Method extractIsotopicIntensities

src/topp/MetaProSIP.cpp:2333–2380

collects intensities starting at seed_mz/_rt, if no peak is found at the expected position a 0 is added

  // collects intensities starting at seed_mz/_rt, if no peak is found at the expected position a 0 is added
  vector<double> extractIsotopicIntensities(Size element_count, double mass_diff, double mz_tolerance_ppm,
                                            double seed_rt, double seed_mz, double seed_charge,
                                            const PeakMap& peak_map)
  {
    vector<double> isotopic_intensities;
    for (Size k = 0; k != element_count; ++k)
    {
      double min_rt = seed_rt - 0.01; // feature rt
      double max_rt = seed_rt + 0.01;
      double mz = seed_mz + k * mass_diff / seed_charge;

      double min_mz;
      double max_mz;

      if (k <= 5)
      {
        double ppm = std::max(10.0, mz_tolerance_ppm); // restrict ppm to 10 for low intensity peaks
        min_mz = mz - mz * ppm * 1e-6;
        max_mz = mz + mz * ppm * 1e-6;
      }
      else
      {
        min_mz = mz - mz * mz_tolerance_ppm * 1e-6;
        max_mz = mz + mz * mz_tolerance_ppm * 1e-6;
      }

      double found_peak_int = 0;

      PeakMap::ConstAreaIterator aait = peak_map.areaBeginConst(min_rt, max_rt, min_mz, max_mz);

      // find 13C/15N peak in window around theoretical predicted position
      vector<double> found_peaks;
      for (; aait != peak_map.areaEndConst(); ++aait)
      {
        double peak_int = aait->getIntensity();
        if (peak_int > 1) // we found a valid 13C/15N peak
        {
          found_peaks.push_back(peak_int);
        }
      }

      found_peak_int = std::accumulate(found_peaks.begin(), found_peaks.end(), 0.0);

      // assign peak intensity to first peak in small area around theoretical predicted position (should be usually only be 1)
      isotopic_intensities.push_back(found_peak_int);
    }
    return isotopic_intensities;
  }

  void writePeakIntensities_(SVOutStream& out_stream, vector<double> isotopic_intensities, bool write_13Cpeaks)
  {