FeatureFinderAlgorithm for MRM experiments. More...

#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmMRM.h>

Inheritance diagram for FeatureFinderAlgorithmMRM:

Collaboration diagram for FeatureFinderAlgorithmMRM:

Type definitions
enum	{ RT = Peak2D::RT , MZ = Peak2D::MZ }

typedef FeatureFinderAlgorithm::MapType	MapType

typedef MapType::SpectrumType	SpectrumType

typedef SpectrumType::FloatDataArrays	FloatDataArrays

	FeatureFinderAlgorithmMRM ()
	default constructor More...

void	run () override
	Main method for actual FeatureFinder. More...

void	run (PeakMap &input_map, FeatureMap &features, const Param &param, const FeatureMap &seeds)

double	fitRT_ (std::vector< Peak1D > &rt_input_data, std::unique_ptr< InterpolationModel > &model) const

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

FeatureMap *	features_
	Output data pointer. More...

const MapType *	map_
	Input data pointer. More...

Additional Inherited Members
Public Types inherited from FeatureFinderAlgorithm
typedef PeakMap	MapType
	Input map type. More...

typedef MapType::CoordinateType	CoordinateType
	Coordinate/Position type of peaks. More...

typedef MapType::IntensityType	IntensityType
	Intensity type of peaks. More...

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Types inherited from FeatureFinderDefs
enum	Flag { UNUSED , USED }
	Flags that indicate if a peak is already used in a feature. More...

typedef IsotopeCluster::IndexPair	IndexPair
	Index to peak consisting of two UInts (scan index / peak index) More...

typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	Index to peak consisting of two UInts (scan index / peak index) with charge information. More...

typedef IsotopeCluster::IndexSet	IndexSet
	A set of peak indices. More...

Public Member Functions inherited from FeatureFinderAlgorithm
	FeatureFinderAlgorithm ()
	default constructor More...

	~FeatureFinderAlgorithm () override
	destructor More...

virtual Param	getDefaultParameters () const
	Returns the default parameters. Reimplement. More...

void	setData (const MapType &map, FeatureMap &features)
	Sets a reference to the calling FeatureFinder. More...

virtual void	setSeeds (const FeatureMap &seeds)
	Sets a reference to the calling FeatureFinder. 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...

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...

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

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 FeatureFinderAlgorithm
const MapType *	map_
	Input data pointer. More...

FeatureMap *	features_
	Output data pointer. 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

FeatureFinderAlgorithm for MRM experiments.

Experimental classes:: This tool has not been tested thoroughly and might behave not as expected!

This very simple algorithm has mainly been tested on data generated on an ABI/SCIEX QTrap 4000. Maybe this algorithm cannot be directly applied on data generated by other mass spectrometers.

Precursor m/z information (Q1) is stored in the "MZ" metavalue of each feature! The feature's m/z itself is the Q3's ion m/z.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
min_rt_distance	float	10.0	min: 0.0	Minimal distance of MRM features in seconds.
min_num_peaks_per_feature	int	5	min: 1	Minimal number of peaks which are needed for a single feature
min_signal_to_noise_ratio	float	2.0	min: 0.0	Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.
write_debug_files	string	false	true, false	If set to true, for each feature a plot will be created, in the subdirectory 'debug'
resample_traces	string	false	true, false	If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension
write_debuginfo	string	false	true, false	If set to true, debug messages are written, the output can be somewhat lengthy.

Note:

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

Member Typedef Documentation

◆ FloatDataArrays

typedef SpectrumType::FloatDataArrays FloatDataArrays

◆ MapType

typedef FeatureFinderAlgorithm::MapType MapType

◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Enumerator
RT
MZ

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmMRM()

FeatureFinderAlgorithmMRM ( )

default constructor

Member Function Documentation

◆ fitRT_()

double fitRT_	(	std::vector< Peak1D > &	rt_input_data,
		std::unique_ptr< InterpolationModel > &	model
	)		const

protected

◆ run() [1/2]

void run ( )

overridevirtual

Main method for actual FeatureFinder.

Implements FeatureFinderAlgorithm.

◆ run() [2/2]

void run	(	PeakMap &	input_map,
		FeatureMap &	features,
		const Param &	param,
		const FeatureMap &	seeds
	)

◆ 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

◆ features_

FeatureMap* features_

Output data pointer.

◆ map_

const MapType* map_

Input data pointer.

Type definitions

Additional Inherited Members