--- a/OPPL/Tool.java	Wed Sep 07 10:46:29 2011 +0200
+++ b/OPPL/Tool.java	Wed Sep 14 19:52:06 2011 +0200
@@ -25,6 +25,7 @@
 import java.io.OutputStream;
 import java.io.PipedOutputStream;
 import java.io.PrintStream;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
 import java.util.logging.Level;
@@ -44,13 +45,18 @@
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLAxiomChange;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.InferenceType;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.InferredAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredOntologyGenerator;
+import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
 
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 
@@ -74,6 +80,7 @@
 		String OWLFilePath = args [0]; 
 		String OPPL_script_file = args [1];
 		String Output_format = args [2];
+		String Add_inferred = args [3];
 		String OPPL_script_source = "";
 		
 		// Load the flat file with script in memory
@@ -107,15 +114,22 @@
 		List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
 		manager.applyChanges(changes);
 		
+		// Add the inferred axioms as asserted axioms to the original ontology
+		if(Add_inferred.equals("Add_inferred")){
+			reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
+			List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+			gens.add(new InferredSubClassAxiomGenerator());
+			InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+			iog.fillOntology(manager, OWL_ontology);
+		}
+
 		// Print the ontology to the standard output so other galaxy tools can operate on the output
-		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
-		
+		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();	
 		if(Output_format.equals("OBO")){
 			manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
 		}
 		else{
 			manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
 		}
-
 	}
 }