diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 0f7c914f9f914c7709aba14ae6af93a7912c7b67..da6e01178ec8af3627783182ef4648744fc46be3 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -18,11 +18,17 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
+//Raph: are things to change for dealing with multiple cell
+// for one objects
+
package fr.inrialpes.exmo.align.impl;
import java.lang.ClassNotFoundException;
import java.util.Hashtable;
+//Raph:
+import java.util.HashSet;
import java.util.Enumeration;
+import java.util.Iterator;
import java.util.Collections;
import java.util.List;
import java.util.ArrayList;
@@ -96,6 +102,7 @@ public class BasicAlignment implements Alignment {
}
public int nbCells() {
+ // Raph: this is now wrong: I need multi-enumeration
return hash1.size();
}
@@ -109,22 +116,16 @@ public class BasicAlignment implements Alignment {
};
public void setOntology1(Object ontology) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLOntology").isInstance(ontology))
- throw new AlignmentException("setOntollogy1: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- }
+ throw new AlignmentException("setOntollogy1: arguments must be OWLEntities");
+ };
+ public void setOntology1(OWLOntology ontology) throws AlignmentException {
onto1 = (OWLOntology) ontology;
};
public void setOntology2(Object ontology) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLOntology").isInstance(ontology))
- throw new AlignmentException("setOntollogy2: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- }
+ throw new AlignmentException("setOntollogy2: arguments must be OWLEntities");
+ };
+ public void setOntology2(OWLOntology ontology) throws AlignmentException {
onto2 = (OWLOntology) ontology;
};
@@ -144,11 +145,15 @@ public class BasicAlignment implements Alignment {
public void setFile2(URI u) { uri2 = u; };
- public Enumeration getElements() { return hash1.elements(); }
+ public Enumeration getElements() {
+ //Raph: This should be a multi Enumeration:
+ return hash1.elements();
+ }
/*
* Please note that all the following methods must be changed because they
* consider that only ONE Entity can be aligned with another !!
+ * A number of modifications are considered in the //Raph:
*/
/** Cell methods * */
public Cell addAlignCell(Object ob1, Object ob2, String relation,
@@ -161,8 +166,22 @@ public class BasicAlignment implements Alignment {
try {
Cell cell = (Cell) new BasicCell((OWLEntity) ob1, (OWLEntity) ob2,
relation, measure);
- hash1.put((Object) (((OWLEntity) ob1).getURI()), cell);
- hash2.put((Object) (((OWLEntity) ob2).getURI()), cell);
+ //Raph:
+ //HashSet s1 = hash1.get((Object)(((OWLEntity)ob1).getURI()));
+ //if ( s1 == null ){
+ // s1 = new HashSet();
+ // hash1.put((Object)(((OWLEntity)ob1).getURI()),s1);
+ //}
+ //s1.add(cell);
+ hash1.put((Object)(((OWLEntity)ob1).getURI()), cell);
+ //Raph:
+ //HashSet s1 = hash1.get((Object)(((OWLEntity)ob1).getURI()));
+ //if ( s2 == null ){
+ // s2 = new HashSet();
+ // hash2.put((Object)(((OWLEntity)ob2).getURI()),s2);
+ //}
+ //s2.add(cell);
+ hash2.put((Object)(((OWLEntity)ob2).getURI()), cell);
return cell;
} catch (OWLException e) {
throw new AlignmentException("getURI problem", e);
@@ -173,86 +192,83 @@ public class BasicAlignment implements Alignment {
return addAlignCell( ob1, ob2, "=", 1. );
}
+ // Raph:
+ public Iterator getAlignCells1(Object ob) throws AlignmentException {
+ throw new AlignmentException("getAlignCell1: arguments must be OWLEntities");
+ }
+ // Raph:
+ public Iterator getAlignCells1(OWLEntity ob) throws AlignmentException {
+ HashSet s = null;
+ try { s = (HashSet)hash1.get(((OWLEntity)ob).getURI()); }
+ catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ if ( s == null ) { return null; }
+ else { return s.iterator(); }
+ }
+
public Cell getAlignCell1(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignCell1: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
- try {
- return (Cell) hash1.get(((OWLEntity) ob).getURI());
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ throw new AlignmentException("getAlignCell1: arguments must be OWLEntities");
+ }
+ public Cell getAlignCell1(OWLEntity ob) throws AlignmentException {
+ try { return (Cell) hash1.get(((OWLEntity) ob).getURI()); }
+ catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
}
public Cell getAlignCell2(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignCell2: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
