├── .gitignore ├── CMakeLists.txt ├── LICENSE ├── README.md ├── example ├── README.md ├── example_match.png ├── example_results_control.csv ├── yeast_1000.msp └── yeast_exp.mgf ├── include ├── LICENSE └── cxxopts.hpp ├── scripts ├── merge_pin_output.py └── test.csv └── src ├── DefineConstants.h ├── build_index.cpp ├── configuration.cpp ├── configuration.h ├── fragment_ion_index.cpp ├── fragment_ion_index.h ├── index_file_reader.cpp ├── index_file_reader.h ├── index_file_writer.cpp ├── index_file_writer.h ├── indexing_manager.cpp ├── indexing_manager.h ├── library.cpp ├── library.h ├── main.cpp ├── match.cpp ├── match.h ├── mgf_reader.cpp ├── mgf_reader.h ├── msp_reader.cpp ├── msp_reader.h ├── naive_search.cpp ├── precursor_index.cpp ├── precursor_index.h ├── quick_scan.cpp ├── scanner.cpp ├── scanner.h ├── scores.cpp ├── scores.h ├── search_index.cpp ├── search_manager.cpp ├── search_manager.h ├── settings.cpp ├── settings.h ├── spectral_search.cpp ├── spectral_search.h ├── 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