MassTraceDetection Class Reference

#include <OpenMS/FEATUREFINDER/MassTraceDetection.h>

Inheritance diagram for MassTraceDetection:

Classes
struct	Apex
struct	PeakCandidate
	Encapsulates peak finding logic for both up and down directions. More...
struct	TraceExtensionState
	Encapsulates trace extension state. More...

Public Types
enum	TraceTerminationCriterion { OUTLIER , SAMPLE_RATE }
	Trace termination criteria enum for performance optimization. More...
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	MassTraceDetection ()
	Default constructor.
	~MassTraceDetection () override
	Default destructor.
Main computation methods
void	run (const PeakMap &, std::vector< MassTrace > &, const Size max_traces=0)
void	run (PeakMap::ConstAreaIterator &begin, PeakMap::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
	Invokes the run method (see above) on merely a subregion of a MSExperiment map.
bool	hasFwhmMz () const
	determine if meta array is available
bool	hasFwhmIm () const
bool	hasCentroidIm () const
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Private methods and members
bool	has_fwhm_mz_ = false
bool	has_fwhm_im_ = false
bool	has_centroid_im_ = false
double	mass_error_ppm_
double	mass_error_da_
double	noise_threshold_int_
double	chrom_peak_snr_
double	ion_mobility_tolerance_
MassTrace::MT_QUANTMETHOD	quant_method_
TraceTerminationCriterion	trace_termination_criterion_
Size	trace_termination_outliers_
double	min_sample_rate_
double	min_trace_length_
double	max_trace_length_
bool	reestimate_mt_sd_
int	fwhm_meta_idx_ = -1
int	ion_mobility_idx_ = -1
int	im_fwhm_idx_ = -1
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.
static void	updateIterativeWeightedMean_ (const double &added_value, const double &added_intensity, double &centroid_value, double &prev_counter, double &prev_denom)
	allows for the iterative computation of intensity weighted of a mass trace's centroid m/z or ion mobility
void	run_ (const std::vector< Apex > &chrom_apices, const Size peak_count, const PeakMap &work_exp, const std::vector< Size > &spec_offsets, std::vector< MassTrace > &found_masstraces, const Size max_traces=0)
	The internal run method.
void	getIMIndices_ (const PeakMap &spectra, int &fwhm_meta_idx, bool &has_fwhm_mz, int &im_idx, bool &has_centroid_im, int &im_fwhm_idx, bool &has_fwhm_im) const
	Internal helper to extract and validate metadata float array indices.
PeakCandidate	findBestPeak_ (const MSSpectrum &spectrum, double centroid_mz, double ftl_sd, double centroid_im=-1.0) const
	Find the best matching peak in a spectrum considering m/z and optionally ion mobility.
bool	isPeakAcceptable_ (const PeakCandidate &candidate, double centroid_mz, double ftl_sd, double centroid_im, Size spectrum_idx, const std::vector< Size > &spec_offsets, const std::vector< bool > &peak_visited) const
	Check if peak candidate meets acceptance criteria.
void	processPeak_ (const PeakCandidate &candidate, const MSSpectrum &spectrum, std::list< PeakType > &current_trace, std::vector< std::pair< Size, Size > > &gathered_idx, std::vector< double > &fwhms_mz, std::vector< double > &fwhms_im, double &centroid_mz, double &centroid_im, double &prev_counter, double &prev_denom, double &prev_counter_im, double &prev_denom_im, double &ftl_sd, double &intensity_so_far, Size spectrum_idx, bool is_upward_extension)
	Process a single peak during trace extension.
bool	isTraceValid_ (const std::list< PeakType > &trace, Size total_scans_visited, Size consecutive_missed_down, Size consecutive_missed_up) const
	Check if a mass trace meets quality criteria.

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static std::atomic< int >	recursion_depth_

Member Enumeration Documentation

TraceTerminationCriterion

enum TraceTerminationCriterion

Trace termination criteria enum for performance optimization.

Enumerator
OUTLIER	Terminate when consecutive outliers exceed threshold.
SAMPLE_RATE	Terminate when sample rate falls below threshold.

Constructor & Destructor Documentation

MassTraceDetection()

MassTraceDetection

(

)

Default constructor.

~MassTraceDetection()

~MassTraceDetection ( )

override

Default destructor.

