Method findFeatures

src/openms/source/ANALYSIS/TOPDOWN/MassFeatureTrace.cpp:36–169

  }

  std::vector<FLASHDeconvHelperStructs::MassFeature> MassFeatureTrace::findFeatures(const PrecalculatedAveragine& averagine)
  {
    MSExperiment map;
    std::map<int, MSSpectrum> index_spec_map;
    int min_abs_charge = INT_MAX;
    int max_abs_charge = INT_MIN;
    bool is_positive = true;
    std::vector<FLASHDeconvHelperStructs::MassFeature> mass_features;
    for (auto& item : peak_group_map_)
    {
      double rt = item.first;
      MSSpectrum deconv_spec;
      deconv_spec.setRT(rt);
      for (auto& pg : item.second)
      {
        is_positive = pg.second.isPositive();
        auto [z1, z2] = pg.second.getAbsChargeRange();
        max_abs_charge = max_abs_charge > z2 ? max_abs_charge : z2;
        min_abs_charge = min_abs_charge < z1 ? min_abs_charge : z1;

        Peak1D tp(pg.first, (float)pg.second.getIntensity());
        deconv_spec.push_back(tp);
      }
      map.addSpectrum(deconv_spec);
    }

    // when map size is less than 3, MassTraceDetection aborts - too few spectra for mass tracing.
    if (map.size() < 3)
    {
      return mass_features;
    }

    MassTraceDetection mtdet;
    Param mtd_param = getParameters().copy("");
    mtd_param.remove("min_isotope_cosine");

    mtdet.setParameters(mtd_param);
    std::vector<MassTrace> m_traces;

    mtdet.run(map, m_traces); // m_traces : output of this function
    int charge_range = max_abs_charge - min_abs_charge + 1;

    for (auto& mt : m_traces)
    {
      double max_qscore = .0;
      int min_feature_abs_charge = INT_MAX; // min feature charge
      int max_feature_abs_charge = INT_MIN; // max feature charge

      auto per_isotope_intensity = std::vector<float>(averagine.getMaxIsotopeIndex(), .0f);
      auto per_charge_intensity = std::vector<float>(charge_range + min_abs_charge + 1, .0f);

      double mass = mt.getCentroidMZ();
      double max_iso = 0;
      int max_iso_off = 0;
      boost::dynamic_bitset<> charges(charge_range + 1);
      std::vector<PeakGroup> pgs;
      pgs.reserve(mt.getSize());