Implements the isotope wavelet feature finder. More...

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

Inheritance diagram for FeatureFinderAlgorithmIsotopeWavelet:

Collaboration diagram for FeatureFinderAlgorithmIsotopeWavelet:

Classes
struct	BoxElement
	Internally used data structure for the sweep line algorithm. More...

Public Types
typedef FeatureFinderAlgorithm	Base

typedef Peak1D	PeakType

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 Member Functions
	FeatureFinderAlgorithmIsotopeWavelet ()
	Default Constructor. More...

	~FeatureFinderAlgorithmIsotopeWavelet () override
	Destructor. More...

MSSpectrum *	createHRData (const UInt i)

void	run () override
	The working horse of this class. 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, FeatureFinder &ff)
	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...

Static Public Member Functions
static const String	getProductName ()

static FeatureFinderAlgorithm *	create ()

Static Public Member Functions inherited from FeatureFinderAlgorithm
static void	registerChildren ()
	register all derived classes here (see FeatureFinderAlgorithm_impl.h) 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 Types
typedef std::map< UInt, BoxElement >	Box
	Key: RT (index), value: BoxElement. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. 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	max_charge_
	The maximal absolute charge state we will consider. More...

double	intensity_threshold_
	The only parameter of the isotope wavelet. More...

UInt	RT_votes_cutoff_

UInt	real_RT_votes_cutoff_

UInt	RT_interleave_
	The number of subsequent scans a pattern must cover in order to be considered as signal. More...

String	use_gpus_

String	intensity_type_

bool	check_PPMs_

bool	hr_data_

std::vector< UInt >	gpu_ids_
	A list of all GPU devices that can be used. More...

Int	progress_counter_

Protected Attributes inherited from FeatureFinderAlgorithm
const MapType *	map_
	Input data pointer. More...

FeatureMap *	features_
	Output data pointer. More...

FeatureFinder *	ff_
	Pointer to the calling FeatureFinder that is used to access the feature flags. 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

Implements the isotope wavelet feature finder.

The FeatureFinderAlgorithmIsotopeWavelet class has been designed for finding features in 1D or 2D MS data sets using the isotope wavelet. In the case of two dimensional data, the class provides additionally the sweep line algorithm. Please note that the algorithm implemented here is only marginally related to the algorithm presented in Schulz-Trieglaff et al. (2007, 2008), as no fitting procedure is applied anymore after the wavelet-based seeding step. The wavelet has been designed to extract even very lowly-abundant features (see Hussong et al. (2007, 2009)), usually featuring a very low signal-to-noise ratio. The wavelet in its current implementation is not able to resolve overlapping patterns (see also Hussong et al. (2009)) and slightly shifts masses to the right due to the construction of the wavelet.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
max_charge	int	3	min: 1	The maximal charge state to be considered.
intensity_threshold	float	-1.0		The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform. If you set intensity_threshold=-1, t' will be zero. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g.
intensity_type	string	ref	ref, trans, corrected	Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet).
check_ppm	string	false	true, false	Enables/disables a ppm test vs. the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied.
hr_data	string	false	true, false	Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure.
sweep_line:rt_votes_cutoff	int	5	min: 0	Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature.
sweep_line:rt_interleave	int	1	min: 0	Defines the maximum number of scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value.

Note:

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

Class Documentation

◆ OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement

struct OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement

Internally used data structure for the sweep line algorithm.

Collaboration diagram for FeatureFinderAlgorithmIsotopeWavelet::BoxElement:

[legend]

Class Members
UInt	c	Note, this is not the charge (it is charge-1!!!)
double	intens
double	mz
double	RT	The elution time (not the scan index)
double	score

Member Typedef Documentation

◆ Base

typedef FeatureFinderAlgorithm Base

◆ Box

typedef std::map<UInt, BoxElement> Box

protected

Key: RT (index), value: BoxElement.

◆ PeakType

typedef Peak1D PeakType

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmIsotopeWavelet()

FeatureFinderAlgorithmIsotopeWavelet ( )

Default Constructor.

◆ ~FeatureFinderAlgorithmIsotopeWavelet()

~FeatureFinderAlgorithmIsotopeWavelet ( )

override

Destructor.

Member Function Documentation

◆ create()

static FeatureFinderAlgorithm* create ( )

static

◆ createHRData()

MSSpectrum* createHRData ( const UInt i )

◆ getProductName()

static const String getProductName ( )

static

◆ run()

void run ( )

overridevirtual

The working horse of this class.

Implements FeatureFinderAlgorithm.

◆ 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

◆ check_PPMs_

bool check_PPMs_

protected

◆ gpu_ids_

std::vector<UInt> gpu_ids_

protected

A list of all GPU devices that can be used.

◆ hr_data_

bool hr_data_

protected

◆ intensity_threshold_

double intensity_threshold_

protected

The only parameter of the isotope wavelet.

◆ intensity_type_

String intensity_type_

protected

◆ max_charge_

UInt max_charge_

protected

The maximal absolute charge state we will consider.

◆ progress_counter_

Int progress_counter_

protected

◆ real_RT_votes_cutoff_

UInt real_RT_votes_cutoff_

protected

◆ RT_interleave_

UInt RT_interleave_

protected

The number of subsequent scans a pattern must cover in order to be considered as signal.

◆ RT_votes_cutoff_

UInt RT_votes_cutoff_

protected

◆ use_gpus_

String use_gpus_

protected

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Class Documentation

◆ OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement

Member Typedef Documentation

◆ Base

◆ Box

◆ PeakType

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmIsotopeWavelet()

◆ ~FeatureFinderAlgorithmIsotopeWavelet()

Member Function Documentation

◆ create()

◆ createHRData()

◆ getProductName()

◆ run()

◆ updateMembers_()

Member Data Documentation

◆ check_PPMs_

◆ gpu_ids_

◆ hr_data_

◆ intensity_threshold_

◆ intensity_type_

◆ max_charge_

◆ progress_counter_

◆ real_RT_votes_cutoff_

◆ RT_interleave_

◆ RT_votes_cutoff_

◆ use_gpus_