OpenSwathWorkflowBase Class Reference

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

Inheritance diagram for OpenSwathWorkflowBase:

Protected Member Functions
	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...

Protected Attributes
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_

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()

OpenSwathWorkflowBase ( bool  use_ms1_traces )

inlineexplicitprotected

Member Function Documentation

MS1Extraction_()

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  )

protected

Perform MS1 extraction and store result in ms1_chromatograms.

prepareExtractionCoordinates_()

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

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_

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

use_ms1_traces_

bool use_ms1_traces_

protected

Whether to use the MS1 traces.