- adapted code to multiple alignments (suppressed deprecated primitives)

src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java

@@ -84,7 +84,7 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
 	return (1 - getAlignedStrength1(ob));
     };
     public double getAlignedDistance2( Object ob ) throws AlignmentException{
-	return (1 - getAlignedStrength1(ob));
+	return (1 - getAlignedStrength2(ob));
     };
 
     /**
@@ -96,7 +96,8 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
     public void align( Alignment alignment, Parameters params ) throws AlignmentException, OWLException {
       if (  params.getParameter("type") != null ) 
 	  setType((String)params.getParameter("type"));
-      else setType("**");
+      // This is a 1:1 alignment in fact
+      else setType("11");
 
       getSimilarity().initialize( (OWLOntology)getOntology1(), (OWLOntology)getOntology2(), alignment );
       getSimilarity().compute( params );
@@ -219,18 +220,52 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
       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();
+					}}});*/
       SortedSet cellSet = new TreeSet(
 			    new Comparator() {
 				public int compare( Object o1, Object o2 )
 				    throws ClassCastException{
+				    try {
+					//System.err.println(((Cell)o1).getObject1()+" -- "+((Cell)o1).getObject2()+" // "+((Cell)o2).getObject1()+" -- "+((Cell)o2).getObject2());
 				    if ( o1 instanceof Cell
 					 && o2 instanceof Cell ) {
 					if ( ((Cell)o1).getStrength() > ((Cell)o2).getStrength() ){
 					    return -1;
+					} else if ( ((Cell)o1).getStrength() < ((Cell)o2).getStrength() ){
+					    return 1;
+					} else if ( (((OWLEntity)((Cell)o1).getObject1()).getURI().getFragment() == null)
+						    || (((OWLEntity)((Cell)o2).getObject1()).getURI().getFragment() == null) ) {
+					    return -1;
+					} else if ( ((OWLEntity)((Cell)o1).getObject1()).getURI().getFragment().compareTo(((OWLEntity)((Cell)o2).getObject1()).getURI().getFragment()) > 0) {
+					    return -1;
+					} else if ( ((OWLEntity)((Cell)o1).getObject1()).getURI().getFragment().compareTo(((OWLEntity)((Cell)o2).getObject1()).getURI().getFragment()) < 0 ) {
+					    return 1;
+					} else if ( (((OWLEntity)((Cell)o1).getObject2()).getURI().getFragment() == null)
+						    || (((OWLEntity)((Cell)o2).getObject2()).getURI().getFragment() == null) ) {
+					    return -1;
+					} else if ( ((OWLEntity)((Cell)o1).getObject2()).getURI().getFragment().compareTo(((OWLEntity)((Cell)o2).getObject2()).getURI().getFragment()) > 0) {
+					    return -1;
+					// On va supposer qu'ils n'ont pas le meme nom
 					} else { return 1; }
 				    } else {
 					throw new ClassCastException();
-				    }}});
+				    }
+				    } catch ( OWLException e) { 
+					e.printStackTrace(); return 0;}
+				}
+			    }
+			    );
 
       try {
 	  // Get all the matrix above threshold in the SortedSet
@@ -284,9 +319,9 @@ public class DistanceAlignment extends BasicAlignment implements AlignmentProces
 	      Cell cell = (Cell)it.next();
 	      ent1 = (OWLEntity)cell.getObject1();
 	      ent2 = (OWLEntity)cell.getObject2();
-	      if ( (getAlignCell1( ent1 ) == null) && (getAlignCell2( ent2 ) == null) ){
+	      if ( (getAlignCells1( ent1 ) == null) && (getAlignCells2( ent2 ) == null) ){
 		  // The cell is directly added!
-		  addCell( ent1, ent2, cell );
+		  addCell( cell );
 	      }
 	  };
 

src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java

@@ -130,12 +130,19 @@ public class ClassStructAlignment extends DistanceAlignment implements Alignment
 		    // check that there is a correspondance
 		    // in list of class2 atts and add their weights
 		    for ( Iterator prp = properties1.iterator(); prp.hasNext(); ){
-			Cell cell = getAlignCell1( (OWLEntity)prp.next() );
-			if ( cell != null ) {
-			    if ( properties2.contains((Object)cell.getObject2() ) ) {
-				attsum = attsum + 1 - cell.getStrength();
+			Set s2 = getAlignCells1( (OWLEntity)prp.next() );
+			// Find the property with the higest similarity
+			// that is matched here
+			double currentValue = 0.;
+			for( Iterator it2 = s2.iterator(); it2.hasNext(); ){
+			    Cell c2 = (Cell)it2.next();
+			    if ( properties2.contains((Object)c2.getObject2() ) ) {
+				double val = c2.getStrength();
+				if ( val > currentValue )
+				    currentValue = val;
 			    }
 			}
+			attsum = attsum + 1 - currentValue;
 		    }
 		    classmatrix[i][j] = classmatrix[i][j]
 			+ pic2 * (2 * attsum / (nba1 + nba2));

