1 files changed, 368 insertions, 368 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
index f3cc937..d8ebc55 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
@@ -1,387 +1,387 @@
 package uk.ac.ox.cs.pagoda.tracking;
 
-import java.io.BufferedWriter;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Map;
-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.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.DatatypeRestriction;
-import org.semanticweb.HermiT.model.Equality;
-import org.semanticweb.HermiT.model.Individual;
-import org.semanticweb.HermiT.model.Inequality;
-import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.JRDFox.model.Datatype;
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.model.Literal;
 import uk.ac.ox.cs.pagoda.MyPrefixes;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.query.*; 
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.GapTupleIterator;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
 import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
+
+import java.io.BufferedWriter;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.*;
+
+public abstract class TrackingRuleEncoder extends Disposable {
+    public static final String trackingPredicateRelation = Namespace.PAGODA_AUX + "isTrackingPredicateFor";
+    public static final String QueryPredicate = Namespace.PAGODA_AUX + "Query";
+    protected BasicQueryEngine store;
+    protected QueryRecord currentQuery;
+    protected Set<String> unaryPredicates = new HashSet<String>();
+    protected Set<String> binaryPredicates = new HashSet<String>();
+    UpperDatalogProgram program;
+    Collection<DLClause> trackingClauses = new HashSet<DLClause>();
+    Collection<DLClause> queryClauses = new LinkedList<DLClause>();
+    Map<Integer, DLClause> index2clause = new HashMap<Integer, DLClause>();
+    Map<DLClause, Integer> clause2index = new HashMap<DLClause, Integer>();
+    String equalityRelatedRuleText = null;
+    boolean ruleEncoded = false;
+    DLPredicate selected;
+    private boolean queryEncoded = false;
+    private LinkedList<int[]> addedData = new LinkedList<int[]>();
+    private String trackingSuffix;
+
+    public TrackingRuleEncoder(UpperDatalogProgram program, BasicQueryEngine store) {
+        this.program = program;
+        this.store = store;
+    }
+
+    public static String getRawTerm(GroundTerm r) {
+        if(r instanceof uk.ac.ox.cs.JRDFox.model.Individual)
+            return ((uk.ac.ox.cs.JRDFox.model.Individual) r).getIRI();
+        else {
+            Literal l = (Literal) r;
+            if(l.getDatatype().equals(Datatype.XSD_STRING) && l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL))
+                return "\"" + l.getLexicalForm() + "\"";
+            else
+                return "\"" + l.getLexicalForm() + "\"^^<" + l.getDatatype().getIRI() + ">";
+        }
+    }
+
+    protected static String getTrackingSuffix(String queryID) {
+        return "_AUXt" + queryID;
+    }
+
+    public boolean encodingRules() {
+        if(isDisposed()) throw new DisposedException();
+        if(ruleEncoded) return false;
+        ruleEncoded = true;
 
-public abstract class TrackingRuleEncoder {
-        UpperDatalogProgram program;
-        Collection<DLClause> trackingClauses = new HashSet<DLClause>();
-        Collection<DLClause> queryClauses = new LinkedList<DLClause>();
-        
-        Map<Integer, DLClause> index2clause = new HashMap<Integer, DLClause>();
-        Map<DLClause, Integer> clause2index = new HashMap<DLClause, Integer>();
-        
-        String equalityRelatedRuleText = null; 
-        protected BasicQueryEngine store;  
-        
-        public TrackingRuleEncoder(UpperDatalogProgram program, BasicQueryEngine store) {
-                this.program = program;
-                this.store = store; 
-        }
-        
-        protected abstract String getEqualityRelatedRuleText();
-
-        boolean ruleEncoded = false; 
-        
-        public boolean encodingRules() {
-                if (ruleEncoded) return false;
-                ruleEncoded = true; 
-                
 //              for (DLClause clause: program.getClauses(currentQuery.getClause())) {
-                for (DLClause clause: program.getClauses()) {
-                        encodingRule(clause);
-                }
-                return true; 
-        }
-        
-        protected String getIRI(String name) {
-                return program.getOntology().getOntologyID().getOntologyIRI().toString() + "#" + name;
