OfflinePrecursorIonSelection::OfflinePrecursorIonSelection() :
DefaultParamHandler("OfflinePrecursorIonSelection")
{
defaults_.setValue("ms2_spectra_per_rt_bin", 5, "Number of allowed MS/MS spectra in a retention time bin.");
defaults_.setMinInt("ms2_spectra_per_rt_bin", 1);
defaults_.setValue("min_peak_distance", 3., "The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.");
defaults_.setMinFloat("min_peak_distance", 0.);
defaults_.setValue("selection_window", 2., "All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.");
defaults_.setMinFloat("selection_window", 0.);
defaults_.setValue("exclude_overlapping_peaks", "false", "If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection.");
defaults_.setValidStrings("exclude_overlapping_peaks", ListUtils::create<String>("true,false"));
defaults_.setValue("Exclusion:use_dynamic_exclusion", "false", "If true dynamic exclusion is applied.");
defaults_.setValidStrings("Exclusion:use_dynamic_exclusion", ListUtils::create<String>("true,false"));
defaults_.setValue("Exclusion:exclusion_time", 100., "The time (in seconds) a feature is excluded.");
defaults_.setMinFloat("Exclusion:exclusion_time", 0.);
defaults_.insert("ProteinBasedInclusion:", PSLPFormulation().getDefaults());
defaults_.remove("ProteinBasedInclusion:mz_tolerance");
defaults_.remove("ProteinBasedInclusion:combined_ilp:");
defaults_.remove("ProteinBasedInclusion:thresholds:min_protein_probability");
defaults_.remove("ProteinBasedInclusion:thresholds:min_pred_pep_prob");
defaults_.remove("ProteinBasedInclusion:thresholds:min_rt_weight");
defaults_.removeAll("ProteinBasedInclusion:feature_based");
defaults_.setValue("ProteinBasedInclusion:max_list_size", 1000, "The maximal number of precursors in the inclusion list.");
defaults_.setMinInt("ProteinBasedInclusion:max_list_size", 1);
defaultsToParam_();
}
void ItraqEightPlexQuantitationMethod::setDefaultParams_()
{
defaults_.setValue("channel_113_description", "", "Description for the content of the 113 channel.");
defaults_.setValue("channel_114_description", "", "Description for the content of the 114 channel.");
defaults_.setValue("channel_115_description", "", "Description for the content of the 115 channel.");
defaults_.setValue("channel_116_description", "", "Description for the content of the 116 channel.");
defaults_.setValue("channel_117_description", "", "Description for the content of the 117 channel.");
defaults_.setValue("channel_118_description", "", "Description for the content of the 118 channel.");
defaults_.setValue("channel_119_description", "", "Description for the content of the 119 channel.");
defaults_.setValue("channel_121_description", "", "Description for the content of the 121 channel.");
defaults_.setValue("reference_channel", 113, "Number of the reference channel (113-121). Please note that 120 is not valid.");
defaults_.setMinInt("reference_channel", 113);
defaults_.setMaxInt("reference_channel", 121);
// {0.00, 0.00, 6.89, 0.22}, //113
// {0.00, 0.94, 5.90, 0.16},
// {0.00, 1.88, 4.90, 0.10},
// {0.00, 2.82, 3.90, 0.07},
// {0.06, 3.77, 2.99, 0.00},
// {0.09, 4.71, 1.88, 0.00},
// {0.14, 5.66, 0.87, 0.00},
// {0.27, 7.44, 0.18, 0.00} //121
defaults_.setValue("correction_matrix", StringList::create("0.00/0.00/6.89/0.22," //113
"0.00/0.94/5.90/0.16,"
"0.00/1.88/4.90/0.10,"
"0.00/2.82/3.90/0.07,"
"0.06/3.77/2.99/0.00,"
"0.09/4.71/1.88/0.00,"
"0.14/5.66/0.87/0.00,"
"0.27/7.44/0.18/0.00"), //121
"Override default values (see Documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'");
defaultsToParam_();
}
void TMTSixPlexQuantitationMethod::setDefaultParams_()
{
defaults_.setValue("channel_126_description", "", "Description for the content of the 126 channel.");
defaults_.setValue("channel_127_description", "", "Description for the content of the 127 channel.");
