Method writeTopFD

src/openms/source/FORMAT/FLASHDeconvSpectrumFile.cpp:301–377

  }

  void FLASHDeconvSpectrumFile::writeTopFD(DeconvolvedSpectrum& dspec, std::fstream& fs, const double snr_threshold, const uint min_ms_level, const bool randomize_precursor_mass,
                                           const bool randomize_fragment_mass)
  {
    UInt ms_level = dspec.getOriginalSpectrum().getMSLevel();
    if (ms_level > min_ms_level)
    {
      if (dspec.getPrecursorPeakGroup().empty() || dspec.getPrecursorPeakGroup().getChargeSNR(dspec.getPrecursor().getCharge()) < snr_threshold)
      {
        return;
      }
    }

    if (dspec.size() < topFD_min_peak_count_)
    {
      return;
    }

    fs << std::fixed << std::setprecision(2);
    fs << "BEGIN IONS\n"
       << "ID=" << dspec.getScanNumber() << "\n"
       << "FRACTION_ID=" << 0 << "\n"
       << "SCANS=" << dspec.getScanNumber() << "\n"
       << "RETENTION_TIME=" << dspec.getOriginalSpectrum().getRT() << "\n"
       << "LEVEL=" << dspec.getOriginalSpectrum().getMSLevel() << "\n";


    if (ms_level > 1)
    {
      double precursor_mass = dspec.getPrecursorPeakGroup().getMonoMass();
      if (dspec.getActivationMethod() < Precursor::ActivationMethod::SIZE_OF_ACTIVATIONMETHOD)
      {
        fs << "ACTIVATION=" << Precursor::NamesOfActivationMethodShort[dspec.getActivationMethod()] << "\n";
      }
      fs << "MS_ONE_ID=" << dspec.getPrecursorScanNumber() << "\n"
         << "MS_ONE_SCAN=" << dspec.getPrecursorScanNumber() << "\n"
         << "PRECURSOR_MZ=" << std::to_string(dspec.getPrecursor().getMZ()) << "\n"
         << "PRECURSOR_CHARGE=" << (int)(dspec.getPrecursor().getCharge()) << "\n"
         << "PRECURSOR_MASS=" << std::to_string(precursor_mass + (randomize_precursor_mass ? (((double)rand() / (RAND_MAX)) * 200.0 - 100.0) : .0)) << "\n" // random number between 0 to 100.
         << "PRECURSOR_INTENSITY=" << dspec.getPrecursor().getIntensity() << "\n";
    }

    fs << std::setprecision(-1);

    double qscore_threshold = 0;
    std::vector<double> qscores;

    if (dspec.size() > topFD_max_peak_count_) // max peak count for TopPic = 500
    {
      qscores.reserve(dspec.size());
      for (auto& pg : dspec)
      {
        qscores.push_back(pg.getQscore());
      }
      std::sort(qscores.begin(), qscores.end());
      qscore_threshold = qscores[qscores.size() - topFD_max_peak_count_];
      std::vector<double>().swap(qscores);
    }