-        }
-
-        protected abstract void encodingRule(DLClause clause);
-        
-        protected Individual getIndividual4GeneralRule(DLClause clause) {
-                clause = program.getCorrespondingClause(clause);
+        for(DLClause clause : program.getClauses()) {
+            encodingRule(clause);
+        }
+        return true;
+    }
+
+    public Collection<int[]> getAddedData() {
+        if(isDisposed()) throw new DisposedException();
+        return addedData;
+    }
+
+    public String getTrackingPredicate(String predicateIRI) {
+        if(isDisposed()) throw new DisposedException();
+        if(predicateIRI.startsWith("<"))
+            return predicateIRI.replace(">", getTrackingSuffix(currentQuery.getQueryID()) + ">");
+        else
+            return predicateIRI + getTrackingSuffix(currentQuery.getQueryID());
+    }
+
+    public void setCurrentQuery(QueryRecord record) {
+        if(isDisposed()) throw new DisposedException();
+        deprecateTrackingAndQueryRules();
+        currentQuery = record;
+        selected = AtomicConcept.create(getSelectedPredicate());
+        trackingSuffix = "_AUXt" + currentQuery.getQueryID();
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        deprecateTrackingAndQueryRules();
+    }
+
+    public String getTrackingProgram() {
+        if(isDisposed()) throw new DisposedException();
+        StringBuilder sb = getTrackingProgramBody();
+        sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText());
+        return sb.toString();
+    }
+
+    public void saveTrackingRules(String fileName) {
+        if(isDisposed()) throw new DisposedException();
+        BufferedWriter writer = null;
+        try {
+            writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileName)));
+            writer.write(getTrackingProgram());
+            writer.close();
+        } catch(IOException e) {
+            e.printStackTrace();
+            return;
+        }
+        Utility.logDebug("The tracking rules are saved in " + fileName + ".");
+    }
+
+    public String getSelectedPredicate() {
+        if(isDisposed()) throw new DisposedException();
+        return getIRI("_selected" + currentQuery.getQueryID());
+    }
+
+    public DLClause getSelectedClause(String iri) {
+        if(isDisposed()) throw new DisposedException();
+        int index = iri.lastIndexOf("_r") + 2;
+        int ruleIndex = Integer.parseInt(iri.substring(index));
+        return index2clause.get(ruleIndex);
+    }
+
+    /**
+     * SELECT ?X
+     * WHERE {
+     * ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#:type> :_selected?
+     * }
+     */
+    public String getSelectedSPARQLQuery() {
+        if(isDisposed()) throw new DisposedException();
+        StringBuilder builder = new StringBuilder();
+        builder.append("SELECT ?X\nWHERE {\n?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ");
+        builder.append(selected.toString()).append("\n}");
+        return builder.toString();
+    }
+
+    public OWLOntology getOntology() {
+        if(isDisposed()) throw new DisposedException();
+        return program.getOntology();
+    }
+
+    public UpperDatalogProgram getProgram() {
+        if(isDisposed()) throw new DisposedException();
+        return program;
+    }
+
+    public String getOriginalPredicate(String p) {
+        if(isDisposed()) throw new DisposedException();
+        if(p.startsWith("<")) {
+            if(!p.endsWith(trackingSuffix + ">")) return null;
+        }
+        else if(!p.endsWith(trackingSuffix)) return null;
+
+        return p.replace(trackingSuffix, "");
+    }
+
+    public boolean isAuxPredicate(String p) {
+        if(isDisposed()) throw new DisposedException();
+        return false;
+    }
+
+    protected abstract String getEqualityRelatedRuleText();
+
+    protected String getIRI(String name) {
+        return program.getOntology().getOntologyID().getOntologyIRI().toString() + "#" + name;
+    }
+
+    protected abstract void encodingRule(DLClause clause);
+
+    protected Individual getIndividual4GeneralRule(DLClause clause) {
+        clause = program.getCorrespondingClause(clause);
 //              if (clause == null)
-//                      return Individual.create(getIRI("_r0")); 
-                        
-                int index; 
-                if (clause2index.containsKey(clause)) 
-                        index = clause2index.get(clause); 
-                else {
-                        index = clause2index.size() + 1; 
