[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 0 insertions, 173 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java b/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
deleted file mode 100644
index 43c5849..0000000
--- a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package uk.ac.ox.cs.pagoda.hermit;
-
-import org.semanticweb.HermiT.model.*;
-import uk.ac.ox.cs.pagoda.MyPrefixes;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.util.Namespace;
-
-import java.security.InvalidParameterException;
-import java.util.ArrayList;
-
-public class RuleHelper {
-    private static final String OR = "|";
-    private static final String IF = ":-";
-    private static final String AND = ",";
-
-//      public static String abbreviateIRI(String text) {
-//              String prefixName, prefixIRI; 
-//              int start = -1, ends = -1;
-//              while (true) {
-//                      start = text.indexOf('<', ends + 1);
-//                      if (start == -1) return text;
-//                      ends = text.indexOf('>', start + 1);
-//                      if (ends == -1) return text;
-//                      String sub = text.substring(start, ends + 1), newSub = text.substring(start + 1, ends);
-//                      
-//                      int index = splitPoint(newSub); 
-//                      if (index >= 0) {
-//                              prefixIRI = newSub.substring(0, index + 1);
-//                              if ((prefixName = MyPrefixes.PAGOdAPrefixes.getPrefixName(prefixIRI)) == null) {
-//                                      prefixName = getNewPrefixName();
-//                                      MyPrefixes.PAGOdAPrefixes.declarePrefix(prefixName, prefixIRI);
-//                              }
-//                              newSub = newSub.replace(prefixIRI, prefixName); 
-//                              text = text.replaceAll(sub, newSub);
-//                              ends -= sub.length() - newSub.length();
-//                      }
-//              }
-//      }
-        
-        public static String getText(DLClause clause) {
-                StringBuffer buf = new StringBuffer();
-                String atomText; 
-                
-                boolean lastSpace = true;
-                for (Atom headAtom: clause.getHeadAtoms()) {
-                        if ((atomText = getText(headAtom)) == null) continue; 
-                        if (!lastSpace) buf.append(" ").append(OR).append(" ");
-                        buf.append(atomText);
-                        lastSpace = false;
-                }
-        buf.append(" ").append(IF).append(" ");
-                lastSpace = true;
-                for (Atom bodyAtom: clause.getBodyAtoms()) {
-//              for (String str: strs[1].split(", ")) {
-                        if ((atomText = getText(bodyAtom)) == null) continue; 
-                        if (!lastSpace) buf.append(AND).append(" ");
-                        buf.append(atomText);
-                        lastSpace = false;
-                }
-                buf.append('.');
-                return buf.toString();
-        }
-
-        
-        private static String getText(Atom atom) {
-                if (atom.getDLPredicate() instanceof NodeIDsAscendingOrEqual ||
-                                atom.getDLPredicate() instanceof NodeIDLessEqualThan) 
-                        return null;
-                
-                StringBuilder builder = new StringBuilder(); 
-                if (atom.getArity() == 1) {
-                        builder.append(getText(atom.getDLPredicate())); 
-                        builder.append("("); 
-                        builder.append(getText(atom.getArgument(0)));
-                        builder.append(")"); 
-                }
-                else {
-                        DLPredicate p = atom.getDLPredicate();
-                        if (p instanceof Equality || p instanceof AnnotatedEquality) builder.append(Namespace.EQUALITY_ABBR); 
-                        else if (p instanceof Inequality) builder.append(Namespace.INEQUALITY_ABBR); 
-                        else builder.append(getText(p));
-                        builder.append("("); 
-                        builder.append(getText(atom.getArgument(0))); 
-                        builder.append(",");
-                        builder.append(getText(atom.getArgument(1))); 
-                        builder.append(")"); 
-                }
-                return builder.toString(); 
-        }
-
-        public static String getText(DLPredicate p) {
-                if (p instanceof Equality || p instanceof AnnotatedEquality) return Namespace.EQUALITY_ABBR; 
-                if (p instanceof Inequality) return Namespace.INEQUALITY_ABBR;
-                if (p instanceof AtomicRole && ((AtomicRole) p).getIRI().startsWith("?"))
-                        return ((AtomicRole) p).getIRI(); 
-                return MyPrefixes.PAGOdAPrefixes.abbreviateIRI(p.toString());
-        }
-
-        public static String getText(Term t) {
-                if (t instanceof Variable)
-                        return "?" + ((Variable) t).getName(); 
-                return MyPrefixes.PAGOdAPrefixes.abbreviateIRI(t.toString());
-        }
-
-        public static Term parseTerm(String s) {
-                s = s.trim();
-                if(s.startsWith("?")) return Variable.create(s.substring(1));
-                return Individual.create(MyPrefixes.PAGOdAPrefixes.expandIRI(s));
-        }
-
-    public static Atom parseAtom(String s) {
-        s = s.trim();
-
-        String[] split = s.split("\\(");
-        String predicateIri = OWLHelper.removeAngles(MyPrefixes.PAGOdAPrefixes.expandText(split[0]));
-        String[] predicateArgs = split[1].substring(0, split[1].length() - 1).split(",");
-        int numOfargs = predicateArgs.length;
-        Term terms[] = new Term[predicateArgs.length];
-        for (int i = 0; i < terms.length; i++)
-            terms[i] = parseTerm(predicateArgs[i]);
-        if(numOfargs == 1) {
-            AtomicConcept atomicConcept = AtomicConcept.create(predicateIri);
-            return Atom.create(atomicConcept, terms);
-        }
-        else if(numOfargs == 2) {
-            AtomicRole atomicRole = AtomicRole.create(predicateIri);
-            return Atom.create(atomicRole, terms);
-        }
-        else
-            throw new InvalidParameterException();
-        // TODO? add equality (owl:sameAs)?
-    }
-
-    public static DLClause parseClause(String s) {
-        s = s.trim();
-        if(s.endsWith(".")) s = s.substring(0, s.length()-1).trim();
-
-        String[] headAndBody = s.split(IF);
-        String[] headAtomsStr = splitAtoms(headAndBody[0], OR);
-        String[] bodyAtomsStr = splitAtoms(headAndBody[1], AND);
-
-        Atom[] headAtoms = new Atom[headAtomsStr.length];
-        Atom[] bodyAtoms = new Atom[bodyAtomsStr.length];
-        for (int i = 0; i < headAtoms.length; i++)
-            headAtoms[i] = parseAtom(headAtomsStr[i]);
-        for (int i = 0; i < bodyAtoms.length; i++)
-            bodyAtoms[i] = parseAtom(bodyAtomsStr[i]);
-
-        return DLClause.create(headAtoms, bodyAtoms);
-    }
-
-    private static String[] splitAtoms(String s, String operator) {
-        char op = operator.charAt(0);
-        ArrayList<String> result = new ArrayList<>();
-
-        int b = 0;
-        boolean betweenParenthesis = false;
-        for (int i = 0; i < s.length(); i++) {
-            if(s.charAt(i) == '(')
-                betweenParenthesis = true;
-            else if(s.charAt(i) == ')')
-                betweenParenthesis = false;
-            else if(s.charAt(i) == op && !betweenParenthesis) {
-                result.add(s.substring(b, i));
-                b = i + 1;
-            }
-        }
-        if(b < s.length()) result.add(s.substring(b));
-
-        return result.toArray(new String[0]);
-    }
-
-}