[med-svn] r2722 - trunk/packages/seaview/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Nov 23 12:57:39 UTC 2008
Author: plessy
Date: 2008-11-23 12:57:39 +0000 (Sun, 23 Nov 2008)
New Revision: 2722
Added:
trunk/packages/seaview/trunk/debian/seaview.svg
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/copyright
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/debian/references
Log:
New 3.2 version using a different and free md5 source file.
Other changes are:
- Deletion of the abstract of debian/references (copyrighted).
- Addition of a vecor icon that I made for SeaView (forwarded Upstream).
- Update of debian/copyright to latest spec of machine-readable format and
addition of the license of the files under the FL directory.
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2008-11-20 16:02:00 UTC (rev 2721)
+++ trunk/packages/seaview/trunk/debian/changelog 2008-11-23 12:57:39 UTC (rev 2722)
@@ -1,13 +1,21 @@
-seaview (1:3.2-1) UNRELEASED; urgency=low
+seaview (1:3.2-1) unstable; urgency=low
* New upstream version:
- - Version 3.0
- - Version 3.1
- - Version 3.2
- * debian/copyright, debian/seaview.1*: added year 2008 to copyright
- statements.
+ - Version 3.2: Database import can be done using a keyword.
+ - Version 3.1: now use Fl_Native_File_Chooser.
+ - Version 3.0: sequences can be imported from embl, genbank, swissprot if
+ internet access.
+ * debian/copyright:
+ - Added the FL directory from Upstream sources.
+ - Updated to the latest version of the machine-readable format.
+ * debian/seaview.svg: vector icon made for SeaView and forwarded upstream.
+ * debian/seaview.1*: added year 2008 to copyright statements.
* Updated my email address.
* debian/control, debian/compat: using Debhelper 7.
+ * Experimental handling of bibliographic references:
+ - debian/references contains a BibTeX-formatted reference.
+ - debian/seaview.doc-base.references registers it for Doc-base
+ in a "Bibliography" section to be proposed later.
-- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:02:54 +0900
Modified: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright 2008-11-20 16:02:00 UTC (rev 2721)
+++ trunk/packages/seaview/trunk/debian/copyright 2008-11-23 12:57:39 UTC (rev 2722)
@@ -1,38 +1,16 @@
-NOW CONTAINS A NON-FREE FILE (md5.c); DO NOT UPLOAD UNTIL PROBLEM IS SOLVED.
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=402
+Upstream-Name: SeaView
+Upstream-Maintainer: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+Upstream-Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_3.2.tar.gz
+X-Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
+X-Packaged-Date: Mon, 1 Mar 1999 16:41:51 +0100
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
-X-Debinized-Date: Mon, 1 Mar 1999 16:41:51 +0100
-X-Source-Downloaded-From: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
-X-Upstream-Author: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-
-Files: debian/*
-
-Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
- © 2001 Dr. Guenter Bechly <gbechly at debian.org>
- © 2001 Adrian Bunk <bunk at fs.tum.de>
- © 2001 Doug Porter <dsp at debian.org>
- © 2002 Matej Vela <vela at debian.org>
- © 2003 Colin Watson <cjwatson at debian.org>
- © 2003 Aaron M. Ucko <ucko at debian.org>
- © 2003 Brian R Furry <bfurry at nac.net>
- © 2005 Steve Langasek <vorlon at debian.org>
- © 2007 Nelson A. de Oliveira <naoliv at debian.org>
- © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
-
-License: unknown
- Please treat the contributions of Charles Plessy as if they were in the public domain.
-
-
Files: *
-
Copyright: © 1996-2008 Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-
X-Comment: If you use SeaView in a published work, please cite the following reference:
Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic
tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci.,
12, 543-548.
-
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -47,6 +25,40 @@
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
X-Comment: On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: FL/*
+Copyright: © 2004 Greg Ercolano
+ © 2005 Nathan Vander Wilt
+License: LGPL-2+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Library General Public License for more details.
+ .
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
+X-Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License can be found in `/usr/share/common-licenses/LGPL'.
+
+Files: debian/*
+Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
+ © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+ © 2001 Adrian Bunk <bunk at fs.tum.de>
+ © 2001 Doug Porter <dsp at debian.org>
+ © 2002 Matej Vela <vela at debian.org>
+ © 2003 Colin Watson <cjwatson at debian.org>
+ © 2003 Aaron M. Ucko <ucko at debian.org>
+ © 2003 Brian R Furry <bfurry at nac.net>
+ © 2005 Steve Langasek <vorlon at debian.org>
+ © 2007 Nelson A. de Oliveira <naoliv at debian.org>
+ © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+License: unknown
+ Please treat the contributions of Charles Plessy as if they were in the public domain.
Modified: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install 2008-11-20 16:02:00 UTC (rev 2721)
+++ trunk/packages/seaview/trunk/debian/install 2008-11-23 12:57:39 UTC (rev 2722)
@@ -3,3 +3,4 @@
seaview.help usr/share/seaview
seaview.xpm usr/share/pixmaps
debian/seaview.desktop usr/share/applications
+debian/seaview.svg usr/share/icons/hicolor/scalable/apps
Modified: trunk/packages/seaview/trunk/debian/references
===================================================================
--- trunk/packages/seaview/trunk/debian/references 2008-11-20 16:02:00 UTC (rev 2721)
+++ trunk/packages/seaview/trunk/debian/references 2008-11-23 12:57:39 UTC (rev 2722)
@@ -1,7 +1,3 @@
-
-
-
-
@article{N.Galtier12011996,
author = {Galtier, N. and Gouy, M. and Gautier, C.},
title = {{SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny}},
@@ -11,8 +7,6 @@
pages = {543-548},
doi = {10.1093/bioinformatics/12.6.543},
year = {1996},
-abstract = {SEA VIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEA VIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyonl. fr/pub/ mol_phylogeny or http://acnuc.univ-lyonl.fr, or by e-mail to galtier at biomserv.univ-lyonl.fr.
-},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/12/6/543},
eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/12/6/543.pdf}
}
Added: trunk/packages/seaview/trunk/debian/seaview.svg
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.svg (rev 0)
+++ trunk/packages/seaview/trunk/debian/seaview.svg 2008-11-23 12:57:39 UTC (rev 2722)
@@ -0,0 +1,132 @@
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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+ sodipodi:version="0.32"
+ inkscape:version="0.46"
+ width="32"
+ height="32"
+ version="1.0"
+ sodipodi:docname="seaview.svg"
+ inkscape:output_extension="org.inkscape.output.svg.inkscape">
+ <metadata
+ id="metadata7">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
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+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
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+ inkscape:window-height="790"
+ inkscape:window-width="1396"
+ inkscape:pageshadow="2"
+ inkscape:pageopacity="0.0"
+ guidetolerance="10.0"
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+ id="base"
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+ inkscape:snap-global="true"
+ inkscape:zoom="11.313709"
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