The representation of a group of transitions in a targeted proteomics experiment. More...

#include <OpenMS/KERNEL/MRMTransitionGroup.h>

Inheritance diagram for MRMTransitionGroup< ChromatogramType, TransitionType >:

Collaboration diagram for MRMTransitionGroup< ChromatogramType, TransitionType >:

Public Types
typedef std::vector< MRMFeature >	MRMFeatureListType
	Type definitions. More...

typedef std::vector< TransitionType >	TransitionsType
	List of Reaction Monitoring transitions (meta data) type. More...

typedef ChromatogramType::PeakType	PeakType
	Peak type. More...

Public Member Functions
Constructors and Destructor
	MRMTransitionGroup ()
	Default constructor. More...

	MRMTransitionGroup (const MRMTransitionGroup &rhs)
	Copy Constructor. More...

virtual	~MRMTransitionGroup ()
	Destructor. More...

MRMTransitionGroup &	operator= (const MRMTransitionGroup &rhs)

Size	size () const

const String &	getTransitionGroupID () const

void	setTransitionGroupID (const String &tr_gr_id)

Transition access
const std::vector< TransitionType > &	getTransitions () const

std::vector< TransitionType > &	getTransitionsMuteable ()

void	addTransition (const TransitionType &transition, String key)

bool	hasTransition (String key) const

const TransitionType &	getTransition (String key)

(Fragment ion) chromatogram access
std::vector< ChromatogramType > &	getChromatograms ()

const std::vector< ChromatogramType > &	getChromatograms () const

void	addChromatogram (const ChromatogramType &chromatogram, const String &key)

bool	hasChromatogram (const String &key) const

ChromatogramType &	getChromatogram (const String &key)

const ChromatogramType &	getChromatogram (const String &key) const

(Precursor ion) chromatogram access
std::vector< ChromatogramType > &	getPrecursorChromatograms ()

const std::vector< ChromatogramType > &	getPrecursorChromatograms () const

void	addPrecursorChromatogram (const ChromatogramType &chromatogram, const String &key)

bool	hasPrecursorChromatogram (const String &key) const

ChromatogramType &	getPrecursorChromatogram (const String &key)

const ChromatogramType &	getPrecursorChromatogram (const String &key) const

MRM feature access (positions in RT where a peak was found across all chromatograms)
const std::vector< MRMFeature > &	getFeatures () const

std::vector< MRMFeature > &	getFeaturesMuteable ()

void	addFeature (const MRMFeature &feature)

void	addFeature (MRMFeature &&feature)

Helper functions
String	tr_gr_id_
	transition group id (peak group id) More...

TransitionsType	transitions_
	transition list More...

std::vector< ChromatogramType >	chromatograms_
	chromatogram list More...

std::vector< ChromatogramType >	precursor_chromatograms_
	precursor chromatogram list More...

MRMFeatureListType	mrm_features_
	feature list More...

std::map< String, int >	chromatogram_map_

std::map< String, int >	precursor_chromatogram_map_

std::map< String, int >	transition_map_

bool	isInternallyConsistent () const
	Check whether internal state is consistent, e.g. same number of chromatograms and transitions are present (no runtime overhead in release mode) More...

bool	chromatogramIdsMatch () const
	Ensure that chromatogram native ids match their keys in the map. More...

void	getLibraryIntensity (std::vector< double > &result) const

MRMTransitionGroup	subset (std::vector< std::string > tr_ids) const

MRMTransitionGroup	subsetDependent (std::vector< std::string > tr_ids) const

const MRMFeature &	getBestFeature () const
	Returns the best feature by overall quality. More...

bool	isMappingConsistent_ () const
	Checks that the mapping between chromatograms and transitions is consistent. More...

Detailed Description

template<typename ChromatogramType, typename TransitionType>
class OpenMS::MRMTransitionGroup< ChromatogramType, TransitionType >

The representation of a group of transitions in a targeted proteomics experiment.

The transition group carries information about the transitions (assays), the individual chromatograms as well as features found on these chromatograms.

On the one hand, the MRMTransitionGroup provides a convenient way to store the mapping between the individual transitions (containing the meta-data) and the actual chromatographic data points (measured data) relating to it. In addition, the structure allows storage of features found (regions of the chromatograms) where a potential elution peak was detected (see MRMFeature). Note that these features are usually found on the full collection of chromatograms and therefore relate to the whole collection of chromatograms.

Note that for the data structure to be consistent, it needs to have the same identifiers for the chromatograms as well as for the transitions.

Since not all the functions in OpenMS will work with MSChromatogram data structures, this needs to accept also MSSpectrum as a type for raw data storage.

Member Typedef Documentation

◆ MRMFeatureListType

typedef std::vector<MRMFeature> MRMFeatureListType

Type definitions.

List of MRM Features type

◆ PeakType

typedef ChromatogramType::PeakType PeakType

Peak type.

◆ TransitionsType

typedef std::vector<TransitionType> TransitionsType

List of Reaction Monitoring transitions (meta data) type.

Constructor & Destructor Documentation

◆ MRMTransitionGroup() [1/2]

MRMTransitionGroup ( )

inline

Default constructor.

◆ MRMTransitionGroup() [2/2]

MRMTransitionGroup ( const MRMTransitionGroup< ChromatogramType, TransitionType > & rhs )

inline

Copy Constructor.

◆ ~MRMTransitionGroup()

virtual ~MRMTransitionGroup ( )

inlinevirtual

Destructor.

Member Function Documentation

◆ addChromatogram()

void addChromatogram	(	const ChromatogramType &	chromatogram,
		const String &	key
	)

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ addFeature() [1/2]

void addFeature ( const MRMFeature & feature )

inline

Referenced by MRMTransitionGroupPicker::pickTransitionGroup(), MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ addFeature() [2/2]

void addFeature ( MRMFeature && feature )

inline

◆ addPrecursorChromatogram()

void addPrecursorChromatogram	(	const ChromatogramType &	chromatogram,
		const String &	key
	)

inline

Add a precursor chromatogram (extracted from an MS1 map) to the feature

While any key can be used, it is expected that the monoisotopic trace is called "Precursor_i0" and subsequent traces "Precursor_i1" etc. This policy is not enforced but highly encouraged.

Parameters

chromatogram	Chromatographic traces from the MS1 map to be added
key	Identifier for this trace, please use use consistent naming like "Precursor_i0", "Precursor_i1", "Precursor_i2" ...

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset().

◆ addTransition()

void addTransition	(	const TransitionType &	transition,
		String	key
	)

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ chromatogramIdsMatch()

bool chromatogramIdsMatch ( ) const

inline

Ensure that chromatogram native ids match their keys in the map.

Referenced by MRMTransitionGroupPicker::createMRMFeature(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ getBestFeature()

const MRMFeature& getBestFeature ( ) const

inline

Returns the best feature by overall quality.

For the given transition group, return the best feature as determined by the overall quality