<String> predicatesWithGap = new LinkedList<String>();
-        
         public LinkedList<String> getPredicatesWithGap() {
                 return predicatesWithGap; 
         }
-        
-        private Integer getGapPredicateID(int originalID) {
+
+        protected Integer getGapPredicateID(int originalID) {
                 Integer gapID; 
                 if ((gapID = original2gap.get(originalID)) != null) 
                         return gapID;
@@ -136,11 +136,14 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 return gapID;
         }
 
-        private boolean isAuxPredicate(String originalPredicate) {
-                return originalPredicate.contains("_AUX");
+        protected boolean isAuxPredicate(String originalPredicate) {
+                if(originalPredicate.equals(Namespace.EQUALITY_QUOTED)) return false;
+                return originalPredicate.contains("_AUX") ||
+                                originalPredicate.startsWith("<" + Namespace.OWL_NS) ||
+                                originalPredicate.startsWith("<" + Namespace.PAGODA_ORIGINAL);
         }
 
-        private boolean isRDF_TYPE() {
+        protected boolean isRDF_TYPE() {
 //              return tripleManager.isRdfTypeID(tuple.getTerm(1)); 
                 return tripleManager.isRdfTypeID(tuple[1]); 
         }
@@ -150,8 +153,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 Utility.logError("Unsupported operation!"); 
         }
         
-        private boolean valid = false;
-
         @Override
         public void save(String file) {
                 Utility.logError("Unsupported Operation..."); 
@@ -168,7 +169,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                         ++tupleCounter;
                         tripleManager.addTripleByID(tuple);
                 }
-                valid = true; 
 
                 long tripleCounter = m_store.getTriplesCount(); 
                 Utility.logDebug("There are " + tupleCounter + " tuples in the gap between lower and upper bound materialisation.", 
@@ -183,8 +183,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 }
         }
                 
-        public boolean isValid() {return valid; }
-
         @Override
         public void addTo(DataStore store) throws JRDFStoreException {
                 Utility.logError("Unsupported Operation...");