Method writeProteinTable_

src/topp/ProteinQuantifier.cpp:443–560

Write a table of protein results.

  /// Write a table of protein results.
  void writeProteinTable_(SVOutStream& out, const ProteinQuant& quant, const ExperimentalDesign& ed)
  {
    const bool print_ratios = getFlag_("ratios");
    const bool print_SILACratios = getFlag_("ratiosSILAC");
    // write header:
    out << "protein" << "n_proteins" << "protein_score" << "n_peptides";
    if (ed.getNumberOfSamples() <= 1)
    {
      out << "abundance";
    }
    else
    {
      for (Size i = 0; i < ed.getNumberOfSamples(); ++i)
      {
        out << "abundance_" + String(i+1);
      }

      // TODO MULTIPLEXING: check if correct
      // if ratios-flag is set, print log2-ratios. ratio_1 <sep> ratio_x ....
      if (print_ratios)
      {
        for (Size i = 0; i < ed.getNumberOfSamples(); ++i)
        {
          out << "ratio_" + String(i+1);
        }
      }
      // if ratiosSILAC-flag is set, print SILAC log2-ratios, only if three
      if (print_SILACratios && ed.getNumberOfSamples() == 3)
      {
        for (Size i = 0; i < ed.getNumberOfSamples(); ++i)
        {
          out << "SILACratio_" + String(i+1);
        }
      }
    }

    out << endl;

    // mapping: accession of leader -> (accessions of grouped proteins, score)
    map<String, pair<StringList, double> > leader_to_group;
    if (!proteins_.getIndistinguishableProteins().empty())
    {
      for (auto group : proteins_.getIndistinguishableProteins()) //OMS_CODING_TEST_EXCLUDE
      {
        StringList& accessions = leader_to_group[group.accessions[0]].first;
        accessions = group.accessions;
        for (auto & acc : accessions)
        {
          acc.substitute('/', '_'); // to allow concatenation later
        }
        leader_to_group[group.accessions[0]].second = group.probability;
      }
    }

    for (auto const & q : quant)
    {
      if (q.second.total_abundances.empty())
      {