Method SpectraMerger

src/openms/source/FILTERING/TRANSFORMERS/SpectraMerger.cpp:16–106

{

  SpectraMerger::SpectraMerger() :
    DefaultParamHandler("SpectraMerger")
  {
    // common
    defaults_.setValue("mz_binning_width", 5.0, "minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.", {"advanced"});
    defaults_.setMinFloat("mz_binning_width", 0.0);

    defaults_.setValue("mz_binning_width_unit",
                       "ppm",
                       "Unit in which the distance between two data points or peaks is given.",
                       {"advanced"});
    defaults_.setValidStrings("mz_binning_width_unit", {"Da", "ppm"});

    defaults_.setValue("sort_blocks",
                       "RT_ascending",
                       "Sort blocks by <?> before merging them (useful for precursor order)",
                       {"advanced"});
    defaults_.setValidStrings("sort_blocks", {"RT_ascending", "RT_descending"});

    // Gaussian average
    defaults_.setValue("average_gaussian:spectrum_type", "automatic", "Spectrum type of the MS level to be averaged");
    defaults_.setValidStrings("average_gaussian:spectrum_type", {"profile", "centroid", "automatic"});
    defaults_
        .setValue("average_gaussian:ms_level",
                  1,
                  "If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.");
    defaults_.setMinInt("average_gaussian:ms_level", 0);
    defaults_.setValue("average_gaussian:rt_FWHM", 5.0, "FWHM of Gauss curve in seconds to be averaged over.");
    defaults_.setMinFloat("average_gaussian:rt_FWHM", 0.0);
    defaults_.setMaxFloat("average_gaussian:rt_FWHM", 10e10);
    defaults_.setValue("average_gaussian:cutoff",
                       0.01,
                       "Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.",
                       {"advanced"});
    defaults_.setMinFloat("average_gaussian:cutoff", 0.0);
    defaults_.setMaxFloat("average_gaussian:cutoff", 1.0);
    defaults_.setValue("average_gaussian:precursor_mass_tol",
                       0.0,
                       "PPM mass tolerance for precursor mass. If set, MSn (n>2) spectra of precursor masses within the tolerance are averaged.");
    defaults_.setValue("average_gaussian:precursor_max_charge",
                       1,
                       "Possible maximum precursor ion charge. Effective only when average_gaussian:precursor_mass_tol option is active.");
    defaults_.setMinFloat("average_gaussian:precursor_mass_tol", 0.0);
    defaults_.setMinInt("average_gaussian:precursor_max_charge", 1);

    // top-hat average
    defaults_.setValue("average_tophat:spectrum_type", "automatic", "Spectrum type of the MS level to be averaged");
    defaults_.setValidStrings("average_tophat:spectrum_type", {"profile", "centroid", "automatic"});
    defaults_
        .setValue("average_tophat:ms_level",
                  1,
                  "If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.");
    defaults_.setMinInt("average_tophat:ms_level", 0);
    defaults_.setValue("average_tophat:rt_range",
                       5.0,
                       "RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.");
    defaults_.setMinFloat("average_tophat:rt_range", 0.0);
    defaults_.setMaxFloat("average_tophat:rt_range", 10e10);