RTSimulation::RTSimulation(const RTSimulation& source) :
DefaultParamHandler(source)
{
setParameters(source.getParameters());
rnd_gen_ = source.rnd_gen_;
updateMembers_();
}
CompNovoIdentificationCID::CompNovoIdentificationCID() :
CompNovoIdentificationBase(),
precursor_mass_tolerance_(1.5)
{
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_();
}
RTSimulation& RTSimulation::operator=(const RTSimulation& source)
{
setParameters(source.getParameters());
rnd_gen_ = source.rnd_gen_;
updateMembers_();
return *this;
}
void DefaultParamHandler::setParameters(const Param & param)
{
//set defaults and apply new parameters
Param tmp(param);
tmp.setDefaults(defaults_);
param_ = tmp;
if (check_defaults_)
{
if (defaults_.empty() && warn_empty_defaults_)
{
LOG_WARN << "Warning: No default parameters for DefaultParameterHandler '" << error_name_ << "' specified!" << endl;
}
//remove registered subsections
for (vector<String>::const_iterator it = subsections_.begin(); it != subsections_.end(); ++it)
{
tmp.removeAll(*it + ':');
}
//check defaults
tmp.checkDefaults(error_name_, defaults_);
}
//do necessary changes to other member variables
updateMembers_();
}
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_();
}
IDMapper::IDMapper(const IDMapper & cp) :
DefaultParamHandler(cp),
rt_tolerance_(cp.rt_tolerance_),
mz_tolerance_(cp.mz_tolerance_),
measure_(cp.measure_),
ignore_charge_(cp.ignore_charge_)
{
updateMembers_();
}
CompNovoIdentificationCID & CompNovoIdentificationCID::operator=(const CompNovoIdentificationCID & rhs)
{
if (this != &rhs)
{
CompNovoIdentificationBase::operator=(rhs);
updateMembers_();
}
return *this;
}
GaussTraceFitter::GaussTraceFitter(const GaussTraceFitter& other) :
TraceFitter(other)
{
this->height_ = other.height_;
this->x0_ = other.x0_;
this->sigma_ = other.sigma_;
updateMembers_();
}
/// Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param
ItraqChannelExtractor::ItraqChannelExtractor(Int itraq_type, const Param& param) :
DefaultParamHandler("ItraqChannelExtractor"),
itraq_type_(itraq_type),
channel_map_()
{
init_();
setDefaultParams_();
setParameters(param);
updateMembers_();
}
IDRipper & IDRipper::operator=(const IDRipper & rhs)
{
if (this == &rhs)
return *this;
DefaultParamHandler::operator=(rhs);
updateMembers_();
return *this;
}
CompNovoIdentificationBase & CompNovoIdentificationBase::operator=(const CompNovoIdentificationBase & rhs)
{
if (this != &rhs)
{
DefaultParamHandler::operator=(rhs);
updateMembers_();
// TODO
}
return *this;
}
ExtendedIsotopeFitter1D & ExtendedIsotopeFitter1D::operator=(const ExtendedIsotopeFitter1D & source)
{
if (&source == this)
return *this;
MaxLikeliFitter1D::operator=(source);
updateMembers_();
return *this;
}
BiGaussFitter1D& BiGaussFitter1D::operator=(const BiGaussFitter1D& source)
{
if (&source == this)
return *this;
MaxLikeliFitter1D::operator=(source);
updateMembers_();
return *this;
}
FeatureDistance & FeatureDistance::operator=(const FeatureDistance & other)
{
DefaultParamHandler::operator=(other);
max_intensity_ = other.max_intensity_;
force_constraints_ = other.force_constraints_;
updateMembers_(); // this sets all other member variables
return *this;
}
EGHModel & EGHModel::operator=(const EGHModel & source)
{
if (&source == this)
return *this;
InterpolationModel::operator=(source);
setParameters(source.getParameters());
updateMembers_();
return *this;
}
Fitter1D & Fitter1D::operator=(const Fitter1D & source)
{
if (&source == this)
return *this;
DefaultParamHandler::operator=(source);
setParameters(source.getParameters());
updateMembers_();
return *this;
}
GaussTraceFitter& GaussTraceFitter::operator=(const GaussTraceFitter& source)
{
TraceFitter::operator=(source);
this->height_ = source.height_;
this->x0_ = source.x0_;
this->sigma_ = source.sigma_;
updateMembers_();
return *this;
}
EGHTraceFitter::EGHTraceFitter(const EGHTraceFitter& other) :