Member Function Documentation

findBestPeak_()

PeakCandidate findBestPeak_ ( const MSSpectrum &  spectrum, double  centroid_mz, double  ftl_sd, double  centroid_im = -1.0  ) const

private

Find the best matching peak in a spectrum considering m/z and optionally ion mobility.

getIMIndices_()

void getIMIndices_ ( const PeakMap &  spectra, int &  fwhm_meta_idx, bool &  has_fwhm_mz, int &  im_idx, bool &  has_centroid_im, int &  im_fwhm_idx, bool &  has_fwhm_im  ) const

private

Internal helper to extract and validate metadata float array indices.

hasCentroidIm()

bool hasCentroidIm ( ) const

inline

hasFwhmIm()

bool hasFwhmIm ( ) const

inline

hasFwhmMz()

bool hasFwhmMz ( ) const

inline

determine if meta array is available

isPeakAcceptable_()

bool isPeakAcceptable_ ( const PeakCandidate &  candidate, double  centroid_mz, double  ftl_sd, double  centroid_im, Size  spectrum_idx, const std::vector< Size > &  spec_offsets, const std::vector< bool > &  peak_visited  ) const

private

Check if peak candidate meets acceptance criteria.

isTraceValid_()

bool isTraceValid_ ( const std::list< PeakType > &  trace, Size  total_scans_visited, Size  consecutive_missed_down, Size  consecutive_missed_up  ) const

private

Check if a mass trace meets quality criteria.

processPeak_()

void processPeak_ ( const PeakCandidate &  candidate, const MSSpectrum &  spectrum, std::list< PeakType > &  current_trace, std::vector< std::pair< Size, Size > > &  gathered_idx, std::vector< double > &  fwhms_mz, std::vector< double > &  fwhms_im, double &  centroid_mz, double &  centroid_im, double &  prev_counter, double &  prev_denom, double &  prev_counter_im, double &  prev_denom_im, double &  ftl_sd, double &  intensity_so_far, Size  spectrum_idx, bool  is_upward_extension  )

private

Process a single peak during trace extension.

run() [1/2]

void run	(	const PeakMap &	,
		std::vector< MassTrace > &	,
		const Size	max_traces = 0
	)

Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.

Note

The input MSExperiment's spectra must already be sorted by retention time (see MSExperiment::sortSpectra()). Unsorted input is not checked for tie-order within equal-RT spectra (e.g. ion-mobility data); see run_() precondition.

run() [2/2]

void run	(	PeakMap::ConstAreaIterator &	begin,
		PeakMap::ConstAreaIterator &	end,
		std::vector< MassTrace > &	found_masstraces
	)

Invokes the run method (see above) on merely a subregion of a MSExperiment map.

run_()

void run_ ( const std::vector< Apex > &  chrom_apices, const Size  peak_count, const PeakMap &  work_exp, const std::vector< Size > &  spec_offsets, std::vector< MassTrace > &  found_masstraces, const Size  max_traces = 0  )

private

The internal run method.

updateIterativeWeightedMean_()

static void updateIterativeWeightedMean_ ( const double &  added_value, const double &  added_intensity, double &  centroid_value, double &  prev_counter, double &  prev_denom  )

staticprotected

allows for the iterative computation of intensity weighted of a mass trace's centroid m/z or ion mobility

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

chrom_peak_snr_

double chrom_peak_snr_

private

fwhm_meta_idx_

int fwhm_meta_idx_ = -1

mutableprivate

has_centroid_im_

bool has_centroid_im_ = false

private

has_fwhm_im_

bool has_fwhm_im_ = false

private

has_fwhm_mz_

bool has_fwhm_mz_ = false

private

im_fwhm_idx_

int im_fwhm_idx_ = -1

mutableprivate

ion_mobility_idx_

int ion_mobility_idx_ = -1

mutableprivate

ion_mobility_tolerance_

double ion_mobility_tolerance_

private

mass_error_da_

double mass_error_da_

private

mass_error_ppm_

double mass_error_ppm_

private

max_trace_length_

double max_trace_length_

private

min_sample_rate_

double min_sample_rate_

private

min_trace_length_

double min_trace_length_

private

noise_threshold_int_

double noise_threshold_int_

private

quant_method_

MassTrace::MT_QUANTMETHOD quant_method_

private

reestimate_mt_sd_

bool reestimate_mt_sd_

private

trace_termination_criterion_

TraceTerminationCriterion trace_termination_criterion_

private

trace_termination_outliers_

Size trace_termination_outliers_

private