diff --git a/html/tutorial/MyApp.java b/html/tutorial/MyApp.java
index 99150d1414eb2acde97281beca694a2a1bb3e5cd..d9819a470b92b67acd67fbd5b8076f7397c441dd 100644
--- a/html/tutorial/MyApp.java
+++ b/html/tutorial/MyApp.java
@@ -87,7 +87,7 @@ public class MyApp {
return ;
}
- // Run two diffent alignment methods (e.g., ngram distance and smoa)
+ // Run two different alignment methods (e.g., ngram distance and smoa)
AlignmentProcess a1 = new StringDistAlignment( onto1, onto2 );
params.setParameter("stringFunction","smoaDistance");
a1.align( (Alignment)null, params );
@@ -99,24 +99,31 @@ public class MyApp {
// Merge the two results.
((BasicAlignment)a1).ingest(a2);
- // Test its f-measure.
+ // Threshold at various thresholds
+ // Evaluate them against the references
+ // and choose the one with the best F-Measure
AlignmentParser aparser = new AlignmentParser(0);
Alignment reference = aparser.parse( "file://localhost"+(new File ( "refalign.rdf" ) . getAbsolutePath()), loaded );
Evaluator evaluator = new PRecEvaluator( reference, a1 );
- // Threshold at various thresholds (and maybe various threshold methods)
+ double best = 0.;
+ Alignment result = null;
for ( int i = 0; i <= 10 ; i = i+2 ){
a1.cut( ((double)i)/10 );
evaluator.eval( new BasicParameters() );
System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure());
+ if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
+ result = (BasicAlignment)((BasicAlignment)a1).clone();
+ best = ((PRecEvaluator)evaluator).getFmeasure();
}
+ }
- // If it is over a certain value, output the result as SWRL rules.
+ // Displays it as SWRL Rules
PrintWriter writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( System.out, "UTF-8" )), true);
AlignmentVisitor renderer = new SWRLRendererVisitor(writer);
- a1.render(renderer);
+ result.render(renderer);
writer.flush();
writer.close();
diff --git a/html/tutorial/index.html b/html/tutorial/index.html
index 572437a003dcfcc26d856de8bdfd7ae0d07f8a2c..53164487234b13e6f9148d3084385aa7f4b4bbc9 100644
--- a/html/tutorial/index.html
+++ b/html/tutorial/index.html
@@ -352,7 +352,7 @@ which brings for the same assertions:
through XLST transformations which will transform the OWL instance
files from one ontology to another:
<div class="fragment"><pre>
-$ java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter dist.rdf -r fr.inrialpes.exmo.align.impl.renderer.XSLTRendererVisitor -o results/SMOA5.xsl
+$ java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.XSLTRendererVisitor -o results/SMOA5.xsl
</pre></div>
this transformation can be applied to the data of <a href="data.xml">data.xml</a>:
<div class="fragment"><pre>
@@ -528,38 +528,37 @@ $ java -jar ../../lib/Procalign.jar file://localhost$CWD/rdf/edu.umbc.ebiquity.p
<h2>Embedding</h2>
<p>Of course, the goal of this API is not to be used at the command
- line level (even if it is very often very useful). So if you are
- ready for it, you can develop in Java your own application that take
+ line level (even if it can be very useful). So if you are
+ ready for it, you can develop in Java your own application that takes
advantage of the API.</p>
<p>A skeleton of program using the Alignment API
is <a href="Skeleton.java">Skeleton.java</a>. It can be compiled by
invoking:
<div class="fragment"><pre>
-$ javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar Skeleton.java
+$ javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar -d results Skeleton.java
</div>
and run by:
<div class="fragment"><pre>
-$ java -cp ../../lib/Procalign.jar:. Skeleton myOnto.owl edu.mit.visus.bibtex.owl
+$ java -cp ../../lib/Procalign.jar:results Skeleton myOnto.owl edu.mit.visus.bibtex.owl
</pre></div></p>
<p>Now considering the API (that can be consulted through its thin
- at <a
- href="../../javadoc/org/semanticweb/owl/align/Alignment.html">Javadoc</a>
+ <a href="../../javadoc/org/semanticweb/owl/align/Alignment.html">Javadoc</a>
for instance), can you modify the Skeleton program in order for it
performs the following:
<ul compact="1">
-<li>Run two diffent alignment methods (e.g., ngram distance and
+<li>Run two different alignment methods (e.g., ngram distance and
smoa);</li>
<li>Merge the two results;</li>
-<li>Threshold at various thresholds;</li>
-<li>Evaluate them against the references and choose the one with the
+<li>Trim at various thresholds;</li>
+<li>Evaluate them against the reference alignment and choose the one with the
best F-Measure;</li>
<li>Displays it as SWRL Rules.</li>
</ul>
Of course, you can do it progressively.
