FeatureFinderAlgorithm for picked peaks. More...

#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h>

Inheritance diagram for FeatureFinderAlgorithmPicked:

Collaboration diagram for FeatureFinderAlgorithmPicked:

Protected Attributes
Members for parameters often needed in methods
double	pattern_tolerance_
	Stores mass_trace:mz_tolerance. More...

double	trace_tolerance_
	Stores isotopic_pattern:mz_tolerance. More...

UInt	min_spectra_
	Number of spectra that have to show the same mass (for finding a mass trace) More...

UInt	max_missing_trace_peaks_
	Stores mass_trace:max_missing. More...

double	slope_bound_
	Max slope of mass trace intensities. More...

double	intensity_percentage_
	Isotope pattern intensity contribution of required peaks. More...

double	intensity_percentage_optional_
	Isotope pattern intensity contribution of optional peaks. More...

double	optional_fit_improvement_
	Minimal improvement for leaving out optional isotope. More...

double	mass_window_width_
	Width of the isotope pattern mass bins. More...

UInt	intensity_bins_
	Number of bins (in RT and MZ) for intensity significance estimation. More...

double	min_isotope_fit_
	Minimum isotope pattern fit for a feature. More...

double	min_trace_score_
	Minimum quality of a traces. More...

double	min_rt_span_
	Minimum RT range that has to be left after the fit. More...

double	max_rt_span_
	Maximum RT range the model is allowed to span. More...

double	max_feature_intersection_
	Maximum allowed feature intersection (if larger, that one of the feature is removed) More...

String	reported_mz_
	The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model. 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_

Type definitions
typedef MSExperiment	MapType

typedef MapType::SpectrumType	SpectrumType

typedef SpectrumType::FloatDataArrays	FloatDataArrays

typedef Peak1D	PeakType

typedef FeatureFinderAlgorithmPickedHelperStructs::Seed	Seed

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace	MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces	MassTraces

typedef FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern	TheoreticalIsotopePattern

typedef FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern	IsotopePattern

MapType	map_
	editable copy of the map More...

FeatureMap *	features_

std::ofstream	log_
	Output stream for log/debug info. More...

bool	debug_
	debug flag More...

std::map< String, UInt >	aborts_
	Array of abort reasons. More...

std::map< Seed, String >	abort_reasons_
	Array of abort reasons. More...

FeatureMap	seeds_
	User-specified seed list. More...

	FeatureFinderAlgorithmPicked ()
	default constructor More...

void	setSeeds (const FeatureMap &seeds)

void	setData (const MSExperiment &map, FeatureMap &features)

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

virtual Param	getDefaultParameters () const

void	run ()

Members for intensity significance estimation
double	intensity_rt_step_
	RT bin width. More...

double	intensity_mz_step_
	m/z bin width More...

std::vector< std::vector< std::vector< double > > >	intensity_thresholds_
	Precalculated intensity 20-quantiles (binned) More...

std::vector< TheoreticalIsotopePattern >	isotope_distributions_
	Vector of precalculated isotope distributions for several mass windows. More...

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

void	abort_ (const Seed &seed, const String &reason)
	Writes the abort reason to the log file and counts occurrences for each reason. More...

double	intersection_ (const Feature &f1, const Feature &f2) const

const TheoreticalIsotopePattern &	getIsotopeDistribution_ (double mass) const
	Returns the isotope distribution for a certain mass window. More...

double	findBestIsotopeFit_ (const Seed &center, UInt charge, IsotopePattern &best_pattern) const
	Finds the best fitting position of the isotopic pattern estimate defined by `center`. More...

void	extendMassTraces_ (const IsotopePattern &pattern, MassTraces &traces, Size meta_index_overall) const

void	extendMassTrace_ (MassTrace &trace, SignedSize spectrum_index, double mz, bool increase_rt, Size meta_index_overall, double min_rt=0.0, double max_rt=0.0) const
	Extends a single mass trace in one RT direction. More...

