diff --git a/README.TXT b/README.TXT
index 0d8123fa953eee9daedc58aff6d2a5df567c868e..567b354334b7df5d194b5c832ed58f1645435001 100644
--- a/README.TXT
+++ b/README.TXT
@@ -1,6 +1,6 @@
#######################################################################
# Ontology alignment API and implementation #
-# 03/06/2011, version 4.2 #
+# 03/12/2011, version 4.3 #
# http://alignapi.gforge.inria.fr #
#######################################################################
@@ -61,7 +61,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.4 -o examples/rdf/sample.rdf
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter file:examples/rdf/newsample.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter file:examples/rdf/newsample.rdf
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -a examples/rdf/sample.rdf
@@ -71,7 +71,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publica
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=subStringDistance -t .4 -o examples/rdf/bibref2.rdf
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -DprintMatrix=1 -o /dev/null > examples/rdf/matrix.tex
@@ -123,7 +123,8 @@ plugins/neon/ Plug-in for the NeOn toolkit
src/ Java sources of ontoalign
org.semanticweb.owl.align: the API
fr.inrialpes.exmo.align.impl: basic implementation
- fr.inrialpes.exmo.align.util: utility wrapper functions
+ fr.inrialpes.exmo.align.util: utility functions
+ fr.inrialpes.exmo.align.cli: command line interface
fr.inrialpes.exmo.align.ling: WordNet-based implementation
fr.inrialpes.exmo.align.service: Alignment Service
fr.inrialpes.exmo.ontowrap: Abstract ontology layer
diff --git a/build.xml b/build.xml
index 8fbfa8b3dd21e28b4097fefec77369cca5b1c2eb..e1191b4a09e63aed030548e5418e26591da90dc6 100644
--- a/build.xml
+++ b/build.xml
@@ -183,7 +183,7 @@
<jar jarfile="lib/procalign.jar">
<manifest>
<attribute name="Built-Date" value="${date}"/>
- <attribute name="Main-Class" value="fr.inrialpes.exmo.align.util.Procalign"/>
+ <attribute name="Main-Class" value="fr.inrialpes.exmo.align.cli.Procalign"/>
<attribute name="Class-Path" value="${jarclasspath}"/>
<attribute name="Implementation-Title" value="Alignment API implementation"/>
<attribute name="Implementation-Version" value="${version}.${version.update}"/>
@@ -193,12 +193,13 @@
<attribute name="Bundle-Copyright" value="INRIA, 2003-2011"/>
<attribute name="Bundle-Date" value="${date}"/>
<attribute name="Bundle-License" value="GNU Lesser General Public License 2.1 or above"/>
- <attribute name="Export-package" value="fr.inrialpes.exmo.align.impl,fr.inrialpes.exmo.align.impl.edoal,fr.inrialpes.exmo.align.impl.eval,fr.inrialpes.exmo.align.impl.method,fr.inrialpes.exmo.align.impl.rel,fr.inrialpes.exmo.align.impl.renderer,fr.inrialpes.exmo.align.ling,fr.inrialpes.exmo.align.parser,fr.inrialpes.exmo.align.util,fr.inrialpes.exmo.align.gen"/>
+ <attribute name="Export-package" value="fr.inrialpes.exmo.align.impl,fr.inrialpes.exmo.align.impl.edoal,fr.inrialpes.exmo.align.impl.eval,fr.inrialpes.exmo.align.impl.method,fr.inrialpes.exmo.align.impl.rel,fr.inrialpes.exmo.align.impl.renderer,fr.inrialpes.exmo.align.ling,fr.inrialpes.exmo.align.parser,fr.inrialpes.exmo.align.util,fr.inrialpes.exmo.align.cli,fr.inrialpes.exmo.align.gen"/>
<attribute name="Import-package" value="fr.inrialpes.exmo.ontowrap,fr.inrialpes.exmo.ontowrap.jena25,fr.inrialpes.exmo.ontowrap.owlapi10,fr.inrialpes.exmo.ontowrap.owlapi30,fr.inrialpes.exmo.ontowrap.util,org.semanticweb.owl.align"/>
</manifest>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/impl/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/parser/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/util/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/cli/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/gen/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/ling/**/*.class"/>
<fileset dir="classes" includes="LICENSE.TXT"/>
diff --git a/examples/omwg/README.sh b/examples/omwg/README.sh
index f8ed4b82b70d23e48ff14f51b48370c2812b097e..54f089a1a41feef48ddf0091aff01e3bce1436f2 100644
--- a/examples/omwg/README.sh
+++ b/examples/omwg/README.sh
@@ -1,9 +1,9 @@
#!/bin/sh
echo 1st
-java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter wine.xml > wine2.xml
+java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine.xml > wine2.xml
echo 2nd
-java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter wine2.xml > wine3.xml
+java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine2.xml > wine3.xml
echo diff
diff wine2.xml wine3.xml
diff --git a/examples/tests.sh b/examples/tests.sh
index 657dde20f49b731253ac4814434c3d7830b94a40..609ee39b9b1e056c715a46b529d0f1c2a5b515b6 100644
--- a/examples/tests.sh
+++ b/examples/tests.sh
@@ -45,32 +45,32 @@ java -jar ../lib/procalign.jar file://$CWD/rdf/edu.umbc.ebiquity.publication.owl
# Evaluate their performances
echo "Comparing..."
