- Added the oportunity to encapsulate and already loaded ontology

- fixed copyright notices

src/fr/inrialpes/exmo/align/onto/Ontology.java

 /*
  * $Id$
  *
- * Copyright (C) INRIA Rhne-Alpes, 2008
+ * Copyright (C) INRIA, 2008
  *
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as published by

src/fr/inrialpes/exmo/align/onto/OntologyFactory.java

@@ -46,8 +46,6 @@ public abstract class OntologyFactory {
 	return newInstance(API_NAME);
     }
 
-    // JE: The true question here is that instance being static,
-    // I assume that it is shared by all subclasses! 
     private static OntologyFactory newInstance( String apiName ) {
 	if ( instances == null ) instances = new Hashtable<String,OntologyFactory>();
 	OntologyFactory of = instances.get( apiName );
@@ -82,16 +80,27 @@ public abstract class OntologyFactory {
 	}
     }
 
+    /**
+     * All Ontologies must implement clearCache()
+     * which unload their ontologies if any cache is enabled.
+     */
     public abstract void clearCache();
 
+    /**
+     * Encapsulate an ontology already in the environment
+     * These methods should rather be in a LoadableOntologyFactory
+     */
+    public abstract LoadedOntology newOntology( Object onto ) throws AlignmentException;
+
     /**
      * Load an ontology, cache enabled
+     * These methods should rather be in a LoadableOntologyFactory
      */
     public abstract LoadedOntology loadOntology( URI uri ) throws AlignmentException;
+
     /**
      * Load an ontology, cache enabled if true, disabled otherwise
      * This will disappear: cache will be dispatched in implementations
-     */
     public LoadedOntology loadOntology( URI uri, OntologyCache<LoadedOntology> ontologies ) throws AlignmentException {
 	LoadedOntology onto = null;
 	if ( ontologies != null ) {
@@ -104,4 +113,5 @@ public abstract class OntologyFactory {
 	if ( ontologies != null ) ontologies.recordOntology( uri, onto );
 	return onto;
     };
+     */
 }

src/fr/inrialpes/exmo/align/onto/jena25/JENAOntology.java

+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2003-2008
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
+ */
+
 package fr.inrialpes.exmo.align.onto.jena25;
 
 import java.net.URI;

src/fr/inrialpes/exmo/align/onto/jena25/JENAOntologyFactory.java

+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2003-2008
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
+ */
+
 package fr.inrialpes.exmo.align.onto.jena25;
 
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.NoSuchElementException;
 
 import org.semanticweb.owl.align.AlignmentException;
@@ -15,12 +36,45 @@ import fr.inrialpes.exmo.align.onto.OntologyFactory;
 
 public class JENAOntologyFactory extends OntologyFactory{
 
+    private static URI formalismUri = null;
+    private static String formalismId = "OWL1.0";
+
+    public JENAOntologyFactory() {
+	try { 
+	    formalismUri = new URI("http://www.w3.org/2002/07/owl#");
+	} catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
+    }
+
     // No cache management so far
-    public void clearCache() {
+    public void clearCache() {};
+
+    public JENAOntology newOntology( Object ontology ) throws AlignmentException {
+	if ( ontology instanceof OntModel ) {
+	    JENAOntology onto = new JENAOntology();
+	    onto.setFormalism( formalismId );
+	    onto.setFormURI( formalismUri );
+	    onto.setOntology( (OntModel)ontology );
+	    //onto.setFile( uri );// unknown
+	    // to be checked : why several ontologies in a model ???
+	    // If no URI can be extracted from ontology, then we use the physical URI
+	    try {
+		try {
+		    onto.setURI(new URI(((Ontology)((OntModel)ontology).listOntologies().next()).getURI()));
+		} catch (NoSuchElementException nse) {
+		    // JE: not verysafe
+		    onto.setURI(new URI(((OntModel)ontology).getNsPrefixURI("")));
+		}
+	    } catch ( URISyntaxException usex ){
+		// Better put in the AlignmentException of loaded
+		throw new AlignmentException( "URI Error ", usex );
+	    }
+	    return onto;
+	} else {
+	    throw new AlignmentException( "Argument is not an OntModel: "+ontology );
+	}
     }
 
-    @Override
-    public LoadedOntology loadOntology(URI uri) throws AlignmentException {
+    public JENAOntology loadOntology( URI uri ) throws AlignmentException {
 	try {
 	    OntModel m = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM, null );
 	    m.read(uri.toString());
@@ -30,16 +84,14 @@ public class JENAOntologyFactory extends OntologyFactory{
 	    // If no URI can be extracted from ontology, then we use the physical URI
 	    try {
 		onto.setURI(new URI(((Ontology)m.listOntologies().next()).getURI()));
-	    }
-	    catch (NoSuchElementException nse) {
+	    } catch (NoSuchElementException nse) {
 		onto.setURI(new URI(m.getNsPrefixURI("")));
 		//onto.setFile(uri);
 	    }
 	    //onto.setURI(new URI(m.listOntologies()getOntology(null).getURI()));
 	    onto.setOntology(m);
 	    return onto;
-        }
-	catch (Exception e) {
+        } catch (Exception e) {
 	    throw new AlignmentException("Cannot load "+uri, e );
 	}
     }

src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java

@@ -60,6 +60,26 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
 	cache.clear();
     }
 
+    public OWLAPIOntology newOntology( Object ontology ) throws AlignmentException {
+	if ( ontology instanceof OWLOntology ) {
+	    OWLAPIOntology onto = new OWLAPIOntology();
+	    onto.setFormalism( formalismId );
+	    onto.setFormURI( formalismUri );
+	    onto.setOntology( (OWLOntology)ontology );
+	    //onto.setFile( uri );// unknown
+	    try {
+		onto.setURI( ((OWLOntology)ontology).getLogicalURI() );
+	    } catch (OWLException e) {
+		// Better put in the AlignmentException of loaded
+		e.printStackTrace();
+	    }
+	    //cache.recordOntology( uri, onto );
+	    return onto;
+	} else {
+	    throw new AlignmentException( "Argument is not an OWLOntology: "+ontology );
+	}
+    }
+
     public OWLAPIOntology loadOntology( URI uri ) throws AlignmentException {
 	OWLAPIOntology onto = null;
 	onto = cache.getOntologyFromURI( uri );
@@ -95,3 +115,4 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
 	}
     }
 }
+