[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, 162 insertions, 0 deletions

diff --git a/src/main/java/uk/ac/ox/cs/pagoda/MyPrefixes.java b/src/main/java/uk/ac/ox/cs/pagoda/MyPrefixes.java
new file mode 100644
index 0000000..98a4e97
--- /dev/null
+++ b/src/main/java/uk/ac/ox/cs/pagoda/MyPrefixes.java
@@ -0,0 +1,162 @@
+package uk.ac.ox.cs.pagoda;
+
+import java.util.Map;
+
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class MyPrefixes {
+
+        public final static MyPrefixes PAGOdAPrefixes = new MyPrefixes();
+        
+        private org.semanticweb.HermiT.Prefixes hermit = new org.semanticweb.HermiT.Prefixes(); 
+        private uk.ac.ox.cs.JRDFox.Prefixes rdfox = new uk.ac.ox.cs.JRDFox.Prefixes();
+        
+        public MyPrefixes() {
+                hermit.declareSemanticWebPrefixes(); 
+                hermit.declarePrefix("anony:", Namespace.PAGODA_ANONY);
+                hermit.declarePrefix("aux:", Namespace.PAGODA_AUX);
+                
+                rdfox.declareSemanticWebPrefixes(); 
+                rdfox.declarePrefix("anony:", Namespace.PAGODA_ANONY);
+                rdfox.declarePrefix("aux:", Namespace.PAGODA_AUX);
+        }
+        
+        public org.semanticweb.HermiT.Prefixes getHermiTPrefixes() {
+                return hermit; 
+        }
+        
+        public uk.ac.ox.cs.JRDFox.Prefixes getRDFoxPrefixes() {
+                return rdfox; 
+        }
+        
+        public void declarePrefix(String prefixName, String prefixIRI) {
+                Utility.logDebug("Prefix declared: " + prefixName + "=" + prefixIRI);
+                hermit.declarePrefix(prefixName, prefixIRI); 
+                rdfox.declarePrefix(prefixName, prefixIRI); 
+        }
+        
+        public static boolean isColon4Prefixes(String text, int index) {
+                if (index >= text.length() - 1) return false; 
+                if (index > 0 && text.charAt(index - 1) == '_') return false; // _: blank node
+                char nextCharacter = text.charAt(index + 1);
+                if (nextCharacter == '-') return false; // :-
+                if (nextCharacter == '/') return false; // :/
+                return true;
+        }
+
+        public String expandText(String text) {
+                for (int index = 0; ;) {
+                        index = text.indexOf(':', index);
+                        if (!isColon4Prefixes(text, index)) {
+                                ++index; 
+                                continue;
+                        }
+                        if (index == -1) return text;
+                        int start = index - 1, ends = index + 1;
+                        char ch;
+                        while (start >= 0 && (ch = text.charAt(start)) != ',' && ch != '(' && ch != ' ') --start;
+                        while (ends < text.length() && (ch = text.charAt(ends)) != '(' && ch != ',' && ch != ')') ++ends;
+
+                        String sub = text.substring(start + 1, ends);
+                        String newSub = OWLHelper.addAngles(hermit.expandAbbreviatedIRI(sub)); 
+                        
+                        text = text.replaceAll(sub, newSub);
+                        index = ends + newSub.length() - sub.length();
+                }
+        }
+        
+        public void declareNewPrefix(String iri) {
+                if (!iri.startsWith("<")) return ;
+                int index = splitPoint(iri);
+                if (index >= 0) {
+                        String prefixIRI = iri.substring(1, index + 1), prefixName;
+                        if ((prefixName = getPrefixName(prefixIRI)) == null) {
+                                prefixName = getNewPrefixName();
+                                declarePrefix(prefixName, prefixIRI);
+                        }
+                }
+        }
+        
+        /**
+         * detect the split point of prefix and name for an <url>
+         * 
+         * @param uri
+         * @param index
+         * @return
+         */
+        private int splitPoint(String uri) {
+                int index = uri.lastIndexOf("#"); 
+                if (index != -1) return index; 
+                index = uri.lastIndexOf("/"); 
+                if (index > 0 && uri.charAt(index - 1) != '/')
+                        return index;
+                return -1; 
+        }
+
+
+        private int prefixNumber = 0; 
+        
+        public String getNewPrefixName() {
+                return "prefix" + (prefixNumber ++) + ":"; 
+        }
+
+        public String abbreviateIRI(String iri) {
+                declareNewPrefix(iri);
+                
+                if (iri.startsWith("<"))
+                        return hermit.abbreviateIRI(OWLHelper.removeAngles(iri));
+                else if (iri.contains("^^")) {
+                        int index = iri.indexOf("^^"); 
+                        if (iri.charAt(index + 2) == '<')
+                                return iri.substring(0, index + 2) + abbreviateIRI(iri.substring(index + 2, iri.lastIndexOf('>') + 1)); 
+                }
+                return iri; 
+        }
+        
+        /**
+         * expanded iri without <>
+         * 
+         * @param iri
+         * @return
+         */
+        public String expandIRI(String iri) {           
+                if (hermit.canBeExpanded(iri))
+                        return hermit.expandAbbreviatedIRI(iri); 
+                else if (iri.startsWith("<"))
+                        return iri.substring(1, iri.length() - 1);
+                else 
+                        return iri; 
+        }
+
+        /**
+         * expanded iri with <>
+         * 
+         * @param iri
+         * @return
+         */
+        public String getQuotedIRI(String iri) {
+                if (iri.startsWith("<")) return iri; 
+                if (hermit.canBeExpanded(iri))
+                        return OWLHelper.addAngles(hermit.expandAbbreviatedIRI(iri));
+                return iri; 
+        }
+        
+        public String getPrefixName(String prefixIRI) {
+                return hermit.getPrefixName(prefixIRI);
+        }
+
+        public Map<String, String> getPrefixIRIsByPrefixName() {
+                return hermit.getPrefixIRIsByPrefixName();
+        }
+
+        public String prefixesText() {
+                StringBuffer buf = new StringBuffer();
+                for (Map.Entry<String, String> entry: getPrefixIRIsByPrefixName().entrySet())
+                        buf.append("PREFIX ").append(entry.getKey()).append(" <").append(entry.getValue()).append(">").append(Utility.LINE_SEPARATOR);
+                return buf.toString();
+        }
+
+
+}