diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
deleted file mode 100644
index 977355b51f86e3be15e5367a96fc982bc21dbe00..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ /dev/null
@@ -1,235 +0,0 @@
-/*
- * $Id$
- *
- * 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.impl;
-
-import java.util.Hashtable;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Enumeration;
-import java.util.Set;
-import java.net.URI;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.Level;
-
-import org.xml.sax.SAXException;
-
-import org.semanticweb.owl.model.OWLOntology;
-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;
-import org.semanticweb.owl.align.Relation;
-import org.semanticweb.owl.align.Parameters;
-
-import fr.inrialpes.exmo.align.onto.OntologyFactory;
-import fr.inrialpes.exmo.align.onto.Ontology;
-import fr.inrialpes.exmo.align.onto.LoadedOntology;
-
-/**
- * Represents an OWL ontology alignment. An ontology comprises a number of
- * collections. Each ontology has a number of classes, properties and
- * individuals, along with a number of axioms asserting information about those
- * objects.
- *
- * @author Jérôme Euzenat
- * @version $Id$
- * @deprecated OWLAPIAlignment has been deprecated to the profit of ObjectAlignment
- * It remains here for compatibility purposes and is reimplemented in terms
- * of ObjectAlignment.
- */
-
-@Deprecated
-public class OWLAPIAlignment extends ObjectAlignment {
-
- protected OWLAPIAlignment init = null;
-
- public OWLAPIAlignment() {}
-
- public void init(Object onto1, Object onto2) throws AlignmentException {
- if ( (onto1 instanceof OWLOntology && onto2 instanceof OWLOntology)
- || (onto1 instanceof Ontology && onto2 instanceof Ontology) ){
- super.init( onto1, onto2 );
- } else if ( onto1 instanceof URI && onto2 instanceof URI ) {
- super.init( loadOntology( (URI)onto1 ),
- loadOntology( (URI)onto2 ) );
- } else {
- throw new AlignmentException("arguments must be OWLOntology or URI");
- };
- }
-
- public void loadInit( Alignment al ) throws AlignmentException {
- if ( al instanceof URIAlignment ) {
- try { init = toOWLAPIAlignment( (URIAlignment)al );
- } catch (SAXException e) { e.printStackTrace();
- } catch (OWLException e) { e.printStackTrace(); }
- } else if ( al instanceof OWLAPIAlignment ) {
- init = (OWLAPIAlignment)al;
- }
- }
-
- public URI getOntology1URI() { return onto1.getURI(); };
-
- public URI getOntology2URI() { return onto2.getURI(); };
-
- /** Cell methods **/
- public Cell addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure, Parameters extensions ) throws AlignmentException {
- if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
- throw new AlignmentException("arguments must be OWLEntities");
- return super.addAlignCell( id, ob1, ob2, relation, measure, extensions);
- };
- public Cell addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure) throws AlignmentException {
- if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
- throw new AlignmentException("arguments must be OWLEntities");
- return super.addAlignCell( id, ob1, ob2, relation, measure);
- };
- public Cell addAlignCell(Object ob1, Object ob2, String relation, double measure) throws AlignmentException {
-
- if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
- throw new AlignmentException("arguments must be OWLEntities");
- return super.addAlignCell( ob1, ob2, relation, measure);
- };
- public Cell addAlignCell(Object ob1, Object ob2) throws AlignmentException {
-
- if ( !( ob1 instanceof OWLEntity && ob2 instanceof OWLEntity ) )
- throw new AlignmentException("arguments must be OWLEntities");
- return super.addAlignCell( ob1, ob2 );
- };
- @SuppressWarnings("deprecation")
- public Cell createCell(String id, Object ob1, Object ob2, Relation relation, double measure) throws AlignmentException {
- return (Cell)new OWLAPICell( id, (OWLEntity)ob1, (OWLEntity)ob2, relation, measure); //[W:Deprecated]
- }
-
- public Set<Cell> getAlignCells1(Object ob) throws AlignmentException {
- if ( ob instanceof OWLEntity ){
- return super.getAlignCells1( ob );
- } else {
- throw new AlignmentException("argument must be OWLEntity");
- }
- }
- public Set<Cell> getAlignCells2(Object ob) throws AlignmentException {
- if ( ob instanceof OWLEntity ){
- return super.getAlignCells2( ob );
- } else {
- throw new AlignmentException("argument must be OWLEntity");
- }
- }
-
- /**
- * @deprecated implemented as the one retrieving the highest strength correspondence
- */
- @Deprecated
- public Cell getAlignCell1(Object ob) throws AlignmentException {
- if ( Annotations.STRICT_IMPLEMENTATION == true ){
- throw new AlignmentException("deprecated (use getAlignCells1 instead)");
- } else {
- if ( ob instanceof OWLEntity ){
- return super.getAlignCell1( ob );
- } else {
- throw new AlignmentException("argument must be OWLEntity");
- }
- }
- }
-
- /**
- * @deprecated implemented as the one retrieving the highest strength correspondence
- */
- @Deprecated
- public Cell getAlignCell2(Object ob) throws AlignmentException {
- if ( Annotations.STRICT_IMPLEMENTATION == true ){
- throw new AlignmentException("deprecated (use getAlignCells2 instead)");
- } else {
- if ( ob instanceof OWLEntity ){
- return super.getAlignCell2( ob );
- } else {
- throw new AlignmentException("argument must be OWLEntity");
- }
- }
- }
-
- public OWLAPIAlignment createNewAlignment( Object onto1, Object onto2 ) throws AlignmentException {
- OWLAPIAlignment align = new OWLAPIAlignment();
- align.init( onto1, onto2 );
- return align;
- }
-
- /**
- * This is a clone with the URI instead of OWLAPI objects
- *
- */
- @SuppressWarnings("deprecation")
- public URIAlignment toURIAlignment() throws AlignmentException {
- URIAlignment align = new URIAlignment();
- align.init( getOntology1URI(), getOntology2URI() );
- align.setType( getType() );
- align.setLevel( getLevel() );
- align.setFile1( getFile1() );
- align.setFile2( getFile2() );
- for ( Object ext : ((BasicParameters)extensions).getValues() ){
- align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
- }
- for (Enumeration e = getElements(); e.hasMoreElements();) {
- OWLAPICell c = (OWLAPICell)e.nextElement(); //[W:Deprecated]
- try {
- align.addAlignCell( c.getId(), c.getObject1AsURI(this), c.getObject2AsURI(this), c.getRelation(), c.getStrength() );
- } catch (AlignmentException aex) {
- // Sometimes URIs are null, this is ignored
- }
- };
- return align;
- }
-
- // Here it becomes necessary to load OWL: This is done by init().