defaults_.setValue("channel_128_description", "", "Description for the content of the 128 channel.");
defaults_.setValue("channel_129_description", "", "Description for the content of the 129 channel.");
defaults_.setValue("channel_130_description", "", "Description for the content of the 130 channel.");
defaults_.setValue("channel_131_description", "", "Description for the content of the 131 channel.");
defaults_.setValue("reference_channel", 126, "Number of the reference channel (126-131).");
defaults_.setMinInt("reference_channel", 126);
defaults_.setMaxInt("reference_channel", 131);
// {0.0, 1.0, 5.9, 0.2}, //114
// {0.0, 2.0, 5.6, 0.1},
// {0.0, 3.0, 4.5, 0.1},
// {0.1, 4.0, 3.5, 0.1} //117
defaults_.setValue("correction_matrix", ListUtils::create<String>("0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0"),
"Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
defaultsToParam_();
}
PeakPickerHiRes::PeakPickerHiRes() :
DefaultParamHandler("PeakPickerHiRes"),
ProgressLogger()
{
// set default parameter values
defaults_.setValue("signal_to_noise", 0.0, "Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)");
defaults_.setMinFloat("signal_to_noise", 0.0);
defaults_.setValue("spacing_difference_gap", 4.0, "The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.", ListUtils::create<String>("advanced"));
defaults_.setMinFloat("spacing_difference_gap", 0.0);
defaults_.setValue("spacing_difference", 1.5, "Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.", ListUtils::create<String>("advanced"));
defaults_.setMinFloat("spacing_difference", 0.0);
defaults_.setValue("missing", 1, "Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.", ListUtils::create<String>("advanced"));
defaults_.setMinInt("missing", 0);
defaults_.setValue("ms_levels", ListUtils::create<Int>(""), "List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.");
defaults_.setMinInt("ms_levels", 1);
defaults_.setValue("report_FWHM", "false", "Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.");
defaults_.setValidStrings("report_FWHM", ListUtils::create<String>("true,false"));
defaults_.setValue("report_FWHM_unit", "relative", "Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).");
defaults_.setValidStrings("report_FWHM_unit", ListUtils::create<String>("relative,absolute"));
// parameters for STN estimator
defaults_.insert("SignalToNoise:", SignalToNoiseEstimatorMedian< MSSpectrum >().getDefaults());
// write defaults into Param object param_
defaultsToParam_();
updateMembers_();
}
MRMTransitionGroupPicker::MRMTransitionGroupPicker() :
DefaultParamHandler("MRMTransitionGroupPicker")
{
defaults_.setValue("stop_after_feature", -1, "Stop finding after feature (ordered by intensity; -1 means do not stop).");
defaults_.setValue("stop_after_intensity_ratio", 0.0001, "Stop after reaching intensity ratio");
defaults_.setValue("min_peak_width", -1.0, "Minimal peak width (s), discard all peaks below this value (-1 means no action).", ListUtils::create<String>("advanced"));
defaults_.setValue("background_subtraction", "none", "Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("background_subtraction", ListUtils::create<String>("none,smoothed,original"));
defaults_.setValue("recalculate_peaks", "false", "Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large.", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("recalculate_peaks", ListUtils::create<String>("true,false"));
defaults_.setValue("use_precursors", "false", "Use precursor chromatogram for peak picking", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("use_precursors", ListUtils::create<String>("true,false"));
defaults_.setValue("recalculate_peaks_max_z", 1.0, "Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).", ListUtils::create<String>("advanced"));
