Method run

src/openms/source/ANALYSIS/XLMS/OpenPepXLLFAlgorithm.cpp:160–969

  }

  OpenPepXLLFAlgorithm::ExitCodes OpenPepXLLFAlgorithm::run(PeakMap& unprocessed_spectra, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra)
  {
    ProgressLogger progresslogger;
    progresslogger.setLogType(this->getLogType());

    // preprocess parameters for convenience
    if (fragment_mass_tolerance_xlinks_ < fragment_mass_tolerance_)
    {
      fragment_mass_tolerance_xlinks_ = fragment_mass_tolerance_;
    }
    std::sort(cross_link_mass_mono_link_.begin(), cross_link_mass_mono_link_.end(), std::greater< double >());
    set<String> fixed_unique(fixedModNames_.begin(), fixedModNames_.end());

    // deisotope if "true" or if "auto" and the tolerance is below the threshold (0.1 Da or 100 ppm)
    bool deisotope = (deisotope_mode_ == "true") ||
                      (deisotope_mode_ == "auto" &&
                      ((!fragment_mass_tolerance_unit_ppm_ && fragment_mass_tolerance_ < 0.1) ||
                      (fragment_mass_tolerance_unit_ppm_ && fragment_mass_tolerance_ < 100)));

    if (fixed_unique.size() != fixedModNames_.size())
    {
      OPENMS_LOG_WARN << "duplicate fixed modification provided." << endl;
      return ExitCodes::ILLEGAL_PARAMETERS;
    }

    set<String> var_unique(varModNames_.begin(), varModNames_.end());
    if (var_unique.size() != varModNames_.size())
    {
      OPENMS_LOG_WARN << "duplicate variable modification provided." << endl;
      return ExitCodes::ILLEGAL_PARAMETERS;
    }
    ModifiedPeptideGenerator::MapToResidueType fixed_modifications = ModifiedPeptideGenerator::getModifications(fixedModNames_);
    ModifiedPeptideGenerator::MapToResidueType variable_modifications = ModifiedPeptideGenerator::getModifications(varModNames_);

    protein_ids[0].setPrimaryMSRunPath({}, unprocessed_spectra);

    if (unprocessed_spectra.empty() && unprocessed_spectra.getChromatograms().empty())
    {
      OPENMS_LOG_WARN << "The given file does not contain any conventional peak data, but might"
                  " contain chromatograms. This tool currently cannot handle them, sorry." << endl;
      return INCOMPATIBLE_INPUT_DATA;
    }

    //check if spectra are sorted
    for (Size i = 0; i < unprocessed_spectra.size(); ++i)
    {
      if (!unprocessed_spectra[i].isSorted())
      {
        OPENMS_LOG_WARN << "Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!" << endl;
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    // Peak Picking, check if all levels are picked and pick uncentroided MS levels
    PeakPickerHiRes pp;
    PeakMap picked_spectra;
    progresslogger.startProgress(0, 1, "Centroiding data (if necessary)...");
    pp.pickExperiment(unprocessed_spectra, picked_spectra, true);