FLASHIda.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHHelperClasses.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/ANALYSIS/TOPDOWN/SpectralDeconvolution.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FLASHIda
  {
  public:
    typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine;
    typedef FLASHHelperClasses::LogMzPeak LogMzPeak;
 
    explicit FLASHIda(char *arg);
 
    ~FLASHIda() = default;
 
    FLASHIda(const FLASHIda& ) = default;
 
    FLASHIda(FLASHIda&& other) = default;
 
    FLASHIda& operator=(const FLASHIda& fd) = default;
 
    int getPeakGroups(const double *mzs,
                      const double *intensities,
                      int length,
                      double rt,
                      int ms_level,
                      const char *name,
                      const char *cv);
 
    void getIsolationWindows(double *window_start,
                             double *window_end,
                             double *qscores,
                             int *charges,
                             int *min_charges,
                             int *max_charges,
                             double *mono_masses,
                             double *charge_cos,
                             double *charge_snrs,
                             double *iso_cos,
                             double *snrs, double *charge_scores,
                             double *ppm_errors,
                             double *precursor_intensities,
                             double *peakgroup_intensities,
                             int *ids);
    void removeFromExlusionList(int id);
 
    double getRepresentativeMass();
 
    void getAllMonoisotopicMasses(double *masses, int length);
 
    int GetAllPeakGroupSize();
 
    static std::map<int, std::vector<std::vector<float>>> parseFLASHIdaLog(const String& in_log_file);
 
  private:
    /*struct
    {
      bool operator()(const PeakGroup& a, const PeakGroup& b) const
      {
        return a.getQScore() > b.getQScore();
      }
    } QscoreComparator_;
*/
    std::unordered_map<int, double> tqscore_exceeding_mz_rt_map_; 
    std::unordered_map<int, double> tqscore_exceeding_mass_rt_map_; 
    std::unordered_map<int, double> all_mass_rt_map_; 
    std::unordered_map<int, double> mass_qscore_map_; 
 
 
 
    std::unordered_map<int, int> id_mass_map_;
    std::unordered_map<int, int> id_mz_map_;
    std::unordered_map<int, double> id_qscore_map_;
 
 
    void filterPeakGroupsUsingMassExclusion_(int ms_level, double rt);
 
    static MSSpectrum makeMSSpectrum_(const double *mzs,
                                      const double *ints,
                                      int length,
                                      double rt,
                                      int ms_level,
                                      const char *name);
 
    DeconvolvedSpectrum deconvolved_spectrum_;
    DeconvolvedSpectrum selected_peak_groups_;
    std::vector<int> trigger_charges;
    std::vector<double> trigger_left_isolation_mzs_;
    std::vector<double> trigger_right_isolation_mzs_;
    std::vector<int> trigger_ids_;
 
    SpectralDeconvolution fd_;
 
    double tqscore_threshold = .99;
 
    double qscore_threshold_;
    double rt_window_;
    IntList mass_count_;
 
    int targeting_mode_ = 0; 
 
    std::map<double, std::vector<double>> target_mass_rt_map_;
    std::map<double, std::vector<double>> target_mass_qscore_map_;
    std::vector<double> target_masses_; 
 
    // For the possibility of removal each window is given an id, starting at zero (needed for FAIMS support)
    int window_id_ = 0;
 
    std::map<double, std::vector<double>> exclusion_rt_masses_map_; 
    std::vector<double> excluded_masses_; 
 
    double snr_threshold_ = 1;
 
    DoubleList tol_;
 
    std::map<double, std::vector<double>> cv_to_mass_ = {
      {-80.0, {2400.0, 2900.0}},
      {-70.0, {3500.0, 4000.0}},
      {-60.0, {4500.0, 5000.0}},
      {-50.0, {5100.0, 6500.0}},
      {-40.0, {7500.0, 10000.0}},
      {-30.0, {11000.0, 14000.0}},
      {-20.0, {12000.0, 15000.0}},
      {-10.0, {13000.0, 15500.0}},
      {-0.0, {14000.0, 16000.0}},
      {10.0, {15000.0, 16500.0}},
    };
 
  };
}