- Modified Cell interface so that object URIs can be found in a generic way

        -> solves a database storage bug
- Modified inverse() so that it works when no extensions are there

src/fr/inrialpes/exmo/align/impl/BasicCell.java

@@ -26,6 +26,7 @@ import java.util.Enumeration;
 
 import org.xml.sax.ContentHandler;
 
+import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
 import org.semanticweb.owl.align.Cell;
@@ -100,6 +101,9 @@ public class BasicCell implements Cell, Comparable<Cell> {
      * Use <tt>Ontology.getEntityURI( this )</tt> instead.
      */
     public URI getObject1AsURI() throws AlignmentException {
+	return getObject1AsURI( null );
+    }
+    public URI getObject1AsURI( Alignment al ) throws AlignmentException {
 	if ( object1 instanceof URI ) {
 	    return (URI)object1;
 	} else {
@@ -114,6 +118,9 @@ public class BasicCell implements Cell, Comparable<Cell> {
      * Use <tt>Ontology.getEntityURI( this )</tt> instead.
      */
     public URI getObject2AsURI() throws AlignmentException {
+	return getObject2AsURI( null );
+    }
+    public URI getObject2AsURI( Alignment al ) throws AlignmentException {
 	if ( object2 instanceof URI ) {
 	    return (URI)object2;
 	} else {
@@ -157,8 +164,8 @@ public class BasicCell implements Cell, Comparable<Cell> {
 	    for ( Object ext : ((BasicParameters)extensions).getValues() ){
 		result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
 	    }
+	    result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
 	}
-	result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
 	// The sae should be done for the measure
 	return result;
     }

src/fr/inrialpes/exmo/align/impl/OWLAPICell.java

@@ -33,6 +33,7 @@ import org.xml.sax.SAXException;
 import org.semanticweb.owl.model.OWLEntity;
 import org.semanticweb.owl.model.OWLException;
 
+import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
 import org.semanticweb.owl.align.Cell;
@@ -71,7 +72,7 @@ public class OWLAPICell extends ObjectCell {
     }
 
     // Only OWL
-    public URI getObject1AsURI() throws AlignmentException {
+    public URI getObject1AsURI( Alignment al ) throws AlignmentException {
 	try {
 	    return ((OWLEntity)object1).getURI();
 	} catch (OWLException e) {
@@ -80,7 +81,7 @@ public class OWLAPICell extends ObjectCell {
     }
 
     // Only OWL
-    public URI getObject2AsURI() throws AlignmentException {
+    public URI getObject2AsURI( Alignment al ) throws AlignmentException {
 	try {
 	    return ((OWLEntity)object2).getURI();
 	} catch (OWLException e) {

src/fr/inrialpes/exmo/align/impl/ObjectCell.java

@@ -26,12 +26,16 @@ import java.util.Enumeration;
 
 import org.xml.sax.ContentHandler;
 
+import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
 import org.semanticweb.owl.align.Cell;
 import org.semanticweb.owl.align.Relation;
 import org.semanticweb.owl.align.Parameters;
 
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
+
 /**
  * Represents an ontology alignment correspondence.
  *
@@ -72,20 +76,30 @@ public class ObjectCell extends BasicCell {
     }
      */
 
-    public URI getObject1AsURI() throws AlignmentException {
+    public URI getObject1AsURI( Alignment al ) throws AlignmentException {
+	if ( al instanceof BasicAlignment ) {
+	    Object ontology = ((BasicAlignment)al).getOntologyObject1();
+	    if ( ontology instanceof LoadedOntology ) {
+		return ((LoadedOntology)ontology).getEntityURI( object1 );
+	    }
+	};
 	if ( object1 instanceof URI ) {
 	    return (URI)object1;
 	} else {
-	    // TO BE DONE
-	    return null;
+	    throw new AlignmentException( "Cannot find URI for "+object1 );
 	}
     }
-    public URI getObject2AsURI() throws AlignmentException {
-	if ( object2 instanceof URI ) {
+    public URI getObject2AsURI( Alignment al ) throws AlignmentException {
+	if ( al instanceof BasicAlignment ) {
+	    Object ontology = ((BasicAlignment)al).getOntologyObject2();
+	    if ( ontology instanceof LoadedOntology ) {
+		return ((LoadedOntology)ontology).getEntityURI( object2 );
+	    }
+	};
+        if ( object2 instanceof URI ) {
 	    return (URI)object2;
 	} else {
-	    // TO BE DONE
-	    return null;
+	    throw new AlignmentException( "Cannot find URI for "+object2 );
 	}
     }
     public Cell inverse() throws AlignmentException {
@@ -94,8 +108,8 @@ public class ObjectCell extends BasicCell {
 	    for ( Object ext : ((BasicParameters)extensions).getValues() ){
 		result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
 	    }
+	    result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
 	}
-	result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
 	// The sae should be done for the measure
 	return result;
     }

src/fr/inrialpes/exmo/align/impl/URICell.java

 /*
  * $Id$
  *
- * Copyright (C) INRIA Rhne-Alpes, 2007
+ * Copyright (C) INRIA Rhne-Alpes, 2007-2008
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -30,6 +30,7 @@ import java.net.URI;
 import org.xml.sax.ContentHandler;
 import org.xml.sax.SAXException;
 
+import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
 import org.semanticweb.owl.align.Cell;
@@ -75,8 +76,12 @@ public class URICell extends BasicCell {
 	}
     }
 
-    public URI getObject1AsURI() throws AlignmentException { return (URI)object1; };
-    public URI getObject2AsURI() throws AlignmentException { return (URI)object2; };
+    public URI getObject1AsURI( Alignment al ) throws AlignmentException { 
+	return (URI)object1; 
+    };
+    public URI getObject2AsURI( Alignment al ) throws AlignmentException { 
+	return (URI)object2; 
+    };
     //public Object getObject1(){ return object1; };
     //public Object getObject2(){ return object2; };
     // We could check that the given values are URIs