4 files changed, 26 insertions, 56 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/rules/Approximator.java b/src/uk/ac/ox/cs/pagoda/rules/Approximator.java
index b2edd56..66e676b 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Approximator.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/Approximator.java
@@ -1,16 +1,16 @@
 package uk.ac.ox.cs.pagoda.rules;
 
-import java.util.Collection;
-import java.util.LinkedList;
-
 import org.semanticweb.HermiT.model.AtLeast;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.HermiT.model.DLPredicate;
 
+import java.util.Collection;
+import java.util.LinkedList;
+
 public interface Approximator {
 
-        public Collection<DLClause> convert(DLClause clause, DLClause originalClause); 
+        Collection<DLClause> convert(DLClause clause, DLClause originalClause);
         
 }
 
diff --git a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index 6e17f02..a664ba1 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -1,23 +1,9 @@
 package uk.ac.ox.cs.pagoda.rules;
 
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.Set;
-
 import org.semanticweb.HermiT.Reasoner;
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.Variable;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLObjectInverseOf;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
-import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.HermiT.model.*;
+import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.reasoner.Node;
-
 import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
 import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
 import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
@@ -27,6 +13,11 @@ import uk.ac.ox.cs.pagoda.multistage.RestrictedApplication;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Set;
+
 public class LowerDatalogProgram extends ApproxProgram implements IncrementalProgram {
         
         boolean m_toClassify; 
@@ -68,7 +59,7 @@ public class LowerDatalogProgram extends ApproxProgram implements IncrementalPro
                 norm.process();
                 for (DLClause nClause: norm.getNormlisedClauses()) {
                         if (nClause.getHeadLength() != 1)
-                                for (DLClause newClause: RestrictedApplication.addAddtionalDatalogRules(nClause, tBottom, norm)) {
+                                for (DLClause newClause: RestrictedApplication.addAdditionalDatalogRules(nClause, tBottom, norm)) {
 //                                      System.out.println(newClause); 
                                         if (newClause.getHeadAtom(0).getDLPredicate() instanceof AtomicConcept || newClause.getHeadAtom(0).getDLPredicate() instanceof AtomicRole) {
 //                                              System.out.println(newClause); 
diff --git a/src/uk/ac/ox/cs/pagoda/rules/OverApproxDisj.java b/src/uk/ac/ox/cs/pagoda/rules/OverApproxDisj.java
index 5edb08e..5b298e8 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/OverApproxDisj.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/OverApproxDisj.java
@@ -1,22 +1,19 @@
 package uk.ac.ox.cs.pagoda.rules;
 
-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.Atom;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.Term;
-import org.semanticweb.HermiT.model.Variable;
-
+import org.semanticweb.HermiT.model.*;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 
+import java.util.*;
+
 public class OverApproxDisj implements Approximator {
 
+        /**
+         * Splits a disjunctive rule into a bunch of rules.
+         * <p>
+         * It returns a collection containing a rule for each atom in the head of the input rule.
+         * Each rule has the same body of the input rule,
+         * and the relative head atom as head.
+         * */
         @Override
         public Collection<DLClause> convert(DLClause clause, DLClause originalClause) {
                 LinkedList<DLClause> distincts = new LinkedList<DLClause>();
diff --git a/src/uk/ac/ox/cs/pagoda/rules/OverApproxExist.java b/src/uk/ac/ox/cs/pagoda/rules/OverApproxExist.java
index 7e66411..2ff1673 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/OverApproxExist.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/OverApproxExist.java
@@ -1,30 +1,11 @@
 package uk.ac.ox.cs.pagoda.rules;
 
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.Map;
-
-import org.semanticweb.HermiT.model.AtLeast;
-import org.semanticweb.HermiT.model.AtLeastConcept;
-import org.semanticweb.HermiT.model.AtLeastDataRange;
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicNegationConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.Individual;
-import org.semanticweb.HermiT.model.Inequality;
-import org.semanticweb.HermiT.model.InverseRole;
-import org.semanticweb.HermiT.model.LiteralConcept;
-import org.semanticweb.HermiT.model.Role;
-import org.semanticweb.HermiT.model.Term;
-import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.HermiT.model.*;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 
+import java.util.*;
+
 public class OverApproxExist implements Approximator {
 
         @Override
@@ -142,6 +123,7 @@ public class OverApproxExist implements Approximator {
                         AtomicConcept atomicConcept = null;
                         
                         if (concept instanceof AtomicNegationConcept) {
+                                // is this already in MultiStageUpperProgram?
                                 Atom atom1 = Atom.create(atomicConcept = ((AtomicNegationConcept) concept).getNegatedAtomicConcept(), X);
                                 Atom atom2 = Atom.create(atomicConcept = getNegationConcept(atomicConcept), X);
                                 ret.add(DLClause.create(new Atom[0], new Atom[] {atom1, atom2}));