debian/0000755000000000000000000000000012147656570007203 5ustar debian/copyright0000644000000000000000000000564112147656566011151 0ustar This package was debianized by Julien Dutheil on Tue, 05 Mar 2013 14:34:00 +0100. It was downloaded from Upstream Author: Julien Dutheil Copyright: Copyright (C) 2013 Bio++ Development Team License: 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 the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package 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 General Public License for more details. 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 On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. The Debian packaging is (C) 2013, Julien Dutheil and is licensed under the GPL, see above. The provided software is distributed under the CeCILL license: This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. The complete text of the license may be found here: http://www.cecill.info/licences/Licence_CeCILL_V2-en.html debian/changelog0000644000000000000000000000365612147656566011074 0ustar libbpp-seq (2.1.0-1) unstable; urgency=low * 'omics' tools now in bpp-seq-omics * Extended BppO support * StateProperties renamed to AlphabetIndex -- Julien Dutheil Tue, 05 Mar 2013 14:31:00 +0100 libbpp-seq (2.0.3-1) unstable; urgency=low * Bugs fixed in maf parser + new iterators * Added support for GFF * Added support for FastQ * Several bugs fixed -- Julien Dutheil Thu, 09 Feb 2012 14:00:00 +0100 libbpp-seq (2.0.2-1) unstable; urgency=low * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373). * Packages are now non-native. * Bugs fixed in maf parser. -- Julien Dutheil Thu, 09 Jun 2011 11:00:00 +0100 libbpp-seq (2.0.1) unstable; urgency=low * Fixed copyright and rules file. -- Julien Dutheil Mon, 28 Feb 2011 09:00:00 +0100 libbpp-seq (2.0.0) unstable; urgency=low * New source files organization. * More NGS tools: sequence annotations, quality scores, file parsers, etc. -- Julien Dutheil Mon, 07 Feb 2011 09:00:00 +0100 libbpp-seq (1.7.0) unstable; urgency=low * Several bug fixed. Compilation with -Weffc++. * New compressed sites container. * Improved security by changing several pointers to references. -- Julien Dutheil Thu, 25 Mar 2010 10:02:50 +0100 libbpp-seq (1.6.0) unstable; urgency=low * New support for Nexus sequence files. * Update for version 1.8 of Bio++. -- Julien Dutheil Wed, 10 Jun 2009 11:28:58 +0100 libbpp-seq (1.5.0) unstable; urgency=low * Several bugs fixed, new Phred sequence format, speed improvements. -- Julien Dutheil Thu, 11 Dec 2008 12:21:37 +0100 libbpp-seq (1.4.1) unstable; urgency=low * Initial Release. -- Julien Dutheil Mon, 21 Jul 2008 15:17:26 +0200 debian/prerm0000755000000000000000000000061612147656566010266 0ustar #! /bin/bash # Abort if any command returns an error value set -e removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } if [ "$1" = "remove" ]; then # Actualize .all files removeGeneric /usr/include/Bpp fi exit 0 debian/rules0000755000000000000000000000531112147656566010270 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # 24/01/10 Modification for use with CMake by Julien Dutheil. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # These are used for cross-compiling and for saving the configure script # from having to guess our platform (since we know it already) DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) CFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif # shared library versions version=`ls src/lib*.so.* | \ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'` major=`ls src/lib*.so.* | \ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'` configure: cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . config.status: configure dh_testdir build: build-stamp build-stamp: config.status dh_testdir # Add here commands to compile the package. $(MAKE) touch $@ clean: dh_testdir dh_testroot # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean; [ ! -f Makefile ] || rm Makefile; [ ! -f src/Makefile ] || rm src/Makefile; [ ! -f test/Makefile ] || rm test/Makefile; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f src/*.cmake rm -f test/*.cmake rm -rf CMakeFiles rm -rf src/CMakeFiles rm -rf test/CMakeFiles rm -rf _CPack_Packages rm -rf Testing rm -f DartConfiguration.tcl dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # Add here commands to install the package into debian/tmp $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples dh_install # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_installinit # dh_installcron # dh_installinfo dh_installman dh_link dh_strip dh_compress dh_fixperms # dh_perl # dh_python dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install debian/docs0000644000000000000000000000000012147656566010051 0ustar debian/postrm0000755000000000000000000000152412147656566010464 0ustar #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } if [ "$1" = "remove" ]; then # Automatically added by dh_makeshlibs ldconfig # Actualize .all files createGeneric /usr/include/Bpp fi exit 0 debian/compat0000644000000000000000000000000212147656566010406 0ustar 5 debian/libbpp-seq-dev.install0000644000000000000000000000011012147656566013402 0ustar debian/tmp/usr/include/* debian/tmp/usr/lib/*.a debian/tmp/usr/lib/*.so debian/postinst0000755000000000000000000000144312147656566011023 0ustar #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } if [ "$1" = "configure" ]; then # Actualize .all files createGeneric /usr/include/Bpp fi exit 0 debian/libbpp-seq9.install0000644000000000000000000000003512147656566012725 0ustar debian/tmp/usr/lib/lib*.so.* debian/control0000644000000000000000000000133012147656566010610 0ustar Source: libbpp-seq Section: libs Priority: optional Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), libbpp-core-dev (>= 2.1.0) Standards-Version: 3.9.1 Package: libbpp-seq-dev Section: libdevel Architecture: any Depends: libbpp-seq9 (= ${binary:Version}), ${misc:Depends}, libbpp-core-dev (>= 2.1.0) Description: Bio++ Sequence library development files. Contains the Bio++ classes for sequence analysis. Package: libbpp-seq9 Section: libs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-core2 (>= 2.1.0) Description: Bio++ Sequence library. Contains the Bio++ classes for sequence analysis. debian/source/0000755000000000000000000000000012147656570010503 5ustar debian/source/format0000644000000000000000000000001412147656566011716 0ustar 3.0 (quilt)