-                        index2clause.put(index, clause);
-                        clause2index.put(clause, index); 
-                }
-
-                return Individual.create(getIRI("_r" + index));
-        }
-
-        private boolean queryEncoded = false; 
-        private LinkedList<int[]> addedData = new LinkedList<int[]>();
-        
-        public Collection<int[]> getAddedData() {
-                return addedData; 
-        }
-        
-        private void encodingQuery(QueryRecord[] botQuerRecords) {
-                if (queryEncoded) return ; 
-                queryEncoded = true;
-                
-                if (currentQuery.getArity() > 0 && currentQuery.getArity() < 3) {
-                        encodingAtomicQuery(botQuerRecords);
-
-                } else {
-                        DLClause queryClause = currentQuery.getClause(); 
-                        Atom[] bodyAtoms = queryClause.getBodyAtoms(); 
-                        for (Atom bodyAtom: bodyAtoms) 
-                                addQueryRule(bodyAtom, bodyAtoms); 
-                }
-        }
-        
-        private void addQueryRule(Atom atom, Atom[] atoms) {
-                DLClause newClause; 
-                Atom headAtom; 
-                
-                headAtom = Atom.create(
-                                getTrackingDLPredicate(atom.getDLPredicate()), 
-                                DLClauseHelper.getArguments(atom));
-                newClause = DLClause.create(new Atom[] {headAtom}, atoms); 
-                queryClauses.add(newClause);
-        }
-
-        public static final String trackingPredicateRelation = Namespace.PAGODA_AUX + "isTrackingPredicateFor"; 
-        
-        public static final String QueryPredicate = Namespace.PAGODA_AUX + "Query"; 
-        
-        protected String getCurrentQueryPredicate() {
-                return QueryPredicate + currentQuery.getQueryID(); 
-        }
-
-        protected void encodingAtomicQuery(QueryRecord[] botQuerRecords) {
-                encodingAtomicQuery(botQuerRecords, false);
-        }
-        
-        protected void encodingAtomicQuery(QueryRecord[] botQuerRecords, boolean includingBottom) {
-                DLClause queryClause = currentQuery.getClause(); 
-                AnswerTuples answerTuples = currentQuery.getGapAnswers(); 
-                String[] answerVariables = currentQuery.getAnswerVariables(); 
-                
-                String currentQueryPredicate = getCurrentQueryPredicate();
-                Atom newAtom; 
-                if (answerVariables.length == 1) {
-                        AtomicConcept queryConcept = AtomicConcept.create(currentQueryPredicate);
-                        newAtom = Atom.create(queryConcept, Variable.create(answerVariables[0]));
-                }
-                else {
-                        AtomicRole queryRole = AtomicRole.create(currentQueryPredicate); 
-                        newAtom = Atom.create(queryRole, Variable.create(answerVariables[0]), Variable.create(answerVariables[1]));  
-                }
-                
-                Atom[] bodyAtoms = queryClause.getBodyAtoms();
-                Atom[] newBodyAtoms = new Atom[queryClause.getBodyLength() + 1]; 
-                for (int i = 0; i < bodyAtoms.length; ++i)
-                        newBodyAtoms[i + 1] = bodyAtoms[i]; 
-                newBodyAtoms[0] = newAtom;
-                
-                for (Atom bodyAtom: bodyAtoms) 
-                        addQueryRule(bodyAtom, newBodyAtoms);
-
-                RDFoxTripleManager tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
+//                      return Individual.create(getIRI("_r0"));
+
+        int index;
+        if(clause2index.containsKey(clause))
+            index = clause2index.get(clause);
+        else {
+            index = clause2index.size() + 1;
+            index2clause.put(index, clause);
+            clause2index.put(clause, index);
+        }
+
+        return Individual.create(getIRI("_r" + index));
+    }
+
+    private void encodingQuery(QueryRecord[] botQuerRecords) {
+        if(queryEncoded) return;
+        queryEncoded = true;
+
+        if(currentQuery.getArity() > 0 && currentQuery.getArity() < 3) {
+            encodingAtomicQuery(botQuerRecords);
+
+        }
+        else {
+            DLClause queryClause = currentQuery.getClause();
+            Atom[] bodyAtoms = queryClause.getBodyAtoms();
+            for(Atom bodyAtom : bodyAtoms)
+                addQueryRule(bodyAtom, bodyAtoms);
