Method store

src/openms/source/FORMAT/MzQCFile.cpp:28–276

namespace OpenMS
{ 
  void MzQCFile::store(const String& input_file,
                       const String& output_file,
                       const MSExperiment& exp,
                       const String& contact_name,
                       const String& contact_address,
                       const String& description,
                       const String& label,
                       const FeatureMap& feature_map,
                       vector<ProteinIdentification>& prot_ids,
                       vector<PeptideIdentification>& pep_ids) const
  {
    // --------------------------------------------------------------------
    // preparing output stream, quality metrics json object, CV, status
    // and initialize QC metric classes
    // --------------------------------------------------------------------
    ofstream os(output_file.c_str());
    if (!os)
    {
      throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, output_file);
    }

    using json = nlohmann::ordered_json;
    json quality_metrics = {};

    ControlledVocabulary cv;
    cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
    cv.loadFromOBO("QC", File::find("/CV/qc-cv.obo"));

    QCBase::Status status;
    if (!input_file.empty())
    {
      status |= QCBase::Requires::RAWMZML;
    }
    if (!feature_map.empty())
    {
      status |= QCBase::Requires::PREFDRFEAT;
    }
    if (!prot_ids.empty() && !pep_ids.empty())
    {
      status |= QCBase::Requires::ID;
    }

    TIC tic;
    SpectrumCount spectrum_count;
    FeatureSummary feature_summary;
    IdentificationSummary identification_summary;

    // ---------------------------------------------------------------
    // function to add quality metrics to quality_metrics
    // ---------------------------------------------------------------
    auto addMetric = [&cv, &quality_metrics](const String& accession, const auto& value) -> void
      {
        json qm;
        qm["accession"] = accession;
        if (cv.exists(accession)) 
        {
          qm["name"] = cv.getTerm(accession).name;
        }