mustang (3.2.1-1) debian-dir only changes

--- mustang-3.2.1.orig/debian/mustang.manpages
+++ mustang-3.2.1/debian/mustang.manpages
@@ -0,0 +1 @@
+man/mustang.1
--- mustang-3.2.1.orig/debian/citation.bib
+++ mustang-3.2.1/debian/citation.bib
@@ -0,0 +1,10 @@
+@Article{pmid16736488,
+   Author="Konagurthu, A.S. and Whisstock, J.C. and Stuckey, P.J. and Lesk, A.M.",
+   Title="{{M}{U}{S}{T}{A}{N}{G}: a multiple structural alignment algorithm}",
+   Journal="Proteins",
+   Year="2006",
+   Volume="64",
+   Pages="559--574",
+   Month="Aug"
+}
+
--- mustang-3.2.1.orig/debian/watch
+++ mustang-3.2.1/debian/watch
@@ -0,0 +1,3 @@
+version=3
+# opts="uversionmangle=s/$/.0/" \
+http://www.cs.mu.oz.au/~arun/mustang/ ./mustang_v([.\d]*)\.tgz
--- mustang-3.2.1.orig/debian/copyright
+++ mustang-3.2.1/debian/copyright
@@ -0,0 +1,78 @@
+This package was downloaded from http://www.cs.mu.oz.au/~arun/mustang/
+
+Files: Makefile, src/*, data/test/test_zf-CCHH
+Copyright: (C) 2005, Arun S Konagurthu <arun@bx.psu.edu> and The University
+ of Melbourne.
+License: BSD-like
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ .
+ * Neither the name of the University of Melbourne nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+Files: debian/*
+Copyright: of the Debian packaging is assigned to the copyright holder and
+ condition to the above license.
+License: BSD-like
+
+Files: data/test/pdbs:
+Copyright: PD
+License:
+ ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE
+ .
+ By using the materials available in this archive, the user agrees to abide
+ by the following conditions:
+ .
+ * The archival data files in the PDB archive are made freely available
+ to all users. Data files within the archive may be redistributed in original
+ form without restriction. Redistribution of modified data files using the same
+ file name as is on the FTP server is prohibited. The rules for file names are
+ detailed at http://www.wwpdb.org/wwpdb_charter.html.
+ .
+ * Data files containing PDB content may incorporate the PDB 4-letter entry
+ name (e.g. 1ABC) in standard PDB records only if they are exactly the same
+ as what is residing in the PDB archive. This does not prevent databases
+ from including PDB entry_id's as cross-references where it is clear that
+ they refer to the PDB archive. PDB records refer to the standard PDB format.
+ The distribution of modified PDB format data including the records: HEADER,
+ CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES are not allowed.
+ .
+ * The user assumes all responsibility for insuring that intellectual property
+ claims associated with any data set deposited in the PDB archive are honored.
+ It should be understood that the PDB data files do not contain any information
+ on intellectual property claims with the exception in some cases of a reference
+ for a patent involving the structure.
+ .
+ * Any opinion, findings, and conclusions expressed in the PDB archive by the
+ authors/contributors do not necessarily reflect the views of the wwPDB.
+ .
+ * The data in the PDB archive are provided on an "as is" basis.  The wwPDB
+ nor its comprising institutions cannot be held liable to any party for direct,
+ indirect, special, incidental, or consequential damages, including lost
+ profits, arising from the use of PDB materials.
+ .
+ * Resources on this site are provided without warranty of any kind, either
+ expressed or implied. This includes but is not limited to merchantability or
+ fitness for a particular purpose. The institutions managing this site make
+ no representation that these resources will not infringe any patent or other
+ proprietary right.
--- mustang-3.2.1.orig/debian/mustang.examples
+++ mustang-3.2.1/debian/mustang.examples
@@ -0,0 +1,2 @@
+debian/runtest
+debian/test_zf-CCHH-small
--- mustang-3.2.1.orig/debian/changelog
+++ mustang-3.2.1/debian/changelog
@@ -0,0 +1,80 @@
+mustang (3.2.1-1) unstable; urgency=low
+
+  * New upstream version
+  * Morten Kjeldgaard lost interest in this package because of
+    agressive upstream so I removed him from uploaders and added myself
+  * debhelper 7
+  * prefer single debhelper files in debian/ instead of using
+    arguments do debhelper scripts in the rules file which simplifies
+    transition to short rules file
+  * debian/watch: no uversionmangle which leads to wrong version
+    number
+
+ -- Andreas Tille <tille@debian.org>  Wed, 28 Oct 2009 19:59:33 +0100
+
+mustang (3.2.0-1) unstable; urgency=low
+
+  * New upstream version.
