--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/OWLQueryGalaxy.java	Sat Oct 06 21:50:39 2012 +0200
@@ -0,0 +1,129 @@
+package es.upm.fi.dia.oeg.oppl.galaxy;
+
+import java.util.Set;
+
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+public class OWLQueryGalaxy {
+
+	/**
+	 * @param args
+	 * @throws OWLOntologyCreationException 
+	 * @throws ParserException 
+	 */
+	public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
+		// Get the arguments from command-line
+		String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
+		String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
+		
+		String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
+		String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
+		String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
+		
+		// Create the manager
+		GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
+				
+		// Load the main ontology and hope for the imported URIs to be resolvable		
+		galaxyowlapi.loadMainOntology(OWLFilePath);
+				
+		// Set the reasoner
+		
+		// Pellet
+		if(reasoner_type.equals("Pellet")){
+			galaxyowlapi.setReasonerPellet();
+		}
+		// FaCTPlusPlus
+		else if (reasoner_type.equals("FaCTPlusPlus")){
+			galaxyowlapi.setReasonerFaCT();
+		}
+		// Elk
+		else if (reasoner_type.equals("Elk")){
+			galaxyowlapi.setReasonerElk();
+		}
+		// HermiT
+		else{
+			galaxyowlapi.setReasonerHermit();
+		}
+
+		// Parse the expression to an OWLexpression
+		OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
+		
+		// Execute query and print results
+		if(Answer_type.equals("Individuals")){
+			Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLNamedIndividual ind : inds){
+				print_result_entity(ind.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("EquivalentClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("DirectSuperClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("Ancestors")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		else if (Answer_type.equals("DirectSubClasses")) {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}
+		// Descendants
+		else {
+			Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
+			galaxyowlapi.disposeReasoner();
+			for(OWLClass cls : answer_classes){
+				print_result_entity(cls.getIRI(), Answer_render);
+			}
+		}	
+	}
+	
+	//URI|URIfragment|URIfragment2OBO
+	private static void print_result_entity (IRI iri, String Answer_render){
+		if(Answer_render.equals("URI")){
+			System.out.println(iri);
+		}
+		
+		// Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
+		// done manually
+		else if(Answer_render.equals("URIfragment")){	
+			if(iri.toString().contains("#")){
+				System.out.println(iri.getFragment());
+			}
+			else{
+				String [] iri_tokens = iri.toString().split("/");
+				System.out.println(iri_tokens[iri_tokens.length-1]);
+			}
+		}
+		else{
+			if(iri.toString().contains("#")){
+				System.out.println((iri.getFragment()).replace("_", ":"));
+			}
+			else{
+				String [] iri_tokens = iri.toString().split("/");
+				System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
+			}
+		}
+	}
+}