Method writeTo

src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp:358–942

    }

    void MzIdentMLHandler::writeTo(std::ostream& os)
    {
      String cv_ns = cv_.name();
      String inputs_element;
      std::map<String,String> /* peps, pepevis, */ sil_map, sil_2_date;
      std::set<String> sen_set, sof_set, sip_set;
      std::map<String, String> sdb_ids, sen_ids, sof_ids, sdat_ids, pep_ids;
      //std::map<String, String> pep_pairs_ppxl;
      std::map<String, double> pp_identifier_2_thresh;
      //std::vector< std::pair<String, String> > pepid_pairs_ppxl;

      // file type-specific definitions needed for SpectraData element:
      std::map<FileTypes::Type, std::pair<String, String> > formats_map;
      formats_map[FileTypes::MZML] = make_pair("mzML format", "mzML unique identifier");
      formats_map[FileTypes::MZXML] = make_pair("ISB mzXML format", "scan number only nativeID format");
      formats_map[FileTypes::MZDATA] = make_pair("PSI mzData format", "spectrum identifier nativeID format");
      formats_map[FileTypes::MGF] = make_pair("Mascot MGF format", "multiple peak list nativeID format");


      //TODO if constructed with a msexperiment - not yet implemented
      //~ if(ms_exp_ == 0)
      //~ {
      //~ synthesize spectrum references
      //~ }
      //~ else
      //~ {
      //~ extract peptide and proteinid from msexperiment
      //~ genereate spectrum references from msexperiment foreach peptideidentification
      //~ }

      /*---------------------------------------------------------------------
      DataCollection:
      +Inputs
      -AnalysisData collected in sidlist --> unclosed element string
      ---------------------------------------------------------------------*/
      inputs_element += String("\t<Inputs>\n");
      String spectra_data, search_database;

      /*
      1st: iterate over proteinidentification vector
      */
      //TODO read type of crosslink reagent from settings
      bool is_ppxl = false;
      for (std::vector<ProteinIdentification>::const_iterator it = cpro_id_->begin(); it != cpro_id_->end(); ++it)
      {
        //~ collect analysissoftware in this loop - does not go into inputelement
        String sof_id;
        String sof_name = String(it->getSearchEngine());
        std::map<String, String>::iterator soit = sof_ids.find(sof_name);
        String osecv;
        if (sof_name == "OMSSA")
        {
          osecv = "OMSSA";
        }
        else if (sof_name == "Mascot")
        {
          osecv = "Mascot";
        }