Method registerOptionsAndFlags_

src/topp/SpecLibSearcher.cpp:77–138

protected:
  void registerOptionsAndFlags_() override
  {
    registerInputFileList_("in", "<files>", ListUtils::create<String>(""), "Input files");
    setValidFormats_("in", ListUtils::create<String>("mzML"));
    registerInputFile_("lib", "<file>", "", "searchable spectral library (MSP format)");
    setValidFormats_("lib", ListUtils::create<String>("msp"));
    registerOutputFileList_("out", "<files>", ListUtils::create<String>(""), "Output files. Have to be as many as input files");
    setValidFormats_("out", ListUtils::create<String>("idXML"));

    registerTOPPSubsection_("precursor", "Precursor (Parent Ion) Options");
    registerDoubleOption_("precursor:mass_tolerance", "<tolerance>", 10.0, "Width of precursor mass tolerance window", false);

    StringList precursor_mass_tolerance_unit_valid_strings;
    precursor_mass_tolerance_unit_valid_strings.push_back("ppm");
    precursor_mass_tolerance_unit_valid_strings.push_back("Da");

    registerStringOption_("precursor:mass_tolerance_unit", "<unit>", "ppm", "Unit of precursor mass tolerance.", false, false);
    setValidStrings_("precursor:mass_tolerance_unit", precursor_mass_tolerance_unit_valid_strings);

    registerIntOption_("precursor:min_charge", "<num>", 2, "Minimum precursor charge to be considered.", false, true);
    registerIntOption_("precursor:max_charge", "<num>", 5, "Maximum precursor charge to be considered.", false, true);

    // consider one before annotated monoisotopic peak and the annotated one
    IntList isotopes = {0, 1};
    registerIntList_("precursor:isotopes", "<num>", isotopes, "Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)", false, false);
    
    registerTOPPSubsection_("fragment", "Fragments (Product Ion) Options");
    registerDoubleOption_("fragment:mass_tolerance", "<tolerance>", 10.0, "Fragment mass tolerance", false);
    
//    StringList fragment_mass_tolerance_unit_valid_strings;
//    fragment_mass_tolerance_unit_valid_strings.push_back("ppm");
//    fragment_mass_tolerance_unit_valid_strings.push_back("Da");
    
//    registerStringOption_("fragment:mass_tolerance_unit", "<unit>", "ppm", "Unit of fragment m", false, false);
//    setValidStrings_("fragment:mass_tolerance_unit", fragment_mass_tolerance_unit_valid_strings);

    registerStringOption_("compare_function", "<string>", "ZhangSimilarityScore", "function for similarity comparison", false);
    PeakSpectrumCompareFunctor::registerChildren();
    setValidStrings_("compare_function", Factory<PeakSpectrumCompareFunctor>::registeredProducts());

    registerTOPPSubsection_("report", "Reporting Options");
    registerIntOption_("report:top_hits", "<num>", 10, "Maximum number of top scoring hits per spectrum that are reported.", false, true);

    addEmptyLine_();

    registerTOPPSubsection_("filter", "Filtering options. Most are especially useful when the query spectra are raw.");
    registerDoubleOption_("filter:remove_peaks_below_threshold", "<threshold>", 2.01, "All peaks of a query spectrum with intensities below <threshold> will be zeroed.", false);
    registerIntOption_("filter:min_peaks", "<number>", 5, "required minimum number of peaks for a query spectrum", false);
    registerIntOption_("filter:max_peaks", "<number>", 150, "Use only the top <number> of peaks.", false);
    registerIntOption_("filter:cut_peaks_below", "<number>", 1000, "Remove all peaks which are lower than 1/<number> of the highest peaks. Default equals all peaks which are lower than 0.001 of the maximum intensity peak", false);

    registerTOPPSubsection_("modifications", "Modifications Options");
    vector<String> all_mods;
    ModificationsDB::getInstance()->getAllSearchModifications(all_mods);
    registerStringList_("modifications:fixed", "<mods>", ListUtils::create<String>(""), "Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'", false);
    setValidStrings_("modifications:fixed", all_mods);
    registerStringList_("modifications:variable", "<mods>", ListUtils::create<String>(""), "Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'", false);
    setValidStrings_("modifications:variable", all_mods);