<div class="fragment"><pre>
-$ javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar MyApp.java
-$ java -cp ../../lib/Procalign.jar:. MyApp myOnto.owl edu.mit.visus.bibtex.owl > results/MyApp.owl
+$ javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar -d results MyApp.java
+$ java -cp ../../lib/Procalign.jar:results MyApp myOnto.owl edu.mit.visus.bibtex.owl > results/MyApp.owl
</pre></div></p>
<p>Do you want to see a possible solution?
<div class="button"><form>
@@ -569,7 +568,7 @@ $ java -cp ../../lib/Procalign.jar:. MyApp myOnto.owl edu.mit.visus.bibtex.owl >
<div class="explain" id="qu7"><p>
The main piece of code in Skeleton.java is replaced by
<pre>
-// Run two diffent alignment methods (e.g., ngram distance and smoa)
+// Run two different alignment methods (e.g., ngram distance and smoa)
AlignmentProcess a1 = new StringDistAlignment( onto1, onto2 );
params.setParameter("stringFunction","smoaDistance");
a1.align( (Alignment)null, params );
@@ -581,24 +580,33 @@ a1.align( (Alignment)null, params );
// Merge the two results.
((BasicAlignment)a1).ingest(a2);
-// Test its f-measure.
+// Threshold at various thresholds
+// Evaluate them against the references
+// and choose the one with the best F-Measure
AlignmentParser aparser = new AlignmentParser(0);
Alignment reference = aparser.parse( "file://localhost"+(new File ( "refalign.rdf" ) . getAbsolutePath()), loaded );
Evaluator evaluator = new PRecEvaluator( reference, a1 );
-// Threshold at various thresholds (and maybe various threshold methods)
+double best = 0.;
+Alignment result = null;
for ( int i = 0; i <= 10 ; i = i+2 ){
a1.cut( ((double)i)/10 );
evaluator.eval( new BasicParameters() );
System.err.println("Threshold "+(((double)i)/10)+" : "+((PRecEvaluator)evaluator).getFmeasure());
+ if ( ((PRecEvaluator)evaluator).getFmeasure() > best ) {
+ result = (BasicAlignment)((BasicAlignment)a1).clone();
+ best = ((PRecEvaluator)evaluator).getFmeasure();
+ }
}
-// If it is over a certain value, output the result as SWRL rules.
+// Displays it as SWRL Rules
PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( System.out, "UTF-8" )), true);
+ new BufferedWriter(
+ new OutputStreamWriter( System.out, "UTF-8" )), true);
AlignmentVisitor renderer = new SWRLRendererVisitor(writer);
-a1.render(renderer);
+result.render(renderer);
+writer.flush();
+writer.close();
</pre>
</p></div></p>
</p>
@@ -608,22 +616,15 @@ a1.render(renderer);
be passed at commant-line.
</p></div></p>
-<p><div class="logic"><p><b>More work:</b> Implement the F-measure optimization rule
- presented above so that you automatically select the threshold that
- maximizes F-measure.
-</p></div></p>
-
-<p><div class="logic"><p><b>Advanced:</b>
-What about writing an editor for the alignment API?
-</p></div></p>
-
<p><div class="logic"><p><b>Advanced:</b>
You can develop a specialized matching algorithm
by subclassing the Java programs provided in the Alignment API
implementation (like BasicAlignment or DistanceAlignment).
</p></div></p>
-
+<p><div class="logic"><p><b>Advanced:</b>
+What about writing an editor for the alignment API?
+</p></div></p>
<hr />
<h2>Further exercises</h2>
diff --git a/html/tutorial/script.sh b/html/tutorial/script.sh
index 8af6d644ca1107c5875d0a5643286df32b9b29aa..c6eb9c90de0767a2f774ef1ef5e32dd88af357e3 100644
--- a/html/tutorial/script.sh
+++ b/html/tutorial/script.sh
@@ -54,8 +54,9 @@ cp refalign.rdf results
java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupEval -r refalign.rdf -l "refalign,equal,SMOA,SMOA5,levenshtein,levenshtein33" -c prf -o results/eval.html
#####################
-# Evaluating
-
-javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar MyApp
-java -cp ../../lib/Procalign.jar MyApp file://localhost$CWD/rdf/myOnto.owl file://localhost$CWD/rdf/edu.mit.visus.bibtex.owl
+# Embedding
+javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar -d results Skeleton.java
+java -cp ../../lib/Procalign.jar:results Skeleton myOnto.owl edu.mit.visus.bibtex.owl
+javac -classpath ../../lib/api.jar:../../lib/rdfparser.jar:../../lib/align.jar:../../lib/procalign.jar -d results MyApp.java
+java -cp ../../lib/Procalign.jar:results MyApp myOnto.owl edu.mit.visus.bibtex.owl > results/MyApp.owl