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/NameEq.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/NameEq.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/EditDistName.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/EditDistName.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/SubsDistName.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/SubsDistName.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist4.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist4.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist7.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist7.owl
# Other evaluations
echo "Comparing again..."
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/NameEq.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/NameEq.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/EditDistName.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/EditDistName.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/SubsDistName.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/SubsDistName.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist4.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist4.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist7.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.SymMeanEvaluator file://$CWD/rdf/bibref.owl file://$CWD/aligns/StrucSubsDist7.owl
# Pipelining
echo "Pipelining..."
@@ -78,7 +78,7 @@ java -jar ../lib/procalign.jar file://$CWD/rdf/edu.umbc.ebiquity.publication.owl
java -jar ../lib/procalign.jar file://$CWD/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.ClassStructAlignment -a aligns/PropSubsDist.owl -o aligns/Piped.owl
-java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/aligns/StrucSubsDist.owl file://$CWD/aligns/Piped.owl
+java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/aligns/StrucSubsDist.owl file://$CWD/aligns/Piped.owl
# Rendering
echo "Rendering..."
diff --git a/html/eval.html b/html/eval.html
index d34cfcd0b090ff78317ab2be606439b0630f2949..936a862a7136148e2e6fd6cc0544c81ec7fc545c 100644
--- a/html/eval.html
+++ b/html/eval.html
@@ -16,7 +16,7 @@ implementation described here. It is included in the
<h2>Evaluating</h2>
<p>For demonstrating the use of the API, we implement it and use it
through a particular processor
- (<tt>fr.inrialpes.exmo.align.util.EvalAlign</tt>) which:
+ (<tt>fr.inrialpes.exmo.align.cli.EvalAlign</tt>) which:
<ul compact="1">
<li>Reads two OWL/RDF ontologies;</li>
<li>Creates an alignment object;</li>
@@ -25,7 +25,7 @@ implementation described here. It is included in the
</ul>
Running the program is achieved through:
<div class="fragment"><pre>
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign
Require two alignement filenames
usage: EvalAlign [options] file1 file2
options are:
@@ -35,7 +35,7 @@ options are:
</pre></div>
or ($CWD is the current directory)
<div class="fragment"><pre>
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign file://$CWD/result/align1.owl file://$CWD/result/align2.owl
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign file://$CWD/result/align1.owl file://$CWD/result/align2.owl
</pre></div>
</p>
diff --git a/html/relnotes.html b/html/relnotes.html
index 5bede42533159dbdf8790876a361a305cdf319d8..c138c22c29ab32d65028d97873b32378ed12ece3 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -64,7 +64,11 @@ with a warning:
<h2>Current SVN trunk version</h2>
<!--h2>Version 4.3 (): xx/xx/2011 - Zimt</h2-->
+<p><span style="color: red;">BEWARE:</span> All command-line utilities
+ are now found in the <span style="color: red;">cli</span> package
+ instead of <b>util</b>.</p>
<p><ul compact="1">
+<li>Created new "Command line interface" directory (util/cli)</li>
<li>Full reengineering of the test generator (gen)</li>
<li>Implemented <tt>extractss</tt> for ** alignments in <tt>DistanceAlignment</tt> (impl)</li>
<li>Changed default type of <tt>StringDistAlignment</tt> to "?*" for
@@ -77,6 +81,7 @@ with a warning:
equisimilarity situations (impl)</li>
<li>Slightly modified the parser so that it accepts Alignment URI with
or without # (parser)</li>
+<li>Added better error checking in <tt>toObjectAlignment</tt> (impl)</li>
<li>Fixed a bug on <tt>DistanceAlignment</tt> 1:1 extraction when the
second ontology is larger than the first one (impl)</li>
</ul></p>
diff --git a/html/tutorial/tutorial1/index.html b/html/tutorial/tutorial1/index.html
index 67cf68060b2f106e97354d5b3a7ad2dbdafff899..1a79d89573a2625d389baa62a3f05993d24a3cba 100644
--- a/html/tutorial/tutorial1/index.html
+++ b/html/tutorial/tutorial1/index.html
@@ -100,7 +100,7 @@ between two bibliographic ontologies. They can be seen here:</p>
<h2>Matching</h2>
-<p>For demonstrating the use of our implementation of the Alignment <abbr>API</abbr>, we implemented a particular processor (<tt>fr.inrialpes.exmo.align.util.Procalign</tt>) which:</p>
+<p>For demonstrating the use of our implementation of the Alignment <abbr>API</abbr>, we implemented a particular processor (<tt>fr.inrialpes.exmo.align.cli.Procalign</tt>) which:</p>
<ul>
<li>Reads two <acronym title="Web Ontology Language">OWL</acronym>/<abbr>RDF</abbr> ontologies;</li>
<li>Creates an alignment object;</li>
@@ -209,7 +209,7 @@ $ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.St
a WordNet based distance provided with the <abbr>API</abbr>
implementation by ($WNDIR is the directory where wordnet 3.0 is installed):</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.util.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
+$ java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.cli.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
</div>
<p>See the output in <a href="results/jwnl.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/jwnl.html"><abbr>HTML</abbr></a> (if rendered as before).</p></div>
@@ -239,7 +239,7 @@ $ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.St
<p><b>Other manipulations:</b> It is possible to invert an alignment with the following command:</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter -i results/SMOA5.rdf -o results/AOMS5.rdf
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter -i results/SMOA5.rdf -o results/AOMS5.rdf
</div>
