The ChromatogramExtractor extracts chromatograms from a spectra file. More...

#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>

Inheritance diagram for ChromatogramExtractor:

Collaboration diagram for ChromatogramExtractor:

Public Types
typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates	ExtractionCoordinates

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

Public Member Functions
template<typename ExperimentT >
void	extractChromatograms (const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double mz_extraction_window, bool ppm, TransformationDescription trafo, double rt_extraction_window, const String &filter)
	Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map. More...

void	extractChromatograms (const OpenSwath::SpectrumAccessPtr input, std::vector< OpenSwath::ChromatogramPtr > &output, const std::vector< ExtractionCoordinates > &extraction_coordinates, double mz_extraction_window, bool ppm, const String &filter)
	Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates. More...

void	extractChromatograms (const OpenSwath::SpectrumAccessPtr input, std::vector< OpenSwath::ChromatogramPtr > &output, const std::vector< ExtractionCoordinates > &extraction_coordinates, double mz_extraction_window, bool ppm, double im_extraction_window, const String &filter)
	Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates. More...

template<typename SpectrumT >
void	extract_value_tophat (const SpectrumT &input, const double mz, Size &peak_idx, double &integrated_intensity, const double extract_window, const bool ppm)

template<typename SpectrumT >
void	extract_value_bartlett (const SpectrumT &input, const double mz, Size &peak_idx, double &integrated_intensity, const double extract_window, const bool ppm)

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	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 () const
	Ends the progress display. More...

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

Static Public Member Functions
static void	prepare_coordinates (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ExtractionCoordinates > &coordinates, const OpenMS::TargetedExperiment &transition_exp, const double rt_extraction_window, const bool ms1=false, const int ms1_isotopes=0)
	Prepare the extraction coordinates from a TargetedExperiment. More...

static void	prepare_coordinates (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1=false, const int ms1_isotopes=0)

template<typename TransitionExpT >
static void	return_chromatogram (const std::vector< OpenSwath::ChromatogramPtr > &chromatograms, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, TransitionExpT &transition_exp_used, SpectrumSettings settings, std::vector< OpenMS::MSChromatogram > &output_chromatograms, bool ms1, double im_extraction_width=0.0)
	This converts the ChromatogramPtr to MSChromatogram and adds meta-information. More...

Private Member Functions
template<class SpectrumSettingsT , class ChromatogramT >
void	prepareSpectra_ (SpectrumSettingsT &settings, std::vector< ChromatogramT > &chromatograms, OpenMS::TargetedExperiment &transition_exp)
	This populates the chromatograms vector with empty chromatograms (but sets their meta-information) More...

bool	outsideExtractionWindow_ (const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window)

int	getFilterNr_ (const String &filter)

void	populatePeptideRTMap_ (OpenMS::TargetedExperiment &transition_exp, double rt_extraction_window)

Static Private Member Functions
template<typename TransitionExpT >
static String	extract_id_ (TransitionExpT &transition_exp_used, const String &id, int &prec_charge)
	Extracts id (peptide sequence or compound name) for a compound. More...

Private Attributes
std::map< OpenMS::String, double >	PeptideRTMap_

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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

The ChromatogramExtractor extracts chromatograms from a spectra file.

It will take as input a set of transitions coordinates and will extract the signal of the provided map at the product ion m/z and retention time (rt) values specified by the extraction coordinates. There are two interfaces, the old interface will take a full TargetedExperiment and assume that one wants to extract at the m/z of the transitions present in the TargetedExperiment. The new interface (see also the ChromatogramExtractorAlgorithm class) only expects a set of coordinates which are up to the user to fill but a convenient prepare_coordinates function is provided to create the coordinates for the most common case of an MS2 and MS1 extraction.

In the case of MS2 extraction, the map is assumed to originate from a SWATH (data-independent acquisition or DIA) experiment.

Member Typedef Documentation

◆ ExtractionCoordinates

typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates ExtractionCoordinates

Member Function Documentation

◆ extract_id_()

static String extract_id_	(	TransitionExpT &	transition_exp_used,
		const String &	id,
		int &	prec_charge
	)

staticprivate

Extracts id (peptide sequence or compound name) for a compound.

Parameters

transition_exp_used	The transition experiment used as input (is constant) and either of type LightTargetedExperiment or TargetedExperiment
id	The identifier of the compound or peptide
prec_charge	The charge state of the precursor

◆ extract_value_bartlett()

void extract_value_bartlett	(	const SpectrumT &	input,
		const double	mz,
		Size &	peak_idx,
		double &	integrated_intensity,
		const double	extract_window,
		const bool	ppm
	)

inline

Note: : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

◆ extract_value_tophat()

void extract_value_tophat	(	const SpectrumT &	input,
		const double	mz,
		Size &	peak_idx,
		double &	integrated_intensity,
		const double	extract_window,
		const bool	ppm
	)

inline

Note: : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

◆ extractChromatograms() [1/3]

void extractChromatograms	(	const ExperimentT &	input,
		ExperimentT &	output,
		OpenMS::TargetedExperiment &	transition_exp,
		double	mz_extraction_window,
		bool	ppm,
		TransformationDescription	trafo,
		double	rt_extraction_window,
		const String &	filter
	)

inline

Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map.

Parameters

input	The input spectra from which to extract chromatograms
output	The output vector in which to store the chromatograms
transition_exp	The extraction coordinates (m/z, RT, ion mobility)
mz_extraction_window	Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
ppm	Whether mz windows in in ppm
trafo	A transformation description for RT space
rt_extraction_window	Extracts a window of this size in RT dimension (e.g. a window of 600 seconds means an extraction of 300 seconds on either side)
filter	Which filter to use (bartlett or tophat)

Note: : it will replace chromatograms in the output map, not append to them!; : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

References TargetedExperiment::getTransitions(), TransformationDescription::invert(), OpenMS::Constants::k, and TargetedExperiment::sortTransitionsByProductMZ().

◆ extractChromatograms() [2/3]

void extractChromatograms	(	const OpenSwath::SpectrumAccessPtr	input,
		std::vector< OpenSwath::ChromatogramPtr > &	output,
		const std::vector< ExtractionCoordinates > &	extraction_coordinates,
		double	mz_extraction_window,
		bool	ppm,
		const String &	filter
	)

inline

Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.

Parameters

input	The input spectra from which to extract chromatograms
output	The output vector in which to store the chromatograms (needs to be of the same length as the extraction coordinates, use prepare_coordinates)
extraction_coordinates	The extraction coordinates (m/z, RT, ion mobility)
mz_extraction_window	Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
ppm	Whether mz windows in in ppm
filter	Which filter to use (bartlett or tophat)

Note: : whenever possible, please use this ChromatogramExtractorAlgorithm implementation

References ChromatogramExtractorAlgorithm::extractChromatograms().

◆ extractChromatograms() [3/3]

void extractChromatograms	(	const OpenSwath::SpectrumAccessPtr	input,
		std::vector< OpenSwath::ChromatogramPtr > &	output,
		const std::vector< ExtractionCoordinates > &	extraction_coordinates,
		double	mz_extraction_window,
		bool	ppm,
		double	im_extraction_window,
		const String &	filter
	)

inline

Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.

Parameters

input	The input spectra from which to extract chromatograms
output	The output vector in which to store the chromatograms (needs to be of the same length as the extraction coordinates, use prepare_coordinates)
extraction_coordinates	The extraction coordinates (m/z, RT, ion mobility)
mz_extraction_window	Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
ppm	Whether mz windows in in ppm
im_extraction_window	Extracts a window of this size in ion mobility
filter	Which filter to use (bartlett or tophat)

Note: : whenever possible, please use this ChromatogramExtractorAlgorithm implementation

References ChromatogramExtractorAlgorithm::extractChromatograms().

