From a3c24fa1e34088ce816e06b3a0b30991620d05e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Fri, 17 Jun 2005 08:21:37 +0000
Subject: [PATCH] - Reingeenered DistanceAlignment
---
.../inrialpes/exmo/align/impl/Extractor.java | 30 --
.../inrialpes/exmo/align/impl/SimExtract.java | 309 ------------------
.../exmo/align/impl/alignmentExtractor.java | 37 ---
3 files changed, 376 deletions(-)
delete mode 100644 src/fr/inrialpes/exmo/align/impl/Extractor.java
delete mode 100644 src/fr/inrialpes/exmo/align/impl/SimExtract.java
delete mode 100644 src/fr/inrialpes/exmo/align/impl/alignmentExtractor.java
diff --git a/src/fr/inrialpes/exmo/align/impl/Extractor.java b/src/fr/inrialpes/exmo/align/impl/Extractor.java
deleted file mode 100644
index 1bd36b9a..00000000
--- a/src/fr/inrialpes/exmo/align/impl/Extractor.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * 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);
-}
diff --git a/src/fr/inrialpes/exmo/align/impl/SimExtract.java b/src/fr/inrialpes/exmo/align/impl/SimExtract.java
deleted file mode 100644
index 6da91c50..00000000
--- a/src/fr/inrialpes/exmo/align/impl/SimExtract.java
+++ /dev/null
@@ -1,309 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) INRIA Rhône-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;}
-
-}
diff --git a/src/fr/inrialpes/exmo/align/impl/alignmentExtractor.java b/src/fr/inrialpes/exmo/align/impl/alignmentExtractor.java
deleted file mode 100644
index 133a7131..00000000
--- a/src/fr/inrialpes/exmo/align/impl/alignmentExtractor.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * 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 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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