EmgScoring Class Reference

Scoring of an elution peak using an exponentially modified gaussian distribution model. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgScoring.h>

Collaboration diagram for EmgScoring:

Public Member Functions
	EmgScoring ()=default
	~EmgScoring ()=default
void	setFitterParam (const Param &param)
Param	getDefaults ()
	Get default params for the Emg1D fitting. More...
template<typename SpectrumType , class TransitionT >
double	calcElutionFitScore (MRMFeature &mrmfeature, MRMTransitionGroup< SpectrumType, TransitionT > &transition_group) const
	calculate the elution profile fit score More...
double	elutionModelFit (const ConvexHull2D::PointArrayType &current_section, bool smooth_data) const

Protected Member Functions
template<class LocalPeakType >
double	fitRT_ (std::vector< LocalPeakType > &rt_input_data, std::unique_ptr< InterpolationModel > &model) const
template<class LocalPeakType >
void	prepareFit_ (const ConvexHull2D::PointArrayType &current_section, std::vector< LocalPeakType > &data_to_fit, bool smooth_data) const

Protected Attributes
Param	fitter_emg1D_params_

Detailed Description

Scoring of an elution peak using an exponentially modified gaussian distribution model.

This class uses the original ideas from FeatureFinderAlgorithmMRM to construct an interface that allows scoring of chromatographic peaks.

Constructor & Destructor Documentation

EmgScoring()

EmgScoring ( )

default

~EmgScoring()

~EmgScoring ( )

default

Member Function Documentation

calcElutionFitScore()

double calcElutionFitScore ( MRMFeature &  mrmfeature, MRMTransitionGroup< SpectrumType, TransitionT > &  transition_group  ) const

inline

calculate the elution profile fit score

References EmgScoring::elutionModelFit(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatograms(), Feature::getConvexHulls(), MRMFeature::getFeature(), OpenMS::Constants::k, OPENMS_PRECONDITION, and MRMTransitionGroup< ChromatogramType, TransitionType >::size().

elutionModelFit()

double elutionModelFit ( const ConvexHull2D::PointArrayType &  current_section, bool  smooth_data  ) const

inline

References EmgScoring::fitRT_(), and EmgScoring::prepareFit_().

Referenced by EmgScoring::calcElutionFitScore().

fitRT_()

double fitRT_ ( std::vector< LocalPeakType > &  rt_input_data, std::unique_ptr< InterpolationModel > &  model  ) const

inlineprotected

References EmgFitter1D::fit1d(), EmgScoring::fitter_emg1D_params_, and DefaultParamHandler::setParameters().

Referenced by EmgScoring::elutionModelFit().

getDefaults()

Param getDefaults ( )

inline

Get default params for the Emg1D fitting.

References DefaultParamHandler::getDefaults().

prepareFit_()

void prepareFit_ ( const ConvexHull2D::PointArrayType &  current_section, std::vector< LocalPeakType > &  data_to_fit, bool  smooth_data  ) const

inlineprotected

References GaussFilter::filter(), DefaultParamHandler::getParameters(), Peak1D::setIntensity(), Peak1D::setMZ(), DefaultParamHandler::setParameters(), and Param::setValue().

Referenced by EmgScoring::elutionModelFit().

setFitterParam()

void setFitterParam ( const Param &  param )

inline

overwrites params for the Emg1DFitter. Unspecified params will stay default. use getDefaults to see what you can set.

References EmgScoring::fitter_emg1D_params_.

Member Data Documentation

fitter_emg1D_params_

Param fitter_emg1D_params_

protected

Referenced by EmgScoring::fitRT_(), and EmgScoring::setFitterParam().