Method setProteinIdentificationSettings_

src/topp/ConsensusID.cpp:335–552

  }

  void setProteinIdentificationSettings_(ProteinIdentification& prot_id,
      vector<tuple<String, String, ProteinIdentification::SearchParameters>>& se_ver_settings,
      vector<tuple<String, String, vector<pair<String, String>>>>& rescore_ver_settings)
  {
    // modification params are necessary for further analysis tools (e.g. LuciPHOr2)
    set<String> fixed_mods_set;
    set<String> var_mods_set;
    set<EnzymaticDigestion::Specificity> specs;
    double prec_tol_ppm = 0.;
    double prec_tol_da = 0.;
    double frag_tol_ppm = 0.;
    double frag_tol_da = 0.;
    int min_chg = 10000;
    int max_chg = -10000;
    Size mc = 0;
    // we sort them to pick the same entries, no matter the order of the inputs
    set<String, std::greater<String>> enzymes;
    set<String, std::greater<String>> dbs;

    // use the first settings as basis (i.e. copy over db and enzyme and tolerance)
    // we assume that they are the same or similar
    ProteinIdentification::SearchParameters new_sp = get<2>(se_ver_settings[0]);

    // first check the rescoring procedure. Should at least be the same tool.
    // "" = IDPosteriorProbability. If parts were not rescored at all, they wont have a PEP annotated,
    // and the tool will fail in the next step (beginning of algorithm)
    // TODO maybe also consolidate/merge those settings. But they are currently only used for reporting.
    const auto& final_rescore_ver_setting = rescore_ver_settings[0];
    const String& final_rescore_algo = get<0>(final_rescore_ver_setting);
    const String& final_rescore_algo_version = get<1>(final_rescore_ver_setting);

    for (const auto& rescore_ver_setting : rescore_ver_settings)
    {
      if (get<0>(rescore_ver_setting) != final_rescore_algo
          || get<1>(rescore_ver_setting) != final_rescore_algo_version)
      {
        OPENMS_LOG_WARN << "Warning: Trying to use ConsensusID on searches with different rescoring algorithms. " +
                           get<0>(rescore_ver_setting) + " vs " + final_rescore_algo;
      }
    }
    if (!final_rescore_algo.empty()) new_sp.setMetaValue(final_rescore_algo, final_rescore_algo_version);
    for (const auto& s : get<2>(final_rescore_ver_setting))
    {
      // the metavalue names in s.first already contain the algorithm name. No need to prepend
      new_sp.setMetaValue(s.first, s.second);
    }

    bool allsamese = true;
    for (const auto& se_ver_setting : se_ver_settings)
    {
      allsamese = allsamese &&
          (get<0>(se_ver_setting) == get<0>(se_ver_settings[0]) &&
           get<1>(se_ver_setting) == get<1>(se_ver_settings[0]));

      const ProteinIdentification::SearchParameters& sp = get<2>(se_ver_setting);
      const String& SE = get<0>(se_ver_setting);
      new_sp.setMetaValue("SE:" + SE, get<1>(se_ver_setting));
      new_sp.setMetaValue(SE+":db",sp.db);