Method writeComments_

src/topp/ProteinQuantifier.cpp:564–645

Write comment lines before a peptide/protein table.

  /// Write comment lines before a peptide/protein table.
  void writeComments_(SVOutStream& out, const ExperimentalDesign& ed, const bool proteins = true)
  {
    String what = (proteins ? "Protein" : "Peptide");
    bool old = out.modifyStrings(false);
    bool is_ibaq = algo_params_.getValue("method") == "iBAQ";
    out << "# " + what + " abundances computed from file '" +
      getStringOption_("in") + "'" << endl;
    StringList relevant_params;
    if (proteins) // parameters relevant only for protein output
    {
      relevant_params.push_back("method");
      if (!is_ibaq)
      {
        relevant_params.push_back("top:N");
        Size top = algo_params_.getValue("top:N");
        if (top != 1)
        {
          relevant_params.push_back("top:aggregate");
          if (top != 0)
          {
            relevant_params.push_back("top:include_all");
          }
        }
      }
    }
    relevant_params.push_back("best_charge_and_fraction"); // also for peptide output

    if (ed.getNumberOfSamples() > 1) // flags only for consensusXML input
    {
      relevant_params.push_back("consensus:normalize");
      if (proteins)
      {
        relevant_params.push_back("consensus:fix_peptides");
      }
    }

    String params;
    for (const String& str : relevant_params)
    {
      String value = algo_params_.getValue(str).toString();
      if (value != "false")
      {
        params += str + "=" + value + ", ";
      }
    }
    if (params.empty())
    {
      params = "(none)";
    }
    else
    {
      params.resize(params.size() - 2); // remove trailing ", "
    }
    out << "# Parameters (relevant only): " + params << endl;

    if (ed.getNumberOfSamples() > 1 && ed.getNumberOfLabels() == 1)
    {
      String desc = "# Files/samples associated with abundance values below: ";