Method store

src/openms/source/FORMAT/MSPFile.cpp:346–475

TODO adapt store to write new? format

  //TODO adapt store to write new? format
  void MSPFile::store(const String & filename, const PeakMap & exp) const
  {
    if (!FileHandler::hasValidExtension(filename, FileTypes::MSP))
    {
      throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
          filename, "invalid file extension, expected '" + FileTypes::typeToName(FileTypes::MSP) + "'");
    }

    if (!File::writable(filename))
    {
      throw Exception::FileNotWritable(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
    }

    ofstream out(filename.c_str());

    for (const MSSpectrum& it : exp)
    {
      if (!it.getPeptideIdentifications().empty() && !it.getPeptideIdentifications().begin()->getHits().empty())
      {
        PeptideHit hit = *it.getPeptideIdentifications().begin()->getHits().begin();
        String peptide;
        for (const Residue& pit : hit.getSequence())
        {
          if (pit.isModified() && pit.getOneLetterCode() == "M" &&
              fabs(pit.getModification()->getDiffFormula().getMonoWeight() - 16.0) < 0.01)
          {
            peptide += "M(O)"; // TODO why are we writing specifically only oxidations?
          }
          else
          {
            peptide += pit.getOneLetterCode();
          }
        }
        out << "Name: " << peptide << "/" << hit.getCharge() << "\n";
        out << "MW: " << hit.getSequence().getMonoWeight() << "\n";
        out << "Comment:";

        // modifications
        // e.g. 2/9,C,Carbamidomethyl/12,C,Carbamidomethyl
        Size num_mods(0);
        vector<String> modifications;
        if (hit.getSequence().hasNTerminalModification())
        {
          String mod = hit.getSequence().getNTerminalModificationName();
          ++num_mods;
          String modification = "0," + hit.getSequence().begin()->getOneLetterCode() + "," + mod;
          modifications.push_back(modification);
        }

        // @improvement improve writing support (Andreas)
        UInt pos(0);
        for (AASequence::ConstIterator pit = hit.getSequence().begin(); pit != hit.getSequence().end(); ++pit, ++pos)
        {
          if (!pit->isModified())
          {
            continue;
          }