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Commit 7e439a6e authored by Jérôme Euzenat's avatar Jérôme Euzenat
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suppressed (early) deprecated OWLAPI elements

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src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java deleted 100644 → 0
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View file @ d1370f3e
/*
* $Id$
*
* 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 Jrme 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;
}
}
src/fr/inrialpes/exmo/align/impl/OWLAPICell.java deleted 100644 → 0
+ 0
− 99
View file @ d1370f3e
/*
* $Id$
*
* 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
* 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 Jrme 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
}
}
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