Abstract fitter for RT profile fitting. More...

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

Inheritance diagram for TraceFitter:

Collaboration diagram for TraceFitter:

Classes
class	GenericFunctor

struct	ModelData

Public Member Functions
	TraceFitter ()
	default constructor More...

	TraceFitter (const TraceFitter &source)
	copy constructor More...

TraceFitter &	operator= (const TraceFitter &source)
	assignment operator More...

	~TraceFitter () override
	destructor More...

virtual void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)=0

virtual double	getLowerRTBound () const =0

virtual double	getUpperRTBound () const =0

virtual double	getHeight () const =0

virtual double	getCenter () const =0

virtual double	getFWHM () const =0

virtual double	getValue (double rt) const =0

double	computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, Size k) const

virtual bool	checkMinimalRTSpan (const std::pair< double, double > &rt_bounds, const double min_rt_span)=0

virtual bool	checkMaximalRTSpan (const double max_rt_span)=0

virtual double	getArea ()=0

virtual String	getGnuplotFormula (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, const char function_name, const double baseline, const double rt_shift)=0

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

virtual void	getOptimizedParameters_ (const Eigen::VectorXd &)=0

void	optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor)

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
SignedSize	max_iterations_
	Maximum number of iterations. More...

bool	weighted_
	Whether to weight mass traces by theoretical intensity during the optimization. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Detailed Description

Abstract fitter for RT profile fitting.

This class provides the basic interface and some functionality to fit multiple mass traces to a given RT shape model using the Levenberg-Marquardt algorithm.

Todo:: docu needs update

Class Documentation

◆ OpenMS::TraceFitter::ModelData

struct OpenMS::TraceFitter::ModelData

Collaboration diagram for TraceFitter::ModelData:

[legend]

Class Members
MassTraces *	traces_ptr
bool	weighted

Constructor & Destructor Documentation

◆ TraceFitter() [1/2]

TraceFitter ( )

default constructor

◆ TraceFitter() [2/2]

TraceFitter ( const TraceFitter & source )

copy constructor

◆ ~TraceFitter()

~TraceFitter ( )

override

destructor

Member Function Documentation

◆ checkMaximalRTSpan()

virtual bool checkMaximalRTSpan ( const double max_rt_span )

pure virtual

Checks if the fitted model is not to big

Parameters

max_rt_span Maximum RT span in relation to extended area that the model is allowed to have

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ checkMinimalRTSpan()

virtual bool checkMinimalRTSpan	(	const std::pair< double, double > &	rt_bounds,
		const double	min_rt_span
	)

pure virtual

Checks if the fitted model fills out at least 'min_rt_span' of the RT span

Parameters

rt_bounds	RT boundaries of the fitted model
min_rt_span	Minimum RT span in relation to extended area that has to remain after model fitting

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ computeTheoretical()

double computeTheoretical	(	const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &	trace,
		Size	k
	)		const

Returns the theoretical value of the fitted model at position k in the passed mass trace

Parameters

trace	the mass trace for which the value should be computed
k	use the position of the k-th peak to compute the value

◆ fit()

virtual void fit ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces & traces )

pure virtual

Main method of the TraceFitter which triggers the actual fitting.

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getArea()

virtual double getArea ( )

pure virtual

Returns the peak area of the fitted model

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getCenter()

virtual double getCenter ( ) const

pure virtual

Returns the center position of the fitted model

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getFWHM()

virtual double getFWHM ( ) const

pure virtual

Returns the mass trace width at half max (FWHM)

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getGnuplotFormula()

virtual String getGnuplotFormula	(	const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &	trace,
		const char	function_name,
		const double	baseline,
		const double	rt_shift
	)

pure virtual

Returns a textual representation of the fitted model function, that can be plotted using Gnuplot

Parameters

trace	The mass trace that should be plotted
function_name	The name of the function (e.g. f(x) -> function_name = f)
baseline	The intensity of the baseline
rt_shift	A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality. This should be 0 for the first mass trace and increase by a fixed value for each mass trace.

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getHeight()

virtual double getHeight ( ) const

pure virtual

Returns the height of the fitted model

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getLowerRTBound()

virtual double getLowerRTBound ( ) const

pure virtual

Returns the lower bound of the fitted RT model

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getOptimizedParameters_()

virtual void getOptimizedParameters_ ( const Eigen::VectorXd & )

protectedpure virtual

Updates all member variables to the fitted values stored in the solver.

Parameters

s	The solver containing the fitted parameter values.

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getUpperRTBound()

virtual double getUpperRTBound ( ) const

pure virtual

Returns the upper bound of the fitted RT model

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ getValue()

virtual double getValue ( double rt ) const

pure virtual

Evaluate the fitted model at a time point

Implemented in GaussTraceFitter, and EGHTraceFitter.

◆ operator=()

TraceFitter& operator= ( const TraceFitter & source )

assignment operator

◆ optimize_()

void optimize_	(	Eigen::VectorXd &	x_init,
		GenericFunctor &	functor
	)

protected

Optimize the given parameters using the Levenberg-Marquardt algorithm.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ max_iterations_

SignedSize max_iterations_

protected

Maximum number of iterations.

◆ weighted_

bool weighted_

protected

Whether to weight mass traces by theoretical intensity during the optimization.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::TraceFitter::ModelData

Constructor & Destructor Documentation

◆ TraceFitter() [1/2]

◆ TraceFitter() [2/2]

◆ ~TraceFitter()

Member Function Documentation

◆ checkMaximalRTSpan()

◆ checkMinimalRTSpan()

◆ computeTheoretical()

◆ fit()

◆ getArea()

◆ getCenter()

◆ getFWHM()

◆ getGnuplotFormula()

◆ getHeight()

◆ getLowerRTBound()

◆ getOptimizedParameters_()

◆ getUpperRTBound()

◆ getValue()

◆ operator=()

◆ optimize_()

◆ updateMembers_()

Member Data Documentation

◆ max_iterations_

◆ weighted_