Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: libpwizlite
Upstream-Contact: Filippo Rusconi <lopippo@debian.org>
Source: https://salsa.debian.org/debichem-team/libpwizlite


Files: src/pwiz/data/common/CVTranslator.*pp
 src/pwiz/Version.hpp
 src/pwiz/data/common/ParamTypes.*pp
 src/pwiz/data/common/cv.*pp
 src/pwiz/data/common/cv.inl
 src/pwiz/data/common/diff_std.*pp
 src/pwiz/data/msdata/BinaryDataEncoder.*pp
 src/pwiz/data/msdata/ChromatogramListBase.hpp
 src/pwiz/data/msdata/ChromatogramList_mzML.*pp
 src/pwiz/data/msdata/DefaultReaderList.*pp
 src/pwiz/data/msdata/Diff.hpp
 src/pwiz/data/msdata/IO.*pp
 src/pwiz/data/msdata/LegacyAdapter.*pp
 src/pwiz/data/msdata/MSData.*pp
 src/pwiz/data/msdata/MSDataFile.*pp
 src/pwiz/data/msdata/Reader.*pp
 src/pwiz/data/msdata/References.*pp
 src/pwiz/data/msdata/SHA1OutputObserver.hpp
 src/pwiz/data/msdata/Serializer_mzML.*pp
 src/pwiz/data/msdata/Serializer_mzXML.*pp
 src/pwiz/data/msdata/SpectrumInfo.hpp
 src/pwiz/data/msdata/SpectrumListBase.hpp
 src/pwiz/data/msdata/SpectrumListWrapper.hpp
 src/pwiz/data/msdata/SpectrumList_mzML.*pp
 src/pwiz/data/msdata/SpectrumList_mzXML.*pp
 src/pwiz/data/msdata/TextWriter.hpp
 src/pwiz/data/msdata/Version.*pp
 src/pwiz/data/msdata/examples.hpp
 src/pwiz/utility/minimxml/XMLWriter.*pp
 src/pwiz/utility/math/round.hpp
 src/pwiz/utility/misc/IterationListener.cpp
 src/pwiz/utility/misc/endian.hpp
 src/pwiz/utility/misc/IterationListener.hpp
 src/pwiz/utility/misc/IntegerSet.hpp
 src/pwiz/utility/misc/IntegerSet.cpp
 src/pwiz/utility/misc/SHA1Calculator.*pp
 src/pwiz/data/common/obo.hpp
Copyright: 2007, 2008, 2009, Spielberg Family Center for Applied Proteomics
License: Apache-2.0


Files: src/pwiz/data/misc/FrequencyDataTestData.hpp
 src/pwiz/data/misc/MinimumPepXML.hpp
 src/pwiz/data/misc/PeakData.hpp
 src/pwiz/data/msdata/SpectrumInfo.cpp
 src/pwiz/data/msdata/SpectrumIterator.hpp
 src/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp
 src/pwiz/utility/math/LinearSolver.hpp
 src/pwiz/utility/math/MatchedFilter.hpp
 src/pwiz/utility/misc/MSIHandler.hpp
 src/pwiz/utility/misc/SHA1_ostream.hpp
 src/pwiz/utility/misc/TabReader.hpp
 src/pwiz/utility/misc/Timer.hpp
Copyright: 2007, 2008, 2009 Spielberg Family Center for Applied Proteomics
 2007, 2008, 2009 Cedars Sinai Medical Center, Los Angeles, California
License: Apache-2.0


Files: src/pwiz/utility/misc/CharIndexedVector.hpp
Copyright: 2008 Vanderbilt University - Nashville, TN 37232
 2008 Spielberg Family Center for Applied Proteomics
 2003 Cedars Sinai Medical Center, Los Angeles, California  90048
License: Apache-2.0


