debian/0000775000000000000000000000000012266151412007170 5ustar debian/rules0000775000000000000000000000156212266151333010256 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) %: dh $@ --with autoreconf --parallel .PHONY: override_dh_auto_configure override_dh_auto_configure: dh_auto_configure --parallel -- --enable-doxygen-dot --enable-doxygen-pdf .PHONY: override_dh_auto_build override_dh_auto_build: dh_auto_build --parallel $(MAKE) -C lib doxygen-doc .PHONY: override_dh_strip override_dh_strip: dh_strip --dbg-package=librostlab3-dbg .PHONY: override_dh_compress override_dh_compress: dh_compress -Xlibrostlab.tag .PHONY: get-orig-source get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/watch0000664000000000000000000000013612034237105010216 0ustar version=3 opts=passive \ ftp://rostlab.org/free/librostlab-([0-9.]+)\.tar\.gz debian uupdate debian/changelog0000664000000000000000000001204412266151406011046 0ustar librostlab (1.0.20-3ubuntu1) trusty; urgency=medium * Use dh-autoreconf instead of autotools-dev to also fix FTBFS on ppc64el by getting new libtool macros (still updates config.{sub,guess}). -- Logan Rosen Fri, 17 Jan 2014 01:51:29 -0500 librostlab (1.0.20-3) unstable; urgency=low * debian/control: - cme fix dpkg-control - debhelper 9 - canonical Vcs fields * debian/rules: --with autotools_dev Closes: #727433 * debian/*.install: Multi-Arch locations -- Andreas Tille Thu, 24 Oct 2013 08:49:13 +0200 librostlab (1.0.20-2) unstable; urgency=low * Added handening flags. * Added symbols file for shared library dependency information. -- Laszlo Kajan Wed, 19 Sep 2012 14:03:45 +0200 librostlab (1.0.20-1) unstable; urgency=low [ Laszlo Kajan ] * Moved blast parser out into librostlab-blast. * Initial release in Debian (Closes: #666192) [ Andreas Tille ] * debian/control: - Enhanced long description - Joe Debian-User might possibly not know what rostlab is and from the explanation it did not became clear that the library is useful in computational biology - Priority: optional (just leave the debug package extra) - Short descriptions should be different * debian/librostlab-doc.doc-base: Add doc-base file for the included documentation -- Andreas Tille Fri, 30 Mar 2012 15:21:06 +0200 librostlab (1.0.19) unstable; urgency=low * Added trace_scanning() and changed trace_scanning( bool ) * Fixed multi-result file parsing -- Laszlo Kajan Wed, 21 Mar 2012 14:47:50 +0100 librostlab (1.0.18) unstable; urgency=low * Fixed more std::. -- Laszlo Kajan Wed, 21 Mar 2012 14:41:19 +0100 librostlab (1.0.17) unstable; urgency=low * No using namespace std; any more in headers -- Laszlo Kajan Wed, 21 Mar 2012 13:50:03 +0100 librostlab (1.0.16) unstable; urgency=low * changed library license to LGPL * Changed package name to librostlab0, librostlab0-dbg and librostlab0-dev. * Provides librostlab-dev. * Hit is now a template with hsp type as parameter. * Added NCBI BLOSUM62 matrix data. * Cleaned up grammar for rounds. * Added rostlab_stdio.h -- Laszlo Kajan Fri, 14 Oct 2011 20:41:57 +0200 librostlab (1.0.15) unstable; urgency=low * better description -- Laszlo Kajan Fri, 14 Oct 2011 20:34:30 +0200 librostlab (1.0.14) unstable; urgency=low * added documentation -- Laszlo Kajan Fri, 14 Oct 2011 20:12:30 +0200 librostlab (1.0.13) unstable; urgency=low * parser::parse now returns result_type * cast of result_type to bool is done -- Laszlo Kajan Fri, 14 Oct 2011 19:34:04 +0200 librostlab (1.0.12) unstable; urgency=low * more headers installed -- Laszlo Kajan Fri, 14 Oct 2011 19:18:42 +0200 librostlab (1.0.11) unstable; urgency=low * headers are now installed -- Laszlo Kajan Fri, 14 Oct 2011 19:02:15 +0200 librostlab (1.0.10) unstable; urgency=low * Removed libzerg-based blast parser * Added bison/flex based LGPL blast parser -- Laszlo Kajan Thu, 06 Oct 2011 19:57:29 +0200 librostlab (1.0.9) unstable; urgency=low * flock_resource -> file_lock_resource * locking now with fcntl: also works on NFS -- Laszlo Kajan Mon, 26 Sep 2011 18:50:22 +0200 librostlab (1.0.8) unstable; urgency=low * added missing -dev dependency on librostlab0 * removed private members from doxygen documentation -- Laszlo Kajan Fri, 23 Sep 2011 21:45:02 +0200 librostlab (1.0.7) unstable; urgency=low * renamed _map_split_in_2 to map_split_in_2 * added blastpgp parser * cdbs -- Laszlo Kajan Fri, 23 Sep 2011 21:43:11 +0200 librostlab (1.0.6) unstable; urgency=low * added mapAA2int.h Maximilian Hecht Wed, 29 Jun 2011 09:50:51 +0200 -- Laszlo Kajan Wed, 29 Jun 2011 10:50:51 +0200 librostlab (1.0.5) unstable; urgency=low * added throw() definitions to interface of flock_resource -- Laszlo Kajan Mon, 20 Jun 2011 10:52:36 +0200 librostlab (1.0.4) unstable; urgency=low * FASTA format checking improved -- Laszlo Kajan Fri, 10 Jun 2011 10:29:22 +0200 librostlab (1.0.3) stable; urgency=low * flock debugging added -- Laszlo Kajan Wed, 02 Feb 2011 14:53:19 +0100 librostlab (1.0.2) stable; urgency=low * does not touch lock file any more -- Laszlo Kajan Wed, 02 Feb 2011 13:44:10 +0100 librostlab (1.0.1) stable; urgency=low * now closes lock file before throwing an exception if locking fails * added cwd_resource -- Laszlo Kajan Thu, 20 Jan 2011 23:57:04 +0100 librostlab (1.0.0) stable; urgency=low * Initial release -- Laszlo Kajan Wed, 15 Sep 2010 15:28:53 +0200 debian/compat0000664000000000000000000000000212232141472010364 