Default SRM/MRM chromatogram provider declaration. More...

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

Inheritance diagram for MRMChromHandler:

Collaboration diagram for MRMChromHandler:

Public Member Functions
	MRMChromHandler ()

	~MRMChromHandler () override

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

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

Public Member Functions inherited from IChromatogramHandler
	IChromatogramHandler ()=default

virtual	~IChromatogramHandler ()=default

Static Public Member Functions
static void	normalizeChromatogramMZ (MSChromatogram &chrom)

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

Detailed Description

Default SRM/MRM chromatogram provider declaration.

The MRMChromHandler class is the default implementation of IChromatogramHandler used by OpenSwathWorkflow when running in SRM/MRM mode. It delegates to the internal SRM/MRM helpers implemented in MRMChromHandler.cpp for chromatogram collection and mapping.

This header exposes the provider's public interface (only the class declaration). The implementation is colocated in MRMChromHandler.cpp so the provider can remain a lightweight adapter while keeping implementation details private to the translation unit.

Constructor & Destructor Documentation

◆ MRMChromHandler()

MRMChromHandler ( )

◆ ~MRMChromHandler()

~MRMChromHandler ( )

override

Member Function Documentation

◆ collectIrtChromatogramsForIrt()

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`
	)

overridevirtual

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

Implements IChromatogramHandler.

◆ extractAndMapChromatogramsForTransitions()

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

overridevirtual

Extract (or select) chromatograms for the given transitions and return mapped & filtered chromatograms.

Implements IChromatogramHandler.

◆ normalizeChromatogramMZ()

static void normalizeChromatogramMZ ( MSChromatogram & chrom )

static

Utility function to normalize chromatogram precursor/product m/z and nativeID This handles chromatogram-only files where metadata may not be properly set

Public Member Functions

Static Public Member Functions