Method generateMzTabStringFromModifications

src/openms/source/FORMAT/MzTab.cpp:594–647

  }

  map<Size, MzTabModificationMetaData> MzTab::generateMzTabStringFromModifications(const vector<String>& mods)
  {
    map<Size, MzTabModificationMetaData> mods_mztab;
    Size index(1);
    for (String const & s : mods)
    {
      MzTabModificationMetaData mod;
      MzTabParameter mp;
      ModificationsDB* mod_db = ModificationsDB::getInstance();
      String unimod_accession;
      try
      {
        const ResidueModification* m = mod_db->getModification(s);
        unimod_accession = m->getUniModAccession();
        if (!unimod_accession.empty())
        {
          // MzTab standard is to report Unimod accession.
          mp.setCVLabel("UNIMOD");
          mp.setAccession(unimod_accession.toUpper());
        }
        mp.setName(m->getId());
        mod.modification = mp;

        if (m->getTermSpecificity() == ResidueModification::C_TERM)
        {
          mod.position = MzTabString("Any C-term");
        }
        else if (m->getTermSpecificity() == ResidueModification::N_TERM)
        {
          mod.position = MzTabString("Any N-term");
        }
        else if (m->getTermSpecificity() == ResidueModification::ANYWHERE)
        {
          mod.position = MzTabString("Anywhere");
        }
        else if (m->getTermSpecificity() == ResidueModification::PROTEIN_C_TERM)
        {
          mod.position = MzTabString("Protein C-term");
        }
        else if (m->getTermSpecificity() == ResidueModification::PROTEIN_N_TERM)
        {
          mod.position = MzTabString("Protein N-term");
        }
        mod.site = MzTabString(String(m->getOrigin()));
        mods_mztab[index] = mod;
      }
      catch(...)
      {
        OPENMS_LOG_WARN << "Skipping unknown residue modification: '" + s + "'" << endl; 
      }
      ++index;
    }
    return mods_mztab;
  }

  map<Size, MzTabModificationMetaData> MzTab::generateMzTabStringFromVariableModifications(const vector<String>& mods)
  {