diff --git a/html/cli.html b/html/cli.html
index 7656859191432a9c936f6461f7317be45ec375d2..72346e4e1a33191820f794b9f998b54ff1b9a5b8 100644
--- a/html/cli.html
+++ b/html/cli.html
@@ -16,6 +16,8 @@ the <tt>fr.inrialpes.exmo.align.cli</tt> package:
<dt>Procalign</dt><dd>Runs a matcher on a pair of ontologies</dd>
<dt>ParserPrinter</dt><dd>Parses and alignment and displays it in
various formats.</dd>
+<dt>TransformQuery</dt><dd>Transform a SPARQL query according to an
+ alignment.</dd>
<!--dt>DiffAlign</dt><dd>TODO</dd-->
<dt>EvalAlign</dt><dd>Evaluates and alignment with respect to a
reference alignment.</dd>
@@ -33,18 +35,11 @@ the <tt>fr.inrialpes.exmo.align.cli</tt> package:
These command line operations usually share switch conventions:
<ul>
<li>displaying help (-h);</li>
-<li>taking parameerst (-Dv=n) and parameter files (-P);</li>
+<li>taking parameters (-Dv=n) and parameter files (-P);</li>
<li>directing the output to a file (-o);</li>
</ul></p>
-<h2>Displaying alignments</h2>
-<p>
-Another such utility (<tt>ParserPrinter</tt>) allows to read an
-alignment, to manipulate it and to output it without processing
-the <tt>align</tt> method.
-</p>
-
-<h2>Matching</h2>
+<h3>Matching</h3>
<p>
The implementation offers a stand-alone program (<tt>fr.inrialpes.exmo.align.cli.Procalign</tt>) which:
<ul>
@@ -64,7 +59,7 @@ Additional options are available:
<p>Running the program is achieved through:
<div class="terminal">
-$ java -jar lib/procalign.jar
+$ java -cp lib/procalign.jar --help
usage: java fr.inrialpes.exmo.align.cli.Procalign [options] ontoURI ontoURI
Matches the two ontologies identified by <ontoURI>
@@ -75,20 +70,89 @@ Options:
See http://alignapi.gforge.inria.fr/logging.html
-h,--help Print this page
-i,--impl <CLASS> Use the given CLASS for matcher
- -o,--output <FILENAME> Send output to FILENAME
+ -o,--output <FILE> Send output to FILE
-P,--params <FILE> Read parameters from FILE
-r,--renderer <CLASS> Use the given CLASS for output
-T,--cutmethod <METHOD> Method to use for triming (hard|perc|prop|best|span)
-t,--threshold <DOUBLE> Trim the alignment with regard to threshold
-Alignment API implementation 4.5 (1864M)
+Alignment API implementation 4.6 (1886:1889M)
</div>
</p>
<p>
Parameters can be passed to all the command line interfaces through the "-Dname=value" scheme. These parameters are either used by the command line utility or transmitted to the called programs, e.g., <tt>align()</tt>. Parameters can also be passed through an XML file through the "-P filename" option.
</p>
-<h2>Batch matching</h2>
+<h3>Displaying alignments</h3>
+<p>
+Another such utility (<tt>ParserPrinter</tt>) allows to read an
+alignment, to manipulate it and to output it without processing
+the <tt>align</tt> method.
+</p>
+<div class="terminal">
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter
+usage: java fr.inrialpes.exmo.align.cli.ParserPrinter [options] alignfile
+ Parse the given <alignfile> and prints it
+
+Options:
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -e,--embedded Read the alignment as embedded in a XML file
+ -h,--help Print this page
+ -i,--inverse Inverse first and second ontology
+ -o,--output <FILE> Send output to FILE
+ -P,--params <FILE> Read parameters from FILE
+ -p,--parser <CLASS> Use the given CLASS for parsing
+ -r,--renderer <CLASS> Use the given CLASS for rendering
+ -T,--cutmethod <METHOD> Method to use for triming (hard|perc|prop|best|span)
+ -t,--threshold <DOUBLE> Trim the alignment with regard to threshold
+ -w,--outputDir <DIR> Split the output in a DIRectory (SPARQL)
+
+Alignment API implementation 4.6 (1886:1889M)
+</div>
+<p>
+The utility may be invoked in the following way:
+<div class="terminal">
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter file:examples/rdf/newsample.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
+</div>
+</p>
+
+<h3>Translating queries</h3>
+<p>
+Another such utility (<tt>TransformQuery</tt>) allows to read a
+query (either from the command line, from the standard input or from a
+file) and prints out the same query in which entities of the first
+ontology in the alignment have been replaced by corresponding entities
+of the second ontology. Additional namespaces may be defined for
+simplifying the output.
