diff --git a/lib/align.jar b/lib/align.jar
index 350259b13d126d4804221c71849146ecd14cf139..46333ba5794540445c8a29bf588b17a16e6bbdd0 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/alignwn.jar b/lib/alignwn.jar
index b631f139f89e38e36c20157f66235ad9c70d6787..020946ca1bd9f9cd341b03a36e6a54d1da10f12e 100644
Binary files a/lib/alignwn.jar and b/lib/alignwn.jar differ
diff --git a/lib/procalign.jar b/lib/procalign.jar
index 4c20b64fe3c4a003bb9ecfba8bcc0b7758140df6..411f799bab05bab691489e2ad4cfe013910af5f9 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index e600c97d161d7e32b2df169d6af02a95234d0f58..116b18234e5164e71bc1a802138519868bdbaba2 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -21,10 +21,15 @@
package fr.inrialpes.exmo.align.impl;
import java.lang.ClassNotFoundException;
+import java.lang.ClassCastException;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.Vector;
+import java.util.TreeSet;
+import java.util.SortedSet;
+import java.util.Set;
+import java.util.Comparator;
import java.io.PrintStream;
import java.io.IOException;
import java.net.URI;
@@ -60,7 +65,6 @@ import fr.inrialpes.exmo.align.impl.ConcatenatedIterator;
* @version $Id$
*/
-
public class DistanceAlignment extends BasicAlignment implements AlignmentProcess
{
Similarity sim;
@@ -117,9 +121,10 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
double threshold = 0.;
if ( params.getParameter("threshold") != null )
threshold = ((Double) params.getParameter("threshold")).doubleValue();
-
+
+ //System.err.println("The type is "+type+" with length = "+type.length());
if ( type.equals("?*") || type.equals("1*") || type.equals("?+") || type.equals("1+") ) return extractqs( threshold, params );
- else if ( type.equals("??") || type.equals("1?") || type.equals("?1") || type.equals("11") ) return extractqs( threshold, params );
+ else if ( type.equals("??") || type.equals("1?") || type.equals("?1") || type.equals("11") ) return extractqq( threshold, params );
else if ( type.equals("*?") || type.equals("+?") || type.equals("*1") || type.equals("+1") ) return extractqs( threshold, params );
else if ( type.equals("**") || type.equals("+*") || type.equals("*+") || type.equals("++") ) return extractqs( threshold, params );
// The else should be an error message
@@ -128,6 +133,7 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
/**
* Extract the alignment of a ?* type
+ * Complexity: O(n^2)
*/
public Alignment extractqs( double threshold, Parameters params) {
int i = 0, j = 0;
@@ -168,28 +174,124 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
found = true; max = val; class2 = current;
}
}
- if ( found ) {
- addAlignCell(class1,class2, "=", max);
- }
+ if ( found ) addAlignCell(class1,class2, "=", max);
}
// 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;
- for (Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ) {
- OWLIndividual current = (OWLIndividual)it2.next();
- val = 1 - sim.getIndividualSimilarity(ind1,current);
- if (val > max) {
- found = true; max = val; ind2 = current;
+ if ( params.getParameter("noinst") == null ){
+ for (Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext();) {
+ OWLIndividual ind1 = (OWLIndividual)it1.next();
+ found = false; max = threshold; val = 0;
+ OWLIndividual ind2 = null;
+ for (Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ) {
+ OWLIndividual current = (OWLIndividual)it2.next();
+ val = 1 - sim.getIndividualSimilarity(ind1,current);
+ if (val > max) {
+ found = true; max = val; ind2 = current;
+ }
}
+ System.err.println(ind1+" -- "+ind2+" = "+max);
+ if ( found ) addAlignCell(ind1,ind2, "=", max);
}
- System.err.println(ind1+" -- "+ind2+" = "+max);
- if ( found ) addAlignCell(ind1,ind2, "=", max);
- }*/
+ }
} catch (Exception e2) {e2.printStackTrace();}
return((Alignment)this);
}
+ /**
+ * Extract the alignment of a ?? type
+ *
+ * Basic algorithm:
+ * 1) dump the part of the matrix distance above threshold in a sorted set
+ * 2) traverse the sorted set and each time a correspondence involving two
+ * entities that have no correspondence is encountered, add it to the
+ * alignment.
