The PeakPickerMRM finds peaks a single chromatogram. More...

#include <OpenMS/ANALYSIS/OPENSWATH/PeakPickerMRM.h>

Inheritance diagram for PeakPickerMRM:

Public Types
typedef MSSpectrum< ChromatogramPeak >	RichPeakChromatogram

Public Member Functions
void	pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
	Finds peaks in a single chromatogram and annotates left/right borders. More...


	PeakPickerMRM ()
	Constructor. More...

	~PeakPickerMRM ()
	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...

Protected Member Functions
void	pickChromatogramCrawdad_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)

void	pickChromatogram_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)

void	integratePeaks_ (const RichPeakChromatogram &chromatogram)
	Compute peak area (peak integration) More...

Size	findClosestPeak_ (const RichPeakChromatogram &chromatogram, double target_rt, Size current_peak=0)
	Helper function to find the closest peak in a chromatogram to "target_rt". More...

void	removeOverlappingPeaks_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
	Helper function to remove overlapping peaks in a single Chromatogram. More...

void	updateMembers_ ()
	Synchronize members with param class. More...

PeakPickerMRM &	operator= (const PeakPickerMRM &rhs)
	Assignment operator is protected for algorithm. More...

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

Protected Attributes
UInt	sgolay_frame_length_
	Frame length for the SGolay smoothing. More...

UInt	sgolay_polynomial_order_
	Polynomial order for the SGolay smoothing. More...

double	gauss_width_
	Width of the Gaussian smoothing. More...

bool	use_gauss_
	Whether to use Gaussian smoothing. More...

bool	remove_overlapping_
	Whether to resolve overlapping peaks. More...

double	peak_width_
	Forced peak with. More...

double	signal_to_noise_
	Signal to noise threshold. More...

double	sn_win_len_
	Signal to noise window length. More...

UInt	sn_bin_count_
	Signal to noise bin count. More...

bool	write_sn_log_messages_
	Whether to write out log messages of the SN estimator. More...

String	method_
	Peak picker method. More...

std::vector< double >	integrated_intensities_
	Temporary vector to hold the integrated intensities. More...

std::vector< int >	left_width_
	Temporary vector to hold the peak left widths. More...

std::vector< int >	right_width_
	Temporary vector to hold the peak right widths. 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

The PeakPickerMRM finds peaks a single chromatogram.

It uses the PeakPickerHiRes internally to find interesting seed candidates. These candidates are then expanded and a right/left border of the peak is searched. Additionally, overlapping peaks can be removed.

Member Typedef Documentation

typedef MSSpectrum<ChromatogramPeak> RichPeakChromatogram

Constructor & Destructor Documentation

PeakPickerMRM ( )

Constructor.

~PeakPickerMRM ( )

inline

Destructor.

Member Function Documentation

Size findClosestPeak_	(	const RichPeakChromatogram &	chromatogram,
		double	target_rt,
		Size	current_peak = `0`
	)

protected

Helper function to find the closest peak in a chromatogram to "target_rt".

The search will start from the index current_peak, so the function is assuming the closest peak is to the right of current_peak.

It will return the index of the closest peak in the chromatogram.

void integratePeaks_ ( const RichPeakChromatogram & chromatogram )

protected

Compute peak area (peak integration)

PeakPickerMRM& operator= ( const PeakPickerMRM & rhs )

protected

Assignment operator is protected for algorithm.

void pickChromatogram	(	const RichPeakChromatogram &	chromatogram,
		RichPeakChromatogram &	picked_chrom
	)

Finds peaks in a single chromatogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked chromatogram

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

void pickChromatogram_	(	const RichPeakChromatogram &	chromatogram,
		RichPeakChromatogram &	picked_chrom
	)

protected

void pickChromatogramCrawdad_	(	const RichPeakChromatogram &	chromatogram,
		RichPeakChromatogram &	picked_chrom
	)

protected

void removeOverlappingPeaks_	(	const RichPeakChromatogram &	chromatogram,
		RichPeakChromatogram &	picked_chrom
	)

protected

Helper function to remove overlapping peaks in a single Chromatogram.

void updateMembers_ ( )

protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

double gauss_width_

protected

Width of the Gaussian smoothing.

std::vector<double> integrated_intensities_

protected

Temporary vector to hold the integrated intensities.

std::vector<int> left_width_

protected

Temporary vector to hold the peak left widths.

String method_

protected

Peak picker method.

double peak_width_

protected

Forced peak with.

bool remove_overlapping_

protected

Whether to resolve overlapping peaks.

std::vector<int> right_width_

protected

Temporary vector to hold the peak right widths.

UInt sgolay_frame_length_

protected

Frame length for the SGolay smoothing.

UInt sgolay_polynomial_order_

protected

Polynomial order for the SGolay smoothing.

double signal_to_noise_

protected

Signal to noise threshold.

UInt sn_bin_count_

protected

Signal to noise bin count.

double sn_win_len_

protected

Signal to noise window length.

bool use_gauss_

protected

Whether to use Gaussian smoothing.

bool write_sn_log_messages_

protected

Whether to write out log messages of the SN estimator.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation