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

Inheritance diagram for OpenSwathWorkflowBase:

Collaboration diagram for OpenSwathWorkflowBase:

Protected Member Functions
	OpenSwathWorkflowBase ()
	Default constructor. More...

	OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
	Constructor. More...

void	MS1Extraction_ (const OpenSwath::SpectrumAccessPtr ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1only=false, int ms1_isotopes=0)
	Perform MS1 extraction and store result in ms1_chromatograms. More...

void	prepareExtractionCoordinates_ (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const TransformationDescription trafo_inverse, const ChromExtractParams &cp, const bool ms1=false, const int ms1_isotopes=-1) const
	Function to prepare extraction coordinates that also correctly handles RT transformations. More...

Protected Attributes
OpenSwath::SpectrumAccessPtr	ms1_map_ = nullptr
	Spectrum Access to the MS1 map (note that this is not threadsafe!) More...

bool	use_ms1_traces_
	Whether to use the MS1 traces. More...

bool	use_ms1_ion_mobility_
	Whether to use ion mobility extraction on MS1 traces. More...

bool	prm_
	Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows. More...

int	threads_outer_loop_
	How many threads should be used for the outer loop. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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

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...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Constructor & Destructor Documentation

◆ OpenSwathWorkflowBase() [1/2]

OpenSwathWorkflowBase ( )

inlineprotected

Default constructor.

Will not use any ms1 traces and use all threads in the outer loop.

◆ OpenSwathWorkflowBase() [2/2]

OpenSwathWorkflowBase	(	bool	use_ms1_traces,
		bool	use_ms1_ion_mobility,
		bool	prm,
		int	threads_outer_loop
	)

inlineprotected

Constructor.

Parameters

use_ms1_traces	Whether to use MS1 data
threads_outer_loop	How many threads should be used for the outer loop (-1 will use all threads in the outer loop)

Note: The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).

Member Function Documentation

◆ MS1Extraction_()

void MS1Extraction_	(	const OpenSwath::SpectrumAccessPtr	ms1_map,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		std::vector< MSChromatogram > &	ms1_chromatograms,
		Interfaces::IMSDataConsumer *	chromConsumer,
		const ChromExtractParams &	cp,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const TransformationDescription &	trafo_inverse,
		bool	ms1only = `false`,
		int	ms1_isotopes = `0`
	)

protected

Perform MS1 extraction and store result in ms1_chromatograms.

Parameters

swath_maps	The raw data (swath maps)
ms1_chromatograms	Output vector for MS1 chromatograms
chromConsumer	Chromatogram consumer object to store the extracted chromatograms
cp	Parameter set for the chromatogram extraction
transition_exp	The set of assays to be extracted and scored
trafo_inverse	Inverse transformation function
load_into_memory	Whether to cache the current SWATH map in memory
ms1only	If true, will only score on MS1 level and ignore MS2 level

◆ prepareExtractionCoordinates_()

void prepareExtractionCoordinates_	(	std::vector< OpenSwath::ChromatogramPtr > &	chrom_list,
		std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &	coordinates,
		const OpenSwath::LightTargetedExperiment &	transition_exp_used,
		const TransformationDescription	trafo_inverse,
		const ChromExtractParams &	cp,
		const bool	ms1 = `false`,
		const int	ms1_isotopes = `-1`
	)		const

protected

Function to prepare extraction coordinates that also correctly handles RT transformations.

Creates a set of (empty) chromatograms and extraction coordinates with the correct ids, m/z and retention time start/end points to be extracted by the ChromatogramExtractor.

Handles rt extraction windows by calculating the correct transformation for each coordinate.

Parameters

chrom_list	Output of chromatograms (will be filled with empty chromatogram ptrs)
coordinates	Output of extraction coordinates (will be filled with matching extraction coordinates)
transition_exp_used	The transition experiment used to create the coordinates
ms1	Whether to perform MS1 (precursor ion) or MS2 (fragment ion) extraction
trafo_inverse	Inverse transformation function
cp	Parameter set for the chromatogram extraction

Member Data Documentation

◆ ms1_map_

OpenSwath::SpectrumAccessPtr ms1_map_ = nullptr

protected

Spectrum Access to the MS1 map (note that this is *not* threadsafe!)

Note: This pointer is not threadsafe, please use the lightClone() function to create a copy for each thread; This pointer may be NULL if use_ms1_traces_ is set to false

◆ prm_

bool prm_

protected

Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.

◆ threads_outer_loop_

int threads_outer_loop_

protected

How many threads should be used for the outer loop.

Note: A value of -1 will use all threads in the outer loop; The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).

◆ use_ms1_ion_mobility_

bool use_ms1_ion_mobility_

protected

Whether to use ion mobility extraction on MS1 traces.

◆ use_ms1_traces_

bool use_ms1_traces_

protected

Whether to use the MS1 traces.

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ OpenSwathWorkflowBase() [1/2]

◆ OpenSwathWorkflowBase() [2/2]

Member Function Documentation

◆ MS1Extraction_()

◆ prepareExtractionCoordinates_()

Member Data Documentation

◆ ms1_map_

◆ prm_

◆ threads_outer_loop_

◆ use_ms1_ion_mobility_

◆ use_ms1_traces_