diff --git a/build.xml b/build.xml
index d88860ccda1af9fd8e7dd24a36158a0a78cf21e6..0d0149c1f0e9cb372cd1fbae88c38c9336813cd6 100644
--- a/build.xml
+++ b/build.xml
@@ -78,6 +78,7 @@
<target name="upgrade" description="Upgrade local dependencies">
<copy file="../ontosim/lib/ontosim.jar" todir="lib/ontosim" filtering="false"/>
+ <echo message="Do not forget to upgrade the POM that ontosim has not" />
</target>
<!-- tested -->
@@ -97,7 +98,6 @@
<delete>
<fileset dir="." includes="classes/**/*.class"/>
</delete>
- <delete dir="tattletale" />
<antcall target="cleanjar"/>
<antcall target="jar"/>
<ant dir="plugins/neon" target="compileall" />
@@ -226,7 +226,7 @@
group="fr.inrialpes.exmo.align"
desc="Alignment API implementation"
main="fr.inrialpes.exmo.align.cli.Procalign"
- path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar cli/commons-cli.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
+ path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar cli/commons-cli.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar lucene/lucene-analyzers-common.jar jena/jena.jar jena/iri.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
<files>
<fileset dir="classes">
<include name="fr/inrialpes/exmo/align/impl/**/*.class"/>
@@ -344,12 +344,13 @@
<!-- tested -->
<target name="cleantest" depends="bind" description="Clean up test directory">
<echo message="Cleaning tests..."/>
- <delete>
+ <delete includeemptydirs="true">
<fileset dir="test/classes" includes="**/*.class"/>
<fileset dir="test/output" includes="**/*.*"/>
+ <fileset dir="test/html" includes="**"/>
<fileset dir="test/html" includes="**/*.*"/>
</delete>
- <delete dir="test/html/Ant suite"/>
+ <!--delete dir="test/html/*"/-->
</target>
<!-- tested -->
@@ -536,6 +537,7 @@
<onepom file="slf4j/jcl-over-slf4j" />
<onepom file="slf4j/log4j-over-slf4j" />
<onepom file="lucene/lucene-core" />
+ <onepom file="lucene/lucene-analyzers-common" />
<onepom file="ontosim/ontosim" />
<onepom file="osgi/osgi-core" />
<onepom file="owlapi10/api" />
@@ -559,6 +561,7 @@
<!-- tested -->
<target name="clean" description="Clean up the whole directory">
<echo message="Cleaning..."/>
+ <delete dir="tattletale" />
<antcall target="cleantest"/>
<ant dir="plugins/neon" target="clean" />
<ant dir="plugins/webcontent" target="clean" />
diff --git a/html/lib.html b/html/lib.html
index b5bede0f65ec3ccd398faf4b60002f935ee76f8a..ffbdabd9403ab28f1ed62a342c447c8322b122c9 100644
--- a/html/lib.html
+++ b/html/lib.html
@@ -62,9 +62,9 @@ This is a simplified view: <a href="img/dependencies.png">click here
<h3>Required for some bundled matching methods</h3>
<dl>
-<dt><a href="http://ontosim.gforge.inria.fr">OntoSim</a> 2.3adv: ontosim.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt>
+<dt><a href="http://ontosim.gforge.inria.fr">OntoSim</a> 2.4: ontosim.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt>
<dd>The whole ontosim system requires more libraries, including JWNL. But in our simplest behaviour, these libraries are not needed.</dd>
-<dt><a href="http://lucene.apache.org/">Lucene</a> 3.0.2: lucene-core.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt>
+<dt><a href="http://lucene.apache.org/">Lucene</a> 4.6.0: lucene-core.jar, lucene-analyzers-common.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt>
<dd>This small part of lucene is used for WordNet matching classes.</dd>
</dl>
diff --git a/html/relnotes.html b/html/relnotes.html
index 5599154e4feeb4eba8f95dddb2458cd265ec9a11..6744051d8f3db5b7184aa73d0cf3eacd18f6e762 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -73,12 +73,14 @@ with a warning:
