This class provides the deconvolution of peak regions using non-linear optimization. More...

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h>

Inheritance diagram for OptimizePeakDeconvolution:

Collaboration diagram for OptimizePeakDeconvolution:

Classes
struct	Data
	Class containing the data needed for optimization. More...

Public Types
Type definitions
typedef std::vector< Peak1D >	RawDataVector

typedef RawDataVector::iterator	PeakIterator

Public Member Functions
Constructors and Destructor
	OptimizePeakDeconvolution ()
	Constructor. More...

	OptimizePeakDeconvolution (const OptimizePeakDeconvolution &opt)
	Copy-Constructor. More...

	~OptimizePeakDeconvolution () override
	Destructor. More...

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...

Assignment
OptimizationFunctions::PenaltyFactorsIntensity	penalties_

Int	charge_
	Charge state of the current isotope pattern. More...

static const double	dist_
	distance between two isotopic peaks More...

OptimizePeakDeconvolution &	operator= (const OptimizePeakDeconvolution &opt)

const OptimizationFunctions::PenaltyFactorsIntensity &	getPenalties () const
	Non-mutable access to the penalty parameter. More...

void	setPenalties (const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
	Mutable access to the penalty parameter. More...

Int	getCharge () const
	Non-mutable access to the charge. More...

void	setCharge (const Int charge)
	Mutable access to the charge. More...

bool	optimize (std::vector< PeakShape > &peaks, Data &data)
	Performs a nonlinear optimization of the peaks that belong to the current isotope pattern. More...

Size	getNumberOfPeaks_ (Int charge, std::vector< PeakShape > &temp_shapes, Data &data)

void	setNumberOfPeaks_ (Data &data, const std::vector< PeakShape > &temp_shapes, Int charge)
	A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state. More...

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

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

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

Detailed Description

This class provides the deconvolution of peak regions using non-linear optimization.

Given a vector of peak shapes, this class optimizes all peak shapes parameters using a non-linear optimization. For the non-linear optimization we use the Levenberg-Marquardt algorithm. There are a few constraints for the parameters: the positions are equidistant according to the peptide mass rule, e.g. two consecutive isotopic peaks are 1.003/charge away from each other. Besides the peaks have all the same left and right width, respectively.

Parameters of this class are:

Name	Type	Default	Description
max_iteration	int	10	maximal number of iterations for the fitting step
eps_abs	float	1.0e-04	if the absolute error gets smaller than this value the fitting is stopped
eps_rel	float	1.0e-04	if the relative error gets smaller than this value the fitting is stopped
fwhm_threshold	float	1.0	If a peaks is broader than fwhm_threshold, it is assumed that it contains another peaks and an additional peak is added.
penalties:left_width	float	0.0	penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.
penalties:right_width	float	0.0	penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.
penalties:height	float	0.0	penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.
penalties:position	float	0.0	penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Class Documentation

◆ OpenMS::OptimizePeakDeconvolution::Data

struct OpenMS::OptimizePeakDeconvolution::Data

Class containing the data needed for optimization.

Collaboration diagram for OptimizePeakDeconvolution::Data:

[legend]

Class Members
Int	charge
vector< PeakShape >	peaks
PenaltyFactorsIntensity	penalties
vector< double >	positions
vector< double >	signal

Member Typedef Documentation

◆ PeakIterator

typedef RawDataVector::iterator PeakIterator

◆ RawDataVector

typedef std::vector<Peak1D> RawDataVector

Constructor & Destructor Documentation

◆ OptimizePeakDeconvolution() [1/2]

OptimizePeakDeconvolution ( )

Constructor.

◆ OptimizePeakDeconvolution() [2/2]

OptimizePeakDeconvolution ( const OptimizePeakDeconvolution & opt )

inline

Copy-Constructor.

◆ ~OptimizePeakDeconvolution()

~OptimizePeakDeconvolution ( )

inlineoverride

Destructor.

Member Function Documentation

◆ getCharge()

Int getCharge ( ) const

inline

Non-mutable access to the charge.

◆ getNumberOfPeaks_()

Size getNumberOfPeaks_	(	Int	charge,
		std::vector< PeakShape > &	temp_shapes,
		Data &	data
	)

◆ getPenalties()

const OptimizationFunctions::PenaltyFactorsIntensity& getPenalties ( ) const

inline

Non-mutable access to the penalty parameter.

Accessors

◆ operator=()

OptimizePeakDeconvolution& operator= ( const OptimizePeakDeconvolution & opt )

inline

References OptimizePeakDeconvolution::charge_, DefaultParamHandler::operator=(), and OptimizePeakDeconvolution::penalties_.

◆ optimize()

bool optimize	(	std::vector< PeakShape > &	peaks,
		Data &	data
	)

Performs a nonlinear optimization of the peaks that belong to the current isotope pattern.

◆ setCharge()

void setCharge ( const Int charge )

inline

Mutable access to the charge.

◆ setNumberOfPeaks_()

void setNumberOfPeaks_	(	Data &	data,
		const std::vector< PeakShape > &	temp_shapes,
		Int	charge
	)

protected

A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state.

◆ setPenalties()

void setPenalties ( const OptimizationFunctions::PenaltyFactorsIntensity & penalties )

inline

Mutable access to the penalty parameter.

◆ 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

◆ charge_

Int charge_

protected

Charge state of the current isotope pattern.

Referenced by OptimizePeakDeconvolution::operator=().

◆ dist_

const double dist_

staticprotected

distance between two isotopic peaks

◆ penalties_

OptimizationFunctions::PenaltyFactorsIntensity penalties_

protected

Referenced by OptimizePeakDeconvolution::operator=().

Classes

Public Types

Public Member Functions

Assignment

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::OptimizePeakDeconvolution::Data

Member Typedef Documentation

◆ PeakIterator

◆ RawDataVector

Constructor & Destructor Documentation

◆ OptimizePeakDeconvolution() [1/2]

◆ OptimizePeakDeconvolution() [2/2]

◆ ~OptimizePeakDeconvolution()

Member Function Documentation

◆ getCharge()

◆ getNumberOfPeaks_()

◆ getPenalties()

◆ operator=()

◆ optimize()

◆ setCharge()

◆ setNumberOfPeaks_()

◆ setPenalties()

◆ updateMembers_()

Member Data Documentation

◆ charge_

◆ dist_

◆ penalties_