Size	nearest_ (double pos, const MSSpectrum &spec, Size start) const
	Returns the index of the peak nearest to m/z `pos` in spectrum `spec` (linear search starting from index `start`) More...

void	findIsotope_ (double pos, Size spectrum_index, IsotopePattern &pattern, Size pattern_index, Size &peak_index) const
	Searches for an isotopic peak in the current spectrum and the adjacent spectra. More...

double	positionScore_ (double pos1, double pos2, double allowed_deviation) const
	Calculates a score between 0 and 1 for the m/z deviation of two peaks. More...

double	isotopeScore_ (const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances) const
	Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern. More...

double	intensityScore_ (Size spectrum, Size peak) const
	Compute the intensity score for the peak `peak` in spectrum `spectrum`. More...

std::unique_ptr< TraceFitter >	chooseTraceFitter_ (double &tau)
	Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto) More...

double	intensityScore_ (Size rt_bin, Size mz_bin, double intensity) const

Handling of fitted mass traces
Methods to handle the results of the mass trace fitting process.
void	cropFeature_ (const std::shared_ptr< TraceFitter > &fitter, const MassTraces &traces, MassTraces &new_traces)
	Creates new mass traces `new_traces` based on the fitting result and the original traces `traces`. More...

bool	checkFeatureQuality_ (const std::shared_ptr< TraceFitter > &fitter, MassTraces &feature_traces, const double &seed_mz, const double &min_feature_score, String &error_msg, double &fit_score, double &correlation, double &final_score)
	Checks the feature based on different score thresholds and model constraints. More...

void	writeFeatureDebugInfo_ (const std::shared_ptr< TraceFitter > &fitter, const MassTraces &traces, const MassTraces &new_traces, bool feature_ok, const String &error_msg, const double final_score, const Int plot_nr, const PeakType &peak, const String &path="debug/features/")
	Creates several files containing plots and viewable data of the fitted mass trace. More...

FeatureFinderAlgorithmPicked &	operator= (const FeatureFinderAlgorithmPicked &)
	Not implemented. More...

	FeatureFinderAlgorithmPicked (const FeatureFinderAlgorithmPicked &)
	Not implemented. More...

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

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

FeatureFinderAlgorithm for picked peaks.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
write_debug	string	false	true, false	When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).
intensity:bins	int	10	min: 1	Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is. This parameter should be decreased, if the algorithm is used on small regions of a map.
mass_trace:mz_tolerance	float	0.03	min: 0.0	Tolerated m/z deviation of peaks belonging to the same mass trace. It should be larger than the m/z resolution of the instrument. This value must be smaller than that 1/charge_high!
mass_trace:min_spectra	int	10	min: 1	Number of spectra that have to show a similar peak mass in a mass trace.
mass_trace:max_missing	int	1	min: 0	Number of consecutive spectra where a high mass deviation or missing peak is acceptable. This parameter should be well below 'min_spectra'!
mass_trace:slope_bound	float	0.1	min: 0.0	The maximum slope of mass trace intensities when extending from the highest peak. This parameter is important to separate overlapping elution peaks. It should be increased if feature elution profiles fluctuate a lot.
isotopic_pattern:charge_low	int	1	min: 1	Lowest charge to search for.
isotopic_pattern:charge_high	int	4	min: 1	Highest charge to search for.
isotopic_pattern:mz_tolerance	float	0.03	min: 0.0	Tolerated m/z deviation from the theoretical isotopic pattern. It should be larger than the m/z resolution of the instrument. This value must be smaller than that 1/charge_high!
isotopic_pattern:intensity_percentage	float	10.0	min: 0.0 max: 100.0	Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.
isotopic_pattern:intensity_percentage_optional	float	0.1	min: 0.0 max: 100.0	Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.
isotopic_pattern:optional_fit_improvement	float	2.0	min: 0.0 max: 100.0	Minimal percental improvement of isotope fit to allow leaving out an optional peak.
isotopic_pattern:mass_window_width	float	25.0	min: 1.0 max: 200.0	Window width in Dalton for precalculation of estimated isotope distributions.
isotopic_pattern:abundance_12C	float	98.930000000000007	min: 0.0 max: 100.0	Rel. abundance of the light carbon. Modify if labeled.
isotopic_pattern:abundance_14N	float	99.632000000000005	min: 0.0 max: 100.0	Rel. abundance of the light nitrogen. Modify if labeled.
seed:min_score	float	0.8	min: 0.0 max: 1.0	Minimum seed score a peak has to reach to be used as seed. The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.
fit:max_iterations	int	500	min: 1	Maximum number of iterations of the fit.
feature:min_score	float	0.7	min: 0.0 max: 1.0	Feature score threshold for a feature to be reported. The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.
feature:min_isotope_fit	float	0.8	min: 0.0 max: 1.0	Minimum isotope fit of the feature before model fitting.
feature:min_trace_score	float	0.5	min: 0.0 max: 1.0	Trace score threshold. Traces below this threshold are removed after the model fitting. This parameter is important for features that overlap in m/z dimension.
feature:min_rt_span	float	0.333	min: 0.0 max: 1.0	Minimum RT span in relation to extended area that has to remain after model fitting.
feature:max_rt_span	float	2.5	min: 0.5	Maximum RT span in relation to extended area that the model is allowed to have.
feature:rt_shape	string	symmetric	symmetric, asymmetric	Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.
feature:max_intersection	float	0.35	min: 0.0 max: 1.0	Maximum allowed intersection of features.
feature:reported_mz	string	monoisotopic	maximum, average, monoisotopic	The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.
user-seed:rt_tolerance	float	5.0	min: 0.0	Allowed RT deviation of seeds from the user-specified seed position.
user-seed:mz_tolerance	float	1.1	min: 0.0	Allowed m/z deviation of seeds from the user-specified seed position.
user-seed:min_score	float	0.5	min: 0.0 max: 1.0	Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.
advanced:pseudo_rt_shift	float	500.0	min: 1.0	Pseudo RT shift used when .

