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Commit f5472646 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- full revision of the style of the web pages

- added reference to the tutorial
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<html>
<head>
<title>The alignment API in Java</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
<h1 class="titre">The alignment API in Java</h1>
<p>We develop an alignment toolkit for OWL by:
<p>We have developed an alignment toolkit for OWL by:
<ul compact="1">
<li>Extending the OWL-API towards <a href="format.html">alignment</a>;</li>
<li>Providing an implementation of the API;</li>
<li>Providing an implementation of the Alignment API;</li>
<li>Implementing further alignment methods;</li>
</ul></p>
<p>An extensive presentation of the alignment API can be found <a href="align.pdf">here</a>.</p>
<p>An extensive presentation of the alignment API can be
found <a href="align.pdf">here</a>. We also have
a <a href="tutorial">tutorial</a> on using it.</p>
<h1>Getting ontoalign</h1>
<h2>Getting the Alignment API</h2>
<h2>Fetching the ZIP'ed version</h2>
<h3>Fetching the ZIP'ed version</h3>
<p>The simplest way to use ontoalign is to get the last release
<p>The simplest way to use alignapi is to get the last release
zipfile from the site <a href="http://gforge.inria.fr/frs/?group_id=117">http://gforge.inria.fr/frs/?group_id=117</a>. It contains all the sources, compiled
library, OWL API library.</p>
<h2>Anonymous Subversion</h2>
<h3>Anonymous Subversion</h3>
<p>The very last version of ontoalign can be fetched from the subversion
<p>The very last version of alignapi can be fetched from the subversion
source tree that can be found at:
<a href="http://gforge.inria.fr/scm/?group_id=117">http://gforge.inria.fr/scm/?group_id=117</a>
</p>
......@@ -37,20 +41,20 @@ library, OWL API library.</p>
smoothly upgrade it.</dd>
<dt>Checking out (anonymously) the repository</dt>
<dd>Can be achieved by just doing the following:
<pre>
<!-- $ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft login
&lt;ENTER return when asked for the password&gt;
$ cvs -d :pserver:cvs@cvs-sop.inria.fr:/CVS/exmosoft checkout
ontoalign-->
alignapi-->
<div class="fragment"><pre>
$ svn checkout svn://scm.gforge.inria.fr/svn/alignapi/trunk/
</pre>
</pre></div>
... and you are done.</dd>
</dl>
Note that you may have to fetch separately the <a href="owlapi.html">OWL-API</a>.</p>
<h2>Subversion account</h2>
<h3>Subversion account</h3>
<p>If you have improved ontoalign and want this to be included in the
<p>If you have improved alignapi and want this to be included in the
source base or if you want to seriously work on improving the
software, please contact
Jerome . Euzenat (&Agrave;) inrialpes . fr.</p>
......@@ -61,31 +65,49 @@ Note that you may have to fetch separately the <a href="owlapi.html">OWL-API</a>
<p>Once provided with a password you will be able to check out from and
commit in our repository through:
<pre>
<div class="fragment"><pre>
<!--
$ export CVS_RSH=`which ssh`
$ cvs -d :ext:&lt;loginname&gt;@cvs-sop.inria.fr:/CVS/exmosoft --
--checkout ontoalign
--checkout alignapi
-->
$ svn checkout svn+ssh://username@scm.gforge.inria.fr/svn/alignapi/trunk
</pre>
</pre></div>
(If you are not familliar with subversion, it is worth looking at the
documentation. If you are familiar with CVS, the move is straightforward.)
</p>
<h2>Release notes</h2>
<h3>Running</h3>
<p>Running the program is achieved through:
<div class="fragment"><pre>
$ java -jar lib/procalign.jar
usage: Procalign [options] URI1 URI2
options are:
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
--output=filename -o filename Output the alignment in filename
--alignment=filename -a filename Start from an XML alignment file
--threshold=double -t double Filters the similarities under threshold
--debug[=n] -d [n] Report debug info at level n
--help -h Print this message
</pre></div>
More details are available below.
</p>
<h3>Release notes</h3>
<p>They are provided <a href="relnotes.html">here</a>.</p>
<h2>Documentation</h2>
<h3>Documentation</h3>
<p>The documentation can be found on <a href="http://gforge.inria.fr/docman/?group_id=117">http://gforge.inria.fr/docman/?group_id=117</a>.</p>
<h1>Installation</h1>
<h2>Installation</h2>
<p>"Installing" is really straightforward.</p>
<h2>Files</h2>
<h3>Files</h3>
<p>Whatever your mode of getting ontolign you will get an ontoalign
<p>Whatever your mode of getting ontolign you will get an alignapi
directory containing the following subdirectories:
<ul compact="1">
<li>src: source classes;</li>
......@@ -94,6 +116,7 @@ documentation. If you are familiar with CVS, the move is straightforward.)
