Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: libpwiz Source: http://proteowizard.sourceforge.net/downloads.shtml 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. License: BSL-1.0 Boost Software License - Version 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. 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. License: BSD-2-clause BSD 2-clause "Simplified" License . 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. . 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 HOLDER 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: libraries/boost_aux/boost/nowide/args.hpp libraries/boost_aux/boost/nowide/cenv.hpp libraries/boost_aux/boost/nowide/config.hpp libraries/boost_aux/boost/nowide/convert.hpp libraries/boost_aux/boost/nowide/cstdio.hpp libraries/boost_aux/boost/nowide/cstdlib.hpp libraries/boost_aux/boost/nowide/filebuf.hpp libraries/boost_aux/boost/nowide/fstream.hpp libraries/boost_aux/boost/nowide/iostream.hpp libraries/boost_aux/boost/nowide/stackstring.hpp libraries/boost_aux/boost/nowide/system.hpp libraries/boost_aux/boost/nowide/windows.hpp libraries/boost_aux/libs/nowide/src/iostream.cpp Copyright: 2012, Artyom Beilis (Tonkikh) License: BSL-1.0 Files: libraries/boost_aux/tools/bcp/add_dependent_lib.cpp libraries/boost_aux/tools/bcp/add_path.cpp libraries/boost_aux/tools/bcp/bcp.hpp libraries/boost_aux/tools/bcp/bcp_imp.cpp libraries/boost_aux/tools/bcp/bcp_imp.hpp libraries/boost_aux/tools/bcp/copy_path.cpp libraries/boost_aux/tools/bcp/file_types.cpp libraries/boost_aux/tools/bcp/fileview.cpp libraries/boost_aux/tools/bcp/fileview.hpp libraries/boost_aux/tools/bcp/licence_info.hpp libraries/boost_aux/tools/bcp/main.cpp libraries/boost_aux/tools/bcp/output_licence_info.cpp libraries/boost_aux/tools/bcp/path_operations.cpp Copyright: 2003, Dr John Maddock 2009, Dr John Maddock License: BSL-1.0 Files: libraries/boost_aux/boost/utility/detail/member_dereference.hpp libraries/boost_aux/boost/utility/detail/restricted.hpp libraries/boost_aux/boost/utility/detail/singleton_manager.hpp libraries/boost_aux/boost/utility/mutexed_singleton.hpp libraries/boost_aux/boost/utility/singleton.hpp libraries/boost_aux/boost/utility/thread_specific_singleton.hpp Copyright: 2007, Tobias Schwinger License: BSL-1.0 Files: libraries/boost_aux/boost/enum.hpp libraries/boost_aux/boost/enum/base.hpp libraries/boost_aux/boost/enum/bitfield.hpp libraries/boost_aux/boost/enum/iterator.hpp libraries/boost_aux/boost/enum/macros.hpp Copyright: 2005, Frank Laub License: BSL-1.0 Files: libraries/boost_aux/libs/thread/src/win32/tss_pe-before_1_44.cpp libraries/boost_aux/libs/thread/src/win32/tss_pe.cpp Copyright: 2007, Anthony Williams 2007, David Deakins 2007, Roland Schwarz Aaron W. LaFramboise, Roland Schwarz, Michael Glassford 2004. License: BSL-1.0 Files: libraries/boost_aux/boost/iostreams/arbitrary_positional_facade.hpp libraries/boost_aux/boost/iostreams/filter/base64.hpp Copyright: 2006, 2007, Takeshi Mouri License: BSL-1.0 Files: libraries/libsvm-3.0/svm.cpp libraries/libsvm-3.0/svm.h Copyright: 2000-2010, Chih-Chung Chang 2000-2010, Chih-Jen Lin License: BSD-2-clause Files: libraries/CSpline/CSpline.cpp libraries/CSpline/CSpline.h Copyright: 2014, James Bremner License: BSD-2-clause Files: libraries/libsvm-3.0/svm-model2code.cpp Copyright: 2010, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: libraries/boost_aux/tools/bcp/scan_cvs_path.cpp Copyright: 2003, -7 John Maddock 2007, Bjorn Roald License: BSL-1.0 Files: libraries/boost_aux/boost/foreach_field.hpp Copyright: 2009, Chris Purcell. License: BSL-1.0 Files: libraries/boost_aux/tools/bcp/scan_licence.cpp Copyright: 2003, Dr John Maddock License: BSL-1.0 Files: libraries/boost_aux/boost/interprocess/detail/win32_api.hpp Copyright: Ion Gaztanaga 2005-2012. Distributed under the Boost License: BSL-1.0 Files: libraries/boost_aux/tools/bcp/licence_info.cpp Copyright: 2003 Dr John Maddock License: BSL-1.0 Files: pwiz/Version.hpp pwiz/analysis/common/CwtPeakDetectorTest.cpp pwiz/analysis/common/ExtraZeroSamplesFilter.cpp pwiz/analysis/common/ExtraZeroSamplesFilter.hpp pwiz/analysis/common/ExtraZeroSamplesFilterTest.cpp pwiz/analysis/common/LocalMaximumPeakDetectorTest.cpp pwiz/analysis/common/SavitzkyGolaySmootherTest.cpp pwiz/analysis/common/WhittakerSmootherTest.cpp pwiz/analysis/common/ZeroSampleFillerTest.cpp pwiz/analysis/frequency/MagnitudeLorentzianTestData.cpp pwiz/analysis/frequency/MagnitudeLorentzianTestData.hpp pwiz/analysis/passive/MSDataAnalyzer.cpp pwiz/analysis/passive/MSDataAnalyzer.hpp pwiz/analysis/passive/MSDataAnalyzerTest.cpp pwiz/analysis/passive/MSDataCache.cpp pwiz/analysis/passive/MSDataCache.hpp pwiz/analysis/passive/MSDataCacheTest.cpp pwiz/analysis/passive/MetadataReporter.cpp pwiz/analysis/passive/MetadataReporter.hpp pwiz/analysis/passive/PepXMLCat.cpp pwiz/analysis/passive/PepXMLCat.hpp pwiz/analysis/passive/RegionAnalyzer.cpp pwiz/analysis/passive/RegionAnalyzer.hpp pwiz/analysis/passive/RegionSIC.cpp pwiz/analysis/passive/RegionSIC.hpp pwiz/analysis/passive/RegionSlice.cpp pwiz/analysis/passive/RegionSlice.hpp pwiz/analysis/passive/RegionTIC.cpp pwiz/analysis/passive/RegionTIC.hpp pwiz/analysis/passive/SpectrumBinaryData.cpp pwiz/analysis/passive/SpectrumBinaryData.hpp pwiz/analysis/passive/SpectrumTable.cpp pwiz/analysis/passive/SpectrumTable.hpp pwiz/analysis/peakdetect/FeatureDetector.hpp pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp pwiz/analysis/peakdetect/FeatureDetectorSimple.hpp