defaults_.setValue("minimal_quality", -10000.0, "Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold", ListUtils::create<String>("advanced"));
defaults_.setValue("compute_peak_quality", "false", "Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("compute_peak_quality", ListUtils::create<String>("true,false"));
defaults_.insert("PeakPickerMRM:", PeakPickerMRM().getDefaults());
// write defaults into Param object param_
defaultsToParam_();
updateMembers_();
}
Normalizer::Normalizer() :
DefaultParamHandler("Normalizer")
{
defaults_.setValue("method", "to_one", "Normalize by deviding though the TIC ('to_TIC') or normalize to max intensity of one ('to_one').");
defaults_.setValidStrings("method", ListUtils::create<String>("to_one,to_TIC"));
defaultsToParam_();
}
void DigestSimulation::setDefaultParams_()
{
// supported enzymes
StringList enzymes;
enzymes.resize(EnzymaticDigestion::SIZE_OF_ENZYMES + 1);
for (UInt i = 0; i < EnzymaticDigestion::SIZE_OF_ENZYMES; ++i)
enzymes[i] = EnzymaticDigestion::NamesOfEnzymes[i];
enzymes[EnzymaticDigestion::SIZE_OF_ENZYMES] = "none";
defaults_.setValue("enzyme", enzymes[0], "Enzyme to use for digestion (select 'none' to skip digestion)");
defaults_.setValidStrings("enzyme", enzymes);
// cleavages
defaults_.setValue("model", "naive", "The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).");
defaults_.setValidStrings("model", ListUtils::create<String>("trained,naive"));
defaults_.setValue("model_trained:threshold", 0.50, "Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.");
defaults_.setMinFloat("model_trained:threshold", -2);
defaults_.setMaxFloat("model_trained:threshold", 4);
defaults_.setValue("model_naive:missed_cleavages", 1, "Maximum number of missed cleavages considered. All possible resulting peptides will be created.");
defaults_.setMinInt("model_naive:missed_cleavages", 0);
// pep length
defaults_.setValue("min_peptide_length", 3, "Minimum peptide length after digestion (shorter ones will be discarded)");
defaults_.setMinInt("min_peptide_length", 1);
defaultsToParam_();
}
IsotopeModel::IsotopeModel() :
InterpolationModel(),
charge_(0),
monoisotopic_mz_(0.0)
{
setName(getProductName());
defaults_.setValue("averagines:C", 0.04443989f, "Number of C atoms per Dalton of mass.", ListUtils::create<String>("advanced"));
defaults_.setValue("averagines:H", 0.06981572f, "Number of H atoms per Dalton of mass.", ListUtils::create<String>("advanced"));
defaults_.setValue("averagines:N", 0.01221773f, "Number of N atoms per Dalton of mass.", ListUtils::create<String>("advanced"));
defaults_.setValue("averagines:O", 0.01329399f, "Number of O atoms per Dalton of mass.", ListUtils::create<String>("advanced"));
defaults_.setValue("averagines:S", 0.00037525f, "Number of S atoms per Dalton of mass.", ListUtils::create<String>("advanced"));
defaults_.setValue("isotope:trim_right_cutoff", 0.001, "Cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered.", ListUtils::create<String>("advanced"));
defaults_.setValue("isotope:maximum", 100, "Maximum isotopic rank to be considered.", ListUtils::create<String>("advanced"));
defaults_.setValue("isotope:distance", 1.000495, "Distance between consecutive isotopic peaks.", ListUtils::create<String>("advanced"));
defaults_.setValue("isotope:mode:mode", "Gaussian", "Peak Shape used around each isotope peak.", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("isotope:mode:mode", ListUtils::create<String>("Gaussian,Lorentzian"));
defaults_.setValue("isotope:mode:LorentzFWHM", 0.3, "Full width of the Lorentzian (Cauchy) function applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.", ListUtils::create<String>("advanced"));
defaults_.setValue("isotope:mode:GaussianSD", 0.1, "Standard deviation of Gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.", ListUtils::create<String>("advanced"));
