Method generateInputfileMapping_

src/topp/MSGFPlusAdapter.cpp:299–328

Parse mzML and create RTMapping get RT: it doesn't exist in output from MS-GF+ get m/z: it is rounded after converting to TSV

  // get RT: it doesn't exist in output from MS-GF+
  // get m/z: it is rounded after converting to TSV
  void generateInputfileMapping_(map<String, vector<float> >& rt_mapping)
  {
    String exp_name = getStringOption_("in");

    if (!exp_name.empty())
    {
      PeakMap exp;
      // load only MS2 spectra:
      MzMLFile f;
      f.getOptions().addMSLevel(2);
      f.getOptions().setFillData(false);
      f.load(exp_name, exp);
      exp.getPrimaryMSRunPath(primary_ms_run_path_);
      // if no primary run is assigned, the mzML file is the (unprocessed) primary file
      if (primary_ms_run_path_.empty())
      {
        primary_ms_run_path_.push_back(exp_name);
      }

      for (MSSpectrum& ms : exp)
      {
        String id = ms.getNativeID(); // expected format: "... scan=#"
        if (!id.empty())
        {
          rt_mapping[id].push_back(ms.getRT());
          rt_mapping[id].push_back(ms.getPrecursors()[0].getMZ());
        }
      }
    }
  }

  String makeModString_(const String& mod_name, bool fixed=true)
  {