pwiz/analysis/peakdetect/FeatureDetectorSimpleTest.cpp pwiz/analysis/peakdetect/PeakFamilyDetector.cpp pwiz/analysis/peakdetect/PeakFamilyDetector.hpp pwiz/analysis/peakdetect/PeakFamilyDetectorFT.cpp pwiz/analysis/peakdetect/PeakFamilyDetectorFT.hpp pwiz/analysis/peakdetect/PeakFamilyDetectorFTTest.cpp pwiz/analysis/peakdetect/PeakFamilyDetectorFTTestData.cpp pwiz/analysis/peakdetect/msextract.cpp pwiz/analysis/peptideid/PeptideID.hpp pwiz/analysis/peptideid/PeptideIDMap.cpp pwiz/analysis/peptideid/PeptideIDMap.hpp pwiz/analysis/peptideid/PeptideIDMapTest.cpp pwiz/analysis/peptideid/PeptideID_flat.cpp pwiz/analysis/peptideid/PeptideID_flat.hpp pwiz/analysis/peptideid/PeptideID_flatTest.cpp pwiz/analysis/peptideid/PeptideID_pepXML.cpp pwiz/analysis/peptideid/PeptideID_pepXML.hpp pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp pwiz/analysis/spectrum_processing/PrecursorRecalculator.hpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefault.cpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefault.hpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefaultTest.cpp pwiz/analysis/spectrum_processing/SpectrumListFactory.cpp pwiz/analysis/spectrum_processing/SpectrumListFactory.hpp pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_Filter.cpp pwiz/analysis/spectrum_processing/SpectrumList_Filter.hpp pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculator.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculator.hpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.hpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefineTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_ZeroSamplesFilter.cpp pwiz/analysis/spectrum_processing/SpectrumList_ZeroSamplesFilter.hpp pwiz/data/common/CVTranslator.cpp pwiz/data/common/CVTranslator.hpp pwiz/data/common/CVTranslatorTest.cpp pwiz/data/common/ParamTypes.cpp pwiz/data/common/ParamTypes.hpp pwiz/data/common/ParamTypesTest.cpp pwiz/data/common/cv.cpp pwiz/data/common/cv.inl pwiz/data/common/cvtest.cpp pwiz/data/common/diff_std.cpp pwiz/data/common/diff_std.hpp pwiz/data/common/diff_std_test.cpp pwiz/data/common/obo.cpp pwiz/data/common/obo.hpp pwiz/data/common/obotest.cpp pwiz/data/identdata/DefaultReaderList.cpp pwiz/data/identdata/DefaultReaderList.hpp pwiz/data/identdata/DelimReader.cpp pwiz/data/identdata/DelimReader.hpp pwiz/data/identdata/DelimWriter.cpp pwiz/data/identdata/DelimWriter.hpp pwiz/data/identdata/Diff.cpp pwiz/data/identdata/Diff.hpp pwiz/data/identdata/DiffTest.cpp pwiz/data/identdata/ExtendedReadTest.cpp pwiz/data/identdata/IO.cpp pwiz/data/identdata/IO.hpp pwiz/data/identdata/IOTest.cpp pwiz/data/identdata/IdentData.cpp pwiz/data/identdata/IdentData.hpp pwiz/data/identdata/IdentDataFile.cpp pwiz/data/identdata/IdentDataFile.hpp pwiz/data/identdata/IdentDataTest.cpp pwiz/data/identdata/KwCVMap.cpp pwiz/data/identdata/KwCVMap.hpp pwiz/data/identdata/KwCVMapTest.cpp pwiz/data/identdata/MascotReader.hpp pwiz/data/identdata/MzidPredicates.hpp pwiz/data/identdata/Pep2MzIdent.cpp pwiz/data/identdata/Pep2MzIdent.hpp pwiz/data/identdata/Pep2MzIdentTest.cpp pwiz/data/identdata/Reader.cpp pwiz/data/identdata/Reader.hpp pwiz/data/identdata/ReaderTest.cpp pwiz/data/identdata/References.cpp pwiz/data/identdata/References.hpp pwiz/data/identdata/ReferencesTest.cpp pwiz/data/identdata/Serializer_Text.cpp pwiz/data/identdata/Serializer_Text.hpp pwiz/data/identdata/Serializer_Text_Test.cpp pwiz/data/identdata/Serializer_mzid.cpp pwiz/data/identdata/Serializer_mzid.hpp pwiz/data/identdata/Serializer_mzid_Test.cpp pwiz/data/identdata/Serializer_protXML.cpp pwiz/data/identdata/Serializer_protXML.hpp pwiz/data/identdata/Serializer_protXML_Test.cpp pwiz/data/identdata/TextWriter.hpp pwiz/data/identdata/examples.cpp pwiz/data/identdata/examples.hpp pwiz/data/misc/FrequencyDataTestData.cpp pwiz/data/misc/FrequencyDataTestData.hpp pwiz/data/misc/MinimumPepXML.cpp pwiz/data/misc/MinimumPepXML.hpp pwiz/data/misc/MinimumPepXMLTest.cpp pwiz/data/misc/PeakData.cpp pwiz/data/misc/PeakData.hpp pwiz/data/misc/PeakDataTest.cpp pwiz/data/msdata/BinaryDataEncoder.cpp pwiz/data/msdata/BinaryDataEncoder.hpp pwiz/data/msdata/BinaryDataEncoderTest.cpp pwiz/data/msdata/ChromatogramListBase.hpp pwiz/data/msdata/ChromatogramListBaseTest.cpp pwiz/data/msdata/ChromatogramList_mzML.cpp pwiz/data/msdata/ChromatogramList_mzML.hpp pwiz/data/msdata/ChromatogramList_mzML_Test.cpp pwiz/data/msdata/DefaultReaderList.cpp pwiz/data/msdata/DefaultReaderList.hpp pwiz/data/msdata/Diff.cpp pwiz/data/msdata/Diff.hpp pwiz/data/msdata/DiffTest.cpp pwiz/data/msdata/IO.cpp pwiz/data/msdata/IO.hpp pwiz/data/msdata/IOTest.cpp pwiz/data/msdata/LegacyAdapter.cpp pwiz/data/msdata/LegacyAdapter.hpp pwiz/data/msdata/LegacyAdapterTest.cpp pwiz/data/msdata/MSData.cpp pwiz/data/msdata/MSData.hpp pwiz/data/msdata/MSDataFile.cpp pwiz/data/msdata/MSDataFile.hpp pwiz/data/msdata/MSDataFileTest.cpp pwiz/data/msdata/MSDataTest.cpp pwiz/data/msdata/MSnReaderTest.cpp pwiz/data/msdata/Reader.cpp pwiz/data/msdata/Reader.hpp pwiz/data/msdata/ReaderTest.cpp pwiz/data/msdata/References.cpp pwiz/data/msdata/References.hpp pwiz/data/msdata/ReferencesTest.cpp pwiz/data/msdata/SHA1OutputObserver.hpp pwiz/data/msdata/Serializer_mzML.cpp pwiz/data/msdata/Serializer_mzML.hpp pwiz/data/msdata/Serializer_mzML_Test.cpp pwiz/data/msdata/Serializer_mzXML.cpp pwiz/data/msdata/Serializer_mzXML.hpp pwiz/data/msdata/Serializer_mzXML_Test.cpp pwiz/data/msdata/SpectrumInfo.cpp pwiz/data/msdata/SpectrumInfo.hpp pwiz/data/msdata/SpectrumInfoTest.cpp pwiz/data/msdata/SpectrumIterator.cpp pwiz/data/msdata/SpectrumIterator.hpp pwiz/data/msdata/SpectrumIteratorTest.cpp pwiz/data/msdata/SpectrumListBase.hpp pwiz/data/msdata/SpectrumListBaseTest.cpp pwiz/data/msdata/SpectrumListWrapper.hpp pwiz/data/msdata/SpectrumListWrapperTest.cpp pwiz/data/msdata/SpectrumList_MGF_Test.cpp pwiz/data/msdata/SpectrumList_MSn_Test.cpp pwiz/data/msdata/SpectrumList_mzML.cpp pwiz/data/msdata/SpectrumList_mzML.hpp pwiz/data/msdata/SpectrumList_mzML_Test.cpp pwiz/data/msdata/SpectrumList_mzXML.cpp pwiz/data/msdata/SpectrumList_mzXML.hpp pwiz/data/msdata/SpectrumList_mzXML_Test.cpp pwiz/data/msdata/TextWriter.hpp pwiz/data/msdata/examples.cpp pwiz/data/msdata/examples.hpp pwiz/data/proteome/DefaultReaderList.cpp pwiz/data/proteome/DefaultReaderList.hpp pwiz/data/proteome/Diff.cpp pwiz/data/proteome/Diff.hpp pwiz/data/proteome/DiffTest.cpp pwiz/data/proteome/ProteinListWrapper.hpp pwiz/data/proteome/ProteinListWrapperTest.cpp pwiz/data/proteome/ProteomeDataFile.cpp pwiz/data/proteome/ProteomeDataFile.hpp pwiz/data/proteome/ProteomeDataFileTest.cpp pwiz/data/proteome/Reader_FASTA.cpp pwiz/data/proteome/Reader_FASTA.hpp pwiz/data/vendor_readers/ExtendedReaderList.cpp pwiz/data/vendor_readers/ExtendedReaderList.hpp pwiz/data/vendor_readers/Thermo/ChromatogramList_Thermo.cpp pwiz/data/vendor_readers/Thermo/ChromatogramList_Thermo.hpp pwiz/data/vendor_readers/Thermo/Reader_Thermo.cpp pwiz/data/vendor_readers/Thermo/Reader_Thermo.hpp pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.hpp pwiz/data/vendor_readers/Thermo/Reader_Thermo_Test.cpp pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.hpp pwiz/utility/chemistry/IsotopeEnvelopeEstimator.cpp pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp pwiz/utility/chemistry/IsotopeEnvelopeEstimatorTest.cpp pwiz/utility/math/LinearSolver.hpp pwiz/utility/math/MatchedFilter.hpp pwiz/utility/math/MatchedFilterTest.cpp pwiz/utility/math/round.hpp pwiz/utility/minimxml/SAXParserTest.cpp pwiz/utility/minimxml/XMLWriter.cpp pwiz/utility/minimxml/XMLWriter.hpp pwiz/utility/minimxml/XMLWriterTest.cpp pwiz/utility/misc/Base64Test.cpp pwiz/utility/misc/IntegerSet.cpp pwiz/utility/misc/IntegerSet.hpp pwiz/utility/misc/IntegerSetTest.cpp pwiz/utility/misc/IterationListener.cpp pwiz/utility/misc/IterationListener.hpp pwiz/utility/misc/IterationListenerTest.cpp pwiz/utility/misc/MSIHandler.cpp pwiz/utility/misc/MSIHandler.hpp pwiz/utility/misc/SHA1Calculator.cpp pwiz/utility/misc/SHA1Calculator.hpp pwiz/utility/misc/SHA1CalculatorTest.cpp pwiz/utility/misc/SHA1_ostream.hpp pwiz/utility/misc/SHA1_ostream_test.cpp pwiz/utility/misc/TabReader.cpp pwiz/utility/misc/TabReader.hpp pwiz/utility/misc/Timer.hpp pwiz/utility/misc/endian.hpp pwiz/utility/misc/endian_test.cpp Copyright: 2007, Spielberg Family Center for Applied Proteomics 2008, Spielberg Family Center for Applied Proteomics 2009, Spielberg Family Center for Applied Proteomics 2010, Spielberg Family Center for Applied Proteomics 2012, Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/analysis/common/CwtPeakDetector.cpp pwiz/analysis/common/CwtPeakDetector.hpp pwiz/analysis/common/LocalMaximumPeakDetector.cpp pwiz/analysis/common/LocalMaximumPeakDetector.hpp pwiz/analysis/common/PeakDetector.hpp pwiz/analysis/common/SavitzkyGolaySmoother.cpp pwiz/analysis/common/SavitzkyGolaySmoother.hpp pwiz/analysis/common/Smoother.hpp pwiz/analysis/common/WhittakerSmoother.cpp pwiz/analysis/common/WhittakerSmoother.hpp pwiz/analysis/common/ZeroSampleFiller.cpp pwiz/analysis/common/ZeroSampleFiller.hpp pwiz/analysis/passive/RunSummary.cpp pwiz/analysis/passive/RunSummary.hpp pwiz/analysis/proteome_processing/ProteinListFactory.cpp pwiz/analysis/proteome_processing/ProteinListFactory.hpp pwiz/analysis/proteome_processing/ProteinListFactoryTest.cpp pwiz/analysis/proteome_processing/ProteinList_DecoyGenerator.cpp pwiz/analysis/proteome_processing/ProteinList_DecoyGenerator.hpp pwiz/analysis/proteome_processing/ProteinList_DecoyGeneratorTest.cpp pwiz/analysis/proteome_processing/ProteinList_Filter.cpp pwiz/analysis/proteome_processing/ProteinList_Filter.hpp pwiz/analysis/proteome_processing/ProteinList_FilterTest.cpp pwiz/analysis/spectrum_processing/MS2DeisotoperTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_3D.cpp pwiz/analysis/spectrum_processing/SpectrumList_3D.hpp pwiz/analysis/spectrum_processing/SpectrumList_3D_Test.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotope.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotope.hpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotopeTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.hpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculatorTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.cpp pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.hpp pwiz/analysis/spectrum_processing/SpectrumList_IonMobility_Test.cpp pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.cpp pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.hpp pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefinerTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.cpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.hpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixerTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilter.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilter.hpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilterTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.hpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummerTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_Smoother.cpp pwiz/analysis/spectrum_processing/SpectrumList_Smoother.hpp pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.cpp pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.hpp pwiz/analysis/spectrum_processing/ThresholdFilter.cpp pwiz/analysis/spectrum_processing/ThresholdFilter.hpp pwiz/data/common/BinaryIndexStream.cpp pwiz/data/common/BinaryIndexStream.hpp pwiz/data/common/BinaryIndexStreamTest.cpp pwiz/data/common/Index.hpp pwiz/data/common/MemoryIndex.cpp pwiz/data/common/MemoryIndex.hpp pwiz/data/common/MemoryIndexTest.cpp pwiz/data/common/Unimod.cpp pwiz/data/common/Unimod.hpp pwiz/data/common/UnimodTest.cpp pwiz/data/identdata/Serializer_pepXML.cpp pwiz/data/identdata/Serializer_pepXML.hpp pwiz/data/identdata/Serializer_pepXML_Test.cpp pwiz/data/identdata/Version.hpp pwiz/data/msdata/Index_mzML.cpp pwiz/data/msdata/Index_mzML.hpp pwiz/data/msdata/MSDataMerger.cpp pwiz/data/msdata/MSDataMerger.hpp pwiz/data/msdata/MSDataMergerTest.cpp pwiz/data/msdata/MemoryMRUCache.hpp pwiz/data/msdata/Serializer_MGF.cpp pwiz/data/msdata/Serializer_MGF.hpp pwiz/data/msdata/Serializer_MGF_Test.cpp pwiz/data/msdata/Serializer_MSn.cpp pwiz/data/msdata/Serializer_MSn.hpp pwiz/data/msdata/Serializer_MSn_Test.cpp pwiz/data/msdata/SpectrumListCache.cpp pwiz/data/msdata/SpectrumListCache.hpp pwiz/data/msdata/SpectrumListCacheTest.cpp pwiz/data/msdata/SpectrumWorkerThreads.cpp pwiz/data/msdata/SpectrumWorkerThreads.hpp pwiz/data/proteome/ProteinListCache.cpp pwiz/data/proteome/ProteinListCache.hpp pwiz/data/proteome/ProteinListCacheTest.cpp pwiz/data/proteome/ProteomeData.cpp pwiz/data/proteome/ProteomeData.hpp pwiz/data/proteome/ProteomeDataTest.cpp pwiz/data/proteome/Reader.cpp pwiz/data/proteome/Reader.hpp pwiz/data/proteome/ReaderTest.cpp pwiz/data/proteome/Serializer_FASTA.cpp pwiz/data/proteome/Serializer_FASTA.hpp pwiz/data/proteome/Serializer_FASTA_Test.cpp pwiz/data/proteome/TextWriter.hpp pwiz/data/proteome/examples.cpp pwiz/data/proteome/examples.hpp pwiz/data/tradata/DefaultReaderList.cpp pwiz/data/tradata/DefaultReaderList.hpp pwiz/data/tradata/Diff.cpp pwiz/data/tradata/Diff.hpp pwiz/data/tradata/DiffTest.cpp pwiz/data/tradata/IO.cpp pwiz/data/tradata/IO.hpp pwiz/data/tradata/IOTest.cpp pwiz/data/tradata/Reader.cpp pwiz/data/tradata/Reader.hpp pwiz/data/tradata/ReaderTest.cpp pwiz/data/tradata/References.cpp pwiz/data/tradata/References.hpp pwiz/data/tradata/ReferencesTest.cpp pwiz/data/tradata/Serializer_traML.cpp pwiz/data/tradata/Serializer_traML.hpp pwiz/data/tradata/Serializer_traML_Test.cpp pwiz/data/tradata/TextWriter.hpp pwiz/data/tradata/TraData.cpp pwiz/data/tradata/TraData.hpp pwiz/data/tradata/TraDataFile.cpp pwiz/data/tradata/TraDataFile.hpp pwiz/data/tradata/TraDataFileTest.cpp pwiz/data/tradata/TraDataTest.cpp pwiz/data/tradata/Version.hpp pwiz/data/tradata/examples.cpp pwiz/data/tradata/examples.hpp pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.hpp pwiz/data/vendor_readers/ABI/Reader_ABI.cpp pwiz/data/vendor_readers/ABI/Reader_ABI.hpp pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.cpp pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.hpp pwiz/data/vendor_readers/ABI/Reader_ABI_Test.cpp pwiz/data/vendor_readers/ABI/SpectrumList_ABI.cpp pwiz/data/vendor_readers/ABI/SpectrumList_ABI.hpp pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.hpp pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D_Test.cpp pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.cpp pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.hpp pwiz/data/vendor_readers/Agilent/ChromatogramList_Agilent.cpp pwiz/data/vendor_readers/Agilent/ChromatogramList_Agilent.hpp pwiz/data/vendor_readers/Agilent/Reader_Agilent.cpp pwiz/data/vendor_readers/Agilent/Reader_Agilent.hpp pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.cpp pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.cpp pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.hpp pwiz/data/vendor_readers/Bruker/ChromatogramList_Bruker.cpp pwiz/data/vendor_readers/Bruker/ChromatogramList_Bruker.hpp pwiz/data/vendor_readers/Bruker/Reader_Bruker.cpp pwiz/data/vendor_readers/Bruker/Reader_Bruker.hpp pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.cpp pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.hpp pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.cpp pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.cpp pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.hpp pwiz/data/vendor_readers/Shimadzu/ChromatogramList_Shimadzu.cpp pwiz/data/vendor_readers/Shimadzu/ChromatogramList_Shimadzu.hpp pwiz/data/vendor_readers/Shimadzu/Reader_Shimadzu.cpp pwiz/data/vendor_readers/Shimadzu/Reader_Shimadzu.hpp pwiz/data/vendor_readers/UIMF/Reader_UIMF.cpp pwiz/data/vendor_readers/UIMF/Reader_UIMF.hpp pwiz/data/vendor_readers/UIMF/SpectrumList_UIMF.cpp pwiz/data/vendor_readers/UIMF/SpectrumList_UIMF.hpp pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.cpp pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.hpp pwiz/data/vendor_readers/Waters/Reader_Waters.cpp pwiz/data/vendor_readers/Waters/Reader_Waters.hpp pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.cpp pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.hpp pwiz/data/vendor_readers/Waters/Reader_Waters_Test.cpp pwiz/data/vendor_readers/Waters/SpectrumList_Waters.cpp pwiz/data/vendor_readers/Waters/SpectrumList_Waters.hpp pwiz/utility/misc/ClickwrapPrompter.cpp pwiz/utility/misc/ClickwrapPrompter.hpp pwiz/utility/misc/ClickwrapPrompterTest.cpp pwiz/utility/misc/DateTime.hpp pwiz/utility/misc/DateTimeTest.cpp pwiz/utility/misc/Environment.hpp pwiz/utility/misc/ExceptionTest.cpp pwiz/utility/misc/Once.hpp pwiz/utility/misc/Singleton.hpp pwiz/utility/misc/Std.hpp pwiz/utility/misc/TabReaderTest.cpp pwiz/utility/misc/VendorReaderTestHarness.cpp pwiz/utility/misc/VendorReaderTestHarness.hpp pwiz/utility/misc/cpp_cli_utilities.hpp pwiz/utility/misc/mru_list_test.cpp pwiz/utility/misc/shared_map.hpp Copyright: 2008, Vanderbilt University - Nashville, TN 37232 2009, Vanderbilt University - Nashville, TN 37232 2010, Vanderbilt University - Nashville, TN 37232 2011, Vanderbilt University - Nashville, TN 37232 2012, Vanderbilt University - Nashville, TN 37232 2014, Vanderbilt University - Nashville, TN 37232 2015, Vanderbilt University - Nashville, TN 37232 2016, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: pwiz/analysis/demux/DemuxSolver.cpp pwiz/analysis/demux/DemuxSolver.hpp pwiz/analysis/demux/DemuxTypes.hpp pwiz/analysis/demux/FSDemux.cpp pwiz/analysis/demux/IDemultiplexer.hpp pwiz/analysis/demux/IPrecursorMaskCodec.hpp pwiz/analysis/demux/MSXDemultiplexer.cpp pwiz/analysis/demux/MSXDemultiplexer.hpp pwiz/analysis/demux/OverlapDemultiplexer.cpp pwiz/analysis/demux/OverlapDemultiplexer.hpp pwiz/analysis/demux/PrecursorMaskCodec.cpp pwiz/analysis/demux/PrecursorMaskCodec.hpp pwiz/analysis/demux/SpectrumPeakExtractor.cpp pwiz/analysis/demux/SpectrumPeakExtractor.hpp pwiz/analysis/spectrum_processing/SpectrumList_Demux.cpp pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp Copyright: Jarret Egertson License: Apache-2.0 Files: pwiz/analysis/demux/CubicHermiteSpline.cpp pwiz/analysis/demux/CubicHermiteSpline.cpp pwiz/analysis/demux/CubicHermiteSpline.hpp pwiz/analysis/demux/CubicHermiteSpline.hpp pwiz/analysis/demux/CubicHermiteSplineTest.cpp pwiz/analysis/demux/DemuxDebugReadWriteTest.cpp pwiz/analysis/demux/DemuxDebugReader.cpp pwiz/analysis/demux/DemuxDebugReader.hpp pwiz/analysis/demux/DemuxDebugWriter.cpp pwiz/analysis/demux/DemuxDebugWriter.hpp pwiz/analysis/demux/DemuxHelpers.cpp pwiz/analysis/demux/DemuxHelpers.cpp pwiz/analysis/demux/DemuxHelpers.hpp pwiz/analysis/demux/DemuxHelpersTest.cpp pwiz/analysis/demux/DemuxSolverTest.cpp pwiz/analysis/demux/DemuxTypes.hpp pwiz/analysis/demux/EnumConstantNotPresentException.hpp pwiz/analysis/demux/IInterpolation.hpp pwiz/analysis/demux/MatrixIO.cpp pwiz/analysis/demux/MatrixIO.hpp pwiz/analysis/demux/MatrixIOTest.cpp pwiz/analysis/demux/SpectrumPeakExtractorTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_DemuxTest.cpp Copyright: Austin Keller License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/MS2DeisotoperTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_3D.cpp pwiz/analysis/spectrum_processing/SpectrumList_3D.hpp pwiz/analysis/spectrum_processing/SpectrumList_3D_Test.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotope.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotope.hpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeFromIsotopeTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.hpp pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculatorTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.cpp pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefiner.hpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilter.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilter.hpp pwiz/analysis/spectrum_processing/SpectrumList_PeakFilterTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.cpp pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.hpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.cpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.hpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummerTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_Smoother.cpp pwiz/analysis/spectrum_processing/SpectrumList_Smoother.hpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.cpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.hpp pwiz/analysis/spectrum_processing/ThresholdFilter.cpp pwiz/analysis/spectrum_processing/ThresholdFilter.hpp Copyright: 2008 Vanderbilt University License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.cpp pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.hpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.cpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.hpp pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixerTest.cpp Copyright: 2009 Vanderbilt University License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_LockmassRefinerTest.cpp Copyright: 2015 Vanderbilt University License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_IonMobility_Test.cpp pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.cpp pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.hpp Copyright: 2016 Vanderbilt University License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/PrecursorRecalculator.hpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefault.cpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefault.hpp pwiz/analysis/spectrum_processing/PrecursorRecalculatorDefaultTest.cpp pwiz/analysis/spectrum_processing/SpectrumListFactory.cpp pwiz/analysis/spectrum_processing/SpectrumListFactory.hpp pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_Filter.cpp pwiz/analysis/spectrum_processing/SpectrumList_Filter.hpp pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculator.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculator.hpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.hpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefineTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.cpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.hpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.cpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.hpp pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp Copyright: 2008 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_ZeroSamplesFilter.cpp pwiz/analysis/spectrum_processing/SpectrumList_ZeroSamplesFilter.hpp Copyright: 2012 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_MZWindow.cpp pwiz/analysis/spectrum_processing/SpectrumList_MZWindow.hpp pwiz/analysis/spectrum_processing/SpectrumList_MZWindowTest.cpp Copyright: 2009 Center for Applied Molecular Medicine License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/MS2Deisotoper.cpp pwiz/analysis/spectrum_processing/MS2Deisotoper.hpp pwiz/analysis/spectrum_processing/MS2NoiseFilter.cpp pwiz/analysis/spectrum_processing/MS2NoiseFilter.hpp pwiz/analysis/spectrum_processing/PrecursorMassFilter.cpp pwiz/analysis/spectrum_processing/PrecursorMassFilter.hpp pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.cpp Copyright: 2009 Institute for Systems Biology, Seattle, WAO License: Apache-2.0 Files: pwiz/data/identdata/Serializer_Text.cpp pwiz/data/identdata/Serializer_Text.hpp pwiz/data/identdata/Serializer_mzid.hpp pwiz/data/identdata/examples.cpp pwiz/data/identdata/examples.hpp Copyright: 2008 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/data/identdata/DefaultReaderList.cpp pwiz/data/identdata/DefaultReaderList.hpp pwiz/data/identdata/Diff.cpp pwiz/data/identdata/Diff.hpp pwiz/data/identdata/DiffTest.cpp pwiz/data/identdata/ExtendedReadTest.cpp pwiz/data/identdata/IO.cpp pwiz/data/identdata/IO.hpp pwiz/data/identdata/IOTest.cpp pwiz/data/identdata/IdentData.cpp pwiz/data/identdata/IdentData.hpp pwiz/data/identdata/IdentDataFile.cpp pwiz/data/identdata/IdentDataFile.hpp pwiz/data/identdata/IdentDataTest.cpp pwiz/data/identdata/Pep2MzIdent.cpp pwiz/data/identdata/Pep2MzIdent.hpp pwiz/data/identdata/Pep2MzIdentTest.cpp pwiz/data/identdata/Reader.cpp pwiz/data/identdata/Reader.hpp pwiz/data/identdata/ReaderTest.cpp pwiz/data/identdata/References.cpp pwiz/data/identdata/References.hpp pwiz/data/identdata/ReferencesTest.cpp pwiz/data/identdata/Serializer_mzid.cpp pwiz/data/identdata/Serializer_mzid_Test.cpp pwiz/data/identdata/TextWriter.hpp Copyright: 2009 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/data/identdata/DelimReader.cpp pwiz/data/identdata/DelimReader.hpp pwiz/data/identdata/DelimWriter.cpp pwiz/data/identdata/DelimWriter.hpp pwiz/data/identdata/KwCVMap.cpp pwiz/data/identdata/KwCVMap.hpp pwiz/data/identdata/KwCVMapTest.cpp pwiz/data/identdata/MascotReader.hpp pwiz/data/identdata/MzidPredicates.hpp pwiz/data/identdata/Serializer_Text_Test.cpp Copyright: 2010 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/data/identdata/Serializer_protXML.cpp pwiz/data/identdata/Serializer_protXML.hpp pwiz/data/identdata/Serializer_protXML_Test.cpp Copyright: 2012 Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/utility/findmf/base/base/interpolate.hpp pwiz/utility/findmf/base/base/copy_iftest.cpp pwiz/utility/findmf/base/base/constants.hpp pwiz/utility/findmf/base/base/scale.hpp pwiz/utility/findmf/base/base/diff.hpp pwiz/utility/findmf/base/base/cumsum.hpp pwiz/utility/findmf/base/base/utilities/interpolation.hpp pwiz/utility/findmf/base/base/utilities/base.hpp pwiz/utility/findmf/base/base/cumsumtest.cpp pwiz/utility/findmf/base/base/basetest.cpp pwiz/utility/findmf/base/base/equispaceinterpolationtest.cpp pwiz/utility/findmf/base/base/difftest.cpp pwiz/utility/findmf/base/base/copyif.hpp pwiz/utility/findmf/base/base/base.hpp pwiz/utility/findmf/base/resample/bin1d.hpp pwiz/utility/findmf/base/resample/bucket1d.hpp pwiz/utility/findmf/base/resample/masscomparefunctors.hpp pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp pwiz/utility/findmf/base/resample/convert2dense.hpp pwiz/utility/findmf/base/resample/determinbinwithtest.cpp pwiz/utility/findmf/base/resample/bucket1dtest.cpp pwiz/utility/findmf/base/resample/determinebinwidth.hpp pwiz/utility/findmf/base/resample/convert2densetest.cpp pwiz/utility/findmf/base/resample/breakspec.hpp pwiz/utility/findmf/base/filter/filter.hpp pwiz/utility/findmf/base/filter/utilities/gauss.hpp pwiz/utility/findmf/base/filter/utilities/preparedata.hpp pwiz/utility/findmf/base/filter/utilities/mexhat.hpp pwiz/utility/findmf/base/filter/filterutilstest.cpp pwiz/utility/findmf/base/filter/gaussfilter.hpp pwiz/utility/findmf/base/filter/gaussfiltertest.cpp pwiz/utility/findmf/base/ms/peakpickerqtof.hpp pwiz/utility/findmf/base/ms/simplepickertest.cpp pwiz/utility/findmf/base/ms/simplepicker.hpp Copyright: ETH Zurich - Witold Wolski License: Apache-2.0 Files: pwiz/utility/math/HouseholderQR.hpp pwiz/utility/math/LinearLeastSquares.hpp pwiz/utility/math/LinearLeastSquaresTest.cpp pwiz/utility/math/Types.hpp pwiz/utility/math/qr.hpp Copyright: Robert Burke License: Apache-2.0 Files: pwiz/utility/math/LinearSolver.hpp pwiz/utility/math/LinearSolverTest.cpp pwiz/utility/math/MatchedFilter.hpp pwiz/utility/math/MatchedFilterTest.cpp pwiz/utility/math/OrderedPair.hpp pwiz/utility/math/OrderedPairTest.cpp pwiz/utility/math/Parabola.cpp pwiz/utility/math/Parabola.hpp pwiz/utility/math/ParabolaTest.cpp pwiz/utility/math/Stats.cpp pwiz/utility/math/Stats.hpp pwiz/utility/math/StatsTest.cpp pwiz/utility/math/erf.cpp pwiz/utility/math/erf.hpp pwiz/utility/math/erfTest.cpp pwiz/utility/math/round.hpp Copyright: Darren Kessner License: Apache-2.0 Files: pwiz/utility/misc/FailTest.cpp pwiz/utility/chemistry/iso.cpp pwiz/utility/chemistry/parse_isotopes.cpp pwiz/utility/math/qrTest.cpp pwiz/utility/math/HouseholderQRTest.cpp Copyright: Matthew Chambers License: Apache-2.0 Files: pwiz/analysis/frequency/DerivativeTest.hpp pwiz/analysis/frequency/FrequencyEstimator.hpp pwiz/analysis/frequency/FrequencyEstimatorPhysicalModel.cpp pwiz/analysis/frequency/FrequencyEstimatorPhysicalModel.hpp pwiz/analysis/frequency/FrequencyEstimatorSimple.cpp pwiz/analysis/frequency/FrequencyEstimatorSimple.hpp pwiz/analysis/frequency/FrequencyEstimatorSimpleTest.cpp pwiz/analysis/frequency/MagnitudeLorentzian.cpp pwiz/analysis/frequency/MagnitudeLorentzian.hpp pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp pwiz/analysis/frequency/ParameterEstimator.cpp pwiz/analysis/frequency/ParameterEstimator.hpp pwiz/analysis/frequency/ParametrizedFunction.hpp pwiz/analysis/frequency/ParametrizedFunctionTest.cpp pwiz/analysis/frequency/PeakDetector.hpp pwiz/analysis/frequency/PeakDetectorMatchedFilter.cpp pwiz/analysis/frequency/PeakDetectorMatchedFilter.hpp pwiz/analysis/frequency/PeakDetectorMatchedFilterTest.cpp pwiz/analysis/frequency/PeakDetectorMatchedFilterTestData.cpp pwiz/analysis/frequency/PeakDetectorMatchedFilterTestData.hpp pwiz/analysis/frequency/PeakDetectorNaive.cpp pwiz/analysis/frequency/PeakDetectorNaive.hpp pwiz/analysis/frequency/PeakDetectorNaiveTest.cpp pwiz/analysis/frequency/TruncatedLorentzian.cpp pwiz/analysis/frequency/TruncatedLorentzian.hpp pwiz/analysis/frequency/TruncatedLorentzianEstimator.cpp pwiz/analysis/frequency/TruncatedLorentzianEstimator.hpp pwiz/analysis/frequency/TruncatedLorentzianParameters.cpp pwiz/analysis/frequency/TruncatedLorentzianParameters.hpp pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp pwiz/analysis/frequency/TruncatedLorentzianTest.cpp pwiz/data/misc/CalibrationParameters.hpp pwiz/data/misc/CalibrationParametersTest.cpp pwiz/data/misc/FrequencyData.cpp pwiz/data/misc/FrequencyData.hpp pwiz/data/misc/FrequencyDataTest.cpp pwiz/data/misc/SampleDatum.hpp pwiz/data/misc/SampleDatumTest.cpp pwiz/data/proteome/AminoAcid.cpp pwiz/data/proteome/AminoAcid.hpp pwiz/data/proteome/AminoAcidTest.cpp pwiz/data/proteome/Peptide.cpp pwiz/data/proteome/Peptide.hpp pwiz/data/proteome/PeptideTest.cpp pwiz/utility/chemistry/Chemistry.cpp pwiz/utility/chemistry/Chemistry.hpp pwiz/utility/chemistry/ChemistryData.cpp pwiz/utility/chemistry/ChemistryData.hpp pwiz/utility/chemistry/ChemistryTest.cpp pwiz/utility/chemistry/Ion.hpp pwiz/utility/chemistry/IsotopeCalculator.cpp pwiz/utility/chemistry/IsotopeCalculator.hpp pwiz/utility/chemistry/IsotopeCalculatorTest.cpp pwiz/utility/chemistry/IsotopeTable.cpp pwiz/utility/chemistry/IsotopeTable.hpp pwiz/utility/chemistry/IsotopeTableTest.cpp pwiz/utility/math/LinearLeastSquares.hpp pwiz/utility/math/LinearLeastSquaresTest.cpp pwiz/utility/math/LinearSolverTest.cpp pwiz/utility/math/Parabola.cpp pwiz/utility/math/Parabola.hpp pwiz/utility/math/ParabolaTest.cpp pwiz/utility/math/Stats.cpp pwiz/utility/math/Stats.hpp pwiz/utility/math/StatsTest.cpp pwiz/utility/math/Types.hpp pwiz/utility/math/erf.cpp pwiz/utility/math/erf.hpp pwiz/utility/math/erfTest.cpp pwiz/utility/math/qr.hpp pwiz/utility/misc/Base64.cpp pwiz/utility/misc/Base64.hpp pwiz/utility/misc/Image.hpp pwiz/utility/misc/unit.hpp pwiz/utility/proteome/IPIFASTADatabase.cpp pwiz/utility/proteome/IPIFASTADatabase.hpp pwiz/utility/proteome/IPIFASTADatabaseTest.cpp pwiz/utility/proteome/pepdb.cpp Copyright: 2005, Louis Warschaw Prostate Cancer Center 2006, Louis Warschaw Prostate Cancer Center 2007, Louis Warschaw Prostate Cancer Center License: Apache-2.0 Files: pwiz/analysis/peakdetect/FeatureDetectorPeakel.cpp pwiz/analysis/peakdetect/FeatureDetectorPeakel.hpp pwiz/analysis/peakdetect/FeatureDetectorPeakelTest.cpp pwiz/analysis/peakdetect/FeatureDetectorTuningTest.cpp pwiz/analysis/peakdetect/FeatureModeler.cpp pwiz/analysis/peakdetect/FeatureModeler.hpp pwiz/analysis/peakdetect/FeatureModelerTest.cpp pwiz/analysis/peakdetect/MZRTField.cpp pwiz/analysis/peakdetect/MZRTField.hpp pwiz/analysis/peakdetect/MZRTFieldTest.cpp pwiz/analysis/peakdetect/Noise.cpp pwiz/analysis/peakdetect/Noise.hpp pwiz/analysis/peakdetect/NoiseTest.cpp pwiz/analysis/peakdetect/PeakExtractor.cpp pwiz/analysis/peakdetect/PeakExtractor.hpp pwiz/analysis/peakdetect/PeakExtractorTest.cpp pwiz/analysis/peakdetect/PeakFinder.cpp pwiz/analysis/peakdetect/PeakFinder.hpp pwiz/analysis/peakdetect/PeakFinderTest.cpp pwiz/analysis/peakdetect/PeakFitter.cpp pwiz/analysis/peakdetect/PeakFitter.hpp pwiz/analysis/peakdetect/PeakFitterTest.cpp pwiz/analysis/peakdetect/PeakelGrower.cpp pwiz/analysis/peakdetect/PeakelGrower.hpp pwiz/analysis/peakdetect/PeakelGrowerTest.cpp pwiz/analysis/peakdetect/PeakelPicker.cpp pwiz/analysis/peakdetect/PeakelPicker.hpp pwiz/analysis/peakdetect/PeakelPickerTest.cpp pwiz/analysis/spectrum_processing/SpectrumList_MZWindow.cpp pwiz/analysis/spectrum_processing/SpectrumList_MZWindow.hpp pwiz/analysis/spectrum_processing/SpectrumList_MZWindowTest.cpp pwiz/utility/chemistry/MZTolerance.cpp pwiz/utility/chemistry/MZTolerance.hpp pwiz/utility/chemistry/MZToleranceTest.cpp pwiz/utility/math/OrderedPair.hpp pwiz/utility/math/OrderedPairTest.cpp pwiz/utility/misc/almost_equal.hpp pwiz/utility/misc/almost_equal_test.cpp Copyright: 2009, Center for Applied Molecular Medicine License: Apache-2.0 Files: pwiz/analysis/Version.hpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.cpp pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.hpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.cpp pwiz/analysis/spectrum_processing/SpectrumList_Sorter.hpp pwiz/data/msdata/SpectrumList_BTDX.cpp pwiz/data/msdata/SpectrumList_BTDX.hpp pwiz/data/msdata/SpectrumList_MGF.cpp pwiz/data/msdata/SpectrumList_MGF.hpp pwiz/data/msdata/SpectrumList_MSn.cpp pwiz/data/msdata/SpectrumList_MSn.hpp pwiz/data/msdata/Version.hpp pwiz/data/proteome/Version.hpp pwiz/utility/misc/CharIndexedVector.hpp pwiz/utility/misc/Container.hpp pwiz/utility/misc/Exception.hpp pwiz/utility/misc/Export.hpp pwiz/utility/misc/Filesystem.cpp pwiz/utility/misc/Filesystem.hpp pwiz/utility/misc/FilesystemTest.cpp pwiz/utility/misc/Stream.hpp pwiz/utility/misc/String.hpp pwiz/utility/misc/optimized_lexical_cast.hpp pwiz/utility/misc/virtual_map.hpp Copyright: 2008, Spielberg Family Center for Applied Proteomics 2008, Vanderbilt University - Nashville, TN 37232 2011, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: pwiz/analysis/common/DataFilter.hpp pwiz/analysis/spectrum_processing/MS2Deisotoper.cpp pwiz/analysis/spectrum_processing/MS2Deisotoper.hpp pwiz/analysis/spectrum_processing/MS2NoiseFilter.cpp pwiz/analysis/spectrum_processing/MS2NoiseFilter.hpp pwiz/analysis/spectrum_processing/PrecursorMassFilter.cpp pwiz/analysis/spectrum_processing/PrecursorMassFilter.hpp Copyright: 2009, Institute for Systems Biology, Seattle, WA License: Apache-2.0 Files: pwiz/data/proteome/Digestion.cpp pwiz/data/proteome/Digestion.hpp pwiz/data/proteome/DigestionTest.cpp pwiz/data/proteome/Modification.cpp pwiz/data/proteome/Modification.hpp Copyright: 2006, Louis Warschaw Prostate Cancer Center 2008, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_MZRefiner.cpp pwiz/analysis/spectrum_processing/SpectrumList_MZRefiner.hpp pwiz/analysis/spectrum_processing/SpectrumList_MZRefinerTest.cpp Copyright: 2014, Pacific Northwest National Laboratory License: Apache-2.0 Files: pwiz/utility/math/MatrixInverse.hpp Copyright: http://www.crystalclearsoftware.com/cgi-bin/boost_wiki/wiki.pl?Effective_UBLAS/Matrix_Inversion License: Public-domain or Boost Public Domain or Boost Software License - Version 1.0 Files: pwiz/utility/misc/SHA1.cpp pwiz/utility/misc/SHA1.h Copyright: Dominik Reichl License: Public-domain The work is in the public domain. Files: pwiz/utility/minimxml/SAXParser.cpp pwiz/utility/minimxml/SAXParser.hpp Copyright: 2007, Spielberg Family Center for Applied Proteomics 2011, Insilicos LLC License: Apache-2.0 Files: pwiz/data/msdata/MSNumpress.cpp pwiz/data/msdata/MSNumpress.hpp Copyright: 2013, Johan Teleman License: Apache-2.0 Files: pwiz/analysis/passive/TabularConfig.cpp pwiz/analysis/passive/TabularConfig.hpp Copyright: 2012, University of Minnesota - Minneapolis, MN 55455 License: Apache-2.0 Files: pwiz/utility/misc/random_access_compressed_ifstream.cpp pwiz/utility/misc/random_access_compressed_ifstream.hpp Copyright: 1995-2005, Jean-loup Gailly. 2005, Mark Adler Insilicos LLC 2008,2011 License: Zlib Files: pwiz/data/common/cvgen.cpp Copyright: 2007, Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.cpp Copyright: 2010, Institute for Systems Biology License: Apache-2.0 Files: pwiz/analysis/frequency/FrequencyEstimatorPhysicalModelTest.cpp Copyright: 2007, Spielberg Family Center for Appled Proteomics License: Apache-2.0 Files: pwiz/data/common/cv.hpp Copyright: 2007, Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp Copyright: 2008, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: pwiz/utility/misc/mru_list.hpp Copyright: 2003-2008, Joaquin M Lopez Munoz. License: BSL-1.0 Files: pwiz_tools/commandline/msconvert.cpp pwiz_tools/commandline/pepcat.cpp pwiz_tools/common/FullReaderList.hpp pwiz_tools/common/MSDataAnalyzerApplication.cpp pwiz_tools/common/MSDataAnalyzerApplication.hpp pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp pwiz_tools/examples/hello_analyzer.cpp pwiz_tools/examples/hello_analyzer_2.cpp pwiz_tools/examples/hello_msdata.cpp pwiz_tools/examples/mscat.cpp pwiz_tools/examples/txt2mzml.cpp pwiz_tools/examples/write_example_files.cpp pwiz_tools/examples/write_mzid_example_files.cpp pwiz_tools/examples/write_traml_example_files.cpp Copyright: 2007, Spielberg Family Center for Applied Proteomics 2008, Spielberg Family Center for Applied Proteomics 2009, Spielberg Family Center for Applied Proteomics 2010, Spielberg Family Center for Applied Proteomics License: Apache-2.0 Files: pwiz_tools/commandline/idconvert.cpp pwiz_tools/examples/write_proteome_example_files.cpp Copyright: 2010, Vanderbilt University - Nashville, TN 37232 2011, Vanderbilt University - Nashville, TN 37232 License: Apache-2.0 Files: libraries/eigen3-nnls/* Copyright: 2013 Hannes Matuschek License: MPL-2.0 This Source Code Form is subject to the terms of the Mozilla Public License v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/. Files: debian/* Copyright: 2012-2017 Filippo Rusconi 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 3 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 . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".