defaults_.setValue("charge", 1, "Charge state of the model.", ListUtils::create<String>("advanced"));
defaults_.setValue("statistics:mean", 0.0, "Centroid m/z (as opposed to monoisotopic m/z).", ListUtils::create<String>("advanced"));
defaultsToParam_();
}
CompNovoIdentificationCID::CompNovoIdentificationCID() :
CompNovoIdentificationBase(),
precursor_mass_tolerance_(1.5)
{
defaultsToParam_();
updateMembers_();
}
PoseClusteringShiftSuperimposer::PoseClusteringShiftSuperimposer() :
BaseSuperimposer()
{
setName(getProductName());
defaults_.setValue("mz_pair_max_distance", 0.5, "Maximum of m/z deviation of corresponding elements in different maps. "
"This condition applies to the pairs considered in hashing.");
defaults_.setMinFloat("mz_pair_max_distance", 0.);
defaults_.setValue("num_used_points", 2000, "Maximum number of elements considered in each map "
"(selected by intensity). Use this to reduce the running time "
"and to disregard weak signals during alignment. For using all points, set this to -1.");
defaults_.setMinInt("num_used_points", -1);
defaults_.setValue("shift_bucket_size", 3.0, "The shift of the retention time "
"interval is being hashed into buckets of this size during pose "
"clustering. A good choice for this would be about "
"the time between consecutive MS scans.");
defaults_.setMinFloat("shift_bucket_size", 0.);
defaults_.setValue("max_shift", 1000.0, "Maximal shift which is considered during histogramming. "
"This applies for both directions.", ListUtils::create<String>("advanced"));
defaults_.setMinFloat("max_shift", 0.);
defaults_.setValue("dump_buckets", "", "[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. "
"A serial number for each invocation will be appended automatically.", ListUtils::create<String>("advanced"));
defaults_.setValue("dump_pairs", "", "[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). "
"A serial number for each invocation will be appended automatically.", ListUtils::create<String>("advanced"));
defaultsToParam_();
return;
}
FeatureDistance::FeatureDistance(DoubleReal max_intensity,
bool force_constraints) :
DefaultParamHandler("FeatureDistance"),
params_rt_(), params_mz_(), params_intensity_(),
max_intensity_(max_intensity), force_constraints_(force_constraints)
{
defaults_.setValue("distance_RT:max_difference", 100.0, "Maximum allowed difference in RT in seconds");
defaults_.setMinFloat("distance_RT:max_difference", 0.0);
defaults_.setValue("distance_RT:exponent", 1.0, "Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)", StringList::create("advanced"));
defaults_.setMinFloat("distance_RT:exponent", 0.0);
defaults_.setValue("distance_RT:weight", 1.0, "RT distances are weighted by this factor", StringList::create("advanced"));
defaults_.setMinFloat("distance_RT:weight", 0.0);
defaults_.setSectionDescription("distance_RT", "Distance component based on RT differences");
defaults_.setValue("distance_MZ:max_difference", 0.3, "Maximum allowed difference in m/z (unit defined by 'unit')");
defaults_.setMinFloat("distance_MZ:max_difference", 0.0);
defaults_.setValue("distance_MZ:unit", "Da", "Unit of the 'max_difference' parameter");
defaults_.setValidStrings("distance_MZ:unit", StringList::create("Da,ppm"));
defaults_.setValue("distance_MZ:exponent", 2.0, "Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)", StringList::create("advanced"));
defaults_.setMinFloat("distance_MZ:exponent", 0.0);
defaults_.setValue("distance_MZ:weight", 1.0, "m/z distances are weighted by this factor", StringList::create("advanced"));
defaults_.setMinFloat("distance_MZ:weight", 0.0);
defaults_.setSectionDescription("distance_MZ", "Distance component based on m/z differences");
defaults_.setValue("distance_intensity:exponent", 1.0, "Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)", StringList::create("advanced"));
defaults_.setMinFloat("distance_intensity:exponent", 0.0);
