Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data) More...

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

Inheritance diagram for OpenSwathWorkflowSonar:

Collaboration diagram for OpenSwathWorkflowSonar:

Public Member Functions
	OpenSwathWorkflowSonar (bool use_ms1_traces)

void	performExtractionSonar (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription &trafo, const ChromExtractParams &cp, const ChromExtractParams &cp_ms1, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, Interfaces::IMSDataConsumer *chromConsumer, int batchSize, bool load_into_memory)
	Execute OpenSWATH analysis on a set of SONAR SwathMaps and transitions. More...

void	computeSonarWindows_ (const std::vector< OpenSwath::SwathMap > &swath_maps, double &sonar_winsize, double &sonar_start, double &sonar_end, int &sonar_total_win)
	Compute start, end and total number of (virtual) SONAR windows. More...

void	performSonarExtraction_ (const std::vector< OpenSwath::SwathMap > &used_maps, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, std::vector< OpenSwath::ChromatogramPtr > &chrom_list, const ChromExtractParams &cp)
	Perform extraction from multiple SONAR windows. More...

OpenSwath::ChromatogramPtr	addChromatograms (OpenSwath::ChromatogramPtr base_chrom, OpenSwath::ChromatogramPtr newchrom)
	Add two chromatograms. More...

Public Member Functions inherited from OpenSwathWorkflow
	OpenSwathWorkflow (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)
	Constructor. More...

void	performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription &rt_trafo, const ChromExtractParams &chromatogram_extraction_params, const ChromExtractParams &ms1_chromatogram_extraction_params, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &assay_library, FeatureMap &result_featureFile, bool store_features_in_featureFile, OpenSwathTSVWriter &result_tsv, OpenSwathOSWWriter &result_osw, Interfaces::IMSDataConsumer *result_chromatograms, int batchSize, int ms1_isotopes, bool load_into_memory)
	Execute OpenSWATH analysis on a set of SwathMaps and transitions. More...

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

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

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

Protected Member Functions inherited from OpenSwathWorkflow
void	writeOutFeaturesAndChroms_ (std::vector< OpenMS::MSChromatogram > &chromatograms, std::vector< MSChromatogram > &ms1_chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)
	Write output features and chromatograms. More...

void	scoreAllChromatograms_ (const std::vector< OpenMS::MSChromatogram > &ms2_chromatograms, const std::vector< OpenMS::MSChromatogram > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, const TransformationDescription &trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, int nr_ms1_isotopes=0, bool ms1only=false) const
	Perform scoring on a set of chromatograms. More...

void	selectCompoundsForBatch_ (const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t batch_idx)
	Select which compounds to analyze in the next batch (and copy to output) More...

void	copyBatchTransitions_ (const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)
	Helper function for selectCompoundsForBatch_() More...

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

	OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, 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, 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. 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 inherited from OpenSwathWorkflowBase
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...

bool	pasef_
	Whether data is diaPASEF data. 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_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)

The workflow will perform a complete OpenSWATH analysis, using scanning SWATH data (SONAR data) instead of regular data. In this case, each fragment ion may appear in multiple SWATH windows and thus needs to be extracted from multiple maps.

The overall execution flow in this class is as follows (see performExtractionSonar() function)

Obtain precursor ion chromatograms (if enabled) through MS1Extraction_()
Compute SONAR windows using computeSonarWindows_()
Iterate through each SONAR window:
- Select which transitions to extract (proceed in batches) using OpenSwathHelper::selectSwathTransitions()
- Identify which SONAR windows to use for current set of transitions
- Iterate through each batch of transitions:
  - Extract current batch of transitions from current SONAR window:
    - Select transitions for current batch (see OpenSwathWorkflow::selectCompoundsForBatch_())
    - Prepare transition extraction (see OpenSwathWorkflow::prepareExtractionCoordinates_())
    - Extract transitions using performSonarExtraction_()
    - Convert data to OpenMS format using ChromatogramExtractor::return_chromatogram()
  - Score extracted transitions (see scoreAllChromatograms_())
  - Write scored chromatograms and peak groups to disk (see writeOutFeaturesAndChroms_())

Constructor & Destructor Documentation

◆ OpenSwathWorkflowSonar()

OpenSwathWorkflowSonar ( bool use_ms1_traces )

inlineexplicit

Member Function Documentation

◆ addChromatograms()

OpenSwath::ChromatogramPtr addChromatograms	(	OpenSwath::ChromatogramPtr	base_chrom,
		OpenSwath::ChromatogramPtr	newchrom
	)

Add two chromatograms.

Parameters

base_chrom	The base chromatogram to which we will add intensity
newchrom	The chromatogram to be added

◆ computeSonarWindows_()

void computeSonarWindows_	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		double &	sonar_winsize,
		double &	sonar_start,
		double &	sonar_end,
		int &	sonar_total_win
	)

Compute start, end and total number of (virtual) SONAR windows.

◆ performExtractionSonar()

void performExtractionSonar	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const TransformationDescription &	trafo,
		const ChromExtractParams &	cp,
		const ChromExtractParams &	cp_ms1,
		const Param &	feature_finder_param,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		FeatureMap &	out_featureFile,
		bool	store_features,
		OpenSwathTSVWriter &	tsv_writer,
		OpenSwathOSWWriter &	osw_writer,
		Interfaces::IMSDataConsumer *	chromConsumer,
		int	batchSize,
		bool	load_into_memory
	)

Execute OpenSWATH analysis on a set of SONAR SwathMaps and transitions.

See OpenSwathWorkflowSonar class for a detailed description of this function.

Note: Given that these are scanning SWATH maps, for each transition multiple maps will be used for chromatogram extraction and scoring.

Parameters

swath_maps	The raw data, expected to be scanning SWATH maps (SONAR)
trafo	Transformation description (translating this runs' RT to normalized RT space)
cp	Parameter set for the chromatogram extraction
cp_ms1	Parameter set for the chromatogram extraction in MS1
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
transition_exp	The set of assays to be extracted and scored
out_featureFile	Output feature map to store identified features
store_features	Whether features should be appended to the output feature map (if this is false, then out_featureFile will be empty)
tsv_writer	TSV Writer object to store identified features in csv format (set store_features to false if using this option)
osw_writer	OSW Writer object to store identified features in SQLite format (set store_features to false if using this option)
chromConsumer	Chromatogram consumer object to store the extracted chromatograms
batchSize	Size of the batches which should be extracted and scored
load_into_memory	Whether to cache the current SONAR map(s) in memory

◆ performSonarExtraction_()

void performSonarExtraction_	(	const std::vector< OpenSwath::SwathMap > &	used_maps,
		const std::vector< ChromatogramExtractor::ExtractionCoordinates > &	coordinates,
		std::vector< OpenSwath::ChromatogramPtr > &	chrom_list,
		const ChromExtractParams &	cp
	)

Perform extraction from multiple SONAR windows.

Public Member Functions

Additional Inherited Members