src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java

@@ -195,12 +195,19 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
 			// check that there is a correspondance
 			// in list of class2 atts and add their weights
 			for ( Iterator prp = properties1.iterator(); prp.hasNext(); ){
-			    Cell cell = getAlignCell1( (OWLEntity)prp.next() );
-			    if ( cell != null ) {
-				if ( properties2.contains((Object)cell.getObject2() ) ) {
-				    attsum = attsum + 1 - cell.getStrength();
+			    Set s2 = getAlignCells1( (OWLEntity)prp.next() );
+			    // Find the property with the higest similarity
+			    // that is matched here
+			    double currentValue = 0.;
+			    for( Iterator it2 = s2.iterator(); it2.hasNext(); ){
+				Cell c2 = (Cell)it2.next();
+				if ( properties2.contains((Object)c2.getObject2() ) ) {
+				    double val = c2.getStrength();
+				    if ( val > currentValue )
+					currentValue = val;
 				}
 			    }
+			    attsum = attsum + 1 - currentValue;
 			}
 			classmatrix[i][j] = classmatrix[i][j]
 			    + pic2 * (2 * attsum / (nba1 + nba2));

src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java

@@ -89,7 +89,7 @@ public class OWLAxiomsRendererVisitor implements AlignmentVisitor
 	URI entity1URI = null;
 	try {
 	    // Not very good but we failed to think subsumed from the first shot.
-	    if ( Class.forName("fr.inrialpes.exmo.align.impl.rel.SubsumedRelation").isInstance(cell.getRelation()) ) {
+	    if ( cell.getRelation() instanceof SubsumedRelation ){
 		onto1 = (OWLOntology)alignment.getOntology2();
 		entity1URI = ((OWLEntity)cell.getObject2()).getURI();
 	    } else {
@@ -116,7 +116,6 @@ public class OWLAxiomsRendererVisitor implements AlignmentVisitor
 	    writer.print("\n");
 	}
 	catch (OWLException e) { throw new AlignmentException("getURI problem", e); }
-	catch (ClassNotFoundException e) { throw new AlignmentException("Class no found", e); };
     }
     public void visit( EquivRelation rel ) throws AlignmentException {
 	OWLOntology onto2 = (OWLOntology)alignment.getOntology2();

src/fr/inrialpes/exmo/align/parser/AlignmentParser.java

 /*
  * $Id$
+ * MULT
  *
  * Copyright (C) 2003-2005 INRIA Rhne-Alpes.
  *
@@ -62,6 +63,7 @@ import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.Cell;
 import org.semanticweb.owl.align.AlignmentException;
 import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.MultipleAlignment;
 
 /**
  * This class allows the creation of a parser for an Alignment file.
@@ -105,7 +107,9 @@ public class AlignmentParser extends DefaultHandler {
      * This is a pitty but the idea of creating a particular alignment
      * is not in accordance with using an interface.
      */
-    protected Alignment alignment = null;
+    //JE: mult
+    //protected Alignment alignment = null;
+    protected MultipleAlignment alignment = null;
     
     /**
      * the content found as text...
@@ -248,7 +252,9 @@ public class AlignmentParser extends DefaultHandler {
 		} else if (pName.equals("level")) {
 		} else if (pName.equals("xml")) {
 		} else if (pName.equals("Alignment")) {
-		    alignment = new BasicAlignment();
+		    //JE: multiple
+		    //alignment = new BasicAlignment();
+		    alignment = new MultipleAlignment();
 		} else {
 		    if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
 		    //throw new SAXException("[AlignmentParser] Unknown element name : "+pName);
@@ -313,8 +319,10 @@ public class AlignmentParser extends DefaultHandler {
 		    }
 		    if ( cl1 == null || cl2 == null ) {
 			// Maybe we could just print this out and fail in the end.
-			throw new SAXException( "Missing entity "+cl1+" "+cl2 ); }
-		    if ( measure == null || relation == null ){
+			//throw new SAXException( "Missing entity "+cl1+" "+cl2 );
+			// The cell is void
+			System.err.println("Warning (cell voided), missing entity "+cl1+" "+cl2 );
+		    } else if ( measure == null || relation == null ){
 			cell = alignment.addAlignCell( cl1, cl2);
 		    } else {
 			cell = alignment.addAlignCell( cl1, cl2, relation, Double.parseDouble(measure) );}

src/fr/inrialpes/exmo/align/util/GroupEval.java

@@ -61,9 +61,9 @@ import gnu.getopt.Getopt;
 
 import fr.inrialpes.exmo.align.parser.AlignmentParser;
 
-/** A basic class for an OWL ontology alignment processing. The processor
-    will parse ontologies, align them and renderings the resulting alignment.
-    Command synopsis is as follows:
+/** A basic class for synthesizing the results of a set of alignments provided by
+    different algorithms. The output is a table showing various classical measures
+    for each test and for each algorithm. Average is also computed.
     