Files: src/pwiz/data/msdata/SpectrumList_BTDX.*pp
 src/pwiz/data/msdata/SpectrumList_MGF.*pp
 src/pwiz/data/msdata/SpectrumList_MSn.*pp
 src/pwiz/utility/misc/Container.hpp
 src/pwiz/utility/misc/Exception.hpp
 src/pwiz/utility/misc/Export.hpp
 src/pwiz/utility/misc/Filesystem.*pp
 src/pwiz/utility/misc/Stream.hpp
 src/pwiz/utility/misc/String.hpp
 src/pwiz/utility/misc/optimized_lexical_cast.hpp
 src/pwiz/utility/misc/virtual_map.hpp
Copyright: 2007, 2008, 2009, Spielberg Family Center for Applied Proteomics
 2008, 2010, 2011, 2014, Vanderbilt University - Nashville, TN 37232
 2017, 2009, Matt Chambers <matt.chambers .@. vanderbilt.edu>
License: Apache-2.0


Files: src/pwiz/utility/misc/String.cpp
Copyright: 2021 Matt Chambers <matt.chambers .@. vanderbilt.edu>
License: Apache-2.0


Files: src/pwiz/data/msdata/Index_mzML.*pp
 src/pwiz/data/msdata/Serializer_MGF.*pp
 src/pwiz/data/msdata/Serializer_MSn.*pp
 src/pwiz/data/msdata/SpectrumWorkerThreads.*pp
 src/pwiz/utility/misc/Environment.hpp
 src/pwiz/utility/misc/BinaryData.*pp
 src/pwiz/utility/misc/DateTime.hpp
 src/pwiz/utility/misc/Std.hpp
 src/pwiz/utility/misc/shared_map.hpp
 src/pwiz/utility/misc/Singleton.hpp
 src/pwiz/data/common/BinaryIndexStream.hpp
 src/pwiz/data/common/Index.hpp
 src/pwiz/data/common/MemoryIndex.hpp
 src/pwiz/data/common/Unimod.hpp
 src/pwiz/data/msdata/MSDataMerger.hpp
 src/pwiz/data/msdata/MemoryMRUCache.hpp
 src/pwiz/data/msdata/SpectrumListCache.hpp
 src/pwiz/utility/misc/COMInitializer.hpp
 src/pwiz/utility/misc/ClickwrapPrompter.hpp
 src/pwiz/utility/misc/Once.hpp
 src/pwiz/utility/misc/VendorReaderTestHarness.hpp
 src/pwiz/utility/misc/cpp_cli_utilities.hpp
Copyright: 2008, 2010, 2011, 2014, Vanderbilt University - Nashville, TN 37232
 2017, 2009, Matt Chambers <matt.chambers .@. vanderbilt.edu>
License: Apache-2.0


Files: src/pwiz/utility/findmf/base/base/base.hpp
 src/pwiz/utility/findmf/base/base/constants.hpp
 src/pwiz/utility/findmf/base/base/copyif.hpp
 src/pwiz/utility/findmf/base/base/diff.hpp
 src/pwiz/utility/findmf/base/base/interpolate.hpp
 src/pwiz/utility/findmf/base/base/scale.hpp
 src/pwiz/utility/findmf/base/base/utilities/base.hpp
 src/pwiz/utility/findmf/base/base/utilities/interpolation.hpp
 src/pwiz/utility/findmf/base/filter/filter.hpp
 src/pwiz/utility/findmf/base/filter/gaussfilter.hpp
 src/pwiz/utility/findmf/base/filter/utilities/gauss.hpp
 src/pwiz/utility/findmf/base/filter/utilities/preparedata.hpp
 src/pwiz/utility/findmf/base/resample/bin1d.hpp
 src/pwiz/utility/findmf/base/resample/breakspec.hpp
 src/pwiz/utility/findmf/base/resample/determinebinwidth.hpp
 src/pwiz/utility/findmf/base/resample/masscomparefunctors.hpp
 src/pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp
Copyright: ETH Zurich
License: Apache-2.0


Files: src/pwiz/data/msdata/MSNumpress.*pp
Copyright: 2013, Johan Teleman
License: Apache-2.0


Files: src/pwiz/data/msdata/Serializer_mz5.hpp
 src/pwiz/data/msdata/ChromatogramList_mz5.hpp
 src/pwiz/data/msdata/SpectrumList_mz5.hpp
Copyright: 2011 Proteomics Center Children's Hospital Boston, Boston, MA 02135
License: Apache-2.0