defaults_.setValue("distance_intensity:weight", 0.0, "Distances based on relative intensity are weighted by this factor", StringList::create("advanced"));
defaults_.setMinFloat("distance_intensity:weight", 0.0);
defaults_.setSectionDescription("distance_intensity", "Distance component based on differences in relative intensity");
defaults_.setValue("ignore_charge", "false", "Compare features normally even if their charge states are different");
defaults_.setValidStrings("ignore_charge", StringList::create("true,false"));
defaultsToParam_();
}
void TMTTenPlexQuantitationMethod::setDefaultParams_()
{
defaults_.setValue("channel_126_description", "", "Description for the content of the 126 channel.");
defaults_.setValue("channel_127N_description", "", "Description for the content of the 127N channel.");
defaults_.setValue("channel_127C_description", "", "Description for the content of the 127C channel.");
defaults_.setValue("channel_128N_description", "", "Description for the content of the 128N channel.");
defaults_.setValue("channel_128C_description", "", "Description for the content of the 128C channel.");
defaults_.setValue("channel_129N_description", "", "Description for the content of the 129N channel.");
defaults_.setValue("channel_129C_description", "", "Description for the content of the 129C channel.");
defaults_.setValue("channel_130N_description", "", "Description for the content of the 130N channel.");
defaults_.setValue("channel_130C_description", "", "Description for the content of the 130C channel.");
defaults_.setValue("channel_131_description", "", "Description for the content of the 131 channel.");
defaults_.setValue("reference_channel", "126", "The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131).");
defaults_.setValidStrings("reference_channel", TMTTenPlexQuantitationMethod::channel_names_);
// {0.0, 1.0, 5.9, 0.2}, //114
// {0.0, 2.0, 5.6, 0.1},
// {0.0, 3.0, 4.5, 0.1},
// {0.1, 4.0, 3.5, 0.1} //117
defaults_.setValue("correction_matrix", ListUtils::create<String>("0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0,"
"0.0/0.0/0.0/0.0"),
"Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'");
defaultsToParam_();
}
TICFilter::TICFilter() :
FilterFunctor()
{
setName(TICFilter::getProductName());
defaults_.setValue("window", 5, "Windowing parameter which defines the windows size");
defaultsToParam_();
}
IntensityBalanceFilter::IntensityBalanceFilter() :
FilterFunctor()
{
check_defaults_ = false;
setName(IntensityBalanceFilter::getProductName());
defaultsToParam_();
}
FeatureGroupingAlgorithmQT::FeatureGroupingAlgorithmQT() :
FeatureGroupingAlgorithm()
{
setName("FeatureGroupingAlgorithmQT");
defaults_.insert("", QTClusterFinder().getParameters());
defaultsToParam_();
}
void IsobaricChannelExtractor::setDefaultParams_()
{
defaults_.setValue("select_activation", Precursor::NamesOfActivationMethod[Precursor::HCID], "Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering.");
StringList activation_list(std::vector<std::string>(Precursor::NamesOfActivationMethod, &Precursor::NamesOfActivationMethod[Precursor::SIZE_OF_ACTIVATIONMETHOD - 1]));
activation_list.push_back(""); // allow disabling this
defaults_.setValidStrings("select_activation", activation_list);
defaults_.setValue("reporter_mass_shift", 0.1, "Allowed shift (left to right) in Da from the expected position.");
defaults_.setMinFloat("reporter_mass_shift", 0.00000001);
defaults_.setMaxFloat("reporter_mass_shift", 0.5);
defaults_.setValue("min_precursor_intensity", 1.0, "Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation.");
defaults_.setMinFloat("min_precursor_intensity", 0.0);
defaults_.setValue("keep_unannotated_precursor", "true", "Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.");
defaults_.setValidStrings("keep_unannotated_precursor", StringList::create("true,false"));
defaults_.setValue("min_reporter_intensity", 0.0, "Minimum intenesity of the individual reporter ions to be used extracted.");
defaults_.setMinFloat("min_reporter_intensity", 0.0);
defaults_.setValue("discard_low_intensity_quantifications", "false", "Remove all reporter intensities if a single reporter is below the threshold given in min_reporter_intensity.");
defaults_.setValidStrings("discard_low_intensity_quantifications", StringList::create("true,false"));
defaults_.setValue("min_precursor_purity", 0.0, "Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor.");
defaults_.setMinFloat("min_precursor_purity", 0.0);
defaults_.setMaxFloat("min_precursor_purity", 1.0);
defaults_.setValue("precursor_isotope_deviation", 0.02, "Maximum allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.");
defaults_.setMinFloat("precursor_isotope_deviation", 0.0);
defaults_.addTag("precursor_isotope_deviation", "advanced");
defaultsToParam_();
}
MassTraceDetection::MassTraceDetection() :
DefaultParamHandler("MassTraceDetection"), ProgressLogger()
{
defaults_.setValue("mass_error_ppm", 20.0, "Allowed mass deviation (in ppm).");
defaults_.setValue("noise_threshold_int", 10.0, "Intensity threshold below which peaks are removed as noise.");
defaults_.setValue("chrom_peak_snr", 3.0, "Minimum intensity above noise_threshold_int (signal-to-noise) a peak should have to be considered an apex.");
defaults_.setValue("reestimate_mt_sd", "true", "Enables dynamic re-estimation of m/z variance during mass trace collection stage.");
defaults_.setValidStrings("reestimate_mt_sd", ListUtils::create<String>("true,false"));
defaults_.setValue("quant_method", String(MassTrace::names_of_quantmethod[0]), "Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data.");
defaults_.setValidStrings("quant_method", std::vector<String>(MassTrace::names_of_quantmethod, MassTrace::names_of_quantmethod +(int)MassTrace::SIZE_OF_MT_QUANTMETHOD));
// advanced parameters
defaults_.setValue("trace_termination_criterion", "outlier", "Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.", ListUtils::create<String>("advanced"));
defaults_.setValidStrings("trace_termination_criterion", ListUtils::create<String>("outlier,sample_rate"));
defaults_.setValue("trace_termination_outliers", 5, "Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.", ListUtils::create<String>("advanced"));
defaults_.setValue("min_sample_rate", 0.5, "Minimum fraction of scans along the mass trace that must contain a peak.", ListUtils::create<String>("advanced"));
defaults_.setValue("min_trace_length", 5.0, "Minimum expected length of a mass trace (in seconds).", ListUtils::create<String>("advanced"));
defaults_.setValue("max_trace_length", -1.0, "Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.", ListUtils::create<String>("advanced"));
defaultsToParam_();
this->setLogType(CMD);
}
void ItraqChannelExtractor::setDefaultParams_()
{
defaults_.setValue("select_activation", Precursor::NamesOfActivationMethod[Precursor::HCID], "Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering.");
StringList activation_list;
activation_list.insert(activation_list.begin(), Precursor::NamesOfActivationMethod, Precursor::NamesOfActivationMethod + Precursor::SIZE_OF_ACTIVATIONMETHOD - 1);
activation_list.push_back(""); // allow disabling this
defaults_.setValidStrings("select_activation", activation_list);
defaults_.setValue("reporter_mass_shift", 0.1, "Allowed shift (left to right) in Da from the expected position.");
defaults_.setMinFloat("reporter_mass_shift", 0.00000001);
defaults_.setMaxFloat("reporter_mass_shift", 0.5);
defaults_.setValue("channel_active",
(itraq_type_ == TMT_SIXPLEX
? ListUtils::create<String>("126:liver,131:lung")
: ListUtils::create<String>("114:liver,117:lung")),
