Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: EMBOSS core development team <emboss-bug@emboss.open-bio.org>
Source: ftp://emboss.open-bio.org/pub/EMBOSS/
Upstream-Name: EMBOSS

Files: *
Copyright: The EMBOSS developers or their employers.
License: emboss
 EMBOSS License (http://emboss.sourceforge.net/licence/)
 .
 The AJAX and NUCLEUS libraries are released under the GNU Lesser General
 Public Licence.
 .
 The EMBOSS Administrator’s Guide can be copied, distributed and/or modified
 under the terms of the GNU Free Documentation License, Version 1.1 or any
 later version published by the Free Software Foundation; with no Invariant
 Sections, with no Front-Cover Texts, and with no Back-Cover Texts.  A copy of
 the license is included in the chapter entitled ”GNU Free Documentation
 License”.
 .
 The EMBOSS Quick Guide has been relicenced and can be used, modified and
 distributed under the same terms as EMBOSS itself.
 .
 EMBOSS applications are released under the GNU General Public Licence.
 .
 Parsing of ACD files does not constitute a "derived work" and developers are
 encouraged to do this, for example to write their own GUIs.
 .
 For developers who have their own licensing conditions already in effect, there
 will be an additional way to contribute. The EMBASSY collection can include
 packages that use the EMBOSS core libraries and interfaces but under their own
 licensing conditions. They will be bound by the Library GPL of the AJAX and
 NUCLEUS libraries, but not necessarily by the full GPL.
 .
 Some of the suggestions and code examples from David Hanson's book
 "C Interfaces and Implementations" are included in the AJAX library.
 This library is available from http://www.cs.princeton.edu/software/cii/
 or ftp://ftp.cs.princeton.edu/pub/packages/cii/
 .
 The COPYRIGHT file in release 1.10 says:
 .
 > The author of this software is David R. Hanson.
 >
 > Copyright (c) 1994,1995,1996 by David R. Hanson. All Rights Reserved.
 >
 > Permission to use, copy, modify, and distribute this software for any
 > purpose, subject to the provisions described below, without fee is
 > hereby granted, provided that this entire notice is included in all
 > copies of any software that is or includes a copy or modification of
 > this software and in all copies of the supporting documentation for
 > such software.
 >
 > THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
 > WARRANTY. IN PARTICULAR, THE AUTHOR DOES MAKE ANY REPRESENTATION OR
 > WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR
 > ITS FITNESS FOR ANY PARTICULAR PURPOSE.
 >
 > David Hanson / drh@cs.princeton.edu / http://www.cs.princeton.edu/~drh/
 > Wed Apr 24 13:44:16 PDT 1996
 > Mon Dec 12 15:58:13 EST 1994
Comment: On Debian systems, the complete text of the GNU General Public License
 version 2, the GNU Free Documentation License version 1.2, and the GNU Library
 General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’,
 ‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’
 respectively.

Files: ajax/pcre/*
Copyright: © 1997-2000 University of Cambridge
License: PCRE_license
 PCRE is a library of functions to support regular expressions whose syntax
 and semantics are as close as possible to those of the Perl 5 language.
 .
 Written by: Philip Hazel <ph10@cam.ac.uk>
 .
 University of Cambridge Computing Service,
 Cambridge, England. Phone: +44 1223 334714.
 .
 Copyright (c) 1997-2000 University of Cambridge
 .
 Permission is granted to anyone to use this software for any purpose on any
 computer system, and to redistribute it freely, subject to the following
 restrictions:
 .
  1. 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.
 .
  2. The origin of this software must not be misrepresented, either by
     explicit claim or by omission. In practice, this means that if you use
     PCRE in software which you distribute to others, commercially or
     otherwise, you must put a sentence like this
 .
       Regular expression support is provided by the PCRE library package,
       which is open source software, written by Philip Hazel, and copyright
       by the University of Cambridge, England.
 .
     somewhere reasonably visible in your documentation and in any relevant
     files or online help data or similar. A reference to the ftp site for
     the source, that is, to
 .
       ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/
 .
     should also be given in the documentation.
 .
  3. Altered versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
 .
  4. If PCRE is embedded in any software that is released under the GNU
     General Purpose Licence (GPL), then the terms of that licence shall
     supersede any condition above with which it is incompatible.

Files: plplot/*
Copyright: © 1987, 1988 by Digital Equipment Corporation, Maynard, Massachusetts,
    © 1991, 1993, 1994  Wesley Ebisuzaki
           © 1992, 1993, 1994, 1995, 2001, 2002, 2004  Maurice LeBrun
           © 1992, 1999, 2001  Geoffrey Furnish
           © 1992,  Maurice J. LeBrun, Geoff Furnish, Tony Richardson.
           © 2000, 2001, 2002, 2004, 2005  Alan W. Irwin
           © 2000, 2001, 2002, 2003, 2004 Joao Cardoso
           © 2001, 2003, 2004, 2005  Rafael Laboissiere
           © 2001, 2002, 2003, 2004  Andrew Roach
           © 2002,  Vincent Darley
           © 2004, 2005  Thomas J. Duck
           © 2004, 2005, 2006  Andrew Ross
           © 2006,  Hazen Babcock
           © 2006,  Jim Dishaw
           © 2006, Werner Smekal
License: GPL-2+
 This library is free software; you can redistribute it and/or
 modify it under the terms of 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.
 .
 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
 Library General Public License for more details.
 .
 On Debian systems you can find a copy of the GNU Library General
 Public License version 2 at /usr/share/common-licenses/LGPL-2.