<p>See the output in <a href="results/AOMS5.rdf"><abbr>RDF</abbr>/<abbr>XML</abbr></a> or <a href="results/AOMS5.html"><abbr>HTML</abbr></a> (if rendered as before). The results is an alignment from the source to the target. Inverting alignment is only the exchange of the order of the elements in the alignment file. This can be useful when you have an alignment of <i>A</i> to <i>B</i>, an alignment from <i>C</i> to <i>B</i> and you want to go from <i>A</i> to <i>C</i>. The solution is then to invert the second alignment and to compose them.</p>
@@ -251,7 +251,7 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter
<p>Once a good alignment has been found, only half of the work has been done. In order to actually use our result it is necessary to transform it into some processable format. For instance, if one wants to merge two OWL ontologies, the alignment can be changed into set of <acronym>OWL</acronym> "bridging" axioms. This is achieved by "rendering" the alignment in <acronym>OWL</acronym> (through the <tt>-r</tt> switch):</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
</div>
<p>The result is a set of OWL assertions of the form:</p>
@@ -267,7 +267,7 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter
<p>If one wants to use the alignments only for infering on instances without actually merging the classes, she can generate SWRL rules:</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
</div>
<p>which brings for the same assertions:</p>
<div class="owl"><pre>
@@ -304,7 +304,7 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter
<p>Exchanging data can also be achieved more simply through <abbr>XSLT</abbr> transformations which will transform the <acronym>OWL</acronym> instance files from one ontology to another:</p>
<div class="fragment">
-$ 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
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.XSLTRendererVisitor -o results/SMOA5.xsl
</div>
<p>this transformation can be applied to the data of <a href="data.xml">data.xml</a>:</p>
<div class="fragment">
@@ -318,7 +318,7 @@ $ xsltproc results/SMOA5.xsl data.xml > results/data.xml
<p>For evaluating we use another class than <tt>Procalign</tt>. It is called <tt>EvalAlign</tt> we should specify this to <tt>java</tt>. By default, it computes precision, recall and associated measures. It can be invoked this way:</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/equal.rdf
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/equal.rdf
</div>
<p>The first argument is always the reference alignment, the second one is the alignment to be evaluated. The result is given here:</p>
@@ -350,7 +350,7 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i
<div class="explain" id="qu5"><p>Since it returns more correspondences by loosening the constraints for being a correspondence, it is expected that the recall will increase at the expense of precision.</p></div>
<p>We can see the results of:</p>
<div class="fragment">
-$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/levenshtein33.rdf
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/levenshtein33.rdf
</div>
<div class="button">
<input type="button" onclick="show('qu6')" value="Show result"/>
@@ -375,7 +375,7 @@ $ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i
<p>It is possible to summarize these results by comparing them to each others. This can be achieved by the <tt>GroupEval</tt> class. This class can output several formats (by default html) and takes all the alignments in the subdirectories of the current directory. Here we only have the <tt>results</tt> directory:</p>
<div class="fragment">
$ 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 -f prm -o results/eval.html
+$ java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.GroupEval -r refalign.rdf -l "refalign,equal,SMOA,SMOA5,levenshtein,levenshtein33" -c -f prm -o results/eval.html
</div>
<p>The results are displayed in the <a href="results/eval.html">results/eval.html</a> file whose main content is the table:</p>
diff --git a/html/tutorial/tutorial1/script.bat b/html/tutorial/tutorial1/script.bat
index edac78d5249a1e12431e05ea837aafa814ad230a..5601bdf7066c30d21d6d6c9fea71b5d10714ee2f 100755
--- a/html/tutorial/tutorial1/script.bat
+++ b/html/tutorial/tutorial1/script.bat
@@ -54,18 +54,18 @@ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.Stri
java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance -t 0.5 file://%CWD%/myOnto.owl file://%CWD%/edu.mit.visus.bibtex.owl -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results\SMOA5.html
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter -i results\SMOA5.rdf -o results\AOMS5.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter -i results\SMOA5.rdf -o results\AOMS5.rdf
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter -i results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results\AOMS5.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter -i results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results\AOMS5.html
rem #####################
rem # Outputing
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
-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
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results\SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.XSLTRendererVisitor -o results\SMOA5.xsl
xsltproc results\SMOA5.xsl data.xml > results\data.xml
@@ -73,11 +73,11 @@ xsltproc results\SMOA5.xsl data.xml > results\data.xml
rem #####################
rem # Evaluating
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter refalign.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results\refalign.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter refalign.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results\refalign.html
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://%CWD%/refalign.rdf file://%CWD%/tutorial1/results/equal.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://%CWD%/refalign.rdf file://%CWD%/tutorial1/results/equal.rdf
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://%CWD%/refalign.rdf file://%CWD%/results/tutorial1/levenshtein33.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://%CWD%/refalign.rdf file://%CWD%/results/tutorial1/levenshtein33.rdf
rem # This is for printing distance matrix
rem #java -jar ../../../lib/Procalign.jar file://%CWD%/rdf/myOnto.owl file://%CWD%/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -DprintMatrix=1 -o /dev/null > matrix.tex
@@ -85,7 +85,7 @@ rem #java -jar ../../../lib/Procalign.jar file://%CWD%/rdf/myOnto.owl file://%CW
rem JE: ??
