Method readFromOBOFile

src/openms/source/CHEMISTRY/ModificationsDB.cpp:554–854

  }

  void ModificationsDB::readFromOBOFile(const String& filename)
  {
    ResidueModification mod;
    // add multiple mods for multiple specificities
    //Map<String, ResidueModification> all_mods;
    multimap<String, ResidueModification> all_mods;

    ifstream is(File::find(filename).c_str());
    String line, line_wo_spaces, id;
    String origin = "";

    bool reading_cross_link = false;

    //parse file
    while (getline(is, line, '\n'))
    {
      line.trim();
      line_wo_spaces = line;
      line_wo_spaces.removeWhitespaces();

      if (line.empty() || line[0] == '!') //skip empty lines and comments
      {
        continue;
      }

      if (line_wo_spaces == "[Term]")       //new term
      {
        // if the last [Term] was a moon-link, then it does not belong in CrossLinksDB
        if (!id.empty() && !reading_cross_link) //store last term
        {
          // split into single residues and make unique (for XL-MS, where equal specificities for both sides are possible)
          vector<String> origins;
          origin.split(",", origins);

          std::sort(origins.begin(), origins.end());
          vector<String>::iterator unique_end = unique(origins.begin(), origins.end());
          origins.resize(distance(origins.begin(), unique_end));

          for (vector<String>::iterator orig_it = origins.begin(); orig_it != origins.end(); ++orig_it)
          {
            // we don't allow modifications with ambiguity codes as origin (except "X"):
            if ((orig_it->size() == 1) && (*orig_it != "B") && (*orig_it != "J") && (*orig_it != "Z"))
            {
              mod.setOrigin((*orig_it)[0]);
              all_mods.insert(make_pair(id, mod));
            }
          }

          // for mono-links from XLMOD.obo:
          if (origin.hasSubstring("ProteinN-term"))
          {
            mod.setTermSpecificity(ResidueModification::PROTEIN_N_TERM);
            mod.setOrigin('X');
            all_mods.insert(make_pair(id, mod));
          }
          if (origin.hasSubstring("ProteinC-term"))
          {
            mod.setTermSpecificity(ResidueModification::PROTEIN_C_TERM);