+  * Patches 02-main.cpp.patch and 04-gcc-4.3-exit.patch have been 
+    incorporated upstream and are no longer required.
+
+ -- Morten Kjeldgaard <mok0@ubuntu.com>  Mon, 05 Oct 2009 13:10:26 +0200
+
+mustang (3.0-2) unstable; urgency=low
+
+  * Converted to quilt patch system.
+  * New uploader email
+  * Added citation.bib file, installed in /usr/share/doc/mustang
+  
+ -- Morten Kjeldgaard <mok0@ubuntu.com>  Sun, 14 Dec 2008 13:55:03 +0100
+
+mustang (3.0-1) unstable; urgency=low
+
+  [ Nelson A. de Oliveira ]
+  * debian/rules: CFLAGS -> CPPFLAGS
+  * debian/control: add ${misc:Depends} to binary package, and 
+    add Suggests: mustang-testdata
+  * Add debian/watch
+  
+  [ Morten Kjeldgaard ]
+  * Upload mustang to Debian  (Closes: #459637).
+  * debian/control: Maintainer and homepage fields set as per
+    Debian policy.
+  * Include test pdb files in a separate package.
+  * debian/rules: add get-orig-source target.
+  * Include new upstream patches.
+  * Upstream now distributes manpage which is installed.
+  * Include pdb files from upstream tarball in a separate package,
+    for a more extensive test.
+
+  [ Andreas Tille ]
+  * Maintainer: Debian-Med Packaging Team
+    Uploaders: Morten Kjeldgaard <mok@bioxray.au.dk>
+  * XS-DM-Upload-Allowed: Yes
+  * Vcs-Browser, Vcs-Svn
+
+  [ Steffen Moeller ]
+  * Policy 3.8.0
+  * Patch for gcc-4.3
+  * debian/control has less redundany and easier working, added ref to paper.
+  * changed debian watch to reflect version mangling in debian/changelog
+
+ -- Morten Kjeldgaard <mok@bioxray.au.dk>  Mon, 04 Aug 2008 10:42:14 +0200
+
+mustang (3.0-0ubuntu1) gutsy; urgency=low
+
+  * Initial release
+  * Manpage mustang.1 authored from information in the README.txt file.
+  * The upstream tarball was repackaged to remove PDB files which have an
+    undetermined copyright status and hence can not be distributed.
+    Furthermore, the license was extracted from one of the source files
+    and placed in the file 'LICENSE'. A note describing the repackaging in
+    detail is placed in debian/copyright.
+  * Instead of the PDB files included in the original tarball, a script is
+    supplied that allows the user to fetch a few PDB files and test that
+    mustang works.
+  * A patch on main.cpp is supplied to beautify the output of the initial
+    author blurb. The tabs in the output were removed to make the output
+    easier to read in a default 80 columns wide terminal window.
+
+ -- Morten Kjeldgaard <mok@bioxray.dk>  Mon, 25 Jun 2007 15:55:12 +0000
--- mustang-3.2.1.orig/debian/README.source
+++ mustang-3.2.1/debian/README.source
@@ -0,0 +1,5 @@
+This package uses quilt to manage all modifications to the upstream source.
+Changes are stored in the source package as diffs in debian/patches and applied
+during the build.
+
+For complete information, please see /usr/share/doc/quilt/README.source.
