Method main_

src/topp/FileFilter.cpp:493–1214

  }

  ExitCodes main_(int, const char**) override
  {

    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input file name and type
    String in = getStringOption_("in");
    FileHandler fh;

    FileTypes::Type in_type = fh.getType(in);
    //only use flag in_type, if the in_type cannot be determined by file
    if (in_type == FileTypes::UNKNOWN)
    {
      in_type = FileTypes::nameToType(getStringOption_("in_type"));
      writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
    }

    //output file name and type
    String out = getStringOption_("out");

    FileTypes::Type out_type = fh.getTypeByFileName(out);

    //only use flag out_type, if the out_type cannot be determined by file
    if (out_type == FileTypes::UNKNOWN)
    {
      out_type = FileTypes::nameToType(getStringOption_("out_type"));
      writeDebug_(String("Output file type: ") + FileTypes::typeToName(out_type), 2);
    }
    //use in_type as out_type, if out_type cannot be determined by file or out_type flag
    if (out_type == FileTypes::UNKNOWN)
    {
      out_type = in_type;
      writeDebug_(String("Output file type: ") + FileTypes::typeToName(out_type), 2);
    }

    bool no_chromatograms(getFlag_("peak_options:no_chromatograms"));

    //ranges
    double mz_l, mz_u, rt_l, rt_u, it_l, it_u, charge_l, charge_u, size_l, size_u, q_l, q_u, pc_left, pc_right, select_collision_l, remove_collision_l, select_collision_u, remove_collision_u, select_isolation_width_l, remove_isolation_width_l, select_isolation_width_u, remove_isolation_width_u, replace_pc_charge_in, replace_pc_charge_out;

    //initialize ranges
    mz_l = rt_l = it_l = charge_l = size_l = q_l = pc_left = select_collision_l = remove_collision_l = select_isolation_width_l = remove_isolation_width_l = replace_pc_charge_in = -1 * numeric_limits<double>::max();
    mz_u = rt_u = it_u = charge_u = size_u = q_u = pc_right = select_collision_u = remove_collision_u = select_isolation_width_u = remove_isolation_width_u = replace_pc_charge_out = numeric_limits<double>::max();

    String rt = getStringOption_("rt");
    String mz = getStringOption_("mz");
    String pc_mz_range = getStringOption_("peak_options:pc_mz_range");
    String it = getStringOption_("int");
    IntList levels = getIntList_("peak_options:level");
    IntList maps = getIntList_("consensus:map");
    double sn = getDoubleOption_("peak_options:sn");
    String charge = getStringOption_("f_and_c:charge");
    String size = getStringOption_("f_and_c:size");
    String q = getStringOption_("feature:q");
    String remove_collision_energy = getStringOption_("spectra:remove_collision_energy");
    String select_collision_energy = getStringOption_("spectra:select_collision_energy");