Function write_out_body_

src/topp/OpenSwathFeatureXMLToTSV.cpp:112–278

}

void write_out_body_(std::ostream &os, Feature *feature_it, TargetedExperiment &transition_exp,
                     std::vector<String> &meta_value_names, int run_id, bool short_format, String identifier, String filename)
{

  String peptide_ref = feature_it->getMetaValue("PeptideRef");
  String precursor_mz = feature_it->getMetaValue("PrecursorMZ");

  String sequence;
  String full_peptide_name = "NA";
  String protein_name = "NA";
  String decoy = "NA";
  String charge = "NA";

  if (!transition_exp.hasPeptide(peptide_ref))
  {
    throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                     "Did not find the peptide " + peptide_ref + " in the targeted experiment.");
  }

  const OpenMS::TargetedExperiment::Peptide &pep = transition_exp.getPeptideByRef(peptide_ref);

  sequence = pep.sequence;
  if (!pep.protein_refs.empty())
  {
    // For now just take the first one, assuming the protein name is the id
    protein_name = pep.protein_refs[0];
  }

  // handle charge
  if (pep.hasCVTerm("MS:1000041"))
  {
    charge = pep.getCVTerms().at("MS:1000041")[0].getValue().toString();
  }
  else if (pep.hasCharge())
  {
    charge = (String)pep.getChargeState();
  }
  if (charge == "NA" && !full_peptide_name.empty())
  {
    // deal with FullPeptideNames like PEPTIDE/2
    std::vector<String> substrings;
    full_peptide_name.split("/", substrings);
    if (substrings.size() == 2)
    {
      charge = substrings[1];
    }
  }

  // handle decoy tag
  if (peptide_transition_map.find(peptide_ref) != peptide_transition_map.end() && !peptide_transition_map[peptide_ref].empty())
  {
    const ReactionMonitoringTransition *transition = peptide_transition_map[peptide_ref][0];
#if 1
    const auto& terms = transition->getCVTerms();
    if (terms.find("decoy") != terms.end())
    {
      decoy = transition->getCVTerms().at("decoy")[0].getValue().toString();
    }