diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 5f21eafdbd05c36c0b9edb8438c06d1799d2d0bc..465683e7bc2754ec3560e839c462999e9c6b708b 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -436,6 +436,14 @@ public class BasicAlignment implements Alignment {
}
};
+ /**
+ * Returns default exception for conversion to URIAlignments
+ *
+ */
+ public URIAlignment toURIAlignment() throws AlignmentException {
+ throw new AlignmentException("[BasicAlignment].toURIAlignment() cannot process");
+ }
+
/***************************************************************************
* The harden function acts like threshold but put all weights to 1.
**************************************************************************/
@@ -562,6 +570,12 @@ public class BasicAlignment implements Alignment {
public void render( AlignmentVisitor renderer ) throws AlignmentException {
accept(renderer);
}
+
+ /**
+ * Can be used for reducing the amount of memory taken by an alignment
+ * Does nothing in BasicAlignment.
+ */
+ public void cleanUp() {}
}
class MEnumeration implements Enumeration {
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index b41ad40155557813dc57849d04c049bc7867f3a1..9e84e6088800df43e1562fa3dc0cce193766304d 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -96,6 +96,9 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
extract( getType(), params );
}
+ /**
+ * Prints the distance matrix
+ */
public void printDistanceMatrix( Parameters params ){
System.out.println("\\documentclass{article}\n");
System.out.println("\\usepackage{graphics}\n");
@@ -109,6 +112,13 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
System.out.println("\n\\end{document}");
}
+ /**
+ * Suppresses the distance matrix
+ */
+ public void cleanUp() {
+ sim = null;
+ }
+
/**
* Extract the alignment form the Similarity
* There are theoretically 16 types of extractors composing the
@@ -186,16 +196,20 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
if ( params.getParameter("noinst") == null ){
for (Iterator it1 = ((OWLOntology)onto1).getIndividuals().iterator(); it1.hasNext();) {
OWLIndividual ind1 = (OWLIndividual)it1.next();
- found = false; max = threshold; val = 0;
- OWLIndividual ind2 = null;
- for (Iterator it2 = ((OWLOntology)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 ( ind1.getURI() != null ) {
+ found = false; max = threshold; val = 0;
+ OWLIndividual ind2 = null;
+ for (Iterator it2 = ((OWLOntology)onto2).getIndividuals().iterator(); it2.hasNext(); ) {
+ OWLIndividual current = (OWLIndividual)it2.next();
+ if ( current.getURI() != null ) {
+ val = 1 - sim.getIndividualSimilarity(ind1,current);
+ if (val > max) {
+ found = true; max = val; ind2 = current;
+ }
+ }
}
+ if ( found ) addAlignCell(ind1,ind2, "=", max);
}
- if ( found ) addAlignCell(ind1,ind2, "=", max);
}
}
} catch (OWLException owlex) { owlex.printStackTrace(); }
@@ -393,12 +407,17 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
if ( params.getParameter("noinst") == null ){
for (Iterator it1 = ((OWLOntology)onto1).getIndividuals().iterator(); it1.hasNext();) {
ent1 = (OWLIndividual)it1.next();
- for (Iterator it2 = ((OWLOntology)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 OWLAPICell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
+ if ( ent1.getURI() != null ) {
+
+ for (Iterator it2 = ((OWLOntology)onto2).getIndividuals().iterator(); it2.hasNext(); ) {
+ ent2 = (OWLIndividual)it2.next();
+ if ( ent2.getURI() != null ) {
+ val = 1 - sim.getIndividualSimilarity((OWLIndividual)ent1,(OWLIndividual)ent2);
+ //val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
+ if ( val > threshold ){
+ cellSet.add( new OWLAPICell( (String)null, ent1, ent2, BasicRelation.createRelation("="), val ) );
+ }
+ }
}
}
}
diff --git a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
index 6e112b9b4a3e87f02bc6ec474e699c61b8723522..99b282f7e4c5a9c70f951e86ee06424247e41246 100644
--- a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
+++ b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
@@ -112,11 +112,23 @@ public abstract class MatrixMeasure implements Similarity {
