[med-svn] r150 - in trunk/packages/seaview/trunk/debian: . patches
Charles Plessy
charles-guest at alioth.debian.org
Sat Oct 28 11:10:18 CEST 2006
Author: charles-guest
Date: 2006-10-28 11:10:18 +0200 (Sat, 28 Oct 2006)
New Revision: 150
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch
trunk/packages/seaview/trunk/debian/seaview.1.xml
trunk/packages/seaview/trunk/debian/seaview.desktop
Log:
Improved the manpage, and added a "made in Debian" comment in the desktop file.
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2006-10-21 02:02:49 UTC (rev 149)
+++ trunk/packages/seaview/trunk/debian/changelog 2006-10-28 09:10:18 UTC (rev 150)
@@ -1,8 +1,11 @@
seaview (20060918-2) unstable; urgency=low
- * New maintainer email: the previous one was not the intended mailing list.
+ * New maintainer email: the previous one was not the intended mailing list.
+ * Removing options passed to x-terminal-emulator if they are not a MUST in
+ the policy chapter 11.8.3.
+ * Improved manpage.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 6 Oct 2006 09:44:31 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 28 Oct 2006 17:27:02 +0900
seaview (20060918-1) unstable; urgency=low
Modified: trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch 2006-10-21 02:02:49 UTC (rev 149)
+++ trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch 2006-10-28 09:10:18 UTC (rev 150)
@@ -2,8 +2,8 @@
## 30-align.cxx.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: Use the Debian alternatives system ; hardocode the location of the
-## DP: helper file
+## DP: Use the Debian alternatives system and discard options not warranted by
+## DP: policy 11.8.3 ; hardocode the location of the helper file.
@DPATCH@
@@ -49,7 +49,7 @@
#else
-sprintf(commande, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 "
- "-e seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
-+sprintf(commande, "x-terminal-emulator -T \"%s alignment\" -n %s -sb -sl 2000 "
++sprintf(commande, "x-terminal-emulator -T \"%s alignment\" "
+ "-e /usr/share/seaview/seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
algo_name[align_algorithm]);
l = strlen(commande);
Modified: trunk/packages/seaview/trunk/debian/seaview.1.xml
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1.xml 2006-10-21 02:02:49 UTC (rev 149)
+++ trunk/packages/seaview/trunk/debian/seaview.1.xml 2006-10-28 09:10:18 UTC (rev 150)
@@ -4,7 +4,7 @@
<!ENTITY dhfirstname "<firstname>Charles</firstname>">
<!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>2006-09-27</date>">
+ <!ENTITY dhdate "<date>2006-10-28</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
@@ -51,14 +51,43 @@
<para><command>&dhpackage;</command> is the program that starts the
SeaView GUI.</para>
- <para>SeaView is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS). It allows one to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally improve the alignment.</para>
+ <para>SeaView is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS). It allows one to manually edit the alignment, and also to run DOT-PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment.</para>
<para>If started from the command line with <filename>filename</filename> as an argument, &dhpackage; will open the alignment stored in <filename>filename</filename>.</para>
</refsect1>
<refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-fast</option></term>
+ <listitem><para>Suppresses double buffering for display. This should only accelerate display on very slow systems.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fontsize</option> <parameter>n</parameter></term>
+ <listitem><para>Sets the font size to <parameter>n</parameter>.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-inverted</option></term>
+ <listitem><para>Residues will appear as black letters on a colored background</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-save</option> <parameter>format_name</parameter></term>
+ <listitem><para>Sets the default file format for saving operations. <parameter>format_name</parameter> can be either mase, clustal, phylip, msf, fasta, or nexus. Without this option, SeaView autodetects the format of the opened file and uses the same for saving.</para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1>
+ <title>FILES</title>
+ <para><filename><varname>$HOME</varname>/.seaviewrc</filename> holds the user's configuration for SeaView.</para>
+ </refsect1>
+
+ <refsect1>
<title>SEE ALSO</title>
-
<para> The program is fully documented online. Press the "help" button in the main window. On Debian systems, the text template for SeaView's help can be found in <filename>/usr/share/seaview/seaview.help</filename> (It is human readable).</para>
<para>The home page of SeaView is pbil.univ-lyon1.fr/software/seaview.html.</para>
@@ -74,7 +103,7 @@
<para><application>SeaView</application> is Copyright (C) 1996-2005 Manolo Gouy <email>mgouy at biomserv.univ-lyon1.fr</email>. It is released under the GNU General Public Licence</para>
- <para>This manual page was written by Stephane Bortzmeyer <email>bortzmeyer at debian.org</email> and updated by &dhusername; (&dhemail;) for the &debian; system (but may be used by others). You can redistribute it and/or modify it under the terms of the GNU General Public License.<!-- This also applies to this xml document. --></para>
+ <para>This manual page was written by Stephane Bortzmeyer <email>bortzmeyer at debian.org</email> and updated by &dhusername; (&dhemail;) for the &debian; system (but may be used by others). You can redistribute it and/or modify it under same terms as SeaView itself.<!-- This also applies to this xml document. --></para>
<para>
On Debian systems, the complete text of the GNU General Public
Modified: trunk/packages/seaview/trunk/debian/seaview.desktop
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.desktop 2006-10-21 02:02:49 UTC (rev 149)
+++ trunk/packages/seaview/trunk/debian/seaview.desktop 2006-10-28 09:10:18 UTC (rev 150)
@@ -1,3 +1,6 @@
+# This file was orignially written for Debian, and can be copied, used,
+# modified and redistributed under the same licence as SeaView itself.
+
[Desktop Entry]
Version=1.0
Encoding=UTF-8
@@ -16,4 +19,3 @@
Type=Application
Categories=Biology;Science;Education;
-
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