--- mustang-3.2.1.orig/debian/test_zf-CCHH-small
+++ mustang-3.2.1/debian/test_zf-CCHH-small
@@ -0,0 +1,22 @@
+###############################################################################################
+## This is a valid desciption file.                                                          ##
+##                                                                                           ##
+## Line starting with '>' symbol is treated as PATH to the directory containing structures   ##
+## to be aligned.                                                                            ##
+##                                                                                           ##
+## Lines starting with '+' symbol are treated as file names. If PATH is specified (as in     ##
+## this case), then only the filenames should be provided. However, if PATH line is NOT      ##
+## provided, then the absolute/relative paths of the structure files should be provided.     ##
+##                                                                                           ##
+## All the lines NOT starting with '>' and '+' are simply ignored.                           ##
+##                                                                                           ##
+## Do NOT use comments in the same lines containg PATH and FILENAMES.                        ##
+##                                                                                           ##
+## Whitespaces are intentionally inserted before and/or after '>' and --in some cases-- '+'  ##
+## symbols to show that the whitespaces are ignored                                          ##
+###############################################################################################
+
+ >  /tmp/mustang
+
++1sp1.pdb
++1sp2.pdb
--- mustang-3.2.1.orig/debian/compat
+++ mustang-3.2.1/debian/compat
@@ -0,0 +1 @@
+7
--- mustang-3.2.1.orig/debian/mustang-testdata.install
+++ mustang-3.2.1/debian/mustang-testdata.install
@@ -0,0 +1,2 @@
+data/test/pdbs/[0-9]*     usr/share/doc/mustang-testdata/examples/pdbs
+data/test/test_zf-CCHH    usr/share/doc/mustang-testdata/examples
--- mustang-3.2.1.orig/debian/rules
+++ mustang-3.2.1/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; mode: font-lock  -*-
+
+%:
+	dh --with quilt $@
+
+override_dh_compress:
+	dh_compress -X.pdb
+
+override_dh_auto_clean:
+	rm -f obj/*.o
+	rm -f bin/mustang-3.2*
+#	dh_clean
+
+override_dh_auto_install:
+	install -D -m755 bin/mustang-3.2* debian/mustang/usr/bin/mustang
--- mustang-3.2.1.orig/debian/runtest
+++ mustang-3.2.1/debian/runtest
@@ -0,0 +1,29 @@
+#!/bin/sh
+# pdbget script for mustang that fetches
+# db entries to run test file.
+#
+set -e
+
+SERVER=www.pdb.org
+entries="1sp1 1sp2 3znf"
+
+pdb_fetch () {
+  for n in $* ; do
+      wget -nv http://${SERVER}/pdb/files/$n.pdb.gz
+  done
+}
+
+# The process will run in this directory:
+tmpdir=/tmp/mustang
+
+savedir=$PWD
+rm -rf $tmpdir
+mkdir -p $tmpdir
+cd $tmpdir
+pdb_fetch $entries
+for f in $entries; do gzip -dc $f.pdb.gz > $f.pdb ; done
+
+mustang -f /usr/share/doc/mustang/examples/test_zf-CCHH-small
+cd $savedir
+
+echo Results are in $tmpdir/results.html and $tmpdir/results.pdb
--- mustang-3.2.1.orig/debian/control
+++ mustang-3.2.1/debian/control
@@ -0,0 +1,40 @@
+Source: mustang
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+DM-Upload-Allowed: yes
+Homepage: http://www.cs.mu.oz.au/~arun/mustang/
+Build-Depends: debhelper (>= 7.1), quilt
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mustang/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mustang/trunk/
+
+Package: mustang
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: mustang-testdata
+Description: multiple structural alignment of proteins
+ Mustang is an algorithm to align multiple protein structures.
+ Given a set of PDB files, the program uses the spatial
+ information in the Calpha atoms of the set to produce a sequence alignment.
+ Based on a progressive pairwise heuristic the algorithm then proceeds
+ through a number of refinement passes. Mustang reports the multiple
+ sequence alignment and the corresponding superposition of structures.
+ .
+ When using this program please cite A.S. Konagurthu, J.C. Whisstock,
+ P.J. Stuckey, A.M. Lesk, "MUSTANG: A multiple structural alignment
+ algorithm." Proteins: Structure, Function, and Bioinformatics. 64(3):559-574.
+
+Package: mustang-testdata
+Architecture: all
+Enhances: mustang
+Depends: ${misc:Depends}
+Description: multiple structural alignment of proteins, test data
+ This package contains a larger set of test data than what
+ comes with the binary package. 
+ .
+ To run the test, change to a directory where you have write access, 
+ then issue the command:
+  mustang -f /usr/share/doc/mustang-testdata/examples/test_zf-CCHH 
+
--- mustang-3.2.1.orig/debian/mustang.docs
+++ mustang-3.2.1/debian/mustang.docs
@@ -0,0 +1 @@
+debian/citation.bib
--- mustang-3.2.1.orig/debian/patches/series
+++ mustang-3.2.1/debian/patches/series
@@ -0,0 +1 @@
+03-test_zf-cchh.patch
--- mustang-3.2.1.orig/debian/patches/03-test_zf-cchh.patch
+++ mustang-3.2.1/debian/patches/03-test_zf-cchh.patch
@@ -0,0 +1,13 @@
+This patch merely changes the name of the directory storing the
+example pdb files.
+--- trunk.orig/data/test/test_zf-CCHH
++++ trunk/data/test/test_zf-CCHH
+@@ -20,7 +20,7 @@
+ ################################################################################
+ 
+ 
+-> ./data/test/pdbs    
++> /usr/share/doc/mustang-testdata/examples/pdbs
+ 
+ +1ard.pdb
+ +1bboN.pdb