MS1LabeledFAIMS Class Reference

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 PeptideIdentificationList &ids, const std::vector< ProteinIdentification > &proteins)
	Map IDs only onto multiplets acquired 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 PeptideIdentificationList &  ids, const std::vector< ProteinIdentification > &  proteins  )

static

Map IDs only onto multiplets acquired at the same CV.

References IDMapper::annotate(), MS1LabeledFAIMS::append_(), ConsensusMap::clear(), ConsensusMap::setUnassignedPeptideIdentifications(), ConsensusMap::sortByPosition(), MS1LabeledFAIMS::split_(), and ConsensusMap::updateRanges().

annotateCompensationVoltages()

void annotateCompensationVoltages ( const MSExperiment &  spectra, PeptideIdentificationList &  ids  )

static

Recover identification CVs from spectrum references before any RT-based reference repair.

References SpectrumLookup::addReferenceFormat(), ExposedVector< VectorElement >::begin(), IMTypes::DRIFTTIME_NOT_SET, ExposedVector< VectorElement >::end(), OpenMS::FAIMS_COMPENSATION_VOLTAGE, OpenMS::Constants::UserParam::FAIMS_CV, SpectrumLookup::findByNativeID(), SpectrumLookup::findByReference(), MS1LabeledFAIMS::getCV_(), MSExperiment::getSpectra(), SpectrumLookup::readSpectra(), SpectrumLookup::rt_tolerance, and MSExperiment::size().

append_()

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

staticprivate

References ConsensusMap::getColumnHeaders(), ConsensusMap::getUnassignedPeptideIdentifications(), and ExposedVector< VectorElement >::push_back().

Referenced by MS1LabeledFAIMS::annotate(), and MS1LabeledFAIMS::group().

getCV_()

MS1LabeledFAIMS::CV getCV_ ( const MetaInfoInterface &  value )

staticprivate

References OpenMS::Constants::UserParam::FAIMS_CV, MetaInfoInterface::getMetaValue(), and MetaInfoInterface::metaValueExists().

Referenced by MS1LabeledFAIMS::annotateCompensationVoltages(), and MS1LabeledFAIMS::split_().

group()

void group ( FeatureGroupingAlgorithmQT &  linker, const std::vector< ConsensusMap > &  maps, ConsensusMap &  result  )

static

Link only within a CV, preserving the input maps' channel subelements.

References MS1LabeledFAIMS::append_(), ConsensusMap::clear(), OpenMS::Constants::UserParam::FAIMS_CV, FeatureGroupingAlgorithmQT::group(), MS1LabeledFAIMS::split_(), FeatureGroupingAlgorithm::transferSubelements(), and ConsensusMap::updateRanges().

split_()

std::map< MS1LabeledFAIMS::CV, std::vector< ConsensusMap > > split_ ( const std::vector< ConsensusMap > &  maps )

staticprivate

References MS1LabeledFAIMS::getCV_().

Referenced by MS1LabeledFAIMS::annotate(), and MS1LabeledFAIMS::group().