Keep FAIMS acquisitions separate while retaining physical run/channel columns. More...

#include <MS1LabeledWorkflow/MS1LabeledFAIMS.h>

Public Types
using	CV = std::optional< double >
	A missing CV denotes conventional, non-FAIMS data; NaN is never used as a map key.

Static Public Member Functions
static void	annotateCompensationVoltages (const MSExperiment &spectra, PeptideIdentificationList &ids)
	Recover identification CVs from spectrum references before any RT-based reference repair.

static void	annotate (IDMapper &mapper, ConsensusMap &map, const FeatureMap &channels, const PeptideIdentificationList &ids, const std::vector< ProteinIdentification > &proteins)
	Map IDs onto multiplets through the elution regions of their channels, only at the same CV.

static void	group (FeatureGroupingAlgorithmQT &linker, const std::vector< ConsensusMap > &maps, ConsensusMap &result)
	Link only within a CV, preserving the input maps' channel subelements.

Static Private Member Functions
static CV	getCV_ (const MetaInfoInterface &value)

static std::map< CV, std::vector< ConsensusMap > >	split_ (const std::vector< ConsensusMap > &maps)

static void	append_ (ConsensusMap &result, ConsensusMap &&part)

Detailed Description

Keep FAIMS acquisitions separate while retaining physical run/channel columns.

Member Typedef Documentation

◆ CV

using CV = std::optional<double>

A missing CV denotes conventional, non-FAIMS data; NaN is never used as a map key.

Member Function Documentation

◆ annotate()

void annotate	(	IDMapper &	mapper,
		ConsensusMap &	map,
		const FeatureMap &	channels,
		const PeptideIdentificationList &	ids,
		const std::vector< ProteinIdentification > &	proteins
	)

static

Map IDs onto multiplets through the elution regions of their channels, only at the same CV.

channels holds one feature per (multiplet, channel) of map, with the unique id of the channel's feature handle and its convex hulls (see the workflow). The IDs are matched against these hulls (IDMapper's feature map mode, i.e. against where the channel elutes rather than its apex) and every match is attached to the channel's multiplet, with the channel as map_index. An ID matching several channels of one multiplet is attached once. IDs without match become unassigned. map receives proteins and the data processing IDMapper records.

References IDMapper::annotate(), MS1LabeledFAIMS::getCV_(), ConsensusMap::getDataProcessing(), ConsensusMap::getProteinIdentifications(), ConsensusMap::getUnassignedPeptideIdentifications(), ExposedVector< VectorElement >::push_back(), MetaInfoInterface::removeMetaValue(), MetaInfoInterface::setMetaValue(), ExposedVector< VectorElement >::size(), OpenMS::StringUtils::toStr(), and ConsensusMap::updateRanges().