7 files changed, 30 insertions, 133 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
deleted file mode 100644
index 9191067..0000000
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
+++ /dev/null
@@ -1,78 +0,0 @@
-package uk.ac.ox.cs.pagoda.reasoner;
-
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
-import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
-import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
-import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-@Deprecated
-public class ConsistencyManager2 extends ConsistencyManager {
-
-        public ConsistencyManager2(MyQueryReasoner reasoner) {
-                super(reasoner);
-                fragmentExtracted = true; 
-        }
-        
-        protected boolean unsatisfiability(double duration) {
-                Utility.logDebug("The ontology and dataset is unsatisfiable."); 
-                return false;
-        }
-
-        protected boolean satisfiability(double duration) {
-                Utility.logDebug("The ontology and dataset is satisfiable."); 
-                return true;
-        }
-        
-        @Override
-        boolean check() {
-//              if (!checkRLLowerBound()) return false; 
-//              if (!checkELLowerBound()) return false;
-                // TODO test
-                if (checkUpper(m_reasoner.lazyUpperStore) && checkUpper(m_reasoner.limitedSkolemUpperStore)) return true;
-                AnswerTuples iter = null; 
-                
-                try {
-                        iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
-                        fullQueryRecord.updateUpperBoundAnswers(iter);
-                } finally {
-                        if (iter != null) iter.dispose();
-                }
-                
-                if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
-                        return satisfiability(t.duration());
-                
-                try {
-                        extractAxioms();
-                } catch (OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                }
-                
-                Checker checker = new HermitSummaryFilter(fullQueryRecord, true);  // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
-//              fullQueryRecord.saveRelevantOntology("fragment_bottom.owl");
-                boolean satisfiable = checker.isConsistent(); 
-                checker.dispose();
-                if (!satisfiable) return unsatisfiability(t.duration()); 
-                
-                return satisfiability(t.duration()); 
-        }
-
-        private void extractAxioms() throws OWLOntologyCreationException {
-                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
-                fullQueryRecord.setRelevantOntology(manager.createOntology());
-                QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, fullQueryRecord); 
-                m_reasoner.encoder.setCurrentQuery(fullQueryRecord);
-                tracker.extract(m_reasoner.trackingStore, null, true); 
-        }
-
-        @Override
-        public QueryRecord[] getQueryRecords() {
-                if (botQueryRecords == null)
-                        botQueryRecords = new QueryRecord[] {fullQueryRecord}; 
-                return botQueryRecords; 
-        }
-
-}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index ab57ccf..2285b5f 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -2,7 +2,6 @@ package uk.ac.ox.cs.pagoda.reasoner;
 
 import org.semanticweb.karma2.profile.ELHOProfile;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
@@ -12,7 +11,7 @@ import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
-public class ELHOQueryReasoner extends QueryReasoner {
+class ELHOQueryReasoner extends QueryReasoner {
 
         LowerDatalogProgram program; 
         
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 6da86ac..a4fa7c3 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -14,7 +14,7 @@ import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
-public class ELHOUQueryReasoner extends QueryReasoner {
+class ELHOUQueryReasoner extends QueryReasoner {
 
         DatalogProgram program; 
         
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index 5511691..d1856c9 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -1,32 +1,22 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.Set;
-
 import org.semanticweb.HermiT.Reasoner;
-import org.semanticweb.owlapi.model.OWLClassExpression;
-import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyStorageException;
-
+import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.JRDFox.model.Individual;
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.owl.QueryRoller;
-import uk.ac.ox.cs.pagoda.query.AnswerTuple;
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
-import uk.ac.ox.cs.pagoda.query.AnswerTuplesImp;
-import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.query.*;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
-public class HermiTReasoner extends QueryReasoner {
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+class HermiTReasoner extends QueryReasoner {
         
         Reasoner hermit;
         
@@ -54,15 +44,8 @@ public class HermiTReasoner extends QueryReasoner {
                 OWLOntology tbox = onto;
                 try {
                         onto = OWLHelper.getImportedOntology(tbox, importedData.toString().split(ImportDataFileSeparator));
-                        importedOntologyPath = OWLHelper.getOntologyPath(onto); 
-                } catch (OWLOntologyCreationException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } catch (OWLOntologyStorageException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } catch (IOException e) {
-                        // TODO Auto-generated catch block
+                        importedOntologyPath = OWLHelper.getOntologyPath(onto);
+                } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
                         e.printStackTrace();
                 }
                 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index b10e2d1..6adbd37 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -25,7 +25,7 @@ import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 import java.util.Collection;
 import java.util.HashMap;
 
-public class MyQueryReasoner extends QueryReasoner {
+class MyQueryReasoner extends QueryReasoner {
 
         OWLOntology ontology;
         DatalogProgram program;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
index 3894874..60f34c6 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
@@ -10,18 +10,17 @@ import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 
-public class RLQueryReasoner extends QueryReasoner {
+class RLQueryReasoner extends QueryReasoner {
         
         RDFoxQueryEngine rlLowerStore = null;
 
-        LowerDatalogProgram program; 
+        LowerDatalogProgram program;
+        Timer t = new Timer();
         
         public RLQueryReasoner() {
-                rlLowerStore = new BasicQueryEngine("rl"); 
+                rlLowerStore = new BasicQueryEngine("rl");
         }
         
-        Timer t = new Timer(); 
-        
         @Override
         public void evaluate(QueryRecord queryRecord) {
                 AnswerTuples rlAnswer = null; 
@@ -56,10 +55,8 @@ public class RLQueryReasoner extends QueryReasoner {
         public boolean preprocess() {
                 rlLowerStore.importRDFData("data", importedData.toString());
                 rlLowerStore.materialise("lower program", program.toString());
-                
-                if (!isConsistent())  
-                        return false; 
-                return true; 
+
+                return isConsistent();
         }
 
         @Override
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
index fe4022d..e5564d9 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
@@ -1,7 +1,6 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
 import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
@@ -12,26 +11,25 @@ import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
-public class RLUQueryReasoner extends QueryReasoner {
+class RLUQueryReasoner extends QueryReasoner {
 
         DatalogProgram program; 
         
         BasicQueryEngine rlLowerStore, rlUpperStore;
         
-        boolean multiStageTag, equalityTag; 
+        boolean multiStageTag, equalityTag;
+        Timer t = new Timer();
         
         public RLUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
                 this.multiStageTag = multiStageTag;
-                this.equalityTag = considerEqualities; 
-                rlLowerStore = new BasicQueryEngine("rl-lower-bound"); 
-                if (!multiStageTag) 
-                        rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
-                else  
-                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
+                this.equalityTag = considerEqualities;
+                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+                if(!multiStageTag)
+                        rlUpperStore = new BasicQueryEngine("rl-upper-bound");
+                else
+                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
         }
         
-        Timer t = new Timer();
-        
         @Override
         public void evaluate(QueryRecord queryRecord) {
                 AnswerTuples ans = null;
@@ -100,11 +98,9 @@ public class RLUQueryReasoner extends QueryReasoner {
                 
                 rlUpperStore.importRDFData("data", datafile);
                 rlUpperStore.materialiseRestrictedly(program, null);
-                
-                if (!isConsistent()) 
-                        return false; 
 
-                return true; 
+                return isConsistent();
+
         }
 
         @Override