<li>dtd: the align.dtd and align.owl alignment specification;</li>
<li>lib: jar-files (in the zip-file the owl-api libraries are included);</li>
<li>html: a few html presentation files</li>
<li>html/tutorial: a tutorial on using the API</li>
<li>build.xml: ant file to compile and generate jar-files.</li>
<li>distrib: contains a few files for building the distribution</li>
<li>classes: the compiled classes (in the zip file, the classes are
......@@ -104,7 +127,7 @@ documentation. If you are familiar with CVS, the move is straightforward.)
</ul>
</p>
<h2>Requirements</h2>
<h3>Requirements</h3>
<p><b>For using</b> you will need <a href="http://java.sun.com">Java
runtime environment</a> (tested in 1.4.1) and the <a href="owlapi.html">OWL-API binary distribution</a> (this is
......@@ -122,7 +145,7 @@ Note that OWL-API needs log4j and getopt packages, but these are
included in the SVN repository). It is also very usefull to
have <a ref="http://ant.apache.org">Ant</a>.</p>
<h2>Required libraries (jar)</h2>
<h3>Required libraries (jar)</h3>
<p>Using the api (align.jar) requires:
<ul compact="1">
......@@ -142,76 +165,43 @@ addition:
<li>The Java WordNet Library (jwnl.jar).</li>
</ul></p>
<h2>Assembling</h2>
<h3>Assembling</h3>
<p>A good way of setting your environment (from the SVN archive) for
developing is to unzip the OWL-API binary distribution and put the
files in the ontoalign directories:
<pre>
files in the alignapi directories:
<div class="fragment"><pre>
$ unzip owlapi-bin-03-10-15.zip
$ mv owl/lib/* lib
$ ant jar
$ mv owl/javadoc/* javadoc
$ ant javadoc
$ rm -rf owl
</pre>
</pre></div>
</p>
<h1>Compilation and use</h1>
<h2>Compilation and use</h2>
<p>Generating the lib/procalign.jar file (and the other libraries) can
be done by launching:
<pre>
<div class="fragment"><pre>
$ ant jar
</pre></p>
</pre></div></p>
<h2>Using the API</h2>
<h1>Using the API</h1>
<p>A <a href="tutorial">tutorial</a> presents how to use the Alignment
API</p>
<p>An extensive presentation of the alignment API can be found
in the documentation section. It documents use and extension of the API.</p>
<p>For demonstrating the use of the API, we implement it and use it
through a particular processor
(<tt>fr.inrialpes.exmo.align.util.Procalign</tt>) which:
<ul compact="1">
<li>Reads two OWL/RDF ontologies;</li>
<li>Creates an alignment object;</li>
<li>Computes the alignment between these ontologies;</li>
<li>Displays the result.</li>
</ul>
Running the program is achieved through:
<pre>
$ java -jar lib/procalign.jar
usage: Procalign [options] URI1 URI2
options are:
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
--output=filename -o filename Output the alignment in filename
--alignment=filename -a filename Start from an XML alignment file
--threshold=double -t double Filters the similarities under threshold
--debug[=n] -d [n] Report debug info at level n
--help -h Print this message
</pre>
or ($CWD is the current directory)
<pre>
$ java -jar lib/procalign.jar file://localhost$CWD/rdf/onto1.owl file://localhost$CWD/rdf/onto2.owl
</pre>
Additionaly a number of options are available:
<ul compact="1">
<li>displaying debug information (-d);</li>
<li>controling the way of rendering the output (-r);</li>
<li>deciding the implementation of the alignment method (-i);</li>
<li>providing an input alignent (-a) [implemented but not used by most
methods].</li>
</ul>
</p>
<h1>License</h1>
<h2>License</h2>
<p>The alignment API and its implementation is distributed under the
GNU <a href="../distrib/LICENSE.TXT">Lesser General Public License</a>.</p>
<h1>The alignment API</h1>
<h2>The alignment API</h2>
<p>The OWL-API is extended with the
(<tt>org.semanticweb.owl.align</tt>) package. Which describes the
Alignment API. This API is, in turns, an "implementation" of the <a
......@@ -233,7 +223,7 @@ Additionaly a number of options are available:
contains a method for calling a particular alignment method (it is
a sub-interface of <tt>Alignment</tt>) and an <tt>AlignmentException</tt>.</p>
<h1>Implementing and extending the API</h1>
<h2>Implementing and extending the API</h2>
<p>A (default) impplementation of this API can be found in
the <tt>fr.inrialpes.exmo.align.impl</tt> package.</p>
<p>Adding new alignments methods amounts to create a
......@@ -253,11 +243,11 @@ Additionaly a number of options are available:
the <tt>EditDistNameAlignment</tt> class which uses an edit
distance on class names. It thus have to build a matrix of distance
and to choose the alignment from the distance. It can be called by:
<pre>
<div class="fragment"><pre>
$ java -jar lib/procalign.jar file://localhost$CWD/rdf/onto1.owl file://localhost$CWD/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
</Pre>
</pre></div>
which returns:
<pre>
<div class="code"><pre>
&lt;?xml version='1.0' encoding='utf-8' standalone='no'?>
&lt;!DOCTYPE rdf:RDF SYSTEM "align.dtd">
......@@ -284,7 +274,7 @@ which returns:
&lt;/map>
&lt;/Alignment>
&lt;/rdf:RDF>
</pre>
</pre></div>
</p>
<address>
......
