Method writeTo

src/openms/source/FORMAT/HANDLERS/FeatureXMLHandler.cpp:69–223

  }

  void FeatureXMLHandler::writeTo(std::ostream& os)
  {
    const FeatureMap& feature_map = *(cmap_);

    os << "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n"
       << "<featureMap version=\"" << version_ << "\"";
    // file id
    if (!feature_map.getIdentifier().empty())
    {
      os << " document_id=\"" << feature_map.getIdentifier() << "\"";
    }
    // unique id
    if (feature_map.hasValidUniqueId())
    {
      os << " id=\"fm_" << feature_map.getUniqueId() << "\"";
    }
    os << " xsi:noNamespaceSchemaLocation=\"https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/FeatureXML_1_9.xsd\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n";

    // user param
    writeUserParam_("UserParam", os, feature_map, 1);

    // write data processing
    for (Size i = 0; i < feature_map.getDataProcessing().size(); ++i)
    {
      const DataProcessing& processing = feature_map.getDataProcessing()[i];
      os << "\t<dataProcessing completion_time=\"" << processing.getCompletionTime().getDate() << 'T' << processing.getCompletionTime().getTime() << "\">\n";
      os << "\t\t<software name=\"" << processing.getSoftware().getName() << "\" version=\"" << processing.getSoftware().getVersion() << "\" />\n";
      for (set<DataProcessing::ProcessingAction>::const_iterator it = processing.getProcessingActions().begin(); it != processing.getProcessingActions().end(); ++it)
      {
        os << "\t\t<processingAction name=\"" << DataProcessing::NamesOfProcessingAction[*it] << "\" />\n";
      }
      writeUserParam_("UserParam", os, processing, 2);
      os << "\t</dataProcessing>\n";
    }

    // throws if protIDs are not unique, i.e. PeptideIDs will be randomly assigned (bad!)
    checkUniqueIdentifiers_(feature_map.getProteinIdentifications());

    // write identification runs
    Size prot_count = 0;
    for (Size i = 0; i < feature_map.getProteinIdentifications().size(); ++i)
    {
      const ProteinIdentification& current_prot_id = feature_map.getProteinIdentifications()[i];
      os << "\t<IdentificationRun ";
      os << "id=\"PI_" << i << "\" ";
      identifier_id_[current_prot_id.getIdentifier()] = String("PI_") + i;
      os << "date=\"" << current_prot_id.getDateTime().getDate() << "T" << current_prot_id.getDateTime().getTime() << "\" ";
      os << "search_engine=\"" << writeXMLEscape(current_prot_id.getSearchEngine()) << "\" ";
      os << "search_engine_version=\"" << writeXMLEscape(current_prot_id.getSearchEngineVersion()) << "\">\n";

      //write search parameters
      const ProteinIdentification::SearchParameters& search_param = current_prot_id.getSearchParameters();
      os << "\t\t<SearchParameters "
         << "db=\"" << writeXMLEscape(search_param.db) << "\" "
         << "db_version=\"" << writeXMLEscape(search_param.db_version) << "\" "
         << "taxonomy=\"" << writeXMLEscape(search_param.taxonomy) << "\" ";
      if (search_param.mass_type == ProteinIdentification::MONOISOTOPIC)
      {