OpenSwathWorkflowBase Class Reference

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

Inheritance diagram for OpenSwathWorkflowBase:

Collaboration diagram for OpenSwathWorkflowBase:

Protected Member Functions
	OpenSwathWorkflowBase ()
	Default constructor.
	OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, bool mrm, int threads_outer_loop)
	Constructor.
void	MS1Extraction_ (const OpenSwath::SpectrumAccessPtr &ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1_only=false, int ms1_isotopes=0)
	Perform MS1 extraction and store result in ms1_chromatograms.
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.

Protected Attributes
OpenSwath::SpectrumAccessPtr	ms1_map_ = nullptr
	Spectrum Access to the MS1 map (note that this is not threadsafe!)
bool	use_ms1_traces_
	Whether to use the MS1 traces.
bool	use_ms1_ion_mobility_
	Whether to use ion mobility extraction on MS1 traces.
bool	prm_
	Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.
bool	pasef_
	Whether data is diaPASEF data.
bool	mrm_
	Whether data is chromatogram-only SRM/MRM data.
int	threads_outer_loop_
	How many threads should be used for the outer loop.
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.
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)
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, bool  pasef, bool  mrm, int  threads_outer_loop  )

inlineprotected

Constructor.

Parameters

[in]	use_ms1_traces	Use MS1 data?
[in]	use_ms1_ion_mobility	Use ion mobility extraction on MS1 traces?
[in]	prm	Is data acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows?
[in]	pasef	Is this diaPASEF data?
[in]	mrm	Is this SRM/MRM data?
[in]	threads_outer_loop	Legacy nested OpenMP outer-loop thread count. Values >= 0 request the old per-SWATH nested parallelism; -1 leaves scheduling automatic and allows the SWATH wave scheduler to be used when its other preconditions are met.

Note

This setting is only relevant when OpenMS is built with nested OpenMP support and the SWATH wave scheduler is not active. For the legacy nested path, the total number of threads should be divisible by this number (e.g. use 8 in the outer loop if 24 threads are available and 3 should be used for each 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, const ChromExtractParams &  cp, const OpenSwath::LightTargetedExperiment &  transition_exp, const TransformationDescription &  trafo_inverse, bool  ms1_only = false, int  ms1_isotopes = 0  )

protected

Perform MS1 extraction and store result in ms1_chromatograms.

Parameters

[in]	ms1_map	Spectrum Access to the MS1 map
[in]	swath_maps	The raw data (swath maps)
[in]	ms1_chromatograms	Output vector for MS1 chromatograms
[in]	cp	Parameter set for the chromatogram extraction
[in]	transition_exp	The set of assays to be extracted and scored
[in]	trafo_inverse	Inverse transformation function
[in]	ms1_only	If true, will only score on MS1 level and ignore MS2 level
[in]	ms1_isotopes	Number of MS1 isotopes to extract (zero means only monoisotopic peak)

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

[out]	chrom_list	Output of chromatograms (will be filled with empty chromatogram ptrs)
[out]	coordinates	Output of extraction coordinates (will be filled with matching extraction coordinates)
[out]	transition_exp_used	The transition experiment used to create the coordinates
[in]	trafo_inverse	Inverse transformation function
[in]	cp	Parameter set for the chromatogram extraction
[in]	ms1	Whether to perform MS1 (precursor ion) or MS2 (fragment ion) extraction
[in]	ms1_isotopes	Number of MS1 isotopes to extract (zero means only monoisotopic peak)

Member Data Documentation

mrm_

bool mrm_

protected

Whether data is chromatogram-only SRM/MRM data.

If set to true, indicates that all swath_maps contain only chromatograms (no spectra) and the workflow should use SRM/MRM-specific processing.

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

pasef_

bool pasef_

protected

Whether data is diaPASEF data.

If set to true, a precursor will only be extracted from a single window that matches both in m/z and whose ion mobility (drift time) center is closest to the library ion mobility of the precursor. This is required if windows overlap in m/z or in ion mobility, as is the case for diaPASEF data.

prm_

bool prm_

protected

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

If set to true, a precursor will only be extracted from a single window that matches in m/z and whose m/z center is closest to the library m/z of the precursor. This is required if windows overlap in m/z as is the case for SRM/MRM / PRM data where often multiple windows with similar (or overlaping) m/z are used to target different precursors at different RT.

threads_outer_loop_

int threads_outer_loop_

protected

How many threads should be used for the outer loop.

Note

A value of -1 leaves scheduling automatic and allows the SWATH wave scheduler to be used when its other preconditions are met.

Values >= 0 select the legacy nested OpenMP outer-loop path when OpenMS is built with nested OpenMP support. In that path, the total number of threads should be divisible by this number (e.g. use 8 in the outer loop if 24 threads are available and 3 should be used for each 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.