Convenience entry point that runs MRMFeatureFinderScoring on a list of already-extracted chromatograms. More...

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

Public Member Functions
	ChromatogramProcessor ()=default
	Default constructor (the class is stateless; the API is a single static method)

	~ChromatogramProcessor ()=default
	Destructor.

Static Public Member Functions
static void	pickExperiment (const std::vector< MSChromatogram > &chromatograms, const OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, FeatureMap &featureFile, OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map)
	Score the supplied chromatograms against the transition list and emit features + transition groups.

Detailed Description

Convenience entry point that runs MRMFeatureFinderScoring on a list of already-extracted chromatograms.

Intended for callers that already hold a list of MS chromatograms (XICs extracted upstream) and only need the feature-finding / scoring step without setting up a full SWATH-map / RT-transformation stack. Typical use is inside RT-normalisation flows in the OpenSwath workflow, where iRT chromatograms are extracted before the analytical-transition scoring runs.

All scoring semantics come from MRMFeatureFinderScoring; see its documentation for the parameter set passed in via feature_finder_param.

Constructor & Destructor Documentation

◆ ChromatogramProcessor()

ChromatogramProcessor ( )

default

Default constructor (the class is stateless; the API is a single static method)

◆ ~ChromatogramProcessor()

~ChromatogramProcessor ( )

default

Destructor.

Member Function Documentation

◆ pickExperiment()

static void pickExperiment	(	const std::vector< MSChromatogram > &	chromatograms,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const Param &	feature_finder_param,
		FeatureMap &	featureFile,
		OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &	transition_group_map
	)

static

Score the supplied chromatograms against the transition list and emit features + transition groups.

Tolerates transitions that have no matching chromatogram (they are simply skipped rather than reported as an error). Scoring is performed with no SWATH map and no RT transformation, so this overload is intended for callers that have already extracted the chromatograms upstream and only need the feature-finding step.

Both outputs are populated in place: featureFile gets one feature per scored precursor, and transition_group_map gets one entry per transition group.

Parameters

[in]	chromatograms	Already-extracted XICs to score (one per transition).
[in]	transition_exp	Transition list to align the chromatograms to.
[in]	feature_finder_param	Parameter set forwarded to MRMFeatureFinderScoring.
[out]	featureFile	Receives the scored features (one per precursor); not cleared first.
[out]	transition_group_map	Receives the per-transition-group scoring state.