[med-svn] r1964 - in trunk/packages/clustalw/trunk: . debian

[plessy at alioth.debian.org]

Author: plessy
Date: 2008-06-04 00:46:30 +0000 (Wed, 04 Jun 2008)
New Revision: 1964

Modified:
   trunk/packages/clustalw/trunk/CHANGELOG
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/clustalw.1
   trunk/packages/clustalw/trunk/debian/clustalw.1.xml
   trunk/packages/clustalw/trunk/debian/copyright
Log:
New upstream release.

Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG	2008-06-04 00:02:00 UTC (rev 1963)
+++ trunk/packages/clustalw/trunk/CHANGELOG	2008-06-04 00:46:30 UTC (rev 1964)
@@ -1,4 +1,23 @@
 ----------------------------------------------------------------------
+Version 2.0.8
+----------------------------------------------------------------------
+
+* Implemented maxseqlen cmdline switch
+
+* Updated help-file
+
+* Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
+
+* Fixed bug 133: providing profiles on command line fails (ClustalX)
+
+* Fixed bug 125: Angle bracket inside sequence
+
+* Fixed bug 129: Early exit on empty sequence
+
+* Fixed a couple of possible memory leaks
+
+
+----------------------------------------------------------------------
 Version 2.0.7
 ----------------------------------------------------------------------
 

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2008-06-04 00:02:00 UTC (rev 1963)
+++ trunk/packages/clustalw/trunk/debian/changelog	2008-06-04 00:46:30 UTC (rev 1964)
@@ -1,3 +1,17 @@
+clustalw (2.0.8-1) unstable; urgency=low
+
+  * New upstream release.
+    - Implemented maxseqlen cmdline switch.
+    - Updated help-file.
+    - Fixed various bugs and possible memory leaks
+      (see /usr/share/doc/clustalw/CHANGELOG)
+  * debian/clustalw.1*:
+    - Added new option;
+    - incremented version number.
+  * debian/copyright lifted to the latest draft format version.
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 04 Jun 2008 18:04:17 +0900
+
 clustalw (2.0.7-1) unstable; urgency=low
 
   * New upstream release.

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1	2008-06-04 00:02:00 UTC (rev 1963)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1	2008-06-04 00:46:30 UTC (rev 1964)
@@ -1,11 +1,11 @@
 .\"     Title: CLUSTALW
 .\"    Author: Des Higgins
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: 05/14/2008
+.\"      Date: 06/04/2008
 .\"    Manual: Clustal Manual
-.\"    Source: Clustal 2.0.7
+.\"    Source: Clustal 2.0.8
 .\"
-.TH "CLUSTALW" "1" "05/14/2008" "Clustal 2.0.7" "Clustal Manual"
+.TH "CLUSTALW" "1" "06/04/2008" "Clustal 2.0.8" "Clustal Manual"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -49,7 +49,7 @@
 .PP
 \fB\-fullhelp\fR
 .RS 4
-Dump the built\-in help file content\&.
+Output full help content\&.
 .RE
 .PP
 \fB\-align\fR
@@ -156,7 +156,12 @@
 to
 \fIm\fR+\fIn\fR\&.
 .RE
+.PP
+\fB\-maxseqlen=\fR\fB\fIn\fR\fR
+.RS 4
+Maximum allowed input sequence length\&.
 .RE
+.RE
 .sp
 .it 1 an-trap
 .nr an-no-space-flag 1

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2008-06-04 00:02:00 UTC (rev 1963)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2008-06-04 00:46:30 UTC (rev 1964)
@@ -18,7 +18,7 @@
   <!ENTITY dhsurname   "Plessy">
   <!ENTITY dhemail     "plessy at debian.org">
   <!ENTITY dhusername  "&dhfirstname; &dhsurname;">
-  <!ENTITY dhrelease   "2.0.7">
+  <!ENTITY dhrelease   "2.0.8">
   <!ENTITY dhtitle     "Clustal Manual">
   <!ENTITY dhucpackage "CLUSTALW">
   <!ENTITY dhpackage   "clustalw">
@@ -195,7 +195,7 @@
             <option>-fullhelp</option>
           </term>
           <listitem>
-            <para>Dump the built-in help file content.</para>
+            <para>Output full help content.</para>
           </listitem>
         </varlistentry>
         
@@ -342,6 +342,15 @@
               <para>Sequence range to write starting <replaceable class="parameter">m</replaceable> to <replaceable class="parameter">m</replaceable>+<replaceable class="parameter">n</replaceable>.</para>
             </listitem>
           </varlistentry>
+
+          <varlistentry>
+            <term>
+              <option>-maxseqlen=<replaceable class="parameter">n</replaceable></option>
+            </term>
+            <listitem>
+              <para>Maximum allowed input sequence length.</para>
+            </listitem>
+          </varlistentry>
         </variablelist>
       </refsect3>
       

Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright	2008-06-04 00:02:00 UTC (rev 1963)
+++ trunk/packages/clustalw/trunk/debian/copyright	2008-06-04 00:46:30 UTC (rev 1964)
@@ -1,8 +1,8 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
-Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
-Debianized-Date: Fri, 28 Aug 1998 16:09:48 +0200
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
+Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
+Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
+Packaged-Date: Fri, 28 Aug 1998 16:09:48 +0200
 Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.7-src.tar.gz
-Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
 X-Non-Free-Autobuild: yes
   The licence does not forbid Debian from using autobuilders to create binary
   packages.