+        }
+    }
+
+    private void addQueryRule(Atom atom, Atom[] atoms) {
+        DLClause newClause;
+        Atom headAtom;
+
+        headAtom = Atom.create(
+                getTrackingDLPredicate(atom.getDLPredicate()),
+                DLClauseHelper.getArguments(atom));
+        newClause = DLClause.create(new Atom[]{headAtom}, atoms);
+        queryClauses.add(newClause);
+    }
+
+    protected String getCurrentQueryPredicate() {
+        return QueryPredicate + currentQuery.getQueryID();
+    }
+
+    protected void encodingAtomicQuery(QueryRecord[] botQuerRecords) {
+        encodingAtomicQuery(botQuerRecords, false);
+    }
+
+    protected void encodingAtomicQuery(QueryRecord[] botQuerRecords, boolean includingBottom) {
+        DLClause queryClause = currentQuery.getClause();
+        AnswerTuples answerTuples = currentQuery.getGapAnswers();
+        String[] answerVariables = currentQuery.getAnswerVariables();
+
+        String currentQueryPredicate = getCurrentQueryPredicate();
+        Atom newAtom;
+        if(answerVariables.length == 1) {
+            AtomicConcept queryConcept = AtomicConcept.create(currentQueryPredicate);
+            newAtom = Atom.create(queryConcept, Variable.create(answerVariables[0]));
+        }
+        else {
+            AtomicRole queryRole = AtomicRole.create(currentQueryPredicate);
+            newAtom = Atom.create(queryRole, Variable.create(answerVariables[0]), Variable.create(answerVariables[1]));
+        }
+
+        Atom[] bodyAtoms = queryClause.getBodyAtoms();
+        Atom[] newBodyAtoms = new Atom[queryClause.getBodyLength() + 1];
+        for(int i = 0; i < bodyAtoms.length; ++i)
+            newBodyAtoms[i + 1] = bodyAtoms[i];
+        newBodyAtoms[0] = newAtom;
+
+        for(Atom bodyAtom : bodyAtoms)
+            addQueryRule(bodyAtom, newBodyAtoms);
+
+        RDFoxTripleManager tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
 //              MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes;
-                int[] triple; 
-                int predicate = tripleManager.getResourceID(AtomicConcept.create(currentQueryPredicate));   
-                int rdftype = tripleManager.getResourceID(AtomicRole.create(Namespace.RDF_TYPE));
-                if (answerVariables.length == 1) {              
-                        for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                answer = answerTuples.getTuple();
-                                triple = new int[] { tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), rdftype, predicate }; 
-                                addedData.add(triple);
-                                tripleManager.addTripleByID(triple);
-//                              System.out.println("To be removed ... \n" + tripleManager.getRawTerm(tripleManager.getResourceID(prefixes.expandIRI(answer.getRawTerm(0)))) + " " + tripleManager.getRawTerm(rdftype) + " " + tripleManager.getRawTerm(predicate)); 
-                        }
-                }
-                else {
-                        for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                answer = answerTuples.getTuple();
-                                triple = new int[] { tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), predicate, tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(1))) }; 
-                                addedData.add(triple);
-                                tripleManager.addTripleByID(triple);
-                        }
-                }
-                answerTuples.dispose();
-
-                if (includingBottom && botQuerRecords != null) {
-                        int index = 0; 
-                        GroundTerm t; 
-                        String raw; 
-                        for (QueryRecord  botQueryRecord: botQuerRecords) {
-                                answerTuples = botQueryRecord.getGapAnswers();
-                                int subID = 0;//botQueryRecord.getSubID(); 
-                                String p = subID == 0 ? AtomicConcept.NOTHING.getIRI() : Namespace.OWL_NS + "Nothing_final" + (++index); 
-                                predicate = tripleManager.getResourceID(AtomicConcept.create(p = getTrackingPredicate(p)));
-                                for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                        answer = answerTuples.getTuple(); 
+        int[] triple;
+        int predicate = tripleManager.getResourceID(AtomicConcept.create(currentQueryPredicate));
