SiriusMSConverter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * 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.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS 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.
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// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $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:
    String sf_path; 
    String sf_type; 
    String sf_filename; 
    String sf_accession; 
    String native_id_accession; 
    String native_id_type; 
  };
 
  class CompoundInfo
  {
  public:
    String cmp; 
    double pmass; 
    double pint_mono; 
    double rt; 
    double fmz; 
    String fid; 
    String formula; 
    int charge; 
    String ionization; 
    String des; 
    String specref_format; 
    String source_file; 
    String source_format; 
    std::vector<String> native_ids; 
    String native_ids_id; 
    std::vector<String> m_ids; 
    String m_ids_id; 
    std::vector<String> scan_indices; 
    std::vector<String> specrefs; 
  };
 
    static void store(const MSExperiment& spectra,
                      const OpenMS::String& msfile,
                      const FeatureMapping::FeatureToMs2Indices& feature_mapping,
                      const bool& feature_only,
                      const int& isotope_pattern_iterations,
                      const bool no_mt_info,
                      std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo);
 
 
  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<String>& v_description,
                             const std::vector<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);
 
 
 
    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