Method add_ionmatches_

src/topp/IDFileConverter.cpp:138–183

private:
  bool add_ionmatches_(vector<PeptideIdentification>& peptide_identifications, String filename, double tolerance)
  {
      TheoreticalSpectrumGenerator tg;
      Param tgp(tg.getDefaults());
      tgp.setValue("add_metainfo", "true");
      tgp.setValue("add_losses", "true");
      tgp.setValue("add_precursor_peaks", "true");
      tgp.setValue("add_abundant_immonium_ions", "true");
      tgp.setValue("add_first_prefix_ion", "true");
      tgp.setValue("add_y_ions", "true");
      tgp.setValue("add_b_ions", "true");
      tgp.setValue("add_a_ions", "true");
      tgp.setValue("add_x_ions", "true");
      tg.setParameters(tgp);

      SpectrumAlignment sa;
      Param sap = sa.getDefaults();
      sap.setValue("tolerance", tolerance, "...");
      sa.setParameters(sap);
      SpectrumAnnotator annot;
      bool ret = true;
      PeakMap expmap;
      SpectrumLookup lookup;
      FileHandler().loadExperiment(filename, expmap);
      lookup.readSpectra(expmap.getSpectra());

#pragma omp parallel for
      for (SignedSize i = 0; i < (SignedSize)peptide_identifications.size(); ++i)
      {
        try
        {
          String ref = peptide_identifications[i].getSpectrumReference();
          Size index = lookup.findByNativeID(ref);
          annot.addIonMatchStatistics(peptide_identifications[i], expmap[index], tg, sa);
        }
        catch (Exception::ElementNotFound&)
        {
#pragma omp critical (IDFileConverter_ERROR)
          {
            OPENMS_LOG_ERROR << "Error: Failed to look up spectrum - none with corresponding native ID found." << endl;
            ret = false;
          }
        }
      }
    return ret;
  }

protected:
  Param getSubsectionDefaults_(const String& /*section*/) const override