- try {
- return (Cell) hash2.get(((OWLEntity) ob).getURI());
- } catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
+ throw new AlignmentException("getAlignCell2: arguments must be OWLEntities");
+ }
+ public Cell getAlignCell2(OWLEntity ob) throws AlignmentException {
+ try { return (Cell) hash2.get(((OWLEntity) ob).getURI()); }
+ catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
}
public Object getAlignedObject1(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedObject1: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell1(ob);
if (c != null) return c.getObject2();
else return null;
};
public Object getAlignedObject2(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedObject2: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell2(ob);
if (c != null) return c.getObject1();
else return null;
};
public Relation getAlignedRelation1(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedRelation1: argument must be OWLEntity");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell1(ob);
if (c != null) return c.getRelation();
else return (Relation) null;
};
public Relation getAlignedRelation2(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedRelation2: argument must be OWLEntity");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell2(ob);
if (c != null) return c.getRelation();
else return (Relation) null;
};
public double getAlignedStrength1(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedStrength1: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell1(ob);
if (c != null) return c.getStrength();
else return 0;
};
public double getAlignedStrength2(Object ob) throws AlignmentException {
- try {
- if (!Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob))
- throw new AlignmentException("getAlignedStrength2: arguments must be OWLEntities");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
Cell c = getAlignCell2(ob);
if (c != null) return c.getStrength();
else return 0;
};
+ //Raph:
+ public void removeAlignCell(Cell c) throws AlignmentException {
+ try {
+ HashSet s1 = (HashSet)hash1.get(((OWLEntity)c.getObject1()).getURI());
+ HashSet s2 = (HashSet)hash2.get(((OWLEntity)c.getObject2()).getURI());
+ s1.remove(c);
+ s2.remove(c);
+ } catch (OWLException ex) {
+ throw new AlignmentException("getURI problem", ex);
+ }
+ }
+
/***************************************************************************
* The cut function suppresses from an alignment all the cell over a
* particulat threshold
@@ -264,6 +280,8 @@ public class BasicAlignment implements Alignment {
// Beware, this suppresses all cells with these keys
// There is only one of them
try {
+ //Raph:
+ //removeAlignCell( c );
hash1.remove(((OWLEntity) c.getObject1()).getURI());
hash2.remove(((OWLEntity) c.getObject2()).getURI());
} catch (OWLException ex) {
@@ -295,6 +313,7 @@ public class BasicAlignment implements Alignment {
if ( threshold > 1. || threshold < 0. )
throw new AlignmentException( "Not a percentage or threshold : "+threshold );
// Create a sorted list of cells
+ // Raph: this will not work anymore
List buffer = new ArrayList( hash1.values() );
Collections.sort( buffer );
int size = buffer.size();
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index af9df66a185b5d950cc441eb9d2890769a6a361f..c6e8494da7901cd3892c719751fafc2b12423a19 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -72,19 +72,19 @@ public class BasicCell implements Cell, Comparable {
}
public BasicCell( Object ob1, Object ob2, String rel, double m ) throws AlignmentException {
- try {
- if ( !Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob1) ||
- !Class.forName("org.semanticweb.owl.model.OWLEntity").isInstance(ob2) )
- throw new AlignmentException("BasicCell: must take two OWLEntity as argument");
- } catch (ClassNotFoundException e) { e.printStackTrace(); }
- object1 = (OWLEntity)ob1;
- object2 = (OWLEntity)ob2;
+ throw new AlignmentException("BasicCell: must take two OWLEntity as argument");
+ }
+ public BasicCell( OWLEntity ob1, OWLEntity ob2, String rel, double m ) throws AlignmentException {
+ object1 = ob1;
+ object2 = ob2;
if ( rel.equals("=") ) {
relation = new EquivRelation();
} else if ( rel.equals("<") ) {
relation = new SubsumeRelation();
} else if ( rel.equals("%") ) {
relation = new IncompatRelation();
+ } else if ( rel.equals("~>") ) {
+ relation = new NonTransitiveImplicationRelation();
} else {
// I could use the class name for relation,
// this would be more extensible...
