Method parseString_

src/openms/source/CHEMISTRY/NASequence.cpp:355–412

  }

  void NASequence::parseString_(const String& s, NASequence& nas)
  {
    nas.clear();

    if (s.empty())
      return;

    static RibonucleotideDB* rdb = RibonucleotideDB::getInstance();

    String::ConstIterator str_it = s.begin();
    if (*str_it == 'p') // special case for 5' phosphate
    {
      nas.setFivePrimeMod(rdb->getRibonucleotide("5'-p"));
      ++str_it;
    }
    else if (*str_it == '*') // special case for 5' phosphorothioate
    {
      nas.setFivePrimeMod(rdb->getRibonucleotide("5'-p*"));
      ++str_it;
    }
    String::ConstIterator stop = s.end();
    if ((s.size() > 1) && (s.back() == 'p')) // special case for 3' phosphate
    {
      nas.setThreePrimeMod(rdb->getRibonucleotide("3'-p"));
      --stop;
    }
    else if ((s.size() > 1) && (s.back() == 'c')) // special case for 3' cyclo-phosphate
    {
      nas.setThreePrimeMod(rdb->getRibonucleotide("3'-c"));
      --stop;
    }
    for (; str_it != stop; ++str_it)
    {
      // skip spaces
      if (*str_it == ' ')
        continue;

      // default case: add unmodified, standard ribonucleotide
      if (*str_it != '[')
      {
        try
        {
          ConstRibonucleotidePtr r = rdb->getRibonucleotide(string(1, *str_it));
          nas.seq_.push_back(r);
        }
        catch (Exception::ElementNotFound&)
        {
          String msg = "Cannot convert string to nucleic acid sequence: invalid character '" + String(*str_it) + "'";
          throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, s, msg);
        }
      }
      else // if (*str_it == '[') // non-standard ribonucleotide
      {
        // parse modified ribonucleotide and add it to the sequence:
        str_it = parseMod_(str_it, s, nas);
      }
    }
  }