+        int rdftype = tripleManager.getResourceID(AtomicRole.create(Namespace.RDF_TYPE));
+        if(answerVariables.length == 1) {
+            for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                answer = answerTuples.getTuple();
+                triple =
+                        new int[]{tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), rdftype, predicate};
+                addedData.add(triple);
+                tripleManager.addTripleByID(triple);
+//                              System.out.println("To be removed ... \n" + tripleManager.getRawTerm(tripleManager.getResourceID(prefixes.expandIRI(answer.getRawTerm(0)))) + " " + tripleManager.getRawTerm(rdftype) + " " + tripleManager.getRawTerm(predicate));
+            }
+        }
+        else {
+            for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                answer = answerTuples.getTuple();
+                triple =
+                        new int[]{tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), predicate, tripleManager
+                                .getResourceID(getRawTerm(answer.getGroundTerm(1)))};
+                addedData.add(triple);
+                tripleManager.addTripleByID(triple);
+            }
+        }
+//        answerTuples.dispose();
+
+        if(includingBottom && botQuerRecords != null) {
+            int index = 0;
+            GroundTerm t;
+            String raw;
+            for(QueryRecord botQueryRecord : botQuerRecords) {
+                answerTuples = botQueryRecord.getGapAnswers();
+                int subID = 0;//botQueryRecord.getSubID();
+                String p = subID == 0 ? AtomicConcept.NOTHING.getIRI() : Namespace.OWL_NS + "Nothing_final" + (++index);
+                predicate = tripleManager.getResourceID(AtomicConcept.create(p = getTrackingPredicate(p)));
+                for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                    answer = answerTuples.getTuple();
 //                                      System.out.println("To be removed ... " + answer.getRawTerm(0));
-                                        raw = ((t = answer.getGroundTerm(0)) instanceof uk.ac.ox.cs.JRDFox.model.Individual) ? ((uk.ac.ox.cs.JRDFox.model.Individual) t).getIRI() : t.toString(); 
-                                        triple = new int[] { tripleManager.getResourceID(raw), rdftype, predicate }; 
-                                        addedData.add(triple);
-                                        tripleManager.addTripleByID(triple);
-                                }
-                                answerTuples.dispose();
-                        }
-                }
-                
-                Utility.logInfo(addedData.size() + " triples are added into the store.");
-        }
-        
-        public static String getRawTerm(GroundTerm r) {
-                if (r instanceof uk.ac.ox.cs.JRDFox.model.Individual)
-                        return ((uk.ac.ox.cs.JRDFox.model.Individual) r).getIRI(); 
-                else {
-                        Literal l = (Literal) r; 
-                        if (l.getDatatype().equals(Datatype.XSD_STRING) && l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL))
-                                return "\"" + l.getLexicalForm() + "\""; 
-                        else
-                                return "\"" + l.getLexicalForm() + "\"^^<" + l.getDatatype().getIRI() + ">"; 
-                }
-        }
-
-        protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) {
-                return getDLPredicate(dlPredicate, GapTupleIterator.gapPredicateSuffix); 
-        }
-
-        DLPredicate getDLPredicate(DLPredicate p, String suffix) {
-                if (p instanceof AtomicConcept) 
-                        return AtomicConcept.create(((AtomicConcept) p).getIRI() + suffix);
-                else if (p instanceof DatatypeRestriction) {
-                        DatatypeRestriction restriction = (DatatypeRestriction) p; 
-                        String newURI = restriction.getDatatypeURI() + suffix; 
-                        return getDatatypeRestriction(restriction, newURI);
-                }
-                else if (p instanceof AtomicRole)
-                        return AtomicRole.create(((AtomicRole) p).getIRI() + suffix);
-                else if (p instanceof AnnotatedEquality || p instanceof Equality) 
-                        return AtomicRole.create(Namespace.EQUALITY + suffix);
-                else if (p instanceof Inequality) 