+</p>
+<div class="terminal">
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.TransformQuery --help
+usage: java fr.inrialpes.exmo.align.cli.TransformQuery [options] QUERY
+ Transforms the given QUERY according to an alignment
+
+Options:
+ -a,--alignment <URI> use the alignment identified by URI
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -e,--echo Echo the input query
+ -h,--help Print this page
+ -o,--output <FILE> Send output to FILE
+ -P,--params <FILE> Read parameters from FILE
+ -q,--query <FILE> get the query from the corresponding FILE
+
+Alignment API implementation 4.6 (1886:1889M)
+</div>
+<p>
+The utility may be invoked in the following way:
+<div class="terminal">
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.TransformQuery -a file:examples/rdf/newsample.rdf -q examples/rdf/query.sparql -Donto2=http://www.example.org/ontology2#
+</div>
+</p>
+
+<h3>Batch matching</h3>
<p>There is a small utility (<tt>GroupAlign</tt>) which allows to implement batch matching. It starts with a directory containing a set of subdirectories. Each subdirectory contains an ontology to align (usually called <tt>onto.rdf</tt>) and there exist an ontology to be aligned againts these (-n argument, e.g., named <tt>./onto.rdf</tt>).</p>
<div class="terminal">
@@ -97,29 +161,27 @@ usage: java fr.inrialpes.exmo.align.cli.GroupAlign [options]
Matches pairs of ontologies in subdirectories
Options:
- -a,--alignment <FILE> Use an initial alignment FILE
- -D <NAME=VALUE> Use value for given property
- -d,--debug <LEVEL> debug argument is deprecated, use logging instead
- See http://alignapi.gforge.inria.fr/logging.html
- -h,--help Print this page
- -i,--impl <CLASS> Use the given Alignment implementation
- -n,--name <URI> Use the given URI as common source ontology
- -o,--output <FILENAME> Send output to FILENAME
- -P,--params <FILE> Read parameters from FILE
- -r,--renderer <CLASS> Use the given CLASS for rendering
- -s,--source <FILE> Source ontology FILEname (default onto1.rdf)
- -t,--target <FILE> Target ontology FILEname (default onto.rdf)
- -u,--uriprefix <URI> URI prefix of the target
- -w,--directory <DIR> The DIRectory containing the data to match
-
-Alignment API implementation 4.5 (1864M)
+ -a,--alignment <FILE> Use an initial alignment FILE
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -h,--help Print this page
+ -i,--impl <CLASS> Use the given Alignment implementation
+ -n,--name <URI> Use the given URI as common source ontology
+ -o,--output <FILE> Send output to FILE
+ -P,--params <FILE> Read parameters from FILE
+ -r,--renderer <CLASS> Use the given CLASS for rendering
+ -s,--source <FILE> Source ontology FILEname (default onto1.rdf)
+ -t,--target <FILE> Target ontology FILEname (default onto.rdf)
+ -u,--uriprefix <URI> URI prefix of the target
+ -w,--directory <DIR> The DIRectory containing the data to match
+
+Alignment API implementation 4.6 (1886:1889M)
</div>
<p>Invoking <tt>GroupAlign</tt> with some implementation (-i argument), some set of parameters (-P argument), the name of the output file (-o argument) and optionally a renderer (-r argument) will output the resulting alignment in each of these directories:
<div class="terminal">
-$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.cli@.GroupAlign
- -o edna -n file://$CWD/101/onto.rdf
- -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
+$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.cli@.GroupAlign -o edna -n file://$CWD/101/onto.rdf -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
</div>
</p>
<p>
@@ -129,14 +191,14 @@ This will compare each onto.rdf file in each of the subdirectory to the <tt>file
The output is ready to be evaluated by <tt>GroupEval</tt>.
</p>
-<h3>Generating tests</h3>
+<h2>Generating tests</h2>
<p>
Tools for generating matching tests (<tt>TestGen</tt>) are described
in the <a href="testgen.html">test generation page</a>.
</p>
-<h3>Evaluating alignments</h3>
+<h2>Evaluating alignments</h2>
<p>
Tools for evaluating (<tt>EvalAlign</tt>) and batch evaluating