ChromatogramExtractorAlgorithm Class Reference

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

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

Inheritance diagram for ChromatogramExtractorAlgorithm:

Collaboration diagram for ChromatogramExtractorAlgorithm:

Classes
struct	ExtractionCoordinates

Public Member Functions
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...
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, const bool ppm)
	Extract the next mz value and add the integrated intensity to integrated_intensity. 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, std::vector< double >::const_iterator &im_it, const double mz, const double im, double &integrated_intensity, const double mz_extraction_window, const double im_extraction_window, const bool ppm)
	Extract the next m/z 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...
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
int	getFilterNr_ (const 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() [1/2]

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,
		const bool	ppm
	)

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

This function will sum up all intensities within a window of mass-to-charge. It will extract around mz +/- mz_extract_window / 2.0 and add the result to integrated_intensity.

Parameters

mz_start	Start of the spectrum (m/z coordinates)
mz_it	Current m/z position (will be modified)
mz_end	End of the spectrum (m/z coordinates)
int_int	Current intensity position (will be modified)
mz	Target m/z for the current ion
integrated_intensity	Resulting intensity (will be overwritten)
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 the parameter mz_extraction_window is given in ppm or Th

Note

This function 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!

extract_value_tophat() [2/2]

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,
		std::vector< double >::const_iterator &	im_it,
		const double	mz,
		const double	im,
		double &	integrated_intensity,
		const double	mz_extraction_window,
		const double	im_extraction_window,
		const bool	ppm
	)

Extract the next m/z value and add the integrated intensity to integrated_intensity.

This function will sum up all intensities within a two-dimensional window of mass-to-charge and ion mobility. It will extract around mz +/- mz_extract_window / 2.0 and im +/- im_extraction_window / 2.0 and add the result to integrated_intensity.

Parameters

mz_start	Start of the spectrum (m/z coordinates)
mz_it	Current m/z position (will be modified)
mz_end	End of the spectrum (m/z coordinates)
int_int	Current intensity position (will be modified)
im_int	Current ion mobility position (will be modified)
mz	Target m/z for the current ion
im	Target ion mobility for the current ion
integrated_intensity	Resulting intensity (will be overwritten)
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)
im_extraction_window	Extracts a window of this size in ion mobility dimension.
ppm	Whether the parameter mz_extraction_window is given in ppm or Th

Note

This function will change the position of the iterators mz_it, int_it and im_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,
		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.

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_ ( const String &  filter )

private