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 ()
	~EmgScoring ()
void	setFitterParam (Param param)
Param	getDefaults ()
template<typename SpectrumType , class TransitionT >
double	calcElutionFitScore (MRMFeature &mrmfeature, MRMTransitionGroup< SpectrumType, TransitionT > &transition_group)
	calculate the elution profile fit score More...
double	elutionModelFit (ConvexHull2D::PointArrayType current_section, bool smooth_data)

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

Protected Attributes
EmgFitter1D	fitter_emg1D_

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 ( )

inline

~EmgScoring()

~EmgScoring ( )

inline

Member Function Documentation

calcElutionFitScore()

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

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 ( ConvexHull2D::PointArrayType  current_section, bool  smooth_data  )

inline

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

Referenced by EmgScoring::calcElutionFitScore().

fitRT_()

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

inlineprotected

References EmgFitter1D::fit1d(), and EmgScoring::fitter_emg1D_.

Referenced by EmgScoring::elutionModelFit().

getDefaults()

Param getDefaults ( )

inline

References EmgScoring::fitter_emg1D_, and DefaultParamHandler::getDefaults().

prepareFit_()

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

inlineprotected

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

Referenced by EmgScoring::elutionModelFit().

setFitterParam()

void setFitterParam ( Param  param )

inline

References EmgScoring::fitter_emg1D_, and DefaultParamHandler::setParameters().

Member Data Documentation

fitter_emg1D_

EmgFitter1D fitter_emg1D_

protected

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