PeakPickerIterative Class Reference

This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data). More...

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

Inheritance diagram for PeakPickerIterative:

Public Member Functions
	PeakPickerIterative ()
	Constructor. More...
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...
	~PeakPickerIterative () override
	Destructor. More...
void	pick (const MSSpectrum &input, MSSpectrum &output)
void	pickExperiment (const PeakMap &input, PeakMap &output)
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...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress () const
	Ends the progress display. More...
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
void	pickRecenterPeaks_ (const MSSpectrum &input, std::vector< PeakCandidate > &PeakCandidates, SignalToNoiseEstimatorMedian< MSSpectrum > &snt)

Private Attributes
double	signal_to_noise_
double	peak_width_
double	spacing_difference_
int	sn_bin_count_
int	nr_iterations_
double	sn_win_len_
bool	check_width_internally_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data).

This peak-picking algorithm detects ion signals in profile data and reconstructs the corresponding peak shape by identifying the left and right borders of the peak. It reports the area under the peak as intensity and the weighted m/z values as the m/z value as well as left/right border. Furthermore, it next tries to improve the peak positioning iteratively using the m/z center computed in the last iteration. This allows for refinement in the peak boundaries and more accurate determination of peak center and borders.

Its approach is similar to the PeakPickerHiRes but additionally uses an iterative approach to find and re-center peaks.

• First, it uses the PeakPickerHiRes to find seeds or candidate peaks.
• Next it uses n iterations to re-center those peaks and compute left/right borders for each peak.
• Finally it removes peaks that are within the borders of other peaks.

So far, this peak picker was mainly tested on high resolution TOF-MS data.

Note

The peaks must be sorted according to ascending m/z!

Constructor & Destructor Documentation

PeakPickerIterative()

PeakPickerIterative ( )

inline

Constructor.

~PeakPickerIterative()

~PeakPickerIterative ( )

inlineoverride

Destructor.

Member Function Documentation

pick()

void pick ( const MSSpectrum &  input, MSSpectrum &  output  )

inline

References SpectrumSettings::CENTROID, MSSpectrum::clear(), DefaultParamHandler::getDefaults(), MSSpectrum::getFloatDataArrays(), MSSpectrum::getMSLevel(), MSSpectrum::getName(), MSSpectrum::getRT(), OpenMS::Constants::k, OPENMS_LOG_DEBUG, PeakPickerHiRes::pick(), Peak1D::setIntensity(), MSSpectrum::setMSLevel(), Peak1D::setMZ(), MSSpectrum::setName(), DefaultParamHandler::setParameters(), MSSpectrum::setRT(), SpectrumSettings::setType(), Param::setValue(), OpenMS::sort_peaks_by_intensity(), and MSSpectrum::sortByPosition().

pickExperiment()

void pickExperiment ( const PeakMap &  input, PeakMap &  output  )

inline

References MSExperiment::clear(), MSExperiment::resize(), and MSExperiment::size().

pickRecenterPeaks_()

void pickRecenterPeaks_ ( const MSSpectrum &  input, std::vector< PeakCandidate > &  PeakCandidates, SignalToNoiseEstimatorMedian< MSSpectrum > &  snt  )

inlineprivate

References SignalToNoiseEstimator< Container >::getSignalToNoise(), and OpenMS::Constants::k.

updateMembers_()

void updateMembers_ ( )

inlineoverridevirtual

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

check_width_internally_

bool check_width_internally_

private

nr_iterations_

int nr_iterations_

private

peak_width_

double peak_width_

private

signal_to_noise_

double signal_to_noise_

private

sn_bin_count_

int sn_bin_count_

private

sn_win_len_

double sn_win_len_

private

spacing_difference_

double spacing_difference_

private