SiriusMSConverter.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka, Axel Walter $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <fstream>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI SiriusMSFile
  {
public:
 
  class AccessionInfo
  {
  public:
    std::string sf_path; 
    std::string sf_type; 
    std::string sf_filename; 
    std::string sf_accession; 
    std::string native_id_accession; 
    std::string native_id_type; 
  };
 
  class CompoundInfo
  {
  public:
    std::string cmp; 
    double pmass; 
    double pint_mono; 
    double rt; 
    double fmz; 
    std::string fid; 
    std::string formula; 
    int charge; 
    std::string ionization; 
    std::string des; 
    std::string specref_format; 
    std::string source_file; 
    std::string source_format; 
    std::vector<std::string> native_ids; 
    std::string native_ids_id; 
    std::vector<std::string> m_ids; 
    std::string m_ids_id; 
    std::vector<std::string> scan_indices; 
    std::vector<std::string> specrefs; 
    int file_index; 
  };
 
    static void store(const MSExperiment& spectra,
                      std::ofstream& os,
                      const FeatureMapping::FeatureToMs2Indices& feature_mapping,
                      const bool& feature_only,
                      const int& isotope_pattern_iterations,
                      const bool no_masstrace_info_isotope_pattern,
                      std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                      const size_t& file_index);
    static void saveFeatureCompoundInfoAsTSV(const std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                                      const std::string& filename);
 
  protected:
    static void writeMsFile_(std::ofstream& os,
                             const MSExperiment& spectra,
                             const std::vector<size_t>& ms2_spectra_index,
                             const SiriusMSFile::AccessionInfo& ainfo,
                             const StringList& adducts,
                             const std::vector<std::string>& v_description,
                             const std::vector<std::string>& v_sumformula,
                             const std::vector<std::pair<double,double>>& f_isotopes,
                             int& feature_charge,
                             uint64_t& feature_id,
                             const double& feature_rt,
                             const double& feature_mz,
                             bool& writecompound,
                             const bool& no_masstrace_info_isotope_pattern,
                             const int& isotope_pattern_iterations,
                             int& count_skipped_spectra,
                             int& count_assume_mono,
                             int& count_no_ms1,
                             std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                             const size_t& file_index);
    static Int getHighestIntensityPeakInMZRange_(double test_mz,
                                                 const MSSpectrum& spectrum,
                                                 double tolerance,
                                                 bool ppm);
 
    static std::vector<Peak1D> extractPrecursorIsotopePattern_(const double& precursor_mz,
                                                               const MSSpectrum& precursor_spectrum,
                                                               int& iterations,
                                                               const int& charge);
 
 
 
  };
 
} // namespace OpenMS