4 files changed, 162 insertions, 24 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..84929ad 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
@@ -8,6 +8,7 @@ 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;
@@ -17,14 +18,14 @@ import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 //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; 
         
         public GapByStore4ID(BasicQueryEngine engine) {
                 m_engine = engine; 
@@ -32,7 +33,7 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 tripleManager = new RDFoxTripleManager(m_store, false); 
         }
         
-        long multi; 
+        protected long multi; 
         
         @Override
         public void compile(String program) throws JRDFStoreException {
@@ -117,7 +118,7 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 return predicatesWithGap; 
         }
         
-        private Integer getGapPredicateID(int originalID) {
+        protected Integer getGapPredicateID(int originalID) {
                 Integer gapID; 
                 if ((gapID = original2gap.get(originalID)) != null) 
                         return gapID;
@@ -136,11 +137,14 @@ 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 +154,6 @@ 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 +170,6 @@ 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 +184,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
                 }
         }
                 
-        public boolean isValid() {return valid; }
-
         @Override
         public void addTo(DataStore store) throws JRDFStoreException {
                 Utility.logError("Unsupported Operation..."); 
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
new file mode 100644
index 0000000..f8e1709
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
@@ -0,0 +1,146 @@
+package uk.ac.ox.cs.pagoda.query;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.Map;
+import java.util.Set;
+
+import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
+import uk.ac.ox.cs.pagoda.util.UFS;
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+
+public class GapByStore4ID2 extends GapByStore4ID {
+        
+        private BasicQueryEngine m_baseEngine; 
+        private UFS<String> m_equality = null, m_baseEquality = null; 
+        
+        public GapByStore4ID2(BasicQueryEngine engine, BasicQueryEngine baseEngine) {
+                super(engine);
+                m_baseEngine = baseEngine;
+        }
+        
+        @Override
+        public boolean hasNext() {
+                if (getNewGapTuple(iterator, -1)) return true; 
+                if (iterator != null) {
+                        iterator.dispose();
+                        iterator = null; 
+                }
+                return getNextGapFactAboutEquality(); 
+        }
+        
+        private boolean getNewGapTuple(TupleIterator it, int firstElement) {
+                if (it == null) return false;
+                int firstIndex = 0; 
+                tuple = new int[3]; 
+                if (firstElement > 0) {
+                        tuple[0] = firstElement;
+                        firstIndex = 1; 
+                }               
+                Integer predicate; 
+                try {
+                        for (; multi != 0; multi = it.getNext()) {
+                                for (int i = firstIndex; i < 3; ++i)
+                                        tuple[i] = (int) it.getResourceID(i - firstIndex); 
+                                
+                                if (isRDF_TYPE()) {
+                                        predicate = getGapPredicateID(tuple[2]); 
+                                        if (predicate == null) continue; 
+                                        tuple[2] = predicate; 
+                                }
+                                else {
+                                        predicate = getGapPredicateID(tuple[1]); 
+                                        if (predicate == null) continue;  
+                                        tuple[1] = predicate; 
+                                }
+                                return true; 
+                        }
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                        return false; 
+                }
+                return false; 
+        }
+
+        private LinkedList<String> toAddedIndividuals = null; 
+        private TupleIterator iter_individual = null; 
+        private int currentID = -1; 
+        
+        private boolean getNextGapFactAboutEquality() {
+                if (toAddedIndividuals == null) {
+                        m_equality = m_engine.getEqualityGroups(false); 
+                        m_baseEquality = m_baseEngine.getEqualityGroups(false);
+                        toAddedIndividuals = new LinkedList<String>(); 
+                        Map<String, Integer> rep2cnt = new HashMap<String, Integer>();  
+                        Map<String, Integer> rep2cnt_base = new HashMap<String, Integer>();  
+                        count(m_engine, m_equality, rep2cnt); 
+                        count(m_baseEngine, m_baseEquality, rep2cnt_base);
+                        Set<String> visitedrep = new HashSet<String>();
+                        for (String individual : m_equality.keySet()) {
+                                String rep = m_equality.find(individual);
+                                if (visitedrep.contains(rep)) continue; 
+                                visitedrep.add(rep);
+                                String rep_base = m_baseEquality.find(individual);
+                                if (!rep2cnt.get(rep).equals(rep2cnt_base.get(rep_base))) {
+                                        toAddedIndividuals.add(rep); 
+                                }
+                        }
+
+                }
+                while (true) {
+                        if (getNewGapTuple(iter_individual, currentID)) return true;
+                        if (iter_individual != null) {
+                                iter_individual.dispose();
+                                iter_individual = null; 
+                        }
+                        if (toAddedIndividuals.isEmpty()) {
+                                currentID = -1; 
+                                return false;
+                        }
+                        String individual = toAddedIndividuals.remove();
+                        currentID = tripleManager.getResourceID(individual); 
+                        try {
+                                iter_individual = m_engine.internal_evaluateNotExpanded(String.format("select distinct ?y ?z where { <%s> ?y ?z }", individual));
+                                multi = iter_individual.open(); 
+                        } catch (JRDFStoreException e) {
+                                e.printStackTrace();
+                        }
+                }
+        }
+
+        private void count(BasicQueryEngine engine, UFS<String> equality, Map<String, Integer> map) {
+                for (String ind : equality.keySet()) {
+                        Integer exist = map.get(ind);
+                        if (exist == null)
+                                map.put(equality.find(ind), 1); 
+                        else 
+                                map.put(equality.find(ind), ++exist); 
+                }
+        }
+
+        @Override
+        public int[] next() {
+                try {
+                        if (iterator != null)
+                                multi = iterator.getNext();
+                        else if (iter_individual != null)
+                                multi = iter_individual.getNext();
+                        else 
+                                multi = 0; 
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } 
+                return tuple; 
+        }
+        
+        public void clear() {
+                super.clear();
+                if (iter_individual != null) {
+                        iter_individual.dispose();
+                        iter_individual = null; 
+                }
+        }
+        
+}
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
index a1c1b0e..d2e9b90 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
@@ -164,11 +164,6 @@ public class GapByTriple extends GapTupleIterator<String> {
         }
         
         @Override
-        public boolean isValid() {
-                return true;
-        }
-
-        @Override
         public void clear() {
                 iterator.dispose();             
         }
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java b/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
index 58303bb..61b6364 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
@@ -17,8 +17,6 @@ public abstract class GapTupleIterator<T> implements Iterator<T> {
         
         public void compile(String programText) throws JRDFStoreException {}
         
-        public abstract boolean isValid();
-        
         public abstract void save(String file); 
         
         public abstract void addBackTo() throws JRDFStoreException;
@@ -26,5 +24,5 @@ public abstract class GapTupleIterator<T> implements Iterator<T> {
         public abstract void addTo(DataStore store) throws JRDFStoreException;
         
         public abstract void clear();
-
+        
 }