<!--h2>Version 4.9 (1xxx): ??/??/201X - Al pesto</h2-->
<!--h2>Version 4.8 (1xxx): ??/??/201x - Antésine</h2-->
<!--h2>Version 4.7 (1xxx): ??/??/201x - Letraset</h2-->
-<!--h2>Version 4.6 (18xx): ??/01/2014 - Da lec'h all</h2-->
+
+<h2>Version 4.6 (1875): 22/01/2014 - Da lec'h all</h2>
+
<p><ul compact="1">
<li>Fixed a bug in <tt>EDOALAlignment.init()</tt> which would prohibit rendering (edoal)</li>
<li>Fixed a bug in <tt>OWLAxiomsRendererVisitor</tt>, <tt>SWRLRendererVisitor</tt>, <tt>SEKTMappingRendererVisitor</tt>, <tt>COWLMappingRendererVisitor</tt> <tt>SPARQLConstructRendererVisitor</tt>, and <tt>SPARQLSelectRendererVisitor</tt> which sometimes rendered alignments empty (impl)</li>
<li>All logging and signaling is now through slf4j (impl/server)</li>
-<li>Replaced getopt by <span style="color: green">commons cli</span> 1.2 as command line interpreter (lib/cli)</li>
+<li>Replaced getopt by <span style="color: green">commons cli 1.2</span> as command line interpreter (lib/cli)</li>
<li>Completed <tt>SWRLRendererVisitor</tt> to fill equivalence and subsumption statements (impl)</li>
<li>Declared Alignment server as an OSGi service (server)</li>
<li>Made EDOAL vocabulary dereferenceable (edoal)</li>
@@ -89,13 +91,14 @@ with a warning:
<li>Changed <tt>-o</tt> option in <tt>GroupAlign</tt> to be homogeneous (cli)</li>
<li>Updated tutorial2 with deprecated <tt>BasicParameters</tt> (tutorial)</li>
<li>Added complete command line option tests in <tt>tests/clitest.sh</tt> (cli)</li>
-<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.5 (lib)</li>
-<li>Upgraded to <span style="color: green">xercesImpl</span> to 2.11.0 (lib)</li>
-<!--li>Upgraded to <span style="color: green">Lucene</span> to 4.6.0 (lib)</li-->
-<li>Upgraded to <span style="color: green">mysql</span> to 5.1.28 and <span style="color: green">postgres</span> to 9.3-1100 (lib)</li>
-<li>Upgraded to <span style="color: green">Jena</span> to 2.9.0 (lib)</li>
-<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.8 (lib)</li>
-<li>Upgraded to <span style="color: green">HermiT</span> to 1.3.8 (lib)</li>
+<li>Upgraded to <span style="color: green">SLF4J 1.7.5</span> (lib)</li>
+<li>Upgraded to <span style="color: green">xercesImpl 2.11.0</span> (lib)</li>
+<li>Upgraded to <span style="color: green">Lucene 4.6.0</span> (lib)</li>
+<li>Upgraded to <span style="color: green">OntoSim 2.4</span> (lib)</li>
+<li>Upgraded to <span style="color: green">mysql 5.1.28</span> and <span style="color: green">postgres 9.3-1100</span> (lib)</li>
+<li>Upgraded to <span style="color: green">Jena 2.9.0</span> (lib)</li>
+<li>Upgraded to <span style="color: green">OWL API 3.4.8</span> (lib)</li>
+<li>Upgraded to <span style="color: green">HermiT 1.3.8</span> (lib)</li>
</ul></p>
<h2>Version 4.5 (1847): 25/03/2013 - Building 16</h2>
@@ -119,9 +122,9 @@ with a warning:
<li>Simplified and rewritten <tt>SemPRecEvaluator</tt> (impl)</li>
<li>Fixed all issues but IDDL in <a href="tutorial/tutorial4/index.html">tutorial4</a> (impl)</li>
<li>Fixed display bug in <tt>HTMLMetadataRenderer</tt> (impl)</li>
-<li>Upgraded to <span style="color: green">IDDL</span> to 1.5 (lib)</li>
-<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.2 (lib)</li>
-<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.2; suppressed slf4j-log4j (lib)</li>
+<li>Upgraded to <span style="color: green">IDDL 1.5</span> (lib)</li>
+<li>Upgraded to <span style="color: green">OWL API 3.4.2</span> (lib)</li>
+<li>Upgraded to <span style="color: green">SLF4J 1.7.2</span>; suppressed slf4j-log4j (lib)</li>
<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
