Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: UGENE Upstream-Contact: UniPro Yuliya Algaer Source: https://github.com/ugeneunipro/ugene/releases Files-Excluded: */src/libs_3rdparty/zlib/src */src/libs_3rdparty/sqlite3/src */macosx */windows */windows_x64 */i686 */x86_64 */ubuntu src/plugins_3rdparty/phylip/src/c* src/plugins_3rdparty/phylip/src/d* src/plugins_3rdparty/phylip/src/n* src/plugins_3rdparty/phylip/src/p* src/plugins_3rdparty/phylip/src/s* src/plugins_3rdparty/psipred/src/s* src/plugins_3rdparty/psipred/src/LICENSE src/plugins_3rdparty/psipred/datafiles src/plugins_3rdparty/psipred/psipred.license */CMakeLists.txt Files: * Copyright: © 2008-2015 UniPro License: GPL-2+ Files: src/corelibs/U2Formats/src/ABIFormat.cpp src/corelibs/U2Formats/src/SCFFormat.cpp Copyright: © 1994 Medical Research Council. All rights reserved. License: MCR Permission to use, copy, modify and distribute this software and its documentation for any purpose is hereby granted without fee, provided that this copyright and notice appears in all copies. . MRC disclaims all warranties with regard to this software. Comment: Upstream did the following clarification here: https://lists.debian.org/debian-med/2019/02/msg00020.html . These 2 files have a non-standard license, but I believe the license itself is similar to MIT. . The "without fee" text in the license means that we can use this code without any fee. The only limitation is to keep the copyright text. . See: * Permission to use, copy, modify and distribute this software and its * documentation for any purpose is hereby granted without fee, provided that * this copyright and notice appears in all copies. . Hope this was a simple misunderstanding and there is no bigger issue here. Files: src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp Copyright: © 1998 Todd C. Miller License: ISC Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. . THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. Files: src/plugins_3rdparty/hmm2/* Copyright: © 1992-2003 HHMI/Washington University School of Medicine License: GPL-2+ Files: src/plugins_3rdparty/umuscle/src/muscle/* Copyright: © 2004-2011 Robert C. Edgar License: PD The software is provided as PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm) Files: src/plugins_3rdparty/primer3/src/primer3_core/* Copyright: © 1996-2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), and Helen Skaletsky License: BSD-3-clause 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 names of the copyright holders nor 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 OWNERS 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: src/plugins/biostruct3d_view/src/gl2ps/* Copyright: © 1999-2006 Christophe Geuzaine License: GPL-2+ Comment: Debian just contains this code in libgl2ps-dev Note: Alternatively you can choose the GL2PS License as published by Christophe Geuzaine, either version 2 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 either the GNU Library General Public License or the GL2PS License for more details. Files: src/plugins_3rdparty/ball/src/include/* src/plugins_3rdparty/ball/src/source/* Copyright: © 1996-2012 Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt License: LGPL-2.1 This library 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 2.1 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 Lesser General Public License for more details. . On Debian systems, see /usr/share/common-licenses/LGPL-2.1 for the full text of the license. Files: src/plugins_3rdparty/kalign/src/* Copyright: © 2006 Timo Lassmann License: GPL-2+ Files: src/include/opencl/legacy/* Copyright: © 2008-2010 The Khronos Group Inc. License: BSD+Khronos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and/or associated documentation files (the "Materials"), to deal in the Materials without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Materials, and to permit persons to whom the Materials are furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Materials. . THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS. Files: src/corelibs/U2Private/src/crash_handler/StackWalker.* Copyright: © 2005-2011 Jochen Kalmbach License: BSD-2-clause 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 Jochen Kalmbach 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: src/libs_3rdparty/breakpad/src/common/convert_UTF.c src/libs_3rdparty/breakpad/src/common/convert_UTF.h Copyright: 1991-2015 Unicode, Inc. License: Unicode Permission is hereby granted, free of charge, to any person obtaining a copy of the Unicode data files and any associated documentation (the "Data Files") or Unicode software and any associated documentation (the "Software") to deal in the Data Files or Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, and/or sell copies of the Data Files or Software, and to permit persons to whom the Data Files or Software are furnished to do so, provided that (a) this copyright and permission notice appear with all copies of the Data Files or Software, (b) this copyright and permission notice appear in associated documentation, and (c) there is clear notice in each modified Data File or in the Software as well as in the documentation associated with the Data File(s) or Software that the data or software has been modified. . THE DATA FILES AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THE DATA FILES OR SOFTWARE. . Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in these Data Files or Software without prior written authorization of the copyright holder. Files: debian/* Copyright: © 2008-2011 Ivan Efremov © 2012-2017 Andreas Tille License: GPL-3+ License: GPL-2+ This suite of programs 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. . In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. . If you wish to use Unipro UGENE code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact us (ugene@unipro.ru) for permission. . Incorporation into commercial software under non-GPL terms is possible by obtaining a specially licensed version from Unipro. Contact 'ugene@unipro.ru' to arrange licensing terms. . This software 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 Unipro UGENE release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, see /usr/share/common-licenses/GPL-2 for the complete text of the GPL. 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. . On Debian systems, see /usr/share/common-licenses/GPL-3 for the complete text of the GPL.