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Commit a3c24fa1 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- Reingeenered DistanceAlignment

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src/fr/inrialpes/exmo/align/impl/Extractor.java deleted 100644 → 0
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View file @ 9e78443b
/*
* Copyright (C) INRIA Rhône-Alpes, 2004-2005
*
* 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 org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Parameters;
/**
* @author jpierson
* JE: WHAT THE HELL DOES THAT INTERFACE OUT OF THE API !!!
*/
public interface Extractor {
public Alignment extract(String type, Parameters param);
}
src/fr/inrialpes/exmo/align/impl/SimExtract.java deleted 100644 → 0
+ 0
− 309
View file @ 9e78443b
/*
* $Id$
*
* Copyright (C) INRIA Rhne-Alpes, 2004
*
* 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.net.URI;
import java.util.Iterator;
import java.util.Vector;
import java.lang.ClassNotFoundException;
import java.lang.InstantiationException;
import java.lang.IllegalAccessException;
import java.lang.reflect.InvocationTargetException;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLProperty;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.Similarity;
/**
* Extract a alignment from a distance of similarity Measure
* //JE: I am pretty sure that most of this class is useless.
* As a matter of fact, it copies the similarity into a matrix...
* instead of asking it (and iterating on the objects).
*
* @author jpierson
*
*/
public class SimExtract extends alignmentExtractor implements PreAlignment {
private OWLOntology onto1;
private OWLOntology onto2;
private Similarity sim;
/** properties similarity matrix
*
*/
private double propmatrix[][];
/** class similarity matrix
*
*/
private double classmatrix[][];
/** Individual similarity matrix
*
*/
private double individualmatrix[][];
private int nbclass1 = 0; // number of classes in onto1
private int nbclass2 = 0; // number of classes in onto2
private int nbprop1 = 0; // number of properties in onto1
private int nbprop2 = 0; // number of properties in onto2
private int nbindividu1 = 0; // number of individual in onto1
private int nbindividu2 = 0; // number of individual in onto2
private Vector classlist2 = new Vector(10); // onto2 classes
private Vector classlist1 = new Vector(10); // onto1 classes
private Vector proplist2 = new Vector(10); // onto2 properties
private Vector proplist1 = new Vector(10); // onto1 properties
private Vector individulist2 = new Vector(10); // onto2 Individuals
private Vector individulist1 = new Vector(10); // onto1 Individuals
private double threshold;
public SimExtract( String simClassName ) throws ClassNotFoundException, IllegalAccessException, InstantiationException, InvocationTargetException {
//sim = new SimilarityMeasure();
// Create similarity object
Object[] mparams = {};
Class similarityMeasureClass = Class.forName(simClassName);
java.lang.reflect.Constructor[] simConstructors = similarityMeasureClass.getConstructors();
sim = (Similarity) simConstructors[0].newInstance(mparams);
}
/**
* Intialize the Alignment extraction process.
* @param param
*/
public void align( Parameters param) {
onto1 = (OWLOntology) param.getParameter("ontology1");
onto2 = (OWLOntology) param.getParameter("ontology2");
sim.initialize( onto1, onto2 );
threshold = ((Double) param.getParameter("Threshold")).doubleValue();
createDistanceMatrix();
}
/**
* Create a Similarity Matrix between the terms of the two ontologies
*/
public void createDistanceMatrix() {
// Create similarity matrix
int i, j = 0; // index for onto1 and onto2 classes
try {
// Create property lists and matrix
for (Iterator it = onto1.getObjectProperties().iterator(); it.hasNext(); nbprop1++) {
proplist1.add(it.next());}
for (Iterator it = onto1.getDataProperties().iterator(); it.hasNext(); nbprop1++) {
proplist1.add(it.next());}
for (Iterator it = onto2.getObjectProperties().iterator(); it.hasNext(); nbprop2++) {
proplist2.add(it.next());}
for (Iterator it = onto2.getDataProperties().iterator(); it.hasNext(); nbprop2++) {
proplist2.add(it.next());}
} catch (OWLException e) { e.printStackTrace();}
propmatrix = new double[nbprop1 + 1][nbprop2 + 1];
try {
// Create class lists
for (Iterator it = onto2.getClasses().iterator(); it.hasNext(); nbclass2++) {
classlist2.add(it.next());}
for (Iterator it = onto1.getClasses().iterator(); it.hasNext(); nbclass1++) {
classlist1.add(it.next());}
} catch (OWLException e1) {e1.printStackTrace();}
classmatrix = new double[nbclass1 + 1][nbclass2 + 1];
try {
// Create individual lists
for (Iterator it = onto2.getIndividuals().iterator(); it.hasNext(); nbindividu2++) {
individulist2.add(it.next());}
for (Iterator it = onto1.getIndividuals().iterator(); it.hasNext(); nbindividu1++) {
individulist1.add(it.next());}
} catch (OWLException e1) {e1.printStackTrace();}
individualmatrix = new double[nbindividu1 + 1][nbindividu2 + 1];
// Computing the similarity measure between the onlogies entities
try {
for (i = 0; i < nbprop1; i++) {
OWLProperty cl = (OWLProperty) proplist1.get(i);
URI U1 = cl.getURI();
for (j = 0; j < nbprop2; j++) {
OWLProperty cl2 = (OWLProperty) proplist2.get(j);
URI U2;
U2 = cl.getURI();
propmatrix[i][j] = sim.getPropertySimilarity(cl, cl2);
}
}
} catch (Exception e2) {e2.printStackTrace();}
try {
for (i = 0; i < nbclass1; i++) {
OWLClass cl = (OWLClass) classlist1.get(i);
for (j = 0; j < nbclass2; j++) {
classmatrix[i][j] = sim.getClassSimilarity(cl,(OWLClass) classlist2.get(j));
}
}
} catch (Exception e2) {e2.printStackTrace();}
try {
for (i = 0; i < nbindividu1; i++) {
OWLIndividual In = (OWLIndividual) individulist1.get(i);
for (j = 0; j < nbindividu2; j++) {
individualmatrix[i][j] = sim.getIndividualSimilarity(In,(OWLIndividual) individulist2.get(j));
}
}
} catch (Exception e2) {e2.printStackTrace();}
}
/**
* Extract an alignment form the Similarity Matrix.