     <pre>
     java -cp procalign.jar fr.inrialpes.exmo.align.util.GroupEval [options]
@@ -79,8 +79,11 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
     -t output --type=output: xml/tex/html/ascii
    </pre>
 
-    If output is
-    requested (<CODE>-o</CODE> flags), then output will be written to
+   The input is taken in the current directory in a set of subdirectories (one per
+   test which will be rendered by a line) each directory contains a number of
+   alignment files (one per algorithms which will be renderer as a column).
+
+    If output is requested (<CODE>-o</CODE> flags), then output will be written to
     <CODE>output</CODE> if present, stdout by default.
 
 <pre>
@@ -110,7 +113,7 @@ public class GroupEval {
     }
 
     public static void run(String[] args) throws Exception {
-	String listFile = "std,ssda5,nea,edna5,sdna5,karlsruhe,karlsruhe2,fujitsu,umontreal,stanford";
+	String listFile = "";
 	LongOpt[] longopts = new LongOpt[8];
 	loaded = new Hashtable();
 
@@ -166,6 +169,7 @@ public class GroupEval {
 	    }
 	}
 
+	// JE: StringTokenizer is obsoleted in Java 1.4 in favor of split: to change
 	listAlgo = new Vector();
 	StringTokenizer st = new StringTokenizer(listFile,",");
 	while (st.hasMoreTokens()) {
@@ -337,12 +341,9 @@ public class GroupEval {
 		// For each record print the values <td>bla</td>
 		Enumeration f = test.elements();
 		f.nextElement();
-		System.err.println(" Test#"+test);
 		for( int k = 0 ; f.hasMoreElements() ; k++) {
 		    PRecEvaluator eval = (PRecEvaluator)f.nextElement();
 		    if ( eval != null ){
-			// JE: It might seem that the analogy with kilometers is not correct? This is because of when we have found=0 then the rate is 0, then the value must worsen... which is not the case with our new stuff:
-			// I must reconstuct P & R: this is doable.
 			// iterative H-means computation
 			if ( nexpected == -1 ){
 			    nexpected = eval.getExpected();
@@ -356,20 +357,6 @@ public class GroupEval {
 			int ocorrect = correctVect[k];
 			correctVect[k] = ocorrect + ncorrect;
 
-			//System.err.println("  Algo "+k+" hprec[k-1]="+hMeansPrec[k]+" exp[k-1]="+oexpected+" Prec[k]="+eval.getPrecision()+" exp[k]="+nexpected);
-			// JE: not sure it is precision or recall
-			//if ( eval.getRecall() == 0 ) {
-			//    hMeansRec[k] = (expected)/((oexpected/hMeansRec[k])); 
-			//} else {
-			//    hMeansRec[k] = (expected)/((nexpected/eval.getRecall())+(oexpected/hMeansRec[k])); 
-			//};
-			//if ( eval.getPrecision() == 0 ){
-			//    hMeansPrec[k] = (foundVect[k])/((ofound/hMeansPrec[k])); 
-			//} else {
-			//    hMeansPrec[k] = (foundVect[k])/((nfound/eval.getPrecision())+(ofound/hMeansPrec[k])); 
-			//};
-			// Update data structures
-			//System.err.println("          hprec[k]="+hMeansPrec[k]+" exp[k]="+expected);
 			for ( int i = 0 ; i < fsize; i++){
 			    writer.print("<td>");
 			    if ( format.charAt(i) == 'p' ) {
@@ -443,7 +430,6 @@ public class GroupEval {
     public static void usage() {
 	System.out.println("usage: GroupEval [options]");
 	System.out.println("options are:");
-	System.out.println("\t--impl=className -i classname\t\tUse the given alignment implementation.");
 	System.out.println("\t--format=prfmo -r prfmo\tSpecifies the output order (precision/recall/fallout/f-measure/overall)");
 	System.out.println("\t--dominant=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
 	System.out.println("\t--type=html|xml|tex|ascii -t html|xml|tex|ascii\tSpecifies the output format");

src/fr/inrialpes/exmo/align/util/Procalign.java

 /*
  * $Id$
+ * MULT
  *
  * Copyright (C) 2003 The University of Manchester
  * Copyright (C) 2003 The University of Karlsruhe