Class to execute an OpenSwath Workflow. More...

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

Inheritance diagram for OpenSwathWorkflow:

Public Member Functions
	OpenSwathWorkflow (bool use_ms1_traces)

void	performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &cp, 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 the OpenSWATH workflow on a set of SwathMaps and transitions. 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...

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

void	scoreAllChromatograms (const OpenSwath::SpectrumAccessPtr input, const std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, bool ms1only=false)
	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 j)
	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)
	Copy the required transitions to output. More...

Protected Member Functions inherited from OpenSwathWorkflowBase
	OpenSwathWorkflowBase (bool use_ms1_traces)

void	MS1Extraction_ (const std::vector< OpenSwath::SwathMap > &swath_maps, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool load_into_memory, bool ms1only=false)
	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 bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const
	Function to prepare extraction coordinates that also correctly handles RT transformations. More...

Private Types
typedef OpenSwath::LightTransition	TransitionType

typedef MRMTransitionGroup< MSChromatogram, TransitionType >	MRMTransitionGroupType

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

bool	use_ms1_traces_
	Whether to use the MS1 traces. 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

Class to execute an OpenSwath Workflow.

The workflow will perform a complete OpenSWATH analysis. Optionally, an RT transformation (mapping peptides to normalized space) can be obtained beforehand using the OpenSwathRetentionTimeNormalization class.

Member Typedef Documentation

◆ MRMTransitionGroupType

typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType

private

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

◆ OpenSwathWorkflow()

OpenSwathWorkflow ( bool use_ms1_traces )

inlineexplicit

Member Function Documentation

◆ copyBatchTransitions_()

void copyBatchTransitions_	(	const std::vector< OpenSwath::LightCompound > &	used_compounds,
		const std::vector< OpenSwath::LightTransition > &	all_transitions,
		std::vector< OpenSwath::LightTransition > &	output
	)

protected

Copy the required transitions to output.

Copy all transitions matching to one of the compounds in the selected peptide vector from all_transitions to the output.

Parameters

used_compounds	Which peptides or metabolites to be used
all_transitions	Transitions vector from which to select transitions
output	Output vector containing matching transitions (taken from all_transitions)

◆ performExtraction()

void performExtraction	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const TransformationDescription	trafo,
		const ChromExtractParams &	cp,
		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 the OpenSWATH workflow on a set of SwathMaps and transitions.

Executes the following operations on the given input:

1. Selecting the appropriate transitions for each SWATH window (using OpenSwathHelper::selectSwathTransitions) 2. Extract the chromatograms from the SWATH maps (MS1 and MS2) using (ChromatogramExtractor) 3. Pick peaks in the chromatograms and perform peak scoring (inside scoreAllChromatograms function) 4. Write out chromatograms and found features

Parameters

swath_maps	The raw data (swath maps)
trafo	Transformation description (translating this runs' RT to normalized RT space)
cp	Parameter set for the chromatogram extraction
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
tsv_writer	TSV Writer object to store identified features in csv format
osw_writer	OSW Writer object to store identified features in SQLite format
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 SWATH map in memory

◆ scoreAllChromatograms()

void scoreAllChromatograms	(	const OpenSwath::SpectrumAccessPtr	input,
		const std::map< std::string, OpenSwath::ChromatogramPtr > &	ms1_chromatograms,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		const Param &	feature_finder_param,
		TransformationDescription	trafo,
		const double	rt_extraction_window,
		FeatureMap &	output,
		OpenSwathTSVWriter &	tsv_writer,
		OpenSwathOSWWriter &	osw_writer,
		bool	ms1only = `false`
	)

protected

Perform scoring on a set of chromatograms.

Will iterate over all assays contained in transition_exp and for each assay fetch the corresponding chromatograms and find peak groups.

Parameters

input	Input chromatograms (MS2 level)
ms1_chromatograms	Input chromatograms for MS1-level
swath_maps	Set of swath map(s) for the current swath window (for SONAR multiple maps are provided)
transition_exp	The transition experiment (assay library)
feature_finder_param	Parameters for the MRMFeatureFinderScoring
trafo	RT Transformation function
rt_extraction_window	RT extraction window
output	Output map
tsv_writer	TSV writer for storing output (on the fly)
osw_writer	OSW Writer object to store identified features in SQLite format

◆ selectCompoundsForBatch_()

void selectCompoundsForBatch_	(	const OpenSwath::LightTargetedExperiment &	transition_exp_used_all,
		OpenSwath::LightTargetedExperiment &	transition_exp_used,
		int	batch_size,
		size_t	j
	)

protected

Select which compounds to analyze in the next batch (and copy to output)

This function will select which compounds to analyze in the next batch j and will copy the corresponding compounds and transitions into the output structure. The output will contain batch_size compounds.

Parameters

transition_exp_used_all	input (all transitions for this swath)
transition_exp_used	output (will contain only transitions for the next batch)
batch_size	how many compounds per batch
j	batch number (peptides from jbatch_size to jbatch_size+batch_size will be copied)

Note: The proteins will be copied completely without checking for a match

◆ writeOutFeaturesAndChroms_()

void writeOutFeaturesAndChroms_	(	std::vector< OpenMS::MSChromatogram > &	chromatograms,
		const FeatureMap &	featureFile,
		FeatureMap &	out_featureFile,
		bool	store_features,
		Interfaces::IMSDataConsumer *	chromConsumer
	)

protected

Write output features and chromatograms to disk.

Public Member Functions

Protected Member Functions

Private Types

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ MRMTransitionGroupType

◆ TransitionType

Constructor & Destructor Documentation

◆ OpenSwathWorkflow()

Member Function Documentation

◆ copyBatchTransitions_()

◆ performExtraction()

◆ scoreAllChromatograms()

◆ selectCompoundsForBatch_()

◆ writeOutFeaturesAndChroms_()