String("Each channel that was used in the experiment and its description (")
+ (itraq_type_ == TMT_SIXPLEX
? String("126-131 for TMT-6-plex")
: String("114-117 for 4plex; 113-121 for 8-plex"))
+ String(") in format <channel>:<name>, e.g. \"114:myref\",\"115:liver\"."));
defaultsToParam_();
return;
}
TheoreticalSpectrumGenerator::TheoreticalSpectrumGenerator() :
DefaultParamHandler("TheoreticalSpectrumGenerator")
{
defaults_.setValue("add_isotopes", "false", "If set to 1 isotope peaks of the product ion peaks are added");
defaults_.setValidStrings("add_isotopes", ListUtils::create<String>("true,false"));
defaults_.setValue("max_isotope", 2, "Defines the maximal isotopic peak which is added, add_isotopes must be set to 1");
defaults_.setValue("add_metainfo", "false", "Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++");
defaults_.setValidStrings("add_metainfo", ListUtils::create<String>("true,false"));
defaults_.setValue("add_losses", "false", "Adds common losses to those ion expect to have them, only water and ammonia loss is considered");
defaults_.setValidStrings("add_losses", ListUtils::create<String>("true,false"));
defaults_.setValue("add_precursor_peaks", "false", "Adds peaks of the precursor to the spectrum, which happen to occur sometimes");
defaults_.setValidStrings("add_precursor_peaks", ListUtils::create<String>("true,false"));
defaults_.setValue("add_abundant_immonium_ions", "false", "Add most abundant immonium ions");
defaults_.setValidStrings("add_abundant_immonium_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_first_prefix_ion", "false", "If set to true e.g. b1 ions are added");
defaults_.setValidStrings("add_first_prefix_ion", ListUtils::create<String>("true,false"));
defaults_.setValue("add_y_ions", "true", "Add peaks of y-ions to the spectrum");
defaults_.setValidStrings("add_y_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_b_ions", "true", "Add peaks of b-ions to the spectrum");
defaults_.setValidStrings("add_b_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_a_ions", "false", "Add peaks of a-ions to the spectrum");
defaults_.setValidStrings("add_a_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_c_ions", "false", "Add peaks of c-ions to the spectrum");
defaults_.setValidStrings("add_c_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_x_ions", "false", "Add peaks of x-ions to the spectrum");
defaults_.setValidStrings("add_x_ions", ListUtils::create<String>("true,false"));
defaults_.setValue("add_z_ions", "false", "Add peaks of z-ions to the spectrum");
defaults_.setValidStrings("add_z_ions", ListUtils::create<String>("true,false"));
// intensity options of the ions
defaults_.setValue("y_intensity", 1.0, "Intensity of the y-ions");
defaults_.setValue("b_intensity", 1.0, "Intensity of the b-ions");
defaults_.setValue("a_intensity", 1.0, "Intensity of the a-ions");
defaults_.setValue("c_intensity", 1.0, "Intensity of the c-ions");
defaults_.setValue("x_intensity", 1.0, "Intensity of the x-ions");
defaults_.setValue("z_intensity", 1.0, "Intensity of the z-ions");
defaults_.setValue("relative_loss_intensity", 0.1, "Intensity of loss ions, in relation to the intact ion intensity");
// precursor intensity
defaults_.setValue("precursor_intensity", 1.0, "Intensity of the precursor peak");
defaults_.setValue("precursor_H2O_intensity", 1.0, "Intensity of the H2O loss peak of the precursor");
defaults_.setValue("precursor_NH3_intensity", 1.0, "Intensity of the NH3 loss peak of the precursor");
defaultsToParam_();
}
NeutralLossDiffFilter::NeutralLossDiffFilter() :
FilterFunctor()
{
setName(NeutralLossDiffFilter::getProductName());
//value from Bioinformatics, Bern 2004
defaults_.setValue("tolerance", 0.37, "Tolerance value defined by Bern et al.");
defaultsToParam_();
}
SpectrumAlignment::SpectrumAlignment() :
DefaultParamHandler("SpectrumAlignment")