+ * Complexity: O(n^2.logn)
+ * Pitfall: no global optimality is warranted
+ * for instance if there is the following matrix:
+ * (a,a')=1., (a,b')=.9, (b,a')=.9, (b,b')=.1
+ * This algorithm will select the first and last correspondances of
+ * overall similarity 1.1, while the optimum is the second solution
+ * with overall of 1.8.
+ */
+ public Alignment extractqq( double threshold, Parameters params) {
+ OWLEntity ent1=null, ent2=null;
+ double val = 0;
+ //TreeSet could be replaced by something else
+ //The comparator must always tell that things are different!
+ SortedSet cellSet = new TreeSet(
+ new Comparator() {
+ public int compare( Object o1, Object o2 )
+ throws ClassCastException{
+ if ( o1 instanceof Cell
+ && o2 instanceof Cell ) {
+ if ( ((Cell)o1).getStrength() > ((Cell)o2).getStrength() ){
+ return -1;
+ } else { return 1; }
+ } else {
+ throw new ClassCastException();
+ }}});
+
+ try {
+ // Get all the matrix above threshold in the SortedSet
+ // Plus a map from the objects to the cells
+ // O(n^2.log n)
+ ConcatenatedIterator pit1 = new
+ ConcatenatedIterator(onto1.getObjectProperties().iterator(),
+ onto1.getDataProperties().iterator());
+ for (; pit1.hasNext(); ) {
+ ent1 = (OWLProperty)pit1.next();
+ ConcatenatedIterator pit2 = new
+ ConcatenatedIterator(onto2.getObjectProperties().iterator(),
+ onto2.getDataProperties().iterator());
+ for (; pit2.hasNext(); ) {
+ ent2 = (OWLProperty)pit2.next();
+ val = 1 - sim.getPropertySimilarity((OWLProperty)ent1,(OWLProperty)ent2);
+ //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ if ( val > threshold ){
+ cellSet.add( new BasicCell( ent1, ent2, "=", val ) );
+ }
+ }
+ }
+ for (Iterator it1 = onto1.getClasses().iterator(); it1.hasNext(); ) {
+ ent1 = (OWLClass)it1.next();
+ for (Iterator it2 = onto2.getClasses().iterator(); it2.hasNext(); ) {
+ ent2 = (OWLClass)it2.next();
+ val = 1 - sim.getClassSimilarity((OWLClass)ent1,(OWLClass)ent2);
+ //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ if ( val > threshold ){
+ cellSet.add( new BasicCell( ent1, ent2, "=", val ) );
+ }
+ }
+ }
+ // OLA with or without instances
+ if ( params.getParameter("noinst") == null ){
+ for (Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext();) {
+ ent1 = (OWLIndividual)it1.next();
+ for (Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ) {
+ ent2 = (OWLIndividual)it2.next();
+ val = 1 - sim.getIndividualSimilarity((OWLIndividual)ent1,(OWLIndividual)ent2);
+ //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ if ( val > threshold ){
+ cellSet.add( new BasicCell( ent1, ent2, "=", val ) );
+ }
+ }
+ }
+ }
+
+ // O(n^2)
+ for( Iterator it = cellSet.iterator(); it.hasNext(); ){
+ Cell cell = (Cell)it.next();
+ ent1 = (OWLEntity)cell.getObject1();
+ ent2 = (OWLEntity)cell.getObject2();
+ if ( (getAlignCell1( ent1 ) == null) && (getAlignCell2( ent2 ) == null) ){
+ // The cell is directly added!
+ addCell( ent1, ent2, cell );
+ }
+ };
+
+ } catch (Exception e) { e.printStackTrace(); }
+ return((Alignment)this);
+ }
+
}