Files:
 src/pwiz/utility/minimxml/SAXParser.*pp
Copyright: 2008, 2011, Insilicos LLC All Rights Reserved
 2007, 2008, 2009, Spielberg Family Center for Applied Proteomics
License: Apache-2.0


Files: src/pwiz/utility/misc/unit.hpp
 src/pwiz/utility/misc/Base64.*pp
 src/pwiz/utility/chemistry/Chemistry.hpp
 src/pwiz/data/misc/CalibrationParameters.hpp
Copyright: 2005, 2006, Louis Warschaw Prostate Cancer Center
License: Apache-2.0
 

Files: src/pwiz/utility/chemistry/MZTolerance.hpp
 src/pwiz/utility/math/OrderedPair.hpp
 src/pwiz/utility/misc/almost_equal.hpp
Copyright: 2009, Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA
License: Apache-2.0


Files: src/pwiz/data/misc/SampleDatum.hpp
 src/pwiz/data/misc/FrequencyData.hpp
 src/pwiz/utility/chemistry/ChemistryData.hpp
 src/pwiz/utility/chemistry/Ion.hpp
 src/pwiz/utility/chemistry/IsotopeCalculator.hpp
 src/pwiz/utility/chemistry/IsotopeTable.hpp
 src/pwiz/utility/math/LinearLeastSquares.hpp
 src/pwiz/utility/math/Parabola.hpp
 src/pwiz/utility/math/Stats.hpp
 src/pwiz/utility/math/Types.hpp
 src/pwiz/utility/math/erf.hpp
 src/pwiz/utility/math/qr.hpp
 src/pwiz/utility/misc/Image.hpp
Copyright: 2006, Louis Warschaw Prostate Cancer Center
 2006 Cedars Sinai Medical Center, Los Angeles, California
License: Apache-2.0


Files: src/pwiz/data/msdata/RAMPAdapter.hpp
Copyright: 2008 Spielberg Family Center for Applied Proteomics
 2008 Louis Warschaw Prostate Cancer Center
License: Apache-2.0


Files:  src/pwiz/utility/math/HouseholderQR.hpp
Copyright: Robert Burke <robert.burke@gmail.com>
License: Apache-2.0


Files: src/pwiz/analysis/demux/DemuxDataProcessingStrings.hpp
 src/pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp
Copyright: Jarrett Egertson <jegertso .@. uw.edu>
License: Apache-2.0


Files: src/pwiz/data/msdata/SpectrumListBase.cpp
 src/pwiz/utility/chemistry/MzMobilityWindow.hpp
Copyright: 2019 2020 Matt Chambers
License: Apache-2.0


License: Apache-2.0
 Apache License Version 2.0
 .
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 .
 http://www.apache.org/licenses/LICENSE-2.0
 .
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 .
 On Debian systems you can read the full text of the Apache 2.0 
 LICENSE at /usr/share/common-licenses/Apache-2.0.License: Apache-2.0


Files: src/pwiz/utility/misc/SHA1.*
Copyright: Dominik Reichl <dominik.reichl@t-online.de>
License: Public-domain
 .
 This software is in the public domain.


Files:  src/pwiz/utility/misc/automation_vector.h
Copyright: Andrei Alexandrescu
License: Public-domain-email
 http://erdani.org/publications/adapting_automation_arrays.html
 Sent an email to ask for a copyright notice.
 .
 Date: Wed, 3 Jun 2020 16:45:19 -0400
 From: Andrei Alexandrescu <andrei@erdani.com>
 To: Filippo Rusconi <filippo.rusconi@universite-paris-saclay.fr>
 Cc: Andrei Alexandrescu <andrei@metalanguage.com>
 Subject: Re: Copyright notice for your work ?
 . 
 Public domain. You can use this email as confirmation. Have fun!
 . 
 On Wed, Jun 3, 2020 at 1:32 PM Filippo Rusconi <
 filippo.rusconi@universite-paris-saclay.fr> wrote:
 . 
 > Greetings, Mr Alexandrescu,
 >
 > I am currently packaging a software for Debian GNU/Linux and am seeing
 > that some
 > code from http://erdani.org/publications/adapting_automation_arrays.html
 > is
 > included in that software.
 >
 > Could you please tell me what is the license of that page ? Is the code
 > freely
 > redistributable with a Free Software license or is it in the public domain
 > ?
 >
 > Looking forward to your answer, and with my best regards,
 >
 > Filippo Rusconi
 >
 > --
 >
 > ⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
 > ⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
 > ⢿⡄⠘⠷⠚⠋⠀   Debian Developer
 > ⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
 >            http://www.debian.org