copy ..\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 -f prm -o results\eval.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.GroupEval -r refalign.rdf -l "refalign,equal,SMOA,SMOA5,levenshtein,levenshtein33" -c -f prm -o results\eval.html
diff --git a/html/tutorial/tutorial1/script.sh b/html/tutorial/tutorial1/script.sh
index 6c7dcfa5d5194d47e229357451c328be35cf6b6e..656870f8989607aae3a2596fb7821b46d2f8ad03 100644
--- a/html/tutorial/tutorial1/script.sh
+++ b/html/tutorial/tutorial1/script.sh
@@ -32,9 +32,9 @@ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.Stri
java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/SMOA.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/SMOA.html
-java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.util.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
+java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.cli.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/jwnl.rdf
-java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.util.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/jwnl.html
+java -cp ../../../lib/procalign.jar:../../../lib/jwnl/jwnl.jar fr.inrialpes.exmo.align.cli.Procalign -Dwndict=$WNDIR -i fr.inrialpes.exmo.align.ling.JWNLAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/jwnl.html
#####################
# Manipulating
@@ -47,34 +47,34 @@ java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.Stri
java -jar ../../../lib/procalign.jar -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=smoaDistance -t 0.5 file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl -o results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/SMOA5.html
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -i -o results/AOMS5.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -i -o results/AOMS5.rdf
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -i -o results/AOMS5.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/AOMS5.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -i -o results/AOMS5.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/AOMS5.html
#####################
# Outputing
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.SWRLRendererVisitor
-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
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter results/SMOA5.rdf -r fr.inrialpes.exmo.align.impl.renderer.XSLTRendererVisitor -o results/SMOA5.xsl
xsltproc results/SMOA5.xsl data.xml > results/data.xml
#####################
# Evaluating
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter refalign.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/refalign.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter refalign.rdf -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -o results/refalign.html
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/equal.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/equal.rdf
-java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/levenshtein33.rdf
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/refalign.rdf file://$CWD/tutorial1/results/levenshtein33.rdf
# This is for printing distance matrix
#java -jar ../../../lib/Procalign.jar file://$CWD/rdf/myOnto.owl file://$CWD/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -DprintMatrix=1 -o /dev/null > matrix.tex
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 -f prm -o results/eval.html
+java -cp ../../../lib/procalign.jar fr.inrialpes.exmo.align.cli.GroupEval -r refalign.rdf -l "refalign,equal,SMOA,SMOA5,levenshtein,levenshtein33" -c -f prm -o results/eval.html
diff --git a/html/tutorial/tutorial3/index.html b/html/tutorial/tutorial3/index.html
index 9cb8dd4030e8b453020e6c79b6f1ea9ded36df3d..32331e02b4fba64f3f279785e19b496e7dc10596 100644
--- a/html/tutorial/tutorial3/index.html
+++ b/html/tutorial/tutorial3/index.html
@@ -231,7 +231,7 @@ $ javac -classpath .:../../../lib/align.jar:../../../lib/procalign.jar -d result
</div>
and can be used in:
