added :

	- methods Relation::compose (for EquivRelation, Subsum..Relation, and IncompatRelation)
	- methods Cell::compose

new implementation of Alignment::compose -> Now it works

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

@@ -8,12 +8,12 @@
  * 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
@@ -48,10 +48,10 @@ import org.semanticweb.owl.align.Parameters;
  * NOTE(JE): hashtabale are indexed by URI.
  * This is strange, but there might be a reason
  * NOTE(JE): I do not think that this is the case anymore
- * 
+ *
  * In version 3.0 this class is virtually abstract.
  * But it cannot be declared abstract because it uses its own constructor.
- * 
+ *
  * @author Jrme Euzenat, David Loup, Raphal Troncy
  * @version $Id$
  */
@@ -211,7 +211,7 @@ public class BasicAlignment implements Alignment {
 	return (String)namespaces.getParameter( label );
     };
 
-    public Enumeration getElements() { 
+    public Enumeration getElements() {
 	return new MEnumeration( hash1 );
     }
 
@@ -521,7 +521,21 @@ public class BasicAlignment implements Alignment {
      */
     public Alignment compose(Alignment align) throws AlignmentException {
 	BasicAlignment result = new BasicAlignment();
-	result.init(onto1,onto2);
+	result.init(onto1,((BasicAlignment) align).getOntologyObject2());
+	// TODO type and level
+	// TODO extension
+	for ( Enumeration e = getElements() ; e.hasMoreElements(); ){
+		Cell c1 = (Cell) e.nextElement();
+		Set<Cell> cells2 = align.getAlignCells1(c1.getObject2());
+		if (cells2 !=null) {
+			for (Cell c2 : cells2) {
+				Cell newCell = c1.compose(c2);
+				if (newCell != null) {
+					result.addCell(newCell);
+				}
+			}
+		}
+	}
 	return result;
     }
 

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

@@ -7,19 +7,19 @@
  * 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.impl; 
+package fr.inrialpes.exmo.align.impl;
 
 import java.net.URI;
 import java.util.Enumeration;
@@ -33,10 +33,10 @@ import org.semanticweb.owl.align.Relation;
 import org.semanticweb.owl.align.Parameters;
 
 /**
- * Represents an ontology alignment correspondence. 
+ * Represents an ontology alignment correspondence.
  *
  * @author Jrme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class BasicCell implements Cell, Comparable {
@@ -50,11 +50,11 @@ public class BasicCell implements Cell, Comparable {
     protected Object object2 = null;
     protected Relation relation = null;
     protected double strength = 0;
-    protected Parameters extensions = null;    
+    protected Parameters extensions = null;
 
     /** Creation **/
     public BasicCell( String id, Object ob1, Object ob2, Relation rel, double m ) throws AlignmentException {
-	setId( id ); 
+	setId( id );
 	object1 = ob1;
 	object2 = ob2;
 	relation = rel;
@@ -85,23 +85,23 @@ public class BasicCell implements Cell, Comparable {
 
     public String getId(){ return id; };
     public void setId( String id ){ this.id = id; };
-    public String getSemantics(){ 
+    public String getSemantics(){
 	if ( semantics != null ) { return semantics; }
 	else { return "first-order"; }
     };
     public void setSemantics( String sem ){ semantics = sem; };
     public Object getObject1(){ return object1; };
     public Object getObject2(){ return object2; };
-    public URI getObject1AsURI() throws AlignmentException { 
+    public URI getObject1AsURI() throws AlignmentException {
 	if ( object1 instanceof URI ) {
-	    return (URI)object1; 
+	    return (URI)object1;
 	} else {
 	    throw new AlignmentException( "Cannot find URI for "+object1 );
 	}
     }
-    public URI getObject2AsURI() throws AlignmentException { 
+    public URI getObject2AsURI() throws AlignmentException {
 	if ( object2 instanceof URI ) {
-	    return (URI)object2; 
+	    return (URI)object2;
 	} else {
 	    throw new AlignmentException( "Cannot find URI for "+object2 );
 	}
@@ -149,6 +149,14 @@ public class BasicCell implements Cell, Comparable {
 	return result;
     }
 
+    public Cell compose(Cell c) throws AlignmentException {
+    	if (!object2.equals(c.getObject1()) && relation.compose(c.getRelation())==null )
+    		return null;
+    	Cell result = (Cell)new BasicCell( (String)null, object1, c.getObject2(), relation.compose(c.getRelation()), strength*c.getStrength() );
+    	// TODO : extension...
+    	return result;
+    }
+
     /** Housekeeping **/
     public void dump( ContentHandler h ){};
 

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

@@ -7,18 +7,18 @@
  * 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.impl; 
+package fr.inrialpes.exmo.align.impl;
 
 import fr.inrialpes.exmo.align.impl.rel.EquivRelation;
 import fr.inrialpes.exmo.align.impl.rel.SubsumeRelation;
@@ -39,7 +39,7 @@ import org.xml.sax.ContentHandler;
  * Represents an ontology alignment relation.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class BasicRelation implements Relation
@@ -95,6 +95,11 @@ public class BasicRelation implements Relation
 	return this;
     }
 