0ustar 9 debian/copyright0000664000000000000000000000374311735266016011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: librostlab Upstream-Contact: Laszlo Kajan Source: http://rostlab.org/ Files: debian/* Copyright: 2012 Laszlo Kajan , Technical University of Munich, Germany License: GPL-3+ Files: * Copyright: 2012 Laszlo Kajan , Technical University of Munich, Germany License: LGPL-3+ License: GPL-3+ This program 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 3 of the License, or (at your option) any later version. . This program 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 program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. License: LGPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 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 Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU Lesser General Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. debian/librostlab-doc.docs0000664000000000000000000000010011735366446012750 0ustar doxygen-doc/html/ doxygen-doc/librostlab.pdf lib/librostlab.tag debian/source/0000775000000000000000000000000012054175341010472 5ustar debian/source/format0000664000000000000000000000001411735103747011706 0ustar 3.0 (quilt) debian/librostlab-doc.doc-base0000664000000000000000000000162611735366446013513 0ustar Document: librostlab Title: librostlab Documentation Author: Laszlo Kajan Abstract: C++ library for computational biology This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products. . The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource Section: Science/Biology Format: html Files: /usr/share/doc/librostlab-doc/html/*.html Index: /usr/share/doc/librostlab-doc/html/index.html Format: PDF Files: /usr/share/doc/librostlab-doc/librostlab.pdf.gz debian/librostlab3.symbols0000664000000000000000000000011012026335621013012 0ustar librostlab.so.3 librostlab3 #MINVER# _ZN7rostlab8blosum62E@Base 1.0.20 debian/librostlab3.install0000664000000000000000000000003212232144066012773 0ustar usr/lib/*/librostlab.so.* debian/librostlab-doc.lintian-overrides0000664000000000000000000000221011735366446015462 0ustar # Laszlo Kajan : # This jquery.js is copied into the html documentation by the doxygen # version currently in unstable (1.7.6.1). Earlier versions of Doxygen # (e.g. i n stable) do not copy a jquery.js there. The jquery.js copied # by doxygen is much earlier (1.3.2) than the current version in unstable # (1.7.2-1). The jquery.js from doxygen actually is a minified bundle of # several things: # * jQuery JavaScript Library v1.3.2 http://jquery.com/ # * Sizzle CSS Selector Engine - v0.9.3 http://sizzlejs.com/ # * jQuery hashchange event - v1.3 - 7/21/2010 # http://benalman.com/projects/jquery-hashchange-plugin/ # * jQuery UI 1.7.2 http://docs.jquery.com/UI # * jQuery UI Resizable 1.7.2 http://docs.jquery.com/UI/Resizables # * jQuery.ScrollTo - Easy element scrolling using jQuery. # # Out of these Sizzle is not packaged for Debian, neither is the hashchange # event or jQuery.ScrollTo, as far as I can tell. # # Therefore, it is necessary to keep this jquery.js instead of linking to the # file with the same name from libjs-jquery. librostlab-doc: embedded-javascript-library usr/share/doc/librostlab-doc/html/jquery.js debian/librostlab3-dev.install0000664000000000000000000000012512232144106013545 0ustar usr/include/* usr/lib/*/librostlab.a usr/lib/*/librostlab.la usr/lib/*/librostlab.so debian/control0000664000000000000000000000734012266151407010603 0ustar Source: librostlab Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , Andreas Tille Section: libs Priority: optional Build-Depends: debhelper (>= 9), dh-autoreconf, doxygen, graphviz, latex-xcolor, texlive-fonts-recommended, texlive-latex-extra Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/librostlab/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/librostlab/trunk/ Homepage: http://rostlab.org/ Package: librostlab3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ library for computational biology This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products. . The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource . This package contains the shared library. Package: librostlab3-dev Architecture: any Section: libdevel Depends: librostlab3 (= ${binary:Version}), ${misc:Depends} Suggests: librostlab-doc Provides: librostlab-dev Replaces: librostlab0-dev Description: C++ library for computational biology (development) This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products. . The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource . This package contains files necessary for developing applications with librostlab. Package: librostlab-doc Architecture: all Section: doc Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ library for computational biology (documentation) This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products. . The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource . This package contains html documentation. Package: librostlab3-dbg Architecture: any Section: debug Priority: extra Depends: librostlab3 (= ${binary:Version}), ${misc:Depends} Description: debugging symbols for librostlab The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource . This package provides the detached debug symbols for librostlab.