Method main_

src/topp/SpecLibSearcher.cpp:246–589

  }

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    StringList in_spec = getStringList_("in");
    StringList out = getStringList_("out");
    String in_lib = getStringOption_("lib");
    String compare_function = getStringOption_("compare_function");
 
    float precursor_mass_tolerance = getDoubleOption_("precursor:mass_tolerance");
    bool precursor_mass_tolerance_unit_ppm = getStringOption_("precursor:mass_tolerance_unit") == "ppm" ? true : false;

    int pc_min_charge = getIntOption_("precursor:min_charge");
    int pc_max_charge = getIntOption_("precursor:max_charge");

    // consider one before annotated monoisotopic peak and the annotated one
    IntList isotopes = getIntList_("precursor:isotopes");
   
//    float fragment_mass_tolerance = getDoubleOption_("fragment:mass_tolerance");
//    bool fragment_mass_tolerance_unit_ppm = getStringOption_("fragment:mass_tolerance_unit") == "ppm" ? true : false;

    int top_hits = getIntOption_("report:top_hits");

    float remove_peaks_below_threshold = getDoubleOption_("filter:remove_peaks_below_threshold");
    UInt min_peaks = getIntOption_("filter:min_peaks");
    UInt max_peaks = getIntOption_("filter:max_peaks");
    Int cut_peaks_below = getIntOption_("filter:cut_peaks_below");

    StringList fixed_modifications = getStringList_("modifications:fixed");
    StringList variable_modifications = getStringList_("modifications:variable");

    if (top_hits < -1)
    {
      writeLogError_("top_hits (should be  >= -1 )");
      return ILLEGAL_PARAMETERS;
    }

    // -------------------------------------------------------------
    // loading input
    // -------------------------------------------------------------
    if (out.size() != in_spec.size())
    {
      writeLogError_("out (should be as many as input files)");
      return ILLEGAL_PARAMETERS;
    }

    time_t prog_time = time(nullptr);
    MSPFile spectral_library;
    PeakMap query, library;

    // spectra which will be identified
    MzMLFile spectra;
    spectra.setLogType(log_type_);

    time_t start_build_time = time(nullptr);
    // -------------------------------------------------------------
    // building map for faster search