Method writeTo

src/openms/source/FORMAT/HANDLERS/XQuestResultXMLHandler.cpp:878–1230

    }

    void XQuestResultXMLHandler::writeTo(std::ostream& os)
    {
      ProteinIdentification::SearchParameters search_params;
      search_params = (*this->cpro_id_)[0].getSearchParameters();

      String input_filename;
      if (search_params.metaValueExists("input_mzML"))
      {
        input_filename = search_params.getMetaValue("input_mzML");
      }
      String spec_xml_name = search_params.getMetaValue("out_xquest_specxml");

      os << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
      os << "<?xml-stylesheet type=\"text/xsl\" href=\"\"?>\n";

      DateTime time= DateTime::now();
      String timestring = time.getDate() + " " + time.getTime();

      String mono_masses = search_params.getMetaValue("cross_link:mass_monolink");
      mono_masses = mono_masses.substr(1).chop(1);

      String precursor_mass_tolerance_unit = search_params.precursor_mass_tolerance_ppm ? "ppm" : "Da";
      double precursor_mass_tolerance = search_params.precursor_mass_tolerance;
      String fragment_mass_tolerance_unit = search_params.fragment_mass_tolerance_ppm ? "ppm" : "Da";
      double fragment_mass_tolerance = search_params.fragment_mass_tolerance;
      double fragment_mass_tolerance_xlinks = search_params.getMetaValue("fragment:mass_tolerance_xlinks");

      String cross_link_name = search_params.getMetaValue("cross_link:name");
      double cross_link_mass_light = search_params.getMetaValue("cross_link:mass");
      double cross_link_mass_iso_shift = 0;
      if (search_params.metaValueExists("cross_link:mass_isoshift"))
      {
        cross_link_mass_iso_shift = search_params.getMetaValue("cross_link:mass_isoshift");
      }
      String aarequired1, aarequired2;
      aarequired1 = search_params.getMetaValue("cross_link:residue1");
      aarequired1 = aarequired1.substr(1).chop(1);
      aarequired2 = search_params.getMetaValue("cross_link:residue2");
      aarequired2 = aarequired2.substr(1).chop(1);
      bool ntermxlinkable = aarequired1.hasSubstring("N-term") || aarequired2.hasSubstring("N-term");

      String in_fasta = search_params.db;
      String in_decoy_fasta = search_params.getMetaValue("input_decoys");
      String enzyme_name = search_params.digestion_enzyme.getName();
      int missed_cleavages = search_params.missed_cleavages;

      StringList variable_mod_list = search_params.variable_modifications;
      String variable_mods;
      for (Size i = 0; i < variable_mod_list.size(); ++i)
      {
        variable_mods += variable_mod_list[i] + ",";
      }
      variable_mods = variable_mods.chop(1);

      StringList fixed_mod_list = search_params.fixed_modifications;
      String fixed_mods;
      for (Size i = 0; i < fixed_mod_list.size(); ++i)
      {