The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data. More...

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

Inheritance diagram for ChromatogramExtractorAlgorithm:

Classes
struct	ExtractionCoordinates

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

void	extract_value_tophat (const std::vector< double >::const_iterator &mz_start, std::vector< double >::const_iterator &mz_it, const std::vector< double >::const_iterator &mz_end, std::vector< double >::const_iterator &int_it, const double &mz, double &integrated_intensity, const double &mz_extraction_window, bool ppm)
	Extract the next mz value and add the integrated intensity to integrated_intensity. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~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...

Private Member Functions
int	getFilterNr_ (String filter)

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

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 ChromatogramExtractorAlgorithm extracts chromatograms from a MS data.

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. This interface only expects a set of coordinates which are up to the user to fill but a convenient prepare_coordinates function is provided (in the ChromatogramExtractor class) 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 Function Documentation

◆ extract_value_tophat()

void extract_value_tophat	(	const std::vector< double >::const_iterator &	mz_start,
		std::vector< double >::const_iterator &	mz_it,
		const std::vector< double >::const_iterator &	mz_end,
		std::vector< double >::const_iterator &	int_it,
		const double &	mz,
		double &	integrated_intensity,
		const double &	mz_extraction_window,
		bool	ppm
	)

Extract the next mz value and add the integrated intensity to integrated_intensity.

This function will sum up all intensities within mz +/- mz_extract_window / 2.0 and add the result to integrated_intensity.

Parameters

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)

Note: It will change the position of the iterators mz_it and int_it and it can *not* extract any data if the mz-iterator is already passed the mz value given. It is thus critically important to provide all mz values to be extracted in ascending order!

◆ extractChromatograms()

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

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

Parameters

input	Input spectral map
output	Output chromatograms (XICs)
extraction_coordinates	Extracts around these coordinates (from rt_start to rt_end in seconds - extracts the whole chromatogram if rt_end - rt_start < 0).
mz_extraction_window	Extracts a window of this size in m/z dimension in Th or ppm (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
ppm	Whether mz_extraction_window is in ppm or in Th
filter	Which function to apply in m/z space (currently "tophat" only)

Referenced by ChromatogramExtractor::extractChromatograms().

◆ getFilterNr_()

int getFilterNr_ ( String filter )

private

Classes

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ extract_value_tophat()

◆ extractChromatograms()

◆ getFilterNr_()