Copyright for ugene source package in Mantic

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.