Dispatching chromatogram handler that picks SRM/MRM or DIA at runtime based on the input maps. More...

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

Inheritance diagram for DefaultChromHandler:

Collaboration diagram for DefaultChromHandler:

Public Member Functions
	DefaultChromHandler ()
	Default constructor; eagerly constructs the inner SRM/MRM and DIA handlers.

	~DefaultChromHandler () override
	Destructor.

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 by delegating to the SRM/MRM or DIA handler.

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 and map analytical transition chromatograms via the SRM/MRM or DIA handler.

Public Member Functions inherited from IChromatogramHandler
	IChromatogramHandler ()=default

virtual	~IChromatogramHandler ()=default

Private Attributes
std::unique_ptr< MRMChromHandler >	mrm_
	Inner SRM/MRM handler; selected when all input maps are chromatogram-only.

std::unique_ptr< DIAChromHandler >	dia_
	Inner DIA handler; selected when at least one input map carries MS1 or spectra.

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

Detailed Description

Dispatching chromatogram handler that picks SRM/MRM or DIA at runtime based on the input maps.

Wraps an MRMChromHandler and a DIAChromHandler and forwards each call to whichever is appropriate for the supplied SWATH maps. The mode is decided on every call by inspecting swath_maps:

If every map is chromatogram-only (neither flagged as MS1 nor carrying any spectra), the call is routed to the SRM/MRM handler.
Otherwise (any map flagged ms1 or carrying at least one spectrum), the call is routed to the DIA handler.

SRM/MRM error handling: when the SRM/MRM path raises Exception::IllegalArgument (typically "no chromatograms mapped to transitions" — common for chromatogram-only inputs whose precursor/product m/z don't match the supplied transition list), the exception is logged as a warning and an empty vector is returned. All other exceptions, and any exception raised on the DIA path, propagate to the caller.

Construction is cheap (default-constructs both inner handlers up front); no input data is inspected until the first call.

Constructor & Destructor Documentation

◆ DefaultChromHandler()

DefaultChromHandler ( )

Default constructor; eagerly constructs the inner SRM/MRM and DIA handlers.

◆ ~DefaultChromHandler()

~DefaultChromHandler ( )

override

Destructor.

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 by delegating to the SRM/MRM or DIA handler.

Routing rule: SRM/MRM if every swath_maps entry is chromatogram-only (neither ms1 nor any spectra), DIA otherwise. On the SRM/MRM path, Exception::IllegalArgument ("no chromatograms mapped") is logged and converted to an empty result; all other exceptions propagate unchanged.

Parameters

[in]	swath_maps	Input maps (mixed-mode allowed; the per-map check decides routing).
[in]	irt_transitions	iRT transition list used for mapping.
[in]	mrm_mapping_param	Parameters forwarded to the MRMMapping step.
[in]	cp	Chromatogram-extraction parameters (windows, RT range, etc.).
[in]	trafo	Optional RT transformation applied to iRT transitions.
[in]	pasef	If true, enable PASEF/ion-mobility-aware mapping in the delegate.
[in]	load_into_memory	If true, materialise on-disk data before extraction.

Returns: Mapped iRT chromatograms (empty on the recoverable SRM/MRM "no mapping" case).

Exceptions

Exception::BaseException Propagated for non-recoverable SRM/MRM delegate failures and all DIA-path exceptions.

Note: On the SRM/MRM path, Exception::IllegalArgument ("no chromatograms mapped") is logged and converted to an empty result.

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 and map analytical transition chromatograms via the SRM/MRM or DIA handler.

Routing rule and error handling are identical to collectIrtChromatogramsForIrt(): SRM/MRM for chromatogram-only inputs (where Exception::IllegalArgument is downgraded to an empty result), DIA otherwise (all exceptions propagate).

Parameters

[in]	swath_maps	Input maps (mixed-mode allowed; the per-map check decides routing).
[in]	transition_exp	Analytical transition list to map against.
[in]	cp	Chromatogram-extraction parameters.
[in]	mrm_mapping_param	Parameters forwarded to the MRMMapping step.

Returns: Mapped, filtered chromatograms ready for downstream scoring.

Exceptions

Exception::BaseException Propagated for non-recoverable SRM/MRM delegate failures and all DIA-path exceptions.

Note: On the SRM/MRM path, Exception::IllegalArgument ("no chromatograms mapped") is logged and converted to an empty result.

Implements IChromatogramHandler.

Member Data Documentation

◆ dia_

std::unique_ptr<DIAChromHandler> dia_

private

Inner DIA handler; selected when at least one input map carries MS1 or spectra.

◆ mrm_

std::unique_ptr<MRMChromHandler> mrm_