-                        return AtomicRole.create(Namespace.INEQUALITY + suffix);
-                else if (p instanceof DatatypeRestriction)
-                        return AtomicConcept.create(((DatatypeRestriction) p).getDatatypeURI() + suffix);
-                else {
-                        Utility.logDebug("strange DL predicate appeared ... " + p, 
-                                        "the program paused here in TrackingRuleEncoderDisj.java"); 
-                        return null;
-                }
-        }
-
-        protected DLPredicate getTrackingDLPredicate(DLPredicate dlPredicate) {
-                return getDLPredicate(dlPredicate, getTrackingSuffix(currentQuery.getQueryID())); 
-        }
-        
-        protected static String getTrackingSuffix(String queryID) {
-                return "_AUXt" + queryID; 
-        }
-        
-        public String getTrackingPredicate(String predicateIRI) {
-                if (predicateIRI.startsWith("<"))
-                        return predicateIRI.replace(">", getTrackingSuffix(currentQuery.getQueryID()) + ">");
-                else 
-                        return predicateIRI + getTrackingSuffix(currentQuery.getQueryID());
-        }
-
-        protected DLPredicate getDatatypeRestriction(DatatypeRestriction restriction, String newName) {
-                int length = restriction.getNumberOfFacetRestrictions(); 
-                String[] facets = new String[length]; 
-                Constant[] values = new Constant[length]; 
-                for (int i = 0; i < length; ++i) {
-                        facets[i] = restriction.getFacetURI(i);
-                        values[i] = restriction.getFacetValue(i); 
-                }
-                return DatatypeRestriction.create(newName, facets, values); 
-        }
-
-        protected QueryRecord currentQuery;
-        DLPredicate selected; 
-        
-        public void setCurrentQuery(QueryRecord record) {
-                deprecateTrackingAndQueryRules();
-                currentQuery = record;
-                selected = AtomicConcept.create(getSelectedPredicate());
-                trackingSuffix = "_AUXt" + currentQuery.getQueryID(); 
-        }
-        
-        public void dispose() {
-                deprecateTrackingAndQueryRules();
-        }
-        
-        private String getTrackingRuleText() {
-                return DLClauseHelper.toString(trackingClauses);
-        }
-        
-        private String getQueryRuleText() {
-                return DLClauseHelper.toString(queryClauses);
-        }
-        
-        public String getTrackingProgram() {
-                StringBuilder sb = getTrackingProgramBody();
-                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText()); 
-                return sb.toString(); 
-        }
-        
-        protected StringBuilder getTrackingProgramBody() {
-                encodingRules();
-                encodingQuery(new QueryRecord[0]);
-
-                StringBuilder sb = new StringBuilder(); 
-                sb.append(getTrackingRuleText());
-                sb.append(getEqualityRelatedRuleText());
-                sb.append(getQueryRuleText());
-                return sb; 
-        }
-
-        public void saveTrackingRules(String fileName) {
-                BufferedWriter writer = null;
-                try {
-                        writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileName)));
-                        writer.write(getTrackingProgram());
-                        writer.close();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                        return ;
-                }
-                Utility.logDebug("The tracking rules are saved in " + fileName + "."); 
-        }
-
-        private void deprecateTrackingAndQueryRules() {
-                trackingClauses.clear(); 
-                queryClauses.clear();
-                addedData.clear();
-                ruleEncoded = false; 
-                queryEncoded = false; 
-        }
-
-        public String getSelectedPredicate() {
-                return getIRI("_selected" + currentQuery.getQueryID()); 
-        }
-
-        public DLClause getSelectedClause(String iri) {
-                int index = iri.lastIndexOf("_r") + 2;
-                int ruleIndex = Integer.parseInt(iri.substring(index));
-                return index2clause.get(ruleIndex);
-        }
-        
-        /**
-         * SELECT ?X
-         * WHERE {
-         *      ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#:type> :_selected?