<div class="fragment">
-$ java -classpath .:../../../lib/ontowrap.jar:../../../lib/procalign.jar:results fr.inrialpes.exmo.align.util.Procalign -i MyAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl
+$ java -classpath .:../../../lib/ontowrap.jar:../../../lib/procalign.jar:results fr.inrialpes.exmo.align.cli.Procalign -i MyAlignment file://$CWD/myOnto.owl file://$CWD/edu.mit.visus.bibtex.owl
</div>
</p>
<p>
@@ -342,7 +342,7 @@ In order to have this new class directly jar-launchable, it is sufficient to del
Manifest-Version: 1.0
Created-By: Jerome.Euzenat@inrialpes.fr
Class-Path: align.jar ontowrap.jar procalign.jar mymatcher.jar
-Main-Class: fr/inrialpes/exmo/align/util/Procalign
+Main-Class: fr/inrialpes/exmo/align/cli/Procalign
</div>
The jar may then be launched by:
diff --git a/lib/align.jar b/lib/align.jar
index 36859bef46725bca1e73f7c563cf2e58453a24a6..ace2befda68b8f639d907c932c63f2900a3f11af 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/alignsvc.jar b/lib/alignsvc.jar
index 0cec48f07417aa0c381e24dd27cf46dff8644968..14332d4e50b8d587d1e484aa7d21a590befcedb4 100644
Binary files a/lib/alignsvc.jar and b/lib/alignsvc.jar differ
diff --git a/lib/ontowrap.jar b/lib/ontowrap.jar
index c2703846ff87f97e0c42d85b19e843fff8c3d2ea..b56fe8a5053ee206f85dd09e53e92e4805d66974 100644
Binary files a/lib/ontowrap.jar and b/lib/ontowrap.jar differ
diff --git a/lib/procalign.jar b/lib/procalign.jar
index b6eca4b7b2bf48f184ad82b183580979e88776eb..1510cbb8739391d7cda6ec02f104e23761e9276a 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/plugins/android/build.xml b/plugins/android/build.xml
index ba24f084323a2f9b54860c23f96a4a615319ad46..538d94146d08616ec2dacf6409419b8ee74642fe 100644
--- a/plugins/android/build.xml
+++ b/plugins/android/build.xml
@@ -28,7 +28,7 @@
<exclude name="fr/inrialpes/exmo/align/gen/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/ling/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/service/**/*.java"/>
- <exclude name="fr/inrialpes/exmo/align/util/**/*.java"/>
+ <exclude name="fr/inrialpes/exmo/align/cli/**/*.java"/>
<!-- for picoalign -->
<!--exclude name="fr/inrialpes/exmo/align/impl/edoal/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/parser/RDFParser.java"/-->
@@ -126,7 +126,7 @@
<exclude name="fr/inrialpes/exmo/align/gen/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/ling/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/service/**/*.java"/>
- <exclude name="fr/inrialpes/exmo/align/util/**/*.java"/>
+ <exclude name="fr/inrialpes/exmo/align/cli/**/*.java"/>
<!-- for picoalign -->
<!--exclude name="fr/inrialpes/exmo/align/impl/edoal/**/*.java"/>
<exclude name="fr/inrialpes/exmo/align/parser/RDFParser.java"/-->
diff --git a/src/fr/inrialpes/exmo/align/util/EvalAlign.java b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
similarity index 98%
rename from src/fr/inrialpes/exmo/align/util/EvalAlign.java
rename to src/fr/inrialpes/exmo/align/cli/EvalAlign.java
index d78d3eb792c529f0cb8c3a51f242bfe2a0e44e33..257835bacf42fed9ba46e78b2795283be05f2da3 100644
--- a/src/fr/inrialpes/exmo/align/util/EvalAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2008, 2010
+ * Copyright (C) INRIA, 2003-2008, 2010-2011
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -20,7 +20,7 @@
/*
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
diff --git a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
rename to src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
index 2a48d5c730a51fab0ff5e8b9c75e41e2f3c4b7a8..17bb9c289697de1dc0e3e25ee8f1ec20e9836c96 100644
--- a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, 2007-2010 INRIA
+ * Copyright (C) 2003-2005, 2007-2011 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -26,7 +26,7 @@
It uses the generalisations of precision and recall described in
[Ehrig & Euzenat 2005].
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Evaluator;
diff --git a/src/fr/inrialpes/exmo/align/util/GenPlot.java b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/GenPlot.java
