Abstract interface for providing chromatograms. More...

#include <OpenMS/ANALYSIS/TARGETED/IChromatogramHandler.h>

Inheritance diagram for IChromatogramHandler:

Public Member Functions
	IChromatogramHandler ()=default

virtual	~IChromatogramHandler ()=default

virtual std::vector< MSChromatogram >	collectIrtChromatogramsForIrt (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &irt_transitions, const Param &mrm_mapping_param, const ChromExtractParams &cp, const TransformationDescription &trafo=TransformationDescription(), bool pasef=false, bool load_into_memory=false)=0
	Collect iRT chromatograms from the swath maps and try to map them to the provided iRT transitions.

virtual std::vector< MSChromatogram >	extractAndMapChromatogramsForTransitions (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const ChromExtractParams &cp, const Param &mrm_mapping_param)=0
	Extract (or select) chromatograms for the given transitions and return mapped & filtered chromatograms.

Static Public Member Functions
static std::unique_ptr< IChromatogramHandler >	createDefault ()
	Factory: create the default handler (currently SRM/MRM-based)

Detailed Description

Abstract interface for providing chromatograms.

This interface isolates the rest of the OpenSwath workflow from the source and mapping strategy for chromatograms. Implementations are expected to provide two main services:

collectIrtChromatogramsForIrt(...): collect candidate chromatograms used for iRT calibration and attempt to map them to the supplied iRT transitions.
extractAndMapChromatogramsForTransitions(...): either select existing SRM/MRM chromatograms or extract chromatograms from full-scan data (DIA/SWATH/PRM) and map them to the supplied transitions. Implementations should return only chromatograms that are mapped and ready for processing.

Constructor & Destructor Documentation

◆ IChromatogramHandler()

IChromatogramHandler ( )

default

◆ ~IChromatogramHandler()

virtual ~IChromatogramHandler ( )

virtualdefault

Member Function Documentation

◆ collectIrtChromatogramsForIrt()

virtual std::vector< MSChromatogram > collectIrtChromatogramsForIrt	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::LightTargetedExperiment &	irt_transitions,
		const Param &	mrm_mapping_param,
		const ChromExtractParams &	cp,
		const TransformationDescription &	trafo = `TransformationDescription()`,
		bool	pasef = `false`,
		bool	load_into_memory = `false`
	)

pure virtual

Collect iRT chromatograms from the swath maps and try to map them to the provided iRT transitions.

Implemented in DefaultChromHandler, DIAChromHandler, and MRMChromHandler.

◆ createDefault()

static std::unique_ptr< IChromatogramHandler > createDefault ( )

static

Factory: create the default handler (currently SRM/MRM-based)

◆ extractAndMapChromatogramsForTransitions()

virtual std::vector< MSChromatogram > extractAndMapChromatogramsForTransitions	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const ChromExtractParams &	cp,
		const Param &	mrm_mapping_param
	)