Note:

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

Improvement:

RT model with tailing/fronting (Marc)

More general MZ model - e.g. based on co-elution or with sulfur-averagines (Marc)

Todo:

Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)

Implement user-specified seed lists support (Marc)

Member Typedef Documentation

◆ FloatDataArrays

typedef SpectrumType::FloatDataArrays FloatDataArrays

◆ IsotopePattern

typedef FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern IsotopePattern

protected

◆ MapType

typedef MSExperiment MapType

◆ MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace

protected

◆ MassTraces

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces

protected

◆ PeakType

typedef Peak1D PeakType

protected

◆ Seed

typedef FeatureFinderAlgorithmPickedHelperStructs::Seed Seed

protected

◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

◆ TheoreticalIsotopePattern

typedef FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern

protected

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmPicked() [1/2]

FeatureFinderAlgorithmPicked ( )

default constructor

◆ FeatureFinderAlgorithmPicked() [2/2]

FeatureFinderAlgorithmPicked ( const FeatureFinderAlgorithmPicked & )

private

Not implemented.

Member Function Documentation

◆ abort_()

void abort_	(	const Seed &	seed,
		const String &	reason
	)

protected

Writes the abort reason to the log file and counts occurrences for each reason.

◆ checkFeatureQuality_()

bool checkFeatureQuality_	(	const std::shared_ptr< TraceFitter > &	fitter,
		MassTraces &	feature_traces,
		const double &	seed_mz,
		const double &	min_feature_score,
		String &	error_msg,
		double &	fit_score,
		double &	correlation,
		double &	final_score
	)

protected

Checks the feature based on different score thresholds and model constraints.

Feature can get invalid for following reasons:

Invalid fit: Fitted model is bigger than 'max_rt_span'
Invalid feature after fit - too few traces or peaks left
Invalid fit: Center outside of feature bounds
Invalid fit: Less than 'min_rt_span' left after fit
Feature quality too low after fit

Parameters

fitter	The TraceFitter containing the results from the rt profile fitting step.
feature_traces	Cropped feature mass traces.
seed_mz	Mz of the seed
min_feature_score	Minimal required feature score
error_msg	Will be filled with the error message, if the feature is invalid
fit_score	Will be filled with the fit score
correlation	Will be filled with correlation between feature and model
final_score	Will be filled with the final score

Returns: true if the feature is valid

◆ chooseTraceFitter_()

std::unique_ptr<TraceFitter> chooseTraceFitter_ ( double & tau )

protected

Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto)

Returns: A pointer to the trace fitter that should be used.

◆ cropFeature_()

void cropFeature_	(	const std::shared_ptr< TraceFitter > &	fitter,
		const MassTraces &	traces,
		MassTraces &	new_traces
	)

protected

Creates new mass traces new_traces based on the fitting result and the original traces traces.

Parameters

fitter	The TraceFitter containing the results from the rt profile fitting step.
traces	Original mass traces found in the experiment.
new_traces	Mass traces created by cropping the original mass traces.

◆ extendMassTrace_()

void extendMassTrace_	(	MassTrace &	trace,
		SignedSize	spectrum_index,
		double	mz,
		bool	increase_rt,
		Size	meta_index_overall,
		double	min_rt = `0.0`,
		double	max_rt = `0.0`
	)		const

protected

Extends a single mass trace in one RT direction.

How to use this method:

Add the starting peak to the trace
Indicate using increase_rt whether to extend in downstream or upstream direction

Parameters

trace	The trace that should be extended
spectrum_index	The index of the spectrum from which on the mass trace should be extended
mz	The mz location (center) of the trace
increase_rt	Indicator whether the extension is done in forward or backward direction (with respect to the current spectrum)
meta_index_overall	The index of the overall score
min_rt	The rt minimum up to which the trace will be extended.
max_rt	The rt maximum up to which the trace will be extended.

Note: This method assumes that it extends from a local maximum.; If min_rt or max_rt are set to 0.0 no boundary is assumed in the respective direction.

◆ extendMassTraces_()

void extendMassTraces_	(	const IsotopePattern &	pattern,
		MassTraces &	traces,
		Size	meta_index_overall
	)		const

protected

Extends all mass traces of an isotope pattern in one step

Parameters

pattern	The IsotopePattern that should be extended.
traces	The MassTraces datastructure where the extended mass traces will be stored in.
meta_index_overall	The index of the data array where the quality scores for the given charge are stored.

◆ findBestIsotopeFit_()

double findBestIsotopeFit_	(	const Seed &	center,
		UInt	charge,
		IsotopePattern &	best_pattern
	)		const

protected

Finds the best fitting position of the isotopic pattern estimate defined by center.

Parameters

center	the maximum peak of the isotope distribution (contains charge as well)
charge	The charge of the pattern
best_pattern	Returns the indices of the isotopic peaks. If a isotopic peak is missing -1 is returned.

◆ findIsotope_()

void findIsotope_	(	double	pos,
		Size	spectrum_index,
		IsotopePattern &	pattern,
		Size	pattern_index,
		Size &	peak_index
	)		const

protected

Searches for an isotopic peak in the current spectrum and the adjacent spectra.

Parameters

pos	m/z position of the searched for peak
spectrum_index	index of the central spectrum
pattern	IsotopePattern to store found peaks
pattern_index	index of the isotope in the pattern
peak_index	starting index of the search (to avoid multiple binary searches)

◆ getDefaultParameters()

virtual Param getDefaultParameters ( ) const

inlinevirtual

◆ getIsotopeDistribution_()

const TheoreticalIsotopePattern& getIsotopeDistribution_ ( double mass ) const

protected

Returns the isotope distribution for a certain mass window.

◆ intensityScore_() [1/2]

double intensityScore_	(	Size	rt_bin,
		Size	mz_bin,
		double	intensity
	)		const

protected

◆ intensityScore_() [2/2]

double intensityScore_	(	Size	spectrum,
		Size	peak
	)		const

protected

Compute the intensity score for the peak peak in spectrum spectrum.

The intensity score is computed by interpolating the score between the 4 nearest intensity bins. The scores from the different bins are weighted by the distance of the bin center to the peak.

Parameters

spectrum	Index of the spectrum we are currently looking at
peak	Index of the peak that should be scored inside the spectrum `spectrum`

◆ intersection_()

double intersection_	(	const Feature &	f1,
		const Feature &	f2
	)		const

protected

Calculates the intersection between features. The value is normalized by the size of the smaller feature, so it ranges from 0 to 1.

◆ isotopeScore_()

double isotopeScore_	(	const TheoreticalIsotopePattern &	isotopes,
		IsotopePattern &	pattern,
		bool	consider_mz_distances
	)		const

protected

Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern.

◆ nearest_()

Size nearest_	(	double	pos,
		const MSSpectrum &	spec,
		Size	start
	)		const

protected

Returns the index of the peak nearest to m/z pos in spectrum spec (linear search starting from index start)

◆ operator=()

FeatureFinderAlgorithmPicked& operator= ( const FeatureFinderAlgorithmPicked & )

private

Not implemented.

◆ positionScore_()

double positionScore_	(	double	pos1,
		double	pos2,
		double	allowed_deviation
	)		const

protected

Calculates a score between 0 and 1 for the m/z deviation of two peaks.

◆ run() [1/2]

void run ( )

protected

◆ run() [2/2]

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

◆ setData()

void setData	(	const MSExperiment &	map,
		FeatureMap &	features
	)

◆ setSeeds()

void setSeeds ( 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.

◆ writeFeatureDebugInfo_()

void writeFeatureDebugInfo_	(	const std::shared_ptr< TraceFitter > &	fitter,
		const MassTraces &	traces,
		const MassTraces &	new_traces,
		bool	feature_ok,
		const String &	error_msg,
		const double	final_score,
		const Int	plot_nr,
		const PeakType &	peak,
		const String &	path = `"debug/features/"`
	)

protected

Creates several files containing plots and viewable data of the fitted mass trace.

Parameters

fitter	The TraceFitter containing the results from the rt profile fitting step.
traces	Original mass traces found in the spectra
new_traces	Cropped feature mass traces
feature_ok	Status of the feature
error_msg	If the feature is invalid, `error_msg` contains the reason
final_score	Final score of the feature
plot_nr	Index of the feature
peak	The Seed Peak
path	The path where to put the debug files (default is debug/features)

Member Data Documentation

◆ abort_reasons_

std::map<Seed, String> abort_reasons_

protected

Array of abort reasons.