+    /** By default...**/
+    public Relation compose(Relation r) {
+    	return null;
+    }
+
     /** Are the two relations equal **/
     public boolean equals( Relation r ) {
 	if ( r instanceof BasicRelation ){

src/fr/inrialpes/exmo/align/impl/rel/EquivRelation.java

@@ -6,21 +6,22 @@
  * 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.impl.rel; 
+package fr.inrialpes.exmo.align.impl.rel;
 
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Relation;
 
 import fr.inrialpes.exmo.align.impl.BasicRelation;
 
@@ -28,7 +29,7 @@ import fr.inrialpes.exmo.align.impl.BasicRelation;
  * Represents an OWL equivalence relation.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class EquivRelation extends BasicRelation
@@ -45,6 +46,11 @@ public class EquivRelation extends BasicRelation
     public EquivRelation(){
 	super("=");
     }
+
+    public Relation compose(Relation r) {
+		return r;
+    }
+
 }
 
 

src/fr/inrialpes/exmo/align/impl/rel/IncompatRelation.java

@@ -6,21 +6,22 @@
  * 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.impl.rel; 
+package fr.inrialpes.exmo.align.impl.rel;
 
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Relation;
 
 import fr.inrialpes.exmo.align.impl.BasicRelation;
 
@@ -28,7 +29,7 @@ import fr.inrialpes.exmo.align.impl.BasicRelation;
  * Represents an OWL equivalence relation.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class IncompatRelation extends BasicRelation
@@ -45,6 +46,12 @@ public class IncompatRelation extends BasicRelation
     public IncompatRelation(){
 	super("%");
     }
+
+    public Relation compose(Relation r) {
+    	if (r instanceof EquivRelation || r instanceof SubsumeRelation)
+    		return this;
+    	return null;
+    }
 }
 
 

src/fr/inrialpes/exmo/align/impl/rel/NonTransitiveImplicationRelation.java

@@ -47,6 +47,8 @@ public class NonTransitiveImplicationRelation extends BasicRelation
     public NonTransitiveImplicationRelation(){
 	super("~>");
     }
+    
+    
 }
 
 

src/fr/inrialpes/exmo/align/impl/rel/SubsumeRelation.java

@@ -6,29 +6,31 @@
  * 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.impl.rel; 
+package fr.inrialpes.exmo.align.impl.rel;
 
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Relation;
 
 import fr.inrialpes.exmo.align.impl.BasicRelation;
 
+
 /**
  * Represents an OWL subsumption relation.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class SubsumeRelation extends BasicRelation
@@ -45,6 +47,13 @@ public class SubsumeRelation extends BasicRelation
     public SubsumeRelation(){
 	super(">");
     }
+
+    public Relation compose(Relation r) {
+    	if (r.equals(this) || r instanceof EquivRelation)
+    		return this;
+    	return null;
+    }
+
 }
 
 

src/fr/inrialpes/exmo/align/impl/rel/SubsumedRelation.java

@@ -6,21 +6,22 @@
  * 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.impl.rel; 
+package fr.inrialpes.exmo.align.impl.rel;
 
 import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Relation;
 
 import fr.inrialpes.exmo.align.impl.BasicRelation;
 
@@ -30,7 +31,7 @@ import java.io.PrintWriter;
  * Represents an OWL subsumption relation.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 public class SubsumedRelation extends BasicRelation
@@ -48,6 +49,14 @@ public class SubsumedRelation extends BasicRelation
 	super("<");
     }
 
+    public Relation compose(Relation r) {
+    	if (r.equals(this) || r instanceof EquivRelation)
+    		return this;
+    	else if (r instanceof IncompatRelation)
+    		return r;
+    	return null;
+    }
+
     public void write( PrintWriter writer ) {
         writer.print("&lt;");
     }

src/org/semanticweb/owl/align/Cell.java

@@ -7,18 +7,18 @@
  * 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 org.semanticweb.owl.align; 
+package org.semanticweb.owl.align;
 
 import java.io.PrintStream;
 import java.io.PrintWriter;
@@ -36,7 +36,7 @@ import org.xml.sax.SAXException;
  * about those objects.
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 
@@ -72,6 +72,7 @@ public interface Cell
     public void setExtension( String uri, String label, String value );
 
     public Cell inverse() throws AlignmentException;
+    public Cell compose(Cell c) throws AlignmentException;
 
     /** Housekeeping **/
     public void dump(ContentHandler h);

src/org/semanticweb/owl/align/Relation.java

@@ -7,18 +7,18 @@
  * 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 org.semanticweb.owl.align; 
+package org.semanticweb.owl.align;
 
 import java.io.PrintWriter;
 
@@ -27,7 +27,7 @@ import org.xml.sax.ContentHandler;
 /**
  *
  * @author Jérôme Euzenat
- * @version $Id$ 
+ * @version $Id$
  */
 
 
@@ -37,6 +37,7 @@ public interface Relation
     public void accept( AlignmentVisitor visitor ) throws AlignmentException;
 
     public Relation inverse();
+    public Relation compose(Relation r);
 
     public boolean equals( Relation r );