Extract raw mz/RT/IM peak clouds for targeted OpenSWATH coordinates. More...

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

Inheritance diagram for PeakMapExtractor:

Collaboration diagram for PeakMapExtractor:

Classes
struct	ExtractedPeakMap
	One extracted targeted peak map. More...

Public Types
using	ExtractionCoordinates = ChromatogramExtractorAlgorithm::ExtractionCoordinates

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

Public Member Functions
void	extractPeakMaps (const OpenSwath::SpectrumAccessPtr &input, std::vector< ExtractedPeakMap > &output, const std::vector< ExtractionCoordinates > &extraction_coordinates, double mz_extraction_window, bool ppm, double im_extraction_window, const std::string &filter="tophat")
	Extract raw peak maps at the coordinates defined by `extraction_coordinates`.

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 Member Functions
int	getFilterNr_ (const std::string &filter) const

Additional Inherited Members
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

Extract raw mz/RT/IM peak clouds for targeted OpenSWATH coordinates.

The extractor follows the same targeting contract as ChromatogramExtractorAlgorithm. It consumes sorted extraction coordinates and applies RT, m/z, and optionally ion mobility windows. Unlike chromatogram extraction, it retains every matching raw point instead of integrating a scalar intensity per spectrum.

The output is one extracted peak map per coordinate. Each peak map stores parallel arrays for m/z, RT, ion mobility, and intensity.

Class Documentation

◆ OpenMS::PeakMapExtractor::ExtractedPeakMap

struct OpenMS::PeakMapExtractor::ExtractedPeakMap

One extracted targeted peak map.

Collaboration diagram for PeakMapExtractor::ExtractedPeakMap:

[legend]

Class Members
vector< double >	intensity
vector< double >	ion_mobility
vector< double >	mz
string	native_id
vector< double >	rt
double	rt_end {-1.0}
double	rt_start {0.0}
double	target_ion_mobility {-1.0}
double	target_mz {0.0}
double	target_rt {std::numeric_limits<double>::quiet_NaN()}

Member Typedef Documentation

◆ ExtractionCoordinates

using ExtractionCoordinates = ChromatogramExtractorAlgorithm::ExtractionCoordinates

Member Function Documentation

◆ extractPeakMaps()

void extractPeakMaps	(	const OpenSwath::SpectrumAccessPtr &	input,
		std::vector< ExtractedPeakMap > &	output,
		const std::vector< ExtractionCoordinates > &	extraction_coordinates,
		double	mz_extraction_window,
		bool	ppm,
		double	im_extraction_window,
		const std::string &	filter = `"tophat"`
	)

Extract raw peak maps at the coordinates defined by extraction_coordinates.

Parameters

[in]	input	Input spectral map
[out]	output	Output peak maps; one row per extraction coordinate
[in]	extraction_coordinates	Target coordinates to extract
[in]	mz_extraction_window	Full m/z extraction window in Th or ppm
[in]	ppm	Whether `mz_extraction_window` is specified in ppm
[in]	im_extraction_window	Full ion mobility extraction window. A positive value activates ion mobility filtering around the coordinate's target ion mobility. A negative value extracts the full ion mobility range while still recording the raw ion mobility values.
[in]	filter	Extraction profile in m/z space. Only `"tophat"` is supported because the output preserves raw points instead of applying weighted integration.

Exceptions

Exception::IllegalArgument if filter is not "tophat", if a spectrum is missing ion mobility data, or if the m/z, intensity, and ion mobility arrays on a spectrum have inconsistent sizes

◆ getFilterNr_()

int getFilterNr_ ( const std::string & filter ) const

private

Classes

Public Types

Public Member Functions

Private Member Functions

Additional Inherited Members