Method parseMod_

src/openms/source/CHEMISTRY/NASequence.cpp:414–444

  }

  String::ConstIterator NASequence::parseMod_(const String::ConstIterator str_it, const String& str, NASequence& nas)
  {
    static RibonucleotideDB* rdb = RibonucleotideDB::getInstance();
    OPENMS_PRECONDITION(*str_it == '[', "Modification must start with '['.");
    String::ConstIterator mod_start(str_it);
    String::ConstIterator mod_end(++mod_start);
    while ((mod_end != str.end()) && (*mod_end != ']'))
    {
      ++mod_end; // advance to closing bracket
    }
    string mod(mod_start, mod_end);
    if (mod_end == str.end())
    {
      throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, str, "Cannot convert string to modified ribonucleotide: missing ']'");
    }
    ConstRibonucleotidePtr r = rdb->getRibonucleotide(mod);
    // @TODO: check if position is actually 5'/3' and there's no mod already
    if (r->getTermSpecificity() == Ribonucleotide::FIVE_PRIME)
    {
      nas.setFivePrimeMod(r);
    }
    else if (r->getTermSpecificity() == Ribonucleotide::THREE_PRIME)
    {
      nas.setThreePrimeMod(r);
    }
    else
    {
      nas.seq_.push_back(r);
    }
    return mod_end;
  }

  OPENMS_DLLAPI ostream& operator<<(ostream& os, const NASequence& seq)
  {