Merges blocks of MS or MS2 spectra. More...

#include <OpenMS/PROCESSING/SPECTRAMERGING/SpectraMerger.h>

Inheritance diagram for SpectraMerger:

Collaboration diagram for SpectraMerger:

Classes
class	SpectraDistance_

Public Types
typedef std::map< Size, std::vector< Size > >	MergeBlocks
	blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-spectrum)) More...

typedef std::map< Size, std::vector< std::pair< Size, double > > >	AverageBlocks
	blocks of spectra (master-spectrum index to update to spectra to average over) More...

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

Public Member Functions
	SpectraMerger ()
	default constructor More...

	SpectraMerger (const SpectraMerger &source)
	copy constructor More...

	SpectraMerger (SpectraMerger &&source)=default
	move constructor More...

	~SpectraMerger () override
	destructor More...

SpectraMerger &	operator= (const SpectraMerger &source)
	assignment operator More...

SpectraMerger &	operator= (SpectraMerger &&source)=default
	move-assignment operator More...

template<typename MapType >
void	mergeSpectraBlockWise (MapType &exp)

template<typename MapType >
void	mergeSpectraPrecursors (MapType &exp)
	merges spectra with similar precursors (must have MS2 level) More...

template<typename MapType >
void	average (MapType &exp, const String &average_type, int ms_level=-1)
	average over neighbouring spectra 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
static bool	areMassesMatched (double mz1, double mz2, double tol_ppm, int max_c)
	check if the first and second mzs might be from the same mass 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
template<typename MapType >
void	mergeSpectra_ (MapType &exp, const MergeBlocks &spectra_to_merge, const UInt ms_level)
	merges blocks of spectra of a certain level More...

template<typename MapType >
void	averageProfileSpectra_ (MapType &exp, const AverageBlocks &spectra_to_average_over, const UInt ms_level)
	average spectra (profile mode) More...

template<typename MapType >
void	averageCentroidSpectra_ (MapType &exp, const AverageBlocks &spectra_to_average_over, const UInt ms_level)
	average spectra (centroid mode) More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Additional Inherited Members
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

Merges blocks of MS or MS2 spectra.

Parameter's are accessible via the DefaultParamHandler.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mz_binning_width	float	5.0	min: 0.0	minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.
mz_binning_width_unit	string	ppm	Da, ppm	Unit in which the distance between two data points or peaks is given.
sort_blocks	string	RT_ascending	RT_ascending, RT_descending	Sort blocks by before merging them (useful for precursor order)
average_gaussian:spectrum_type	string	automatic	profile, centroid, automatic	Spectrum type of the MS level to be averaged
average_gaussian:ms_level	int	1	min: 0	If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.
average_gaussian:rt_FWHM	float	5.0	min: 0.0 max: 1.0e11	FWHM of Gauss curve in seconds to be averaged over.
average_gaussian:cutoff	float	0.01	min: 0.0 max: 1.0	Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.
average_gaussian:precursor_mass_tol	float	0.0	min: 0.0	PPM mass tolerance for precursor mass. If set, MSn (n>2) spectra of precursor masses within the tolerance are averaged.
average_gaussian:precursor_max_charge	int	1	min: 1	Possible maximum precursor ion charge. Effective only when average_gaussian:precursor_mass_tol option is active.
average_tophat:spectrum_type	string	automatic	profile, centroid, automatic	Spectrum type of the MS level to be averaged
average_tophat:ms_level	int	1	min: 0	If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.
average_tophat:rt_range	float	5.0	min: 0.0 max: 1.0e11	RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.
average_tophat:rt_unit	string	scans	scans, seconds	Unit for RT range.
block_method:ms_levels	int list	[1]	min: 1	Merge spectra of this level. All spectra with other MS levels remain untouched.
block_method:rt_block_size	int	5	min: 1	Maximum number of scans to be summed up.
block_method:rt_max_length	float	0.0	min: 0.0 max: 1.0e11	Maximum RT size of the block in seconds (0.0 = no size restriction).
precursor_method:mz_tolerance	float	1.0e-04	min: 0.0	Max m/z distance of the precursor entries of two spectra to be merged in [Da].
precursor_method:mass_tolerance	float	0.0	min: 0.0	Max mass distance of the precursor entries of two spectra to be merged in [Da]. Active when set to a positive value.
precursor_method:rt_tolerance	float	5.0	min: 0.0	Max RT distance of the precursor entries of two spectra to be merged in [s].

Note:

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

Member Typedef Documentation

◆ AverageBlocks

typedef std::map<Size, std::vector<std::pair<Size, double> > > AverageBlocks

blocks of spectra (master-spectrum index to update to spectra to average over)

◆ MergeBlocks

typedef std::map<Size, std::vector<Size> > MergeBlocks

blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-spectrum))

Constructor & Destructor Documentation

◆ SpectraMerger() [1/3]

SpectraMerger ( )

default constructor

◆ SpectraMerger() [2/3]

SpectraMerger ( const SpectraMerger & source )

copy constructor

◆ SpectraMerger() [3/3]

SpectraMerger ( SpectraMerger && source )

default

move constructor

◆ ~SpectraMerger()

~SpectraMerger ( )

override

destructor

Member Function Documentation

◆ areMassesMatched()

static bool areMassesMatched	(	double	mz1,
		double	mz2,
		double	tol_ppm,
		int	max_c
	)

inlinestatic

check if the first and second mzs might be from the same mass

Parameters

mz1	the first m/z value
mz2	the second m/z value
tol_ppm	tolerance in ppm
max_c	maximum possible charge value

References OpenMS::Constants::ISOTOPE_MASSDIFF_55K_U, and OpenMS::Constants::PROTON_MASS_U.

◆ average()

void average	(	MapType &	exp,
		const String &	average_type,
		int	ms_level = `-1`
	)

inline

average over neighbouring spectra

Parameters

exp	experimental data to be averaged
average_type	averaging type to be used ("gaussian" or "tophat")
ms_level	targe MS level. If it is -1, ms_level will be determined by ms_level parameter.

References MSExperiment::begin(), SpectrumSettings::CENTROID, MSExperiment::end(), SpectrumSettings::PROFILE, MSExperiment::sortSpectra(), and OpenMS::Math::sum().

Referenced by TOPPFLASHDeconv::main_().

◆ averageCentroidSpectra_()

void averageCentroidSpectra_	(	MapType &	exp,
		const AverageBlocks &	spectra_to_average_over,
		const UInt	ms_level
	)

inlineprotected

average spectra (centroid mode)

Averages spectra in centroid mode of one MS level in an experiment. The blocks of spectra to be combined and their relative weights have previously determined. The averaged spectra are generated in two steps: (1) The m/z of all spectra in a block are collected and sorted. Their corresponding intensities are weighted. (2) m/z positions closer than mz_binning_width are combined to a single peak. The m/z are averaged and the corresponding intensities summed.

Parameters

exp	experimental data to be averaged
spectra_to_average_over	mapping of spectral index to set of spectra to average over with corresponding weights
ms_level	MS level of spectra to be averaged

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSSpectrum::clear(), MSExperiment::end(), ProgressLogger::endProgress(), Peak1D::setIntensity(), Peak1D::setMZ(), ProgressLogger::setProgress(), and ProgressLogger::startProgress().

◆ averageProfileSpectra_()

void averageProfileSpectra_	(	MapType &	exp,
		const AverageBlocks &	spectra_to_average_over,
		const UInt	ms_level
	)

inlineprotected

average spectra (profile mode)

Averages spectra in profile mode of one MS level in an experiment. The blocks of spectra to be combined and their relative weights have previously been determined. The averaged spectra are generated in two steps: (1) The m/z of all spectra in a block are collected and sorted. m/z positions closer than mz_binning_width are removed. (2) At these positions the weighted sum of all spline interpolations is calculated.

The first step ensures roughly the same sampling rate as the one of the original spectra. The exact m/z position is not crucial, since not the original intensities but the spline-interpolated intensities are used.

Parameters

exp	experimental data to be averaged
spectra_to_average_over	mapping of spectral index to set of spectra to average over with corresponding weights
ms_level	MS level of spectra to be averaged

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSSpectrum::clear(), MSExperiment::end(), SplineInterpolatedPeaks::Navigator::eval(), SplineInterpolatedPeaks::getNavigator(), SplineInterpolatedPeaks::getPosMax(), SplineInterpolatedPeaks::getPosMin(), Peak1D::setIntensity(), and Peak1D::setMZ().

◆ mergeSpectra_()

void mergeSpectra_	(	MapType &	exp,
		const MergeBlocks &	spectra_to_merge,
		const UInt	ms_level
	)

inlineprotected

merges blocks of spectra of a certain level

Merges spectra belonging to the same block, setting their MS level to ms_level. All old spectra of level ms_level are removed, and the new consensus spectra (one per block) are added. All spectra with other MS levels remain untouched. The resulting map is NOT sorted!

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSExperiment::clear(), MSSpectrum::clear(), MSExperiment::end(), SpectrumSettings::getNativeID(), SpectrumSettings::getPrecursors(), MSSpectrum::getRT(), MSExperiment::getSpectra(), SpectrumAlignment::getSpectrumAlignment(), OPENMS_LOG_INFO, OPENMS_LOG_WARN, MSSpectrum::setMSLevel(), SpectrumSettings::setNativeID(), DefaultParamHandler::setParameters(), SpectrumSettings::setPrecursors(), MSSpectrum::setRT(), Param::setValue(), MSExperiment::size(), MSSpectrum::sortByPosition(), and SpectrumSettings::unify().

◆ mergeSpectraBlockWise()

void mergeSpectraBlockWise ( MapType & exp )

inline

Merges spectra block-wise, i.e. spectra are merged if they are close in RT. Each block consists of at most block_method:rt_block_size spectra and spans at most block_method:rt_max_length seconds. The MS levels to be merged are specified by block_method:ms_levels. Spectra with other MS levels remain untouched.

References MSExperiment::begin(), MSExperiment::end(), and MSExperiment::sortSpectra().

Referenced by TOPPFLASHDeconv::main_().

◆ mergeSpectraPrecursors()

void mergeSpectraPrecursors ( MapType & exp )

inline

merges spectra with similar precursors (must have MS2 level)

References ClusterHierarchical::cluster(), ClusterAnalyzer::cut(), OPENMS_LOG_WARN, Peak2D::setMZ(), DefaultParamHandler::setParameters(), Peak2D::setRT(), MSExperiment::size(), and MSExperiment::sortSpectra().

◆ operator=() [1/2]

SpectraMerger& operator= ( const SpectraMerger & source )

assignment operator

◆ operator=() [2/2]

SpectraMerger& operator= ( SpectraMerger && source )

default

move-assignment operator

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AverageBlocks

◆ MergeBlocks

Constructor & Destructor Documentation

◆ SpectraMerger() [1/3]

◆ SpectraMerger() [2/3]

◆ SpectraMerger() [3/3]

◆ ~SpectraMerger()

Member Function Documentation

◆ areMassesMatched()

◆ average()

◆ averageCentroidSpectra_()

◆ averageProfileSpectra_()

◆ mergeSpectra_()

◆ mergeSpectraBlockWise()

◆ mergeSpectraPrecursors()

◆ operator=() [1/2]

◆ operator=() [2/2]