[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, 38 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/approx/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
deleted file mode 100644
index cff1d1c..0000000
--- a/test/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package uk.ac.ox.cs.pagoda.approx;
-
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.owlapi.model.OWLOntology;
-
-import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
-
-public class ClauseTester {
-
-        public static void main(String... args) {
-                args = new String[] {
-//                              "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-noDPR.ttl", 
-                                "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/biopax-level3-processed.owl", 
-//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/atlas/gxaterms.owl", 
-//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/core-sat-processed.owl",
-//                              PagodaTester.npd_tbox,
-//                              "/users/yzhou/temp/ontologies/core.RLor.rdf",
-//                              "datatype.owl" 
-                }; 
-                
-                String ontoFile = args[0];   
-                OWLOntology ontology = OWLHelper.loadOntology(ontoFile);  
-                GeneralProgram program = new GeneralProgram();; 
-                program.load(ontology, new NullaryBottom());
-                program.transform();
-                program.save();
-                if (program instanceof GeneralProgram) {
-                        GeneralProgram gp = ((GeneralProgram) program); 
-                        for (DLClause clause: gp.getClauses()) {
-                                System.out.println(clause);
-                                System.out.println(OWLHelper.getOWLAxiom(ontology, clause)); 
-                        }
-                }
-        }
-        
-}