Method peptideSectionRowFromConsensusFeature_

src/openms/source/FORMAT/MzTab.cpp:864–1120

  }

  MzTabPeptideSectionRow MzTab::peptideSectionRowFromConsensusFeature_(
    const ConsensusFeature& c, 
    const ConsensusMap& consensus_map,
    const StringList& ms_runs,
    const Size n_study_variables,
    const set<String>& consensus_feature_user_value_keys,
    const set<String>& peptide_identifications_user_value_keys,
    const set<String>& peptide_hit_user_value_keys,
    const map<String, size_t>& idrun_2_run_index,
    const map<pair<size_t,size_t>,size_t>& map_run_fileidx_2_msfileidx,
    const std::map< std::pair< String, unsigned >, unsigned>& path_label_to_assay,
    const vector<String>& fixed_mods,
    bool export_subfeatures)
  {
    MzTabPeptideSectionRow row;

    const ConsensusMap::ColumnHeaders& cm_column_headers = consensus_map.getColumnHeaders();
    const String & experiment_type = consensus_map.getExperimentType();
    const vector<ProteinIdentification>& prot_id = consensus_map.getProteinIdentifications();

    // create opt_ column for peptide sequence containing modification
    MzTabOptionalColumnEntry opt_global_modified_sequence;
    opt_global_modified_sequence.first = "opt_global_cv_MS:1000889_peptidoform_sequence";
    row.opt_.push_back(opt_global_modified_sequence);

    // Defines how to consume user value keys for the upcoming keys
    const auto addUserValueToRowBy = [&row](const function<void(const String &s, MzTabOptionalColumnEntry &entry)>& f) -> function<void(const String &key)>
    {
      return [f,&row](const String &user_value_key)
        {
          MzTabOptionalColumnEntry opt_entry;
          opt_entry.first = "opt_global_" + user_value_key;
          f(user_value_key, opt_entry);

          // Use default column_header for target decoy
          row.opt_.push_back(opt_entry);
        };
    };

    // create opt_ columns for consensus map user values
    for_each(consensus_feature_user_value_keys.begin(), consensus_feature_user_value_keys.end(),
      addUserValueToRowBy([&c](const String &key, MzTabOptionalColumnEntry &opt_entry)
        {
          if (c.metaValueExists(key))
          {
            opt_entry.second = MzTabString(c.getMetaValue(key).toString());
          }
        })
      );

    // add optional columns for first peptide identification in consensus feature
    for_each(peptide_identifications_user_value_keys.begin(), peptide_identifications_user_value_keys.end(),
      addUserValueToRowBy([&c](const String &key, MzTabOptionalColumnEntry &opt_entry)
        {
          opt_entry.second = MzTabString(c.getMetaValue(key).toString());
        })
      );