{
defaults_.setValue("tolerance", 0.3, "Defines the absolute (in Da) or relative (in ppm) tolerance");
defaults_.setValue("is_relative_tolerance", "false", "If true, the 'tolerance' is interpreted as ppm-value");
defaults_.setValidStrings("is_relative_tolerance", ListUtils::create<String>("true,false"));
defaultsToParam_();
}
void DetectabilitySimulation::setDefaultParams_()
{
defaults_.setValue("dt_simulation_on", "false", "Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count");
defaults_.setValidStrings("dt_simulation_on", StringList::create("true,false"));
defaults_.setValue("min_detect", 0.5, "Minimum peptide detectability accepted. Peptides with a lower score will be removed");
defaults_.setValue("dt_model_file", "examples/simulation/DTPredict.model", "SVM model for peptide detectability prediction");
defaultsToParam_();
}
/// default constructor
SteinScottImproveScore::SteinScottImproveScore() :
PeakSpectrumCompareFunctor()
{
setName(SteinScottImproveScore::getProductName());
defaults_.setValue("tolerance", 0.2, "defines the absolute error of the mass spectrometer");
defaults_.setValue("threshold", 0.2, "if the calculated score is smaller than the threshold, a zero is given back");
defaultsToParam_();
}
ComplementMarker::ComplementMarker() :
PeakMarker()
{
setName(ComplementMarker::getProductName());
defaults_.setValue("tolerance", 1.0, "Tolerance value as defined by Bern et al.");
defaults_.setValue("marks", 1, "How often a peak needs to be marked to be returned");
defaultsToParam_();
}
BinnedSumAgreeingIntensities::BinnedSumAgreeingIntensities() :
BinnedSpectrumCompareFunctor()
{
setName(BinnedSumAgreeingIntensities::getProductName());
defaults_.setValue("normalized", 1, "is set 1 if the similarity-measurement is normalized to the range [0,1]");
defaults_.setValue("precursor_mass_tolerance", 3.0, "Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides");
defaultsToParam_();
}
NeutralLossMarker::NeutralLossMarker() :
PeakMarker()
{
setName(NeutralLossMarker::getProductName());
defaults_.setValue("marks", 1, "How often a peak must be marked to be reported");
defaults_.setValue("tolerance", 0.2, "Tolerance in m/z direction");
defaultsToParam_();
}
FeatureGroupingAlgorithmUnlabeled::FeatureGroupingAlgorithmUnlabeled() :
FeatureGroupingAlgorithm()
{
setName("FeatureGroupingAlgorithmUnlabeled");
defaults_.insert("", StablePairFinder().getParameters());
defaultsToParam_();
// The input for the pairfinder is a vector of FeatureMaps of size 2
pairfinder_input_.resize(2);
}
PeakAlignment::PeakAlignment() :
PeakSpectrumCompareFunctor()
{
defaults_.setValue("epsilon", 0.2, "defines the absolute error of the mass spectrometer");
defaults_.setValue("normalized", 1, "is set 1 if the similarity-measurement is normalized to the range [0,1]");
defaults_.setValue("heuristic_level", 0, "set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heurisitcs - in those sets of peaks has to be at least one match to conduct comparison");
defaults_.setValue("precursor_mass_tolerance", 3.0, "Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides");
defaultsToParam_();
}
WindowMower::WindowMower() :
DefaultParamHandler("WindowMower")
{
defaults_.setValue("windowsize", 50.0, "The size of the sliding window along the m/z axis.");
defaults_.setValue("peakcount", 2, "The number of peaks that should be kept.");
defaults_.setValue("movetype", "slide", "Whether sliding window (one peak steps) or jumping window (window size steps) should be used.");
defaults_.setValidStrings("movetype", ListUtils::create<String>("slide,jump"));
defaultsToParam_();
}
FeatureGroupingAlgorithmLabeled::FeatureGroupingAlgorithmLabeled() :
FeatureGroupingAlgorithm()
{
setName("FeatureGroupingAlgorithmLabeled");
defaults_.insert("", LabeledPairFinder().getParameters());
defaultsToParam_();
}
