Sophie: ugene-1.15.1-1.mga5 i586

ugene-1.15.1-1.mga5.i586.rpm

This file contains information about the license of 3rd party code integrated into UGENE.
*****************************************************************************************

Files: src/corelibs/U2Formats/src/ABIFormat.cpp
src/corelibs/U2Formats/src/SCFFormat.cpp
src/corelibs/U2Formats/src/IOLibUtils.cpp
Copyright: 1994 Medical Research Council. All rights reserved.
License:
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.

The File src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp
Copyright (c) 1998 Todd C. Miller <Todd.Miller@courtesan.com>

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.

The Files in src/plugins_3rdparty/hmm2
HMMER - Biological sequence analysis with profile hidden Markov models
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine

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 HMMER 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 me
(eddy@genetics.wustl.edu) for permission.

Incorporation into commercial software under non-GPL terms is possible
by obtaining a specially licensed version from Washington University
School of Medicine. Contact Jack Pincus (jhpincus@cris.com) 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 HMMER release, in the file LICENSE; if not, write to
the Free Software Foundation, Inc.,
51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.

See /usr/share/common-licenses/GPL for the complete text of the GPL

Note:
The Files in src/plugins_3rdparty/uhmmer/src/u_spu and
src/plugins_3rdparty/uhmmer/src/uhmmsearch_cell.cpp
are modified sources from the HMMER-Cell project
(ftp://selab.janelia.org/pub/software/hmmer/contrib-2.3.2/HMMerCell_src_02272008.tar.gz)

Original Copyright: 2008, International Business Machines Corporation
Authors: Kursad Albayraktaroglu, Jizhu Lu

This files are released under the terms of GPL (v2 or any later version).

The Files in src/plugins_3rdparty/umuscle/src/muscle
are PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm)

The Files src/plugins_3rdparty/psipred/src/seq2mtx.cpp
src/plugins_3rdparty/psipred/src/sspred_avpred.cpp
src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp
Copyright (C) 2000 D.T. Jones
These files are distributed under the terms of custom GPL-compatible
license. See src/plugins_3rdparty/psipred/src/license for details.

The Files in src/plugins_3rdparty/primer3/src/primer3_core
Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.

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.

The Files in src/plugins_3rdparty/hmm3/src/hmmer3
(except files in src/plugins_3rdparty/hmm3/src/hmmer3/easel)
Copyright (C) 2009 Howard Hughes Medical Institute.
Other copyrights also apply. See the
src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT file for a full list.

HMMER is distributed under the terms of the GNU General Public License
(GPLv3).

The Files in src/plugins_3rdparty/hmm3/src/hmmer3/easel
Copyright (C) 2009 Howard Hughes Medical Institute.
Other copyrights also apply. See the
src/plugins_3rdparty/hmm3/src/hmmer3/easel/COPYRIGHT file for a full list.

Easel is distributed under the Janelia Farm Software License, a BSD
license. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE file
for more details.

The Files in src/plugins/biostruct3d_view/src/gl2ps
GL2PS, an OpenGL to PostScript Printing Library
Copyright (C) 1999-2006 Christophe Geuzaine <geuz@geuz.org>

This program is free software; you can redistribute it and/or
modify it under the terms of either:

a) the GNU Library General Public License as published by the Free
Software Foundation, either version 2 of the License, or (at your
option) any later version; or

b) 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.

The Files in src/plugins_3rdparty/ball/include and
src/plugins_3rdparty/ball/source
Copyright (C) Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt
and others 1996-2009

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.

The Files in src/plugins_3rdparty/phylyp/src
version 3.6. (c) Copyright 1993-2004 by the University of Washington.
Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
Permission is granted to copy and use this program provided no fee is
charged for it and provided that this copyright notice is not removed.

The Files in src/plugins_3rdparty/kalign/src

Released under GPL - see the 'COPYING' file

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 2 of the License, or
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

Please send bug reports, comments etc. to:
timolassmann@gmail.com

The Files in src/plugins_3rdparty/bowtie/src/bowtie/SeqAn-1.1
Copyright (C) 2007

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 3 of the License, or (at your option) any later version.

The Files in src/plugins_3rdparty/bowtie/src/bowtie/visualstudio
ISO C9x compliant inttypes.h for Microsoft Visual Studio
Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.

2. 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.

3. The name of the author may be used to endorse or promote products
derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.

The Files in src/plugins_3rdparty/bowtie/src/bowtie
This files are distributed under Artistic License. See the 'COPYING' file
for details.

The Files in src/libs_3rdparty/sqlite3/src

The author disclaims copyright to this source code. In place of
a legal notice, here is a blessing:

May you do good and not evil.
May you find forgiveness for yourself and forgive others.
May you share freely, never taking more than you give.

The Files src/include/opencl/legacy/cl.h
src/include/opencl/legacy/cl_platform.h
Copyright (c) 2008-2010 The Khronos Group Inc.

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.

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.

The algorithm "Unique repeats filter"
Built over original UGENE Repeat finder. Filter results combining them in unique repeats.
Author: Sergey Yakovlev (tac@inbox.lv, tac1402@gmail.com)

released under Apache License 2.0
changed files:
src\plugins\repeat_finder\transl\russian.ts
src\plugins\repeat_finder\transl\english.ts
src\plugins\repeat_finder\src\RepeatQuery.cpp
src\plugins\repeat_finder\src\FindRepeatsTask.cpp
src\plugins\repeat_finder\src\RepeatWorker.cpp
src\plugins\repeat_finder\src\FindRepeatsDialog.cpp
src\plugins\repeat_finder\src\ui\FindRepeatsDialog.ui
src\plugins\repeat_finder\src\FindRepeatsTask.h
src\corelibs\U2Algorithm\src\misc\RepeatFinderSettings.h

Packaging:
Copyright (C) 2008-2012 by Ivan Efremov <iefremov@unipro.ru>
released under the GPL.