Class to execute an OpenSwath Workflow for SONAR data. More...

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

Inheritance 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 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 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)

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...

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, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)
	Write output features and chromatograms to disk. More...

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	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...

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...

void	prepare_coordinates_sub (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1) const
	Simple function to prepare extraction coordinates. 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 OpenSwathWorkflow
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 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.

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 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 SONAR 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

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
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 SONAR map(s) in memory

Referenced by SortPairDoubleByFirst().

◆ 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