<html>
<head>
<title>Using the Alignment API with Wordnet</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body>
......
<html>
<head>
<title>Ontologies to compare</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
......
<html>
<head>
<title>Evaluating alignments</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
......
<html>
<head>
<title>A format for ontology alignment</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcollor="#ffffff">
......@@ -18,7 +20,7 @@
some implementations.</p>
<h1>Specifications</h1>
<h2>Specifications</h2>
<p>There are two specifications of the format:
<dl compact="1">
......@@ -33,9 +35,9 @@
<p>The namespace used by these formats is <tt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment</tt>.</p>
<h1>Format descriptions</h1>
<h2>Format descriptions</h2>
<h2><tt>Alignment</tt> class</h2>
<h3><tt>Alignment</tt> class</h3>
<p>The <tt>Alignment</tt> class describes a partlicular alignment. Its
properties are the following:
......@@ -51,7 +53,7 @@
entities of the ontologies.</dd>
</dl></p>
<h2><tt>Cell</tt> class</h2>
<h3><tt>Cell</tt> class</h3>
<dl compact="1">
<dt>entity1</dt><dd>(value: URI) the URI of some entity of the first ontology;</dd>
<dt>entity2</dt><dd>(value: URI) the URI of some entity of the second ontology;</dd>
......@@ -64,13 +66,11 @@
between the first and second entity.</dd>
</dl></p>
<h2><tt>Relation</tt> class</h2>
<h3><tt>Relation</tt> class</h3>
<p>This class does not currently exists in the format (it exists in
its implementation). Currently, the relation is expressed as a string.</p>
<h1>Implementations</h1>
<h2>JAVA implementation</h2>
<p>There is a <a href="align.html">JAVA API</a>, extending the <a href="owlapi.html">OWL API</a> implementing this
format.</p>
......
<html>
<head>
<title>Alignment API</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body>
......@@ -21,19 +23,24 @@
</dt>
<dd>The alignment format in RDF/XML.</dd>
<dt><a href="align.html">Alignment API</a>
<a href="http://gforge.inria.fr/frs/?group_id=117">[<font color="red">Download page</font>]</a></dt>
[<a
href="http://gforge.inria.fr/frs/?group_id=117"><font
color="red">Download page</font></a> + <a href="relnotes.html"><font
color="red">Release notes</font></a>]</dt>
<dd>
An alignment API in Java and implementation on top of the OWL API.</dd>
<dt><a href="owlapi.html">OWL-API</a> <a href="http://sourceforge.net/projects/owlapi">[<font color="red">Download here</font>]</a></dt>
An alignment API in Java and implementation on top of the OWL
API.</dd>
<dt><a href="tutorial">A tutorial</a></dt><dd>on how to use the Alignment API implementation</dd>
<dt><a href="alignwn.html">Using the API with wordnet</a>
[Included with the API zip file]</dt>
<dd>Demonstrate how to use wordnet within the API</dd>
<dt><a href="owlapi.html">OWL-API</a> [Included with the API zip file]</dt>
<dd>Starting quickly with OWL-API.</dd>
<!--dt><a href="data.html">Ontologies</a></dt>
<dd>Some data for aligning.</dd>
<dt><a href="eval.html">Evaluators</a></dt>
<dd>Evaluating alignments from the format.</dd-->
<dt><a href="alignwn.html">Using the API with wordnet</a>
[<font color="red">Included with the API zip file</font>]</a></dt>
<dd>Demonstrate how to use wordnet within the API</dd>
<a href="http://VisOn.gforge.inria.fr">[<font color="red">VisOn</font>]</a></dt>
<dt><a href="http://VisOn.gforge.inria.fr">[<font color="red">VisOn</font>]</a></dt>
<dd>The VisOn ontology visualizer now works with any implementation of
the API. It provides the opportunity to load and display
ontologies, load, run, display and compare alignment algorithms.</dd>
......