- static public OWLAPIAlignment toOWLAPIAlignment( URIAlignment al ) throws AlignmentException, SAXException, OWLException {
- OWLAPIAlignment alignment = new OWLAPIAlignment();
- alignment.init( al.getFile1(), al.getFile2() );
- alignment.setType( al.getType() );
- alignment.setLevel( al.getLevel() );
- for ( Object ext : ((BasicParameters)al.getExtensions()).getValues() ){
- alignment.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
- }
- OWLOntology o1 = (OWLOntology)alignment.getOntology1();
- OWLOntology o2 = (OWLOntology)alignment.getOntology2();
- for (Enumeration e = al.getElements(); e.hasMoreElements();) {
- Cell c = (Cell)e.nextElement();
- alignment.addAlignCell( c.getId(),
- getEntity( o1, c.getObject1AsURI(al) ),
- getEntity( o2, c.getObject2AsURI(al) ),
- c.getRelation(),
- c.getStrength(),
- c.getExtensions() );
- };
- return alignment;
- }
-
- // JE: newOnto --- Onto: should be discarded
- private static OWLEntity getEntity( OWLOntology ontology, URI uri ) throws OWLException, SAXException {
- OWLEntity result = (OWLEntity)ontology.getClass( uri );
- if ( result == null ) result = (OWLEntity)ontology.getDataProperty( uri );
- if ( result == null ) result = (OWLEntity)ontology.getObjectProperty( uri );
- if ( result == null ) result = (OWLEntity)ontology.getIndividual( uri );
- return result;
- }
-}
-
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java b/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java
deleted file mode 100644
index a01e9e2853d9a81ae70b64bfe6c2b6c628099836..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPICell.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) INRIA Rhône-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
- * 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;
-
-import java.io.PrintStream;
-import java.io.IOException;
-import java.util.Comparator;
-import java.lang.ClassNotFoundException;
-import java.net.URI;
-
-import org.xml.sax.ContentHandler;
-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;
-import org.semanticweb.owl.align.Relation;
-
-import fr.inrialpes.exmo.align.impl.rel.*;
-
-/**
- * Represents an ontology alignment correspondence between two URIs
- *
- * @author Jérôme Euzenat
- * @version $Id$
- * @deprecated OWLAPICell as been deprecated to the profit of ObjectCell
- * It remains here for compatibility purposes and is reimplemented in terms
- * of ObjectCell.
- */
-
-@Deprecated
-public class OWLAPICell extends ObjectCell {
- public void accept( AlignmentVisitor visitor) throws AlignmentException {
- visitor.visit( this );
- }
-
- public OWLAPICell( String id, OWLEntity ob1, OWLEntity ob2, Relation rel, double m ) throws AlignmentException {
- super( id, ob1, ob2, rel, m );
- };
-
- // the strength must be compared with regard to abstract types
- // NOOWL
- public boolean equals( Cell c ) {
- if ( c instanceof OWLAPICell ){
- return ( object1.equals(c.getObject1()) && object2.equals(c.getObject2()) && strength == c.getStrength() && (relation.equals( c.getRelation() )) );
- } else {
- return false;
- }
- }
-
- // Only OWL
- public URI getObject1AsURI( Alignment al ) throws AlignmentException {
- try {
- return ((OWLEntity)object1).getURI();
- } catch (OWLException e) {
- throw new AlignmentException( "Cannot convert to URI "+object1, e );
- }
- }
-
- // Only OWL
- public URI getObject2AsURI( Alignment al ) throws AlignmentException {
- try {
- return ((OWLEntity)object2).getURI();
- } catch (OWLException e) {
- throw new AlignmentException( "Cannot convert to URI "+object2, e );
- }
- }
-
- // Only OWL
- public Cell inverse() throws AlignmentException {
- return (Cell)new OWLAPICell( (String)null, (OWLEntity)object2, (OWLEntity)object1, relation.inverse(), strength );
- // The same should be done for the measure
- }
-
-}
-