Files: src/pwiz/utility/misc/random_access_compressed_ifstream.*pp
Copyright: 2008, 2011, Insilicos LLC All Rights Reserved
 1995-2005 Jean-loup Gailly
 2005 Mark Adler
License: Zlib

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.


Files: src/pwiz/utility/misc/mru_list.hpp
Copyright: 2003-2008, Joaquin M Lopez Munoz
License: Boost-1.0


Files:  src/pwiz/utility/math/MatrixInverse.hpp
Copyright: 0000, No Author
License: Boost-1.0


License: Boost-1.0
 . 
 Permission is hereby granted, free of charge, to any person or organization
 obtaining a copy of the software and accompanying documentation covered by
 this license (the "Software") to use, reproduce, display, distribute,
 execute, and transmit the Software, and to prepare derivative works of the
 Software, and to permit third-parties to whom the Software is furnished to
 do so, all subject to the following:
 . 
 The copyright notices in the Software and this entire statement, including
 the above license grant, this restriction and the following disclaimer,
 must be included in all copies of the Software, in whole or in part, and
 all derivative works of the Software, unless such copies or derivative
 works are solely in the form of machine-executable object code generated by
 a source language processor.
 . 
 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
 SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
 FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.


Files: src/boost/foreach_field.hpp
Copyright: 2009 Chris Purcell
License: Boost-1.0


Files: src/boost/utility/detail/member_dereference.hpp
 src/boost/utility/detail/singleton_manager.hpp
 src/boost/utility/detail/restricted.hpp
 src/boost/utility/thread_specific_singleton.hpp
 src/boost/utility/mutexed_singleton.hpp
 src/boost/utility/singleton.hpp
Copyright: 2007 Tobias Schwinger
License: Boost-1.0


Files: src/boost/enum.hpp
 src/boost/enum/bitfield.hpp
 src/boost/enum/iterator.hpp
 src/boost/enum/macros.hpp
 src/boost/enum/base.hpp
Copyright: 2005 Frank Laub
License: Boost-1.0


Files: src/boost/nowide/convert.hpp
 src/boost/nowide/windows.hpp
 src/boost/nowide/config.hpp
 src/boost/nowide/cstdlib.hpp
 src/boost/nowide/filebuf.hpp
 src/boost/nowide/iostream.hpp
 src/boost/nowide/system.hpp
 src/boost/nowide/cenv.hpp
 src/boost/nowide/stackstring.hpp
 src/boost/nowide/fstream.hpp
 src/boost/nowide/cstdio.hpp
 src/boost/nowide/args.hpp
Copyright: 2012 Artyom Beilis (Tonkikh)
License: Boost-1.0 


Files: src/boost/iostreams/arbitrary_positional_facade.hpp
 src/boost/iostreams/filter/base64.hpp
Copyright: 2006, 2007 Takeshi Mouri
License: Boost-1.0 


Files: CMakeLists.txt
 CMakeStuff/*
 src/CMakeLists.txt
 maintainer-scripts/extract-files-from-proteowizard-source-tree.sh
Copyright: 2020 Filippo Rusconi <lopippo@debian.org>
License: GPL-3+


Files: debian/*
Copyright: 2020 Filippo Rusconi <lopippo@debian.org>
License: GPL-3+


License: GPL-3+
 This package 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.
 .
 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 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 <https://www.gnu.org/licenses/>
 .
 On Debian systems, the complete text of the GNU General
 Public License version 2 can be found in "/usr/share/common-licenses/GPL-3".