* It only keeps the best alignment for each entity of ontology1
* under the condition that it is not under threshold.
*
* The algorithm does not even test that the corresponding object in
* ontology2 is not already in an anlignment...
*
* A greedy method for that would be:
* - test it (easy)
* - if it is the case, then choose the best of the two and reiterate the computation on the other.
* - beware of two things: (a) this will require to map the objects to their rank, (b) do change something ONLY if it is stricly better [less optimal but terminates]
*
* @return A basicAligment object
*/
public Alignment extractAlignment(String type) {
BasicAlignment Al = new BasicAlignment();
int i = 0, j = 0;
Al.init(onto1, onto2);
Al.setType(type);
for (i = 0; i < nbprop1; i++) {
boolean found = false;
int best = 0;
double max = threshold;
for (j = 0; j < nbprop2; j++) {
if (propmatrix[i][j] > max) {
found = true;
best = j;
max = propmatrix[i][j];
}
}
try {
if (found && max > threshold) {
Al.addAlignCell((OWLProperty) proplist1.get(i),
(OWLProperty) proplist2.get(best), "=", max);
//System.out.println( ((OWLProperty) proplist1.get(i)).getURI() + " = " + ((OWLProperty) proplist2.get(best)).getURI() );
}
} catch (Exception e2) {e2.printStackTrace();}
}
for (i = 0; i < nbclass1; i++) {
boolean found = false;
int best = 0;
double max = threshold;
for (j = 0; j < nbclass2; j++) {
if (classmatrix[i][j] > max) {
found = true;
best = j;
max = classmatrix[i][j];
}
}
try {
if (found && max > threshold) {
Al.addAlignCell((OWLClass) classlist1.get(i),
(OWLClass) classlist2.get(best), "=", max);
// System.out.println( classlist1.get(i).toString() + " = " + classlist2.get(best).toString() );
}
} catch (Exception e2) {e2.printStackTrace();}
}
for (i = 0; i < nbindividu1; i++) {
boolean found = false;
int best = 0;
double max = threshold;
for (j = 0; j < nbindividu2; j++) {
if (individualmatrix[i][j] > max) {
found = true;
best = j;
max = individualmatrix[i][j];
}
}
try {
if (found && max > threshold) {
Al.addAlignCell((OWLIndividual) individulist1.get(i),
(OWLIndividual) individulist2.get(best), "=", max);
// System.out.println( individulist1.get(i).toString() + " = " + individulist2.get(best).toString() );
}
} catch (Exception e2) {e2.printStackTrace();}
}
return (Al);
}
/* //JE: ARE THESE METHODS OF ANY USE? ? ? */
/**
* @return the Similiraty Measure object
*/
public Similarity getSimilarity(){return (sim);}
public double getProMatrix(int i, int j){return propmatrix[i][j];}
public double getClassMatrix(int i, int j){return classmatrix[i][j];}
public double getIndividualMatrix(int i,int j){return individualmatrix[i][j];}
/**
* @return the number of class for the ontology 1
*/
public int getnbclass1(){return nbclass1;}
/**
* @return the number of class for the ontology 2
*/
public int getnbclass2(){return nbclass2;}
/**
* @return the number of propriete for the ontology 1
*/
public int getnbprop1 (){return nbprop1;}
/**
* @return the number of properties for the ontology 2
*/
public int getnbprop2 (){return nbprop2;}
/**
* @return the number of Individual for the ontology 1
*/
public int getnbindividu1(){return nbindividu1;}
/**
* @return the number of individual for the ontology 2
*/
public int getnbindividu2(){return nbindividu2;}
}
src/fr/inrialpes/exmo/align/impl/alignmentExtractor.java deleted 100644 → 0
+ 0
− 37
View file @ 9e78443b
/*
* Copyright (C) INRIA Rhne-Alpes, 2004-2005
*
* 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 fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Parameters;
/**
* @author jpierson
* JE: THIS CLASS SHOULD BE OBSOLETED!
*/
public class alignmentExtractor implements Extractor {
public Alignment extract(String type, Parameters param) {
BasicAlignment Al = new BasicAlignment();
return ((Alignment)Al);}
public void threshold (String type, Parameters param){}
}
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