<li>Replaced Commons-Logging and Log4j by jcl-over-slf4j and log4j-over-slf4j (lib)</li>
</ul></p>
diff --git a/html/tutorial/tutorial1/results/AOMS5.rdf b/html/tutorial/tutorial1/results/AOMS5.rdf
index 8be6970bba29d385c30c49a9ae4dc02f6bec7627..cbbae927a6caef186dad24e7aaf8028d9fa5ce30 100644
--- a/html/tutorial/tutorial1/results/AOMS5.rdf
+++ b/html/tutorial/tutorial1/results/AOMS5.rdf
@@ -6,11 +6,10 @@
<Alignment>
<xml>yes</xml>
<level>0</level>
- <type>**</type>
- <align:method>fr.inrialpes.exmo.align.impl.method.StringDistAlignment</align:method>
+ <type>?*</type>
<provenance>null</provenance>
+ <time>518</time>
<method>http://exmo.inrialpes.fr/align/impl/BasicAlignment#inverse</method>
- <align:time>356</align:time>
<onto1>
<Ontology rdf:about="http://alignapi.gforge.inria.fr/tutorial/edu.mit.visus.bibtex.owl">
<location>file:///Java/alignapi/html/tutorial/edu.mit.visus.bibtex.owl</location>
diff --git a/html/tutorial/tutorial1/results/SMOA5.rdf b/html/tutorial/tutorial1/results/SMOA5.rdf
index 019c0a0daf21ffc0a44a3967e8a1f90d95ba453d..a70c1a5dfba634bb9b76e50c45f8379bb9b20b06 100644
--- a/html/tutorial/tutorial1/results/SMOA5.rdf
+++ b/html/tutorial/tutorial1/results/SMOA5.rdf
@@ -6,8 +6,8 @@
<Alignment>
<xml>yes</xml>
<level>0</level>
- <type>**</type>
- <time>356</time>
+ <type>?*</type>
+ <time>518</time>
<method>fr.inrialpes.exmo.align.impl.method.StringDistAlignment</method>
<onto1>
<Ontology rdf:about="http://alignapi.gforge.inria.fr/tutorial/myOnto.owl">
diff --git a/html/tutorial/tutorial1/results/equal.html b/html/tutorial/tutorial1/results/equal.html
index 09476704c661d8ad8d946bf2f131bc25c68c1fbe..b3150162512339fa6946f60c142b8b23cf5e1816 100644
--- a/html/tutorial/tutorial1/results/equal.html
+++ b/html/tutorial/tutorial1/results/equal.html
@@ -21,8 +21,8 @@
<tr><td>type:</td><td><span rel="align:formalism"><span typeof="align:Formalism"><span property="align:name">OWL2.0</span><span property="align:uri" content="http://www.w3.org/2002/07/owl#"/></span></span></td></tr></table>
</div></div></td></tr>
<tr><td>level</td><td property="align:level">0</td></tr>
-<tr><td>type</td><td property="align:type">**</td></tr>
-<tr><td>http://knowledgeweb.semanticweb.org/heterogeneity/alignment : time</td><td property="align:time">309</td></tr>
+<tr><td>type</td><td property="align:type">?*</td></tr>
+<tr><td>http://knowledgeweb.semanticweb.org/heterogeneity/alignment : time</td><td property="align:time">464</td></tr>
<tr><td>http://knowledgeweb.semanticweb.org/heterogeneity/alignment : method</td><td property="align:method">fr.inrialpes.exmo.align.impl.method.StringDistAlignment</td></tr>
</table>
<h2>Correspondences</h2>
diff --git a/lib/align.jar b/lib/align.jar
index 40c8fe817250cbe919e33755e722fe75109b300b..779ee7158751af1a5c023bfd94dc1db7bb37d611 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/align.pom b/lib/align.pom
index c5f466f677c3464eee28e476785613be6cf4b46b..e8d450ff45f7d10b2c02da511c7b8c11d7674ea0 100644
--- a/lib/align.pom
+++ b/lib/align.pom
@@ -16,8 +16,8 @@
<groupId>org.semanticweb.owl</groupId>
<artifactId>align</artifactId>
- <version>4.5</version>
- <!-- Rev 1846M 25/03/2013 -->
+ <version>4.6</version>
+ <!-- Rev 1874M 22/01/2014 -->
<name>The Alignment API</name>
<description>The Alignment API is an API for manipulating ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
@@ -25,7 +25,7 @@
<name>INRIA Exmo team</name>
<url>http://exmo.inrialpes.fr</url>
</organization>
- <!-- (C) INRIA, 2003-2013 -->
+ <!-- (C) INRIA, 2003-2014 -->
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999</name>
diff --git a/lib/alignsvc.jar b/lib/alignsvc.jar