<html>
<head>
<title>Comments on OWL-API</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
......
<html>
<head>
<title>Alignment API: Release notes</title>
<style type="text/css">@import url(style.css);</style>
<!--style type="text/css">@import url(style.css);</style-->
<link rel="stylesheet" type="text/css" href="base.css" />
<link rel="stylesheet" type="text/css" href="style.css" />
</head>
<body bgcolor="#ffffff">
......
BODY {
color: Black;
background-color: #D3D3D3;
font-family: Verdana, sans-serif;
font-size: 12px;
text-align: justify;
}
A {
color: #0000CD;
text-decoration: none;
......@@ -15,44 +7,76 @@ A:HOVER {
color: Navy;
text-decoration: none;
}
div.owl {
background: #edd;
border:1pt solid;
}
div.fragment {
background: #dde;
border:1pt solid;
overflow-y: scroll;
}
div.logic {
background: #ded;
border:1pt solid;
}
.detail {
background: lightYellow;
border:1pt solid red;
/* margin-top: 0.6em;
margin-bottom: 0.6em; */
}
.inference {
background: white;
font-weight: bold;
font-size: large;
}
.titreSection {
font-size:18px;
padding-left:10px;
padding-bottom:10px;
padding-top:5px;
.explain {
display:none;
background: lightYellow;
border:1pt solid red;
}
.titre1 {
font-size:16px;
font-weight:bold;
padding-left:14px;
padding-bottom:5px;
padding-top:10px;
.button {
}
.titre {
font-size:28px;
padding-bottom:20px;
/*
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}
.texte {
font-size:12px;
padding-left:20px;
padding-right:20px;
padding-bottom:5px;
padding-top:5px;
.button {
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}
*/
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table {
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}
.puce {
padding-bottom:5px;
td {
border: solid 1pt;
padding: 1px;
}
th {
border: solid 1pt;
padding: 10px;
}
.imgdiv {
text-align: center;
}
.facts {
margin: 10px;
}
body {
text-align: justify;
padding: 2em 1em 2em 1em;
}
h2 { border-bottom: 1px solid #000088; }
/*
Copyright 1997-2003 W3C (MIT, ERCIM, Keio). All Rights Reserved.
The following software licensing rules apply:
http://www.w3.org/Consortium/Legal/copyright-software */
/* $Id: base.css,v 1.24 2003/04/17 13:56:40 bbos Exp $ */
body {
padding: 2em 1em 2em 70px;
margin: 0;
font-family: sans-serif;
color: black;
background: white;
background-position: top left;
background-attachment: fixed;
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:visited { color: #609; background: transparent }
a:active { color: #C00; background: transparent }
a:link img, a:visited img { border-style: none } /* no border on img links */
a img { color: white; } /* trick to hide the border in Netscape 4 */
@media all { /* hide the next rule from Netscape 4 */
a img { color: inherit; } /* undo the color change above */
}
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div.head table { margin-left: 2em; margin-top: 2em }
p.copyright { font-size: small }
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@media screen { /* hide from IE3 */
a[href]:hover { background: #ffa }
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pre { margin-left: 2em }
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p.copyright { volume: x-soft; speech-rate: x-fast }
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}
......@@ -12,10 +12,8 @@ function hide(id) {
}
</script>
<link rel="stylesheet" type="text/css"
href="base.css" />
<link rel="stylesheet" type="text/css"
href="style.css" />
<link rel="stylesheet" type="text/css" href="../base.css" />
<link rel="stylesheet" type="text/css" href="../style.css" />
</head><body bgcolor="white">
<h1>A small tutorial on the Alignment API</h1>
......@@ -35,7 +33,6 @@ http://alignapi.gforge.inria.fr/tutorial/
</dl>
<hr />
<p>Here is a small tutorial for the alignment API. Since the API has no
dedicated GUI, most of the tutorial is based on command-lines
invocations. Of course, it is not the natural way to use this API:
......@@ -43,8 +40,8 @@ dedicated GUI, most of the tutorial is based on command-lines
are working towards implementing an alignment server that can help
programmes to use the API remotely. The complete tutorial is also
available as a self-contained <a href="script.sh">script.sh</a> or <a href="script.bat">script.bat</a>.</p>
<hr />
<h2>Preparation</h2>
<p>For running the alignment API, you must have a Java interpreter
......@@ -79,9 +76,12 @@ options are:
-Dparam=value Set parameter
--help -h Print this message
</pre></div></p>
This should output the command line usage of the Procalign
class. We do not detail it here, this tutorial will present
The above command outputs the command line usage of the Procalign class.