◆ aborts_

std::map<String, UInt> aborts_

protected

Array of abort reasons.

◆ debug_

bool debug_

protected

debug flag

◆ features_

FeatureMap* features_

protected

◆ intensity_bins_

UInt intensity_bins_

protected

Number of bins (in RT and MZ) for intensity significance estimation.

◆ intensity_mz_step_

double intensity_mz_step_

protected

m/z bin width

◆ intensity_percentage_

double intensity_percentage_

protected

Isotope pattern intensity contribution of required peaks.

◆ intensity_percentage_optional_

double intensity_percentage_optional_

protected

Isotope pattern intensity contribution of optional peaks.

◆ intensity_rt_step_

double intensity_rt_step_

protected

RT bin width.

◆ intensity_thresholds_

std::vector<std::vector<std::vector<double> > > intensity_thresholds_

protected

Precalculated intensity 20-quantiles (binned)

◆ isotope_distributions_

std::vector<TheoreticalIsotopePattern> isotope_distributions_

protected

Vector of precalculated isotope distributions for several mass windows.

◆ log_

std::ofstream log_

mutableprotected

Output stream for log/debug info.

◆ map_

MapType map_

protected

editable copy of the map

◆ mass_window_width_

double mass_window_width_

protected

Width of the isotope pattern mass bins.

◆ max_feature_intersection_

double max_feature_intersection_

protected

Maximum allowed feature intersection (if larger, that one of the feature is removed)

◆ max_missing_trace_peaks_

UInt max_missing_trace_peaks_

protected

Stores mass_trace:max_missing.

◆ max_rt_span_

double max_rt_span_

protected

Maximum RT range the model is allowed to span.

◆ min_isotope_fit_

double min_isotope_fit_

protected

Minimum isotope pattern fit for a feature.

◆ min_rt_span_

double min_rt_span_

protected

Minimum RT range that has to be left after the fit.

◆ min_spectra_

UInt min_spectra_

protected

Number of spectra that have to show the same mass (for finding a mass trace)

◆ min_trace_score_

double min_trace_score_

protected

Minimum quality of a traces.

◆ optional_fit_improvement_

double optional_fit_improvement_

protected

Minimal improvement for leaving out optional isotope.

◆ pattern_tolerance_

double pattern_tolerance_

protected

Stores mass_trace:mz_tolerance.

◆ reported_mz_

String reported_mz_

protected

The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.

◆ seeds_

FeatureMap seeds_

protected

User-specified seed list.

◆ slope_bound_

double slope_bound_

protected

Max slope of mass trace intensities.

◆ trace_tolerance_

double trace_tolerance_

protected

Stores isotopic_pattern:mz_tolerance.

Protected Attributes

Type definitions

Members for intensity significance estimation

Handling of fitted mass traces

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ FloatDataArrays

◆ IsotopePattern

◆ MapType

◆ MassTrace

◆ MassTraces

◆ PeakType

◆ Seed

◆ SpectrumType

◆ TheoreticalIsotopePattern

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmPicked() [1/2]

◆ FeatureFinderAlgorithmPicked() [2/2]

Member Function Documentation

◆ abort_()

◆ checkFeatureQuality_()

◆ chooseTraceFitter_()

◆ cropFeature_()

◆ extendMassTrace_()

◆ extendMassTraces_()

◆ findBestIsotopeFit_()

◆ findIsotope_()

◆ getDefaultParameters()

◆ getIsotopeDistribution_()

◆ intensityScore_() [1/2]

◆ intensityScore_() [2/2]

◆ intersection_()

◆ isotopeScore_()

◆ nearest_()

◆ operator=()

◆ positionScore_()

◆ run() [1/2]

◆ run() [2/2]

◆ setData()

◆ setSeeds()

◆ updateMembers_()

◆ writeFeatureDebugInfo_()

Member Data Documentation

◆ abort_reasons_

◆ aborts_

◆ debug_

◆ features_

◆ intensity_bins_

◆ intensity_mz_step_

◆ intensity_percentage_

◆ intensity_percentage_optional_

◆ intensity_rt_step_

◆ intensity_thresholds_

◆ isotope_distributions_

◆ log_

◆ map_

◆ mass_window_width_

◆ max_feature_intersection_

◆ max_missing_trace_peaks_

◆ max_rt_span_

◆ min_isotope_fit_

◆ min_rt_span_

◆ min_spectra_

◆ min_trace_score_

◆ optional_fit_improvement_

◆ pattern_tolerance_

◆ reported_mz_

◆ seeds_

◆ slope_bound_

◆ trace_tolerance_