index 29d914409046143e49b30e11b87d12616f4ac264..a2a535cb0b4ebb4b594df5e1feb7f3d786b0281a 100644
Binary files a/lib/alignsvc.jar and b/lib/alignsvc.jar differ
diff --git a/lib/alignsvc.pom b/lib/alignsvc.pom
index c975d738decde60653f9565d1e8dda9866ad7350..59c6bb748c89931cb4b14586cc5318229066ac1a 100644
--- a/lib/alignsvc.pom
+++ b/lib/alignsvc.pom
@@ -16,8 +16,8 @@
<groupId>fr.inrialpes.exmo.align</groupId>
<artifactId>alignsvc</artifactId>
- <version>4.5</version>
- <!-- Rev 1846M 25/03/2013 -->
+ <version>4.6</version>
+ <!-- Rev 1874M 22/01/2014 -->
<name>Alignment server</name>
<description>A server for storing and sharing ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
@@ -25,7 +25,7 @@
<name>INRIA Exmo team</name>
<url>http://exmo.inrialpes.fr</url>
</organization>
- <!-- (C) INRIA, 2003-2013 -->
+ <!-- (C) INRIA, 2003-2014 -->
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999</name>
@@ -42,19 +42,19 @@
<dependency>
<groupId>org.semanticweb.owl</groupId>
<artifactId>align</artifactId>
- <version>4.5</version>
+ <version>4.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>fr.inrialpes.exmo</groupId>
<artifactId>ontowrap</artifactId>
- <version>4.5</version>
+ <version>4.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>fr.inrialpes.exmo.align</groupId>
<artifactId>procalign</artifactId>
- <version>4.5</version>
+ <version>4.6</version>
<scope>compile</scope>
</dependency>
<dependency>
@@ -77,6 +77,10 @@
<groupId>org.neon_toolkit.registery</groupId>
<artifactId>oyster2</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.knopflerfish</groupId>
+ <artifactId>framework</artifactId>
+ </dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>servlet</artifactId>
diff --git a/lib/lucene/lucene-analyzers-common.jar b/lib/lucene/lucene-analyzers-common.jar
new file mode 100644
index 0000000000000000000000000000000000000000..8306ed731dded40f647a6b2d4f6ea547972214d7
Binary files /dev/null and b/lib/lucene/lucene-analyzers-common.jar differ
diff --git a/lib/lucene/lucene-analyzers-common.pom b/lib/lucene/lucene-analyzers-common.pom
new file mode 100644
index 0000000000000000000000000000000000000000..a71e207af6dd2901be4c716c81387690d3512771
--- /dev/null
+++ b/lib/lucene/lucene-analyzers-common.pom
@@ -0,0 +1,17 @@
+<project>
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-analyzers-common</artifactId>
+ <version>4.6.0</version>
+ <name>Lucene analyzers common</name>
+ <description>Apache Lucene standard analysers</description>
+ <packaging>jar</packaging>
+ <licenses>
+ <license>
+ <name>Apache License Version 2.0, January 2004</name>
+ <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+ </license>
+ </licenses>
+
+</project>
diff --git a/lib/lucene/lucene-core.jar b/lib/lucene/lucene-core.jar
index 15cd6c922a9fa02b2a2e2cf0da2f38703be71270..a71f9d384146f2e4a47dafaae13706f2a308418b 100644
Binary files a/lib/lucene/lucene-core.jar and b/lib/lucene/lucene-core.jar differ
diff --git a/lib/lucene/lucene-core.pom b/lib/lucene/lucene-core.pom
index f2d6250e88ec61beb3e174a44ab7a9c9445732e9..a410721c0e6490a2fa5653b6db4d05f675bc7922 100644
--- a/lib/lucene/lucene-core.pom
+++ b/lib/lucene/lucene-core.pom
@@ -3,7 +3,7 @@
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
- <version>3.0.2</version>
+ <version>4.6.0</version>
<name>Lucene Core</name>
<description>Apache Lucene Java Core</description>
<packaging>jar</packaging>
diff --git a/lib/ontosim/ontosim.jar b/lib/ontosim/ontosim.jar
index e630a4928c77b950398c1ea6071fc07c37993838..1baee1c85f021ee9fe93bb5f3370f6231a07b5a8 100644
Binary files a/lib/ontosim/ontosim.jar and b/lib/ontosim/ontosim.jar differ
diff --git a/lib/ontosim/ontosim.pom b/lib/ontosim/ontosim.pom
index 0f59f39d5444a5f09b91c0a91c74d608fcc9c8a0..5235ca12bc5cfbedd273a3d54f1cbea1443d58a8 100644
--- a/lib/ontosim/ontosim.pom
+++ b/lib/ontosim/ontosim.pom
@@ -3,8 +3,7 @@
<groupId>fr.inrialpes.exmo</groupId>
<artifactId>ontosim</artifactId>
- <version>2.3adv</version>
- <!-- This is a non released OntoSim at revision 139 -->
+ <version>2.4</version>
<name>OntoSim</name>
<description>OntoSim is a library and API for distances and similarities between ontologies.</description>
<licenses>
diff --git a/lib/ontowrap.jar b/lib/ontowrap.jar
index 16dfb07d775a5a191e0c2317efc3a60944f6f96e..7ea883bed77365fc13a4f931a5a5f687abe74eb0 100644
Binary files a/lib/ontowrap.jar and b/lib/ontowrap.jar differ
diff --git a/lib/ontowrap.pom b/lib/ontowrap.pom
index cc38fca150469b5a3320ed660fd5dcd29ce08398..cd11bc2d7cd393e426a29ec05c0b29f34cf28837 100644
--- a/lib/ontowrap.pom
+++ b/lib/ontowrap.pom
@@ -16,8 +16,8 @@
<groupId>fr.inrialpes.exmo</groupId>
<artifactId>ontowrap</artifactId>
- <version>4.5</version>
- <!-- Rev 1846M 25/03/2013 -->
+ <version>4.6</version>
+ <!-- Rev 1874M 22/01/2014 -->
<name>Ontology wrapping API</name>
<description>An ontology wrapping API and library.</description>
<url>http://alignapi.gforge.inria.fr</url>
@@ -25,7 +25,7 @@
<name>INRIA Exmo team</name>
<url>http://exmo.inrialpes.fr</url>
</organization>
- <!-- (C) INRIA, 2003-2013 -->
+ <!-- (C) INRIA, 2003-2014 -->
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999</name>
diff --git a/lib/procalign.jar b/lib/procalign.jar
index 516a438352b3ed8e447c326f50fa8ac53654bc08..a6c717077a4d26e731c7579459ca27feaffadde1 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/lib/procalign.pom b/lib/procalign.pom
index 251912c043145955dff8225b2df905e2b1539ebd..e7a7285bf812f461151dcc01373d71918746947d 100644
--- a/lib/procalign.pom
+++ b/lib/procalign.pom
@@ -16,8 +16,8 @@
<groupId>fr.inrialpes.exmo.align</groupId>
<artifactId>procalign</artifactId>
- <version>4.5</version>
- <!-- Rev 1846M 25/03/2013 -->
+ <version>4.6</version>
+ <!-- Rev 1874M 22/01/2014 -->
<name>Reference implementation of the Alignment API</name>
<description>Implementation of the Alignment API for manipulating ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
@@ -25,7 +25,7 @@
<name>INRIA Exmo team</name>
<url>http://exmo.inrialpes.fr</url>
</organization>
- <!-- (C) INRIA, 2003-2013 -->
+ <!-- (C) INRIA, 2003-2014 -->
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999</name>
@@ -42,13 +42,13 @@
<dependency>
<groupId>org.semanticweb.owl</groupId>
<artifactId>align</artifactId>
- <version>4.5</version>
+ <version>4.6</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>fr.inrialpes.exmo</groupId>
<artifactId>ontowrap</artifactId>
- <version>4.5</version>
+ <version>4.6</version>
<scope>compile</scope>
</dependency>
<dependency>
diff --git a/test/src/JWNLTest.java b/test/src/JWNLTest.java
index e358d4f0659f2891f435a50536b4b2d115bf1875..a328e545340a392f7ec512f40d1868b2479a58a2 100644
--- a/test/src/JWNLTest.java
+++ b/test/src/JWNLTest.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008-2010, 2013
+ * Copyright (C) INRIA, 2008-2010, 2013-2014
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -179,7 +179,7 @@ $ java -jar lib/procalign.jar -Dwndict=$WNDIR file://$CWD/examples/rdf/edu.umbc.
alignment.render( renderer );
writer.flush();
writer.close();
- assertEquals( stream.toString().length(), 11903, "Rendered differently" );
+ assertEquals( stream.toString().length(), 11906, "Rendered differently" );
alignment.cut( "hard", 0.4 );
assertEquals( alignment.nbCells(), 10 );
}