Files: ajax/zlib/*
Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
License: zlib
  This software is provided 'as-is', without any express or implied
  warranty.  In no event will the authors be held liable for any damages
  arising from the use of this software.
 .
  Permission is granted to anyone to use this software for any purpose,
  including commercial applications, and to alter it and redistribute it
  freely, subject to the following restrictions:
 .
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.
 .
  Jean-loup Gailly        Mark Adler
  jloup@gzip.org          madler@alumni.caltech.edu

Files: doc/programs/html/antigenic.html
 doc/programs/html/pasteseq.html
 doc/programs/html/showpep.html
 doc/programs/master/emboss/apps/inc/acdc.input
 doc/programs/master/emboss/apps/inc/acdtrace.input
 doc/programs/master/emboss/apps/inc/antigenic.input
 doc/programs/master/emboss/apps/inc/pasteseq.input
 doc/programs/master/emboss/apps/inc/showpep.input
 doc/programs/text/antigenic.txt
 doc/programs/text/pasteseq.txt
 doc/programs/text/showpep.txt
 test/data/amir.swiss
 test/data/uniprotft.sw
 test/swiss/seq.dat
 test/swnew/trembl.dat
Copyright: none
 These files are marked to be copyrighted by the UniProt Consortium, but this
 applies to the UniProt database as a whole, not to the individual records.
License: not-the-CC-BY-ND-3.0
 Despite the following statement:
 .
  Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
  Distributed under the Creative Commons Attribution-NoDerivs License
 .
 The above files, as individual records, are not copyrighted.  The statement is
 for the UniProt as a whole.

Files: ajax/core/ajvarbcf.c
Copyright: © 2010 Broad Institute
           © The EMBOSS developers
License: LGPL-2.1+ and MIT

Files: emboss/data/TAXONOMY/*.dmp
Homepage: http://www.ncbi.nlm.nih.gov/taxonomy
Copyright: Probably public domain (under investigation).
License: CC-BY-3.0

Files: emboss/data/OBO/*.obo
Homepage: https://github.com/oborel/obo-relations
Copyright: 2008-2013 Chris Mungall <cjmungall@lbl.gov> et all
License: CC-BY-3.0
Comment: see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=694908

Files: emboss/data/OBO/chebi.obo
Homepage: http://www.ebi.ac.uk/chebi/
Copyright: Public domain according to answer or authors available at
           https://lists.debian.org/debian-med/2013/01/msg00012.html
License: CC-BY-3.0

Files: emboss/data/OBO/software.obo
Homepage: http://theswo.sourceforge.net/
Copyright: 2011-2012 James Malone
Comment: The statement of the author can be seen at
         http://bugs.debian.org/694908#92
         as long as the license is not yet published on its homepage
License: Apache-2.0
 On Debian systems you can find the complete text of the Apache License
 Version 2.0 at /usr/share/common-licenses/Apache-2.0.

Files: emboss/data/OBO/pathway.obo
Homepage: http://www.obofoundry.org/cgi-bin/detail.cgi?id=pathway
Source: ftp://rgd.mcw.edu/pub/data_release/
Copyright: 2009-2012 Victoria Petri <vpetri@mcw.edu>
License: CC-BY-3.0
Comment: See ftp://rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc

Files: emboss/data/OBO/eco.obo
Homepage: https://github.com/evidenceontology/evidenceontology
Copyright: 2009-2013 Marcus Chibucos <mchibucos@gmail.com>,
                     Michelle Giglio <mgiglio@som.umaryland.edu>
License: GPL-3+

Files: emboss/data/OBO/ro.obo
Homepage: https://github.com/oborel/obo-relations
Copyright: 2009-2013 Chris Mungall <cjmungall@lbl.gov> and others
License: CC-BY-3.0

Files:  emboss/data/OBO/so.obo
Homepage: http://www.sequenceontology.org/
Copyright: 2009-2013 Sequence Ontology
                     Karen Eilbeck <keilbeck@genetics.utah.edu>
License: PD
 The Sequence Ontology is in the public domain. It is available to
 public and private sector users with no licensing requirements. We ask
 that you cite SO and do not make changes to SO then redistribute under
 the same name.
 .
 See http://www.sequenceontology.org/resources/faq.html#lic

Files: debian/*
Copyright: 2002-2004 Matt Hope <dopey@debian.org>
           2007-2013 Charles Plessy <plessy@debian.org>
           2012-2013 Andreas Tille <tille@debian.org>
License: LGPL-2.1+
Comment:
 The EMBOSS package for Debian was initially prepared by Matt Hope
 (dopey@debian.org) in 2002-2004 and released on
 (http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian
 was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope
 as a starting point. Feel free to use the work of the pkg-emboss project as if
 it were in the public domain.  The license of the packaging (LGPL-2.1+) was
 chosen in 2013 to be as close as possible to upstream's licenses (LGPL-2.1+
 for the libraries, GPL-2+ for the applications, and GFDL-NIV-1.1 for some of
 the documentation).  After applyint patches, please be kind to submit them to
 Upstream under terms that are convenient for them.

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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.
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 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 .
 On Debian systems, the complete text of the GNU General Public License
 version 3 can be found at /usr/share/common-licenses/GPL-3.

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.
 .
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
Comment: On Debian systems, the complete text of the GNU Lesser General Public
 License version 2.1 can be found at /usr/share/common-licenses/LGPL-2.1.

License: MIT
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
    "Software"), to deal in the Software without restriction, including
    without limitation the rights to use, copy, modify, merge, publish,
    distribute, sublicense, and/or sell copies of the Software, and to
    permit persons to whom the Software is furnished to do so, subject to
    the following conditions:
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    The above copyright notice and this permission notice shall be
    included in all copies or substantial portions of the Software.
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    THE SOFTWARE IS 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 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
