diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index 116b18234e5164e71bc1a802138519868bdbaba2..14930a0a3f28aeb155cda52d3a12063bd322b8c2 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/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 );
}
};
diff --git a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
index e7979c1f3592e29432d7f309e98a520e6cf926a3..56a711d575aeb8db382efc24cc280e507c69b6ef 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
+++ b/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));
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
index 5e09a350901423d39f132c4d0f9221fa62d96c98..6008219f377f58bb2771c940c05168518f27c955 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
+++ b/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));
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
index bc016c064e917c3a5da5576e4d6374e53ed308f9..ffc2bb0d4dc058d6165ee8492e2c29fa055fde10 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
+++ b/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();
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index a79c67abb96850949da163054fbccd9f03ca637e..26f7deb2a0a037830c755f97fc96a3c71c99e4a0 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -1,5 +1,6 @@
/*
* $Id$
+ * MULT
*
* Copyright (C) 2003-2005 INRIA Rhône-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) );}
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index c27bddd9e429f7d1d4bae9f7313ccde8c620f49f..f439cc89581759b62f44c2a62a5b34f31efb6dce 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/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");
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/util/Procalign.java
index 2de765efecd0b7cfc33c8bcfb8c04c3228f900bf..a9da4b18199c11bb7df8cadf5215076cf3383b07 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/util/Procalign.java
@@ -1,5 +1,6 @@
/*
* $Id$
+ * MULT
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe