├── .github └── workflows │ └── build_and_release.yml ├── .gitignore ├── .vscode └── settings.json ├── CMakeLists.txt ├── CPack.txt ├── ChangeLog ├── CommonCMake.txt ├── LICENSE ├── NOTICE ├── ReadMe.md ├── admin ├── add_license.sh ├── add_namespace.sh ├── builders │ ├── _init_msvc_.bat │ ├── _urls_and_file_names_.bat │ ├── centos64_build.sh │ ├── download_file.bat │ ├── fedora64_build.sh │ ├── install_proteowizard.bat │ ├── install_proteowizard.sh │ ├── install_qt.sh │ ├── nativew32_build.bat │ ├── nativew64_build.bat │ ├── osx64_build.sh │ ├── tarball64_build.sh │ └── ubuntu64_build.sh ├── dat_converters.py ├── get_download_stats.sh ├── gnuwin32_bin.zip ├── nextflow │ ├── file_list.txt │ ├── nf.config │ ├── params.txt │ ├── run_maracluster.nf │ └── run_nextflow.sh ├── release_checklist.txt └── vagrant │ ├── ReadMe.md │ ├── batch.sh │ └── manager.sh ├── cmake ├── FindCassandra.cmake ├── FindICU.cmake ├── FindProteoWizard.cmake ├── FindPthreads.cmake ├── MacroFindPackage.cmake └── VersionGen.cmake ├── quickbuild.bat ├── quickbuild.sh ├── quickbuild64.bat └── src ├── BinAndRank.cpp ├── BinAndRank.h ├── BinSpectra.cpp ├── BinSpectra.h ├── BinaryFingerprintMethods.cpp ├── BinaryFingerprintMethods.h ├── BinaryInterface.h ├── CMakeLists.txt ├── Globals.cpp ├── Globals.h.cmake ├── MSClusterMerge.cpp ├── MSClusterMerge.h ├── MSFileExtractor.cpp ├── MSFileExtractor.h ├── MSFileHandler.cpp ├── MSFileHandler.h ├── MSFileMerger.cpp ├── MSFileMerger.h ├── MZIntensityPair.cpp ├── MZIntensityPair.h ├── MaRaCluster.cpp ├── MaRaCluster.h ├── MassChargeCandidate.h ├── MatrixLoader.cpp ├── MatrixLoader.h ├── MyException.cpp ├── MyException.h ├── Option.cpp ├── Option.h ├── PeakCounts.cpp ├── PeakCounts.h ├── PeakDistribution.cpp ├── PeakDistribution.h ├── PvalueCalculator.cpp ├── PvalueCalculator.h ├── PvalueFilterAndSort.cpp ├── PvalueFilterAndSort.h ├── PvalueTriplet.cpp ├── PvalueTriplet.h ├── PvalueVector.h ├── PvalueVectors.cpp ├── PvalueVectors.h ├── Pvalues.cpp ├── Pvalues.h ├── ScanId.cpp ├── ScanId.h ├── ScanMergeInfoSet.cpp ├── ScanMergeInfoSet.h ├── SparseClustering.cpp ├── SparseClustering.h ├── SparseEdge.h ├── SparseMatrix.h ├── SparsePoisonedClustering.cpp ├── SparsePoisonedClustering.h ├── Spectra.cpp ├── Spectra.h ├── Spectrum.h ├── SpectrumClusters.cpp ├── SpectrumClusters.h ├── SpectrumFileList.cpp ├── SpectrumFileList.h ├── SpectrumFiles.cpp ├── SpectrumFiles.h ├── SpectrumHandler.cpp ├── SpectrumHandler.h ├── SpectrumMassInfo.h ├── TsvInterface.h ├── Version.h.cmake ├── extractRAWSpectra.cpp ├── extractSpectra.cpp ├── license.txt ├── main.cpp ├── msgfFixMzML.cpp └── qt-gui ├── CMakeLists.txt ├── CPack.txt ├── icon ├── hicolor │ ├── 128x128 │ │ └── apps │ │ │ └── maracluster.png │ ├── 16x16 │ │ └── apps │ │ │ └── maracluster.png │ ├── 22x22 │ │ └── apps │ │ │ └── maracluster.png │ ├── 32x32 │ │ └── apps │ │ │ └── maracluster.png │ ├── 48x48 │ │ └── apps │ │ │ └── maracluster.png │ └── 64x64 │ │ └── apps │ │ └── maracluster.png ├── 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