rename to src/fr/inrialpes/exmo/align/cli/GenPlot.java
index 57e67578831cff40338ee0644bcd318fbaef2539..eca997441ee7a4df834c0fe7ce63267327c2cde2 100644
--- a/src/fr/inrialpes/exmo/align/util/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2010, INRIA
+ * Copyright (C) 2003-2011, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -24,7 +24,7 @@
* This program evaluates the results of several ontology aligners and plot
* these results
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/GroupAlign.java
rename to src/fr/inrialpes/exmo/align/cli/GroupAlign.java
index 0ed8e8ba70fba8fc98853884d698c50e46a380a0..a6f8a540b085a34d73251f1922f06fd00a5ec770 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, 2010, INRIA
+ * Copyright (C) 2003-2008, 2010-2011, INRIA
* Copyright (C) 2004, Université de Montréal
*
* Modifications to the initial code base are copyright of their
@@ -29,7 +29,7 @@
/* This program evaluates the results of several ontology aligners in a row.
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/GroupEval.java
rename to src/fr/inrialpes/exmo/align/cli/GroupEval.java
index 124ab8840668317e6717807f91230ad7b6f5a8e7..fdc7b9a974d924ac923d7c3946323df40268edf8 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -24,7 +24,7 @@
/* This program evaluates the results of several ontology aligners in a row.
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Evaluator;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupOutput.java b/src/fr/inrialpes/exmo/align/cli/GroupOutput.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/GroupOutput.java
rename to src/fr/inrialpes/exmo/align/cli/GroupOutput.java
index 4e1c5013d017928793cd4c5741fac9ab58a64ae4..f9a441b97734961df21df9f637e1a03084a8c63e 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupOutput.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupOutput.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2010, INRIA
+ * Copyright (C) 2003-2011, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -25,7 +25,7 @@
/* This program evaluates the results of several ontology aligners
and generates a LaTeX diagram for each of these
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
diff --git a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
similarity index 98%
rename from src/fr/inrialpes/exmo/align/util/ParserPrinter.java
rename to src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
index 55a74b0edb1790f759c142806eed51b40785af6e..9b2e60542e1b591bcd8facd64d5da0ad15304904 100644
--- a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2004, 2007-2008
+ * Copyright (C) INRIA, 2003-2004, 2007-2008, 2011
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -20,7 +20,7 @@
/*
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
//Imported JAVA classes
import java.lang.Integer;
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/cli/Procalign.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/Procalign.java
rename to src/fr/inrialpes/exmo/align/cli/Procalign.java
index 5ec96803873a22603dffc978cfa5ea435dcf9e46..be94bf2210e180294f9f0521ce860a6de50891d1 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/cli/Procalign.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, 2010 INRIA Rhône-Alpes
+ * Copyright (C) 2003-2008, 2010-2011 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -25,7 +25,7 @@
/* This program is an adaptation of the Processor.java class of the
initial release of the OWL-API
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGen.java b/src/fr/inrialpes/exmo/align/cli/TestGen.java
similarity index 97%
rename from src/fr/inrialpes/exmo/align/gen/TestGen.java
rename to src/fr/inrialpes/exmo/align/cli/TestGen.java
index 593a44df0a5e2068451506a2fe5d926f7b7bced5..efd3db302c69a03f840854be077869229a2dd047 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGen.java
+++ b/src/fr/inrialpes/exmo/align/cli/TestGen.java
@@ -19,13 +19,17 @@
* USA.