}
prmatrix = new double[nbprop1+1][nbprop2+1];
// Create individual lists
- for ( Iterator it = onto2.getIndividuals().iterator(); it.hasNext(); nbind2++ ){
- indlist2.put( it.next(), new Integer(nbind2) );
+ for ( Iterator it = onto2.getIndividuals().iterator(); it.hasNext(); ){
+ OWLIndividual o = (OWLIndividual)it.next();
+ //System.err.println( o );
+ // We suppress anonymous individuals... this is not legitimate
+ if ( o.getURI() != null ) {
+ indlist2.put( o, new Integer(nbind2) );
+ nbind2++;
+ }
}
- for ( Iterator it = onto1.getIndividuals().iterator(); it.hasNext(); nbind1++ ){
- indlist1.put( it.next(), new Integer(nbind1) );
+ for ( Iterator it = onto1.getIndividuals().iterator(); it.hasNext(); ){
+ OWLIndividual o = (OWLIndividual)it.next();
+ //System.err.println( o );
+ // We suppress anonymous individuals... this is not legitimate
+ if ( o.getURI() != null ) {
+ indlist1.put( o, new Integer(nbind1) );
+ nbind1++;
+ }
}
indmatrix = new double[nbind1+1][nbind2+1];
@@ -137,9 +149,13 @@ public abstract class MatrixMeasure implements Similarity {
// (this comes first because otherwise, it2 is defined)
for ( Iterator it2 = onto2.getIndividuals().iterator(); it2.hasNext(); ){
OWLIndividual ind2 = (OWLIndividual)it2.next();
- for ( Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext(); ){
- OWLIndividual ind1 = (OWLIndividual)it1.next();
- indmatrix[((Integer)indlist1.get(ind1)).intValue()][((Integer)indlist2.get(ind2)).intValue()] = measure( ind1, ind2 );
+ if ( indlist2.get(ind2) != null ) {
+ for ( Iterator it1 = onto1.getIndividuals().iterator(); it1.hasNext(); ){
+ OWLIndividual ind1 = (OWLIndividual)it1.next();
+ if ( indlist1.get(ind1) != null ) {
+ indmatrix[((Integer)indlist1.get(ind1)).intValue()][((Integer)indlist2.get(ind2)).intValue()] = measure( ind1, ind2 );
+ }
+ }
}
}
// Compute distances on properties
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index 05aa5a5d90a1971c404efd25a5ac2db3fe82f0af..bfad92bdb8c8c01ded9a7d1a4c94a6b2d36659d3 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -245,7 +245,11 @@ public class OWLAPIAlignment extends BasicAlignment {
}
for (Enumeration e = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
- align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
+ try {
+ align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
+ } catch (AlignmentException aex) {
+ // Sometimes URIs are null, this is ignore
+ }
};
return align;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
index a95407e6b430fed789f5cc536e170c12a9b1f6fb..871ba9a40d99a87558bcc37b4f2b0cd6a91291e7 100644
--- a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
@@ -86,7 +86,6 @@ public class URIAlignment extends BasicAlignment {
/** Cell methods **/
public Cell addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure) throws AlignmentException {
-
if ( !( ob1 instanceof URI && ob2 instanceof URI ) )
throw new AlignmentException("arguments must be URIs");
@@ -153,6 +152,14 @@ public class URIAlignment extends BasicAlignment {
}
}
+ /**
+ * Returns default exception for conversion to URIAlignments
+ *
+ */
+ public URIAlignment toURIAlignment() throws AlignmentException {
+ return this;
+ }
+
/**
* Generate a copy of this alignment object
*/
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index fcc706254de56ead188b2c9f434d9a3acec26517..2e38ce445c8f93e9a7c6c0059cd4a053cbfe3fdc 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -26,6 +26,7 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.BasicEvaluator;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import java.util.Enumeration;
import java.util.Iterator;
@@ -64,8 +65,8 @@ public class PRecEvaluator extends BasicEvaluator {
private int nbcorrect = 0; // nb of cells correctly identified
/** Creation **/
- public PRecEvaluator(Alignment align1, Alignment align2) {
- super(align1, align2);
+ public PRecEvaluator(Alignment align1, Alignment align2) throws AlignmentException {
+ super(((BasicAlignment)align1).toURIAlignment(), ((BasicAlignment)align2).toURIAlignment());
}
public void init(){