-         * }
-         */
-        public String getSelectedSPARQLQuery() {
-                StringBuilder builder = new StringBuilder(); 
-                builder.append("SELECT ?X\nWHERE {\n?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "); 
-                builder.append(selected.toString()).append("\n}");  
-                return builder.toString(); 
-        }
-
-        public OWLOntology getOntology() {
-                return program.getOntology(); 
-        }
-
-        public UpperDatalogProgram getProgram() {
-                return program;
-        }
-        
-        private String trackingSuffix; 
-        
-        public String getOriginalPredicate(String p) {
-                if (p.startsWith("<")) {
-                        if (!p.endsWith(trackingSuffix + ">")) return null;
-                }
-                else 
-                        if (!p.endsWith(trackingSuffix)) return null;
-                
-                return p.replace(trackingSuffix, ""); 
-        }
-
-        public boolean isAuxPredicate(String p) {
-                return false; 
-        }
-        
-        protected Set<String> unaryPredicates = new HashSet<String>(); 
-        protected Set<String> binaryPredicates = new HashSet<String>();
-        
+                    raw = ((t =
+                            answer.getGroundTerm(0)) instanceof uk.ac.ox.cs.JRDFox.model.Individual) ? ((uk.ac.ox.cs.JRDFox.model.Individual) t)
+                            .getIRI() : t.toString();
+                    triple = new int[]{tripleManager.getResourceID(raw), rdftype, predicate};
+                    addedData.add(triple);
+                    tripleManager.addTripleByID(triple);
+                }
+//                answerTuples.dispose();
+            }
+        }
+
+        Utility.logInfo(addedData.size() + " triples are added into the store.");
+    }
+
+    protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) {
+        return getDLPredicate(dlPredicate, GapTupleIterator.gapPredicateSuffix);
+    }
+
+    DLPredicate getDLPredicate(DLPredicate p, String suffix) {
+        if(isDisposed()) throw new DisposedException();
+        if(p instanceof AtomicConcept)
+            return AtomicConcept.create(((AtomicConcept) p).getIRI() + suffix);
+        else if(p instanceof DatatypeRestriction) {
+            DatatypeRestriction restriction = (DatatypeRestriction) p;
+            String newURI = restriction.getDatatypeURI() + suffix;
+            return getDatatypeRestriction(restriction, newURI);
+        }
+        else if(p instanceof AtomicRole)
+            return AtomicRole.create(((AtomicRole) p).getIRI() + suffix);
+        else if(p instanceof AnnotatedEquality || p instanceof Equality)
+            return AtomicRole.create(Namespace.EQUALITY + suffix);
+        else if(p instanceof Inequality)
+            return AtomicRole.create(Namespace.INEQUALITY + suffix);
+        else if(p instanceof DatatypeRestriction)
+            return AtomicConcept.create(((DatatypeRestriction) p).getDatatypeURI() + suffix);
+        else {
+            Utility.logDebug("strange DL predicate appeared ... " + p,
+                             "the program paused here in TrackingRuleEncoderDisj.java");
+            return null;
+        }
+    }
+
+    protected DLPredicate getTrackingDLPredicate(DLPredicate dlPredicate) {
+        return getDLPredicate(dlPredicate, getTrackingSuffix(currentQuery.getQueryID()));
+    }
+
+    protected DLPredicate getDatatypeRestriction(DatatypeRestriction restriction, String newName) {
+        int length = restriction.getNumberOfFacetRestrictions();
+        String[] facets = new String[length];
+        Constant[] values = new Constant[length];
+        for(int i = 0; i < length; ++i) {
+            facets[i] = restriction.getFacetURI(i);
+            values[i] = restriction.getFacetValue(i);
+        }
+        return DatatypeRestriction.create(newName, facets, values);
+    }
+
+    private String getTrackingRuleText() {
+        return DLClauseHelper.toString(trackingClauses);
+    }
+
+    private String getQueryRuleText() {
+        return DLClauseHelper.toString(queryClauses);
+    }
+
+    protected StringBuilder getTrackingProgramBody() {
+        encodingRules();
+        encodingQuery(new QueryRecord[0]);
+
+        StringBuilder sb = new StringBuilder();
+        sb.append(getTrackingRuleText());
+        sb.append(getEqualityRelatedRuleText());
+        sb.append(getQueryRuleText());
+        return sb;
+    }
+
+    private void deprecateTrackingAndQueryRules() {
+        trackingClauses.clear();
+        queryClauses.clear();
+        addedData.clear();
+        ruleEncoded = false;
+        queryEncoded = false;
+    }
+
 }