*/
-package fr.inrialpes.exmo.align.gen;
+package fr.inrialpes.exmo.align.cli;
import gnu.getopt.Getopt;
import gnu.getopt.LongOpt;
import java.util.Properties;
+import fr.inrialpes.exmo.align.gen.TestGenerator;
+import fr.inrialpes.exmo.align.gen.BenchmarkGenerator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
/**
An utility application for generating tests from command line.
It can either generate a single test or a whole test suite from a single ontology.
diff --git a/src/fr/inrialpes/exmo/align/util/WGroupEval.java b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
similarity index 99%
rename from src/fr/inrialpes/exmo/align/util/WGroupEval.java
rename to src/fr/inrialpes/exmo/align/cli/WGroupEval.java
index b67c5cecf8b667d259b208cd4dccf9c797289e8f..42a6819f3698a1fc4a81f858868a4630bb97a3c0 100644
--- a/src/fr/inrialpes/exmo/align/util/WGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
@@ -24,7 +24,7 @@
/* This program evaluates the results of several ontology aligners in a row.
*/
-package fr.inrialpes.exmo.align.util;
+package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Evaluator;
diff --git a/test/src/EDOALTest.java b/test/src/EDOALTest.java
index c0e59c35e59fa0644162fc074735fb8f0ba5009e..fc5f2b4e36ea625ffa71c9f9d09fbcde23d253c9 100644
--- a/test/src/EDOALTest.java
+++ b/test/src/EDOALTest.java
@@ -55,7 +55,7 @@ public class EDOALTest {
@Test(groups = { "full", "omwg", "raw" })
public void loadPrintTest() throws Exception {
/*
-java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter wine.xml > wine2.xml
+java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine.xml > wine2.xml
*/
aparser1 = new AlignmentParser( 0 );
assertNotNull( aparser1 );
@@ -75,7 +75,7 @@ java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter wine
@Test(groups = { "full", "omwg", "raw" }, dependsOnMethods = {"loadPrintTest"})
public void roundTripTest() throws Exception {
/*
-java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter wine2.xml > wine3.xml
+java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine2.xml > wine3.xml
*/
aparser1.initAlignment( null );
alignment = aparser1.parse( "file:test/output/wine2.xml" );
diff --git a/test/src/READMETest.java b/test/src/READMETest.java
index 1873e7b73a53259367acda7e8086134b8042655f..70522bad43fdfddbdd6e3eeb748a1c214ea85d21 100644
--- a/test/src/READMETest.java
+++ b/test/src/READMETest.java
@@ -105,7 +105,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
@Test(groups = { "full", "impl", "raw" })
public void routineTest5() throws Exception {
/*
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter examples/rdf/newsample.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter examples/rdf/newsample.rdf
*/
AlignmentParser aparser = new AlignmentParser( 0 );
assertNotNull( aparser, "AlignmentParser was null" );
@@ -228,7 +228,7 @@ $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publica
@Test(groups = { "full", "impl", "raw" }, dependsOnMethods = {"routineTest8"})
public void routineEvalTest() throws Exception {
/*
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
*/
AlignmentParser aparser1 = new AlignmentParser( 0 );
assertNotNull( aparser1 );
@@ -262,7 +262,7 @@ $ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrial
@Test(groups = { "full", "impl", "raw" }, dependsOnMethods = {"routineTest8"})
public void emptyEvalTest() throws Exception {
/*
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
*/
AlignmentParser aparser1 = new AlignmentParser( 0 );
assertNotNull( aparser1 );