We do not detail it here, this tutorial will present
it entirelly.</p>
<p>If you want to modify the Alignment API and its implementation,
please refer to <a href="../align.html">this page</a>. In this
tutorial, we will simply learn how to use it.</p>
<p>You will then go to the tutorial directory by doing
<div class="fragment"><pre>
$ cd html/tutorial
......@@ -111,7 +111,6 @@ $ xsltproc ../form-align.xsl results/file.rdf > results/file.html
generates <tt>results/file.html</tt> from the alignment file <tt>results/file.rdf</tt>.</p>
<hr />
<h2>The data</h2>
<p>Your mission, if you accept it, will be to find the best alignment
......@@ -130,16 +129,33 @@ These two ontologies have been used for a few year in the <a href="oaei.ontology
Alignment Evaluation Initiative</a>
</p>
<hr />
<h2>Matching</h2>
<p>Let's try to match these two ontologies:
<p>
For demonstrating the use of our implementation of the Alignment API,
we implemented a particular processor
(<tt>fr.inrialpes.exmo.align.util.Procalign</tt>) which:
<ul compact="1">
<li>Reads two OWL/RDF ontologies;</li>
<li>Creates an alignment object;</li>
<li>Computes the alignment between these ontologies;</li>
<li>Displays the result.</li>
</ul>
Let's try to match these two ontologies:
<div class="fragment"><pre>
$ java -jar ../../lib/procalign.jar file://localhost$CWD/myOnto.owl file://localhost$CWD/edu.mit.visus.bibtex.owl
</pre></div>
Additionaly a number of options are available:
<ul compact="1">
<li>displaying debug information (-d);</li>
<li>controling the way of rendering the output (-r);</li>
<li>deciding the implementation of the alignment method (-i);</li>
<li>providing an input alignent (-a) [implemented but not used by most
methods].</li>
</ul>
</p>
<p>The result is displayed on the standard output Since the output is
<p>The result is displayed on the standard output. Since the output is
too long we send it to a file by using the <tt>-o</tt> flag:
<div class="fragment"><pre>
$ java -jar ../../lib/procalign.jar file://localhost$CWD/myOnto.owl file://localhost$CWD/edu.mit.visus.bibtex.owl -o results/equal.rdf
......@@ -231,7 +247,6 @@ $ java -jar ../../lib/alignwn.jar -i fr.inrialpes.exmo.align.ling.JWNLAlignment
</pre></div>
See the output in <a href="jwnl.rdf">RDF/XML</a> or <a href="jwnl.html">HTML</a>.</p></div></p>
<hr />
<h2>Manipulating</h2>
<p>As can be seen there are some correspondences that do not really make
......@@ -290,7 +305,6 @@ to compose them.</p>
levenshteinDistance and smoaDistance.
</p></div></p>
<hr />
<h2>Output</h2>
<p>Once a good alignment has been found, only half of the work has
......@@ -366,7 +380,6 @@ $ xsltproc results/SMOA5.xsl data.xml > results/data.xml
for giving the <a href="results/data.xml">results/data.xml</a> file.
</p>
<hr />
<h2>Evaluating</h2>
<p>We will evaluate alignments by comparing them to some reference
......@@ -529,7 +542,6 @@ $ java -jar ../../lib/Procalign.jar file://localhost$CWD/rdf/edu.umbc.ebiquity.p
is another class, GroupAlign, that allows to run an
</p></div-->
<hr />
<h2>Embedding</h2>
<p>Of course, the goal of this API is not to be used at the command
......@@ -631,7 +643,6 @@ implementation (like BasicAlignment or DistanceAlignment).
What about writing an editor for the alignment API?
</p></div></p>
<hr />
<h2>Further exercises</h2>
<p>
......@@ -645,7 +656,6 @@ Planning:
- Expressive alignment language (with SEKT/François Sharffe)
-->
<hr />
<h2>Acknowledgements</h2>
<p>The format of this tutorial has been shamelessly borrowed from Sean
......@@ -654,6 +664,6 @@ Planning:
<hr />
<center><small>http://alignapi.gforge.inria.fr/tutorial</small></center>
<hr />
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$Id$
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