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index 5076c17f770b5d181ab6ea00f3d60e1d51b78b82..e600c97d161d7e32b2df169d6af02a95234d0f58 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -40,6 +40,7 @@ import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Cell;
@@ -60,7 +61,7 @@ import fr.inrialpes.exmo.align.impl.ConcatenatedIterator;
*/
-public class DistanceAlignment extends BasicAlignment
+public class DistanceAlignment extends BasicAlignment implements AlignmentProcess
{
Similarity sim;
@@ -171,8 +172,9 @@ public class DistanceAlignment extends BasicAlignment
addAlignCell(class1,class2, "=", max);
}
}
- // Extract for properties
- for (Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext();) {
+ // Extract for individuals
+ // This does not work, at least for the OAEI 2005 tests
+ /* for (Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext();) {
OWLIndividual ind1 = (OWLIndividual)it1.next();
found = false; max = threshold; val = 0;
OWLIndividual ind2 = null;
@@ -183,8 +185,9 @@ public class DistanceAlignment extends BasicAlignment
found = true; max = val; ind2 = current;
}
}
+ System.err.println(ind1+" -- "+ind2+" = "+max);
if ( found ) addAlignCell(ind1,ind2, "=", max);
- }
+ }*/
} catch (Exception e2) {e2.printStackTrace();}
return((Alignment)this);
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
index 167904be40250652f471e4818ed5abb429db551e..f5a3f492991e6cabaa5c5b119945f8bba1a050d2 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/EditDistNameAlignment.java
@@ -55,21 +55,24 @@ public class EditDistNameAlignment extends DistanceAlignment implements Alignmen
public double measure( OWLClass cl1, OWLClass cl2 ) throws OWLException{
String s1 = cl1.getURI().getFragment();
String s2 = cl2.getURI().getFragment();
- return StringDistances.levenshteinDistance(
+ if ( s1 == null || s2 == null ) return 1.;
+ else return StringDistances.levenshteinDistance(
s1.toLowerCase(),
s2.toLowerCase()) / max(s1.length(),s2.length());
}
public double measure( OWLProperty pr1, OWLProperty pr2 ) throws OWLException{
String s1 = pr1.getURI().getFragment();
String s2 = pr2.getURI().getFragment();
- return StringDistances.levenshteinDistance(
+ if ( s1 == null || s2 == null ) return 1.;
+ else return StringDistances.levenshteinDistance(
s1.toLowerCase(),
s2.toLowerCase()) / max(s1.length(),s2.length());
}
public double measure( OWLIndividual id1, OWLIndividual id2 ) throws OWLException{
String s1 = id1.getURI().getFragment();
String s2 = id2.getURI().getFragment();
- return StringDistances.levenshteinDistance(
+ if ( s1 == null || s2 == null ) return 1.;
+ else return StringDistances.levenshteinDistance(
s1.toLowerCase(),
s2.toLowerCase()) / max(s1.length(),s2.length());
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StringDistances.java b/src/fr/inrialpes/exmo/align/impl/method/StringDistances.java
index 60eca48ba41b1252e7bdb7d0e971d7d33b06ad08..26004eff3f765e5fbf42c2d790fce2dcdb673673 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StringDistances.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StringDistances.java
@@ -25,10 +25,11 @@
* various kind of strings.
*
* This includes:
- * - subStringDistance
* - equality
+ * - subStringDistance
+ * - pSubStringDistance [not implemented yet]
* - lowenhein (edit) distance
- * - n-gram distance
+ * - n-gram distance [not implemented yet]
*
* @author Jérôme Euzenat
* @version $Id$
@@ -77,6 +78,10 @@ public class StringDistances {
return (1.0 - ((double)2*best / (l1+l2)));
}
+ /* pSubStringDistance:
+ * find all the common substrings (up to length 3)
+ * sum their size / s1+s2
+ */
public static int equalDistance (String s, String t) {
if (s == null || t == null) {