TraceFitter(other)
{
this->height_ = other.height_;
this->apex_rt_ = other.apex_rt_;
this->sigma_ = other.sigma_;
this->tau_ = other.tau_;
this->sigma_5_bound_ = other.sigma_5_bound_;
updateMembers_();
}
IDMapper & IDMapper::operator=(const IDMapper & rhs)
{
if (this == &rhs)
return *this;
DefaultParamHandler::operator=(rhs);
rt_tolerance_ = rhs.rt_tolerance_;
mz_tolerance_ = rhs.mz_tolerance_;
measure_ = rhs.measure_;
ignore_charge_ = rhs.ignore_charge_;
updateMembers_();
return *this;
}
EGHTraceFitter& EGHTraceFitter::operator=(const EGHTraceFitter& source)
{
TraceFitter::operator=(source);
this->height_ = source.height_;
this->apex_rt_ = source.apex_rt_;
this->sigma_ = source.sigma_;
this->tau_ = source.tau_;
this->sigma_5_bound_ = source.sigma_5_bound_;
updateMembers_();
return *this;
}
void DefaultParamHandler::defaultsToParam_()
{
//check if a description is given for all defaults
bool description_missing = false;
String missing_parameters;
for (Param::ParamIterator it = defaults_.begin(); it != defaults_.end(); ++it)
{
//cout << "Name: " << it->getName() << endl;
if (it->description == "")
{
description_missing = true;
missing_parameters += it.getName() + ",";
break;
}
}
if (description_missing)
{
cerr << "Warning: no default parameter description for parameters '" << missing_parameters << "' of DefaultParameterHandler '" << error_name_ << "' given!" << endl;
}
param_.setDefaults(defaults_);
updateMembers_();
}
AbsoluteQuantitation::AbsoluteQuantitation() :
DefaultParamHandler("AbsoluteQuantitation")
{
defaults_.setValue("min_points", 4, "The minimum number of calibrator points.");
defaults_.setValue("max_bias", 30.0, "The maximum percent bias of any point in the calibration curve.");
defaults_.setValue("min_correlation_coefficient", 0.9, "The minimum correlation coefficient value of the calibration curve.");
defaults_.setValue("max_iters", 100, "The maximum number of iterations to find an optimal set of calibration curve points and parameters.");
defaults_.setValue("outlier_detection_method", "iter_jackknife", "Outlier detection method to find and remove bad calibration points.");
defaults_.setValidStrings("outlier_detection_method", ListUtils::create<String>("iter_jackknife,iter_residual"));
defaults_.setValue("use_chauvenet", "true", "Whether to only remove outliers that fulfill Chauvenet's criterion for outliers (otherwise it will remove any outlier candidate regardless of the criterion).");
defaults_.setValidStrings("use_chauvenet", ListUtils::create<String>("true,false"));
defaults_.setValue("optimization_method", "iterative", "Calibrator optimization method to find the best set of calibration points for each method.");
defaults_.setValidStrings("optimization_method", ListUtils::create<String>("iterative"));
// write defaults into Param object param_
defaultsToParam_();
updateMembers_();
}
DetectabilitySimulation::DetectabilitySimulation(const DetectabilitySimulation& source) :
DefaultParamHandler(source)
{
setParameters(source.getParameters());
updateMembers_();
}
EGHModel::EGHModel(const EGHModel & source) :
InterpolationModel(source)
{
setParameters(source.getParameters());
updateMembers_();
}
Fitter1D::Fitter1D(const Fitter1D & source) :
DefaultParamHandler(source)
{
setParameters(source.getParameters());
updateMembers_();
}
BiGaussFitter1D::BiGaussFitter1D(const BiGaussFitter1D& source) :
MaxLikeliFitter1D(source)
{
updateMembers_();
}
CompNovoIdentificationBase::CompNovoIdentificationBase(const CompNovoIdentificationBase & rhs) :
DefaultParamHandler(rhs)
{
updateMembers_();
}
CompNovoIdentificationCID::CompNovoIdentificationCID(const CompNovoIdentificationCID & rhs) :
CompNovoIdentificationBase(rhs)
{
updateMembers_();
}
DetectabilitySimulation& DetectabilitySimulation::operator=(const DetectabilitySimulation& source)
{
setParameters(source.getParameters());
updateMembers_();
return *this;
}
