Method countScansInSwath_

src/openms/source/FORMAT/SwathFile.cpp:308–385

Counts the number of scans in a full Swath file (e.g. concatenated non-split file)

  }
  /// Counts the number of scans in a full Swath file (e.g. concatenated non-split file)
  void SwathFile::countScansInSwath_(const std::vector<MSSpectrum>& exp,
                                     std::vector<int>& swath_counter, int& nr_ms1_spectra,
                                     std::vector<OpenSwath::SwathMap>& known_window_boundaries)
  {
    int ms1_counter = 0;
    for (Size i = 0; i < exp.size(); i++)
    {
      const MSSpectrum& s = exp[i];
      {
        if (s.getMSLevel() == 1)
        {
          ms1_counter++;
        }
        else
        {
          if (s.getPrecursors().empty())
          {
            throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
              "Found SWATH scan (MS level 2 scan) without a precursor. Cannot determine SWATH window.");
          }
          const std::vector<Precursor> prec = s.getPrecursors();
          double center = prec[0].getMZ();


          // check if ion mobility is present
          double lowerIm = -1;
          double upperIm = -1; // these initial values assume ion mobility is not present

          if (s.metaValueExists("ion mobility lower limit"))
          {
            lowerIm = s.getMetaValue("ion mobility lower limit"); // want this to be -1  if no ion mobility
            upperIm = s.getMetaValue("ion mobility upper limit");

          }

          bool found = false;

          for (Size j = 0; j < known_window_boundaries.size(); j++)
          {
            // We group by the precursor mz (center of the window) since this
            // should be present
            // for ion mobility, since the center value is not present in the raw data (it is computed) we use the imLower and upper bounds
            if ((std::fabs(center - known_window_boundaries[j].center) < 1e-6) && (std::fabs(lowerIm - known_window_boundaries[j].imLower) < 1e-6) && (std::fabs(upperIm - known_window_boundaries[j].imUpper < 1e-6)))
            {
              found = true;
              swath_counter[j]++;
            }
          }
          if (!found)
          {
            // we found a new SWATH scan
            swath_counter.push_back(1);
            double lower = prec[0].getMZ() - prec[0].getIsolationWindowLowerOffset();
            double upper = prec[0].getMZ() + prec[0].getIsolationWindowUpperOffset();

            OpenSwath::SwathMap boundary;
            boundary.lower = lower;
            boundary.upper = upper;