◆ getFilterNr_()

int getFilterNr_ ( const String & filter )

private

Note: : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

◆ outsideExtractionWindow_()

bool outsideExtractionWindow_	(	const ReactionMonitoringTransition &	transition,
		double	current_rt,
		const TransformationDescription &	trafo,
		double	rt_extraction_window
	)

private

Note: : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

◆ populatePeptideRTMap_()

void populatePeptideRTMap_	(	OpenMS::TargetedExperiment &	transition_exp,
		double	rt_extraction_window
	)

private

Note: : TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

◆ prepare_coordinates() [1/2]

static void prepare_coordinates	(	std::vector< OpenSwath::ChromatogramPtr > &	output_chromatograms,
		std::vector< ExtractionCoordinates > &	coordinates,
		const OpenMS::TargetedExperiment &	transition_exp,
		const double	rt_extraction_window,
		const bool	ms1 = `false`,
		const int	ms1_isotopes = `0`
	)

static

Prepare the extraction coordinates from a TargetedExperiment.

Will fill the coordinates vector with the appropriate extraction coordinates (transitions for MS2 extraction, peptide m/z for MS1 extraction). The output will be sorted by m/z.

Parameters

output_chromatograms	An empty vector which will be initialized correctly
coordinates	An empty vector which will be filled with the appropriate extraction coordinates in m/z and rt and sorted by m/z (to be used as input to extractChromatograms)
transition_exp	The transition experiment used as input (is constant)
rt_extraction_window	If non-negative, full RT extraction window, centered on the first RT value (`rt_end` - `rt_start` will equal this window size). If negative, `rt_end` will be set to -1 and `rt_start` to 0 (i.e. full RT range). If NaN, exactly two RT entries are expected the first is used as `rt_start` and the second as `rt_end`.
ms1	Whether to extract for MS1 (peptide level) or MS2 (transition level)

Exceptions

Exception::IllegalArgument if RT values are expected (depending on rt_extraction_window) but not provided

◆ prepare_coordinates() [2/2]

static void prepare_coordinates	(	std::vector< OpenSwath::ChromatogramPtr > &	output_chromatograms,
		std::vector< ExtractionCoordinates > &	coordinates,
		const OpenSwath::LightTargetedExperiment &	transition_exp_used,
		const double	rt_extraction_window,
		const bool	ms1 = `false`,
		const int	ms1_isotopes = `0`
	)

static

◆ prepareSpectra_()

void prepareSpectra_	(	SpectrumSettingsT &	settings,
		std::vector< ChromatogramT > &	chromatograms,
		OpenMS::TargetedExperiment &	transition_exp
	)

inlineprivate

This populates the chromatograms vector with empty chromatograms (but sets their meta-information)

It extracts 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) Copy the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition

References ReactionMonitoringTransition::getCompoundRef(), TargetedExperiment::getCompounds(), ReactionMonitoringTransition::getNativeID(), ReactionMonitoringTransition::getPeptideRef(), TargetedExperiment::getPeptides(), ReactionMonitoringTransition::getPrecursorMZ(), ReactionMonitoringTransition::getProductMZ(), TargetedExperiment::getTransitions(), PeptideCompound::id, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, Peptide::sequence, Precursor::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), Peak1D::setMZ(), and Product::setMZ().

◆ return_chromatogram()

static void return_chromatogram	(	const std::vector< OpenSwath::ChromatogramPtr > &	chromatograms,
		const std::vector< ChromatogramExtractor::ExtractionCoordinates > &	coordinates,
		TransitionExpT &	transition_exp_used,
		SpectrumSettings	settings,
		std::vector< OpenMS::MSChromatogram > &	output_chromatograms,
		bool	ms1,
		double	im_extraction_width = `0.0`
	)

inlinestatic

This converts the ChromatogramPtr to MSChromatogram and adds meta-information.

It sets 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition 7) ion mobility extraction target and window (lower/upper)

Member Data Documentation

◆ PeptideRTMap_

std::map<OpenMS::String, double> PeptideRTMap_

private

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ExtractionCoordinates

Member Function Documentation

◆ extract_id_()

◆ extract_value_bartlett()

◆ extract_value_tophat()

◆ extractChromatograms() [1/3]

◆ extractChromatograms() [2/3]

◆ extractChromatograms() [3/3]

◆ getFilterNr_()

◆ outsideExtractionWindow_()

◆ populatePeptideRTMap_()

◆ prepare_coordinates() [1/2]

◆ prepare_coordinates() [2/2]

◆ prepareSpectra_()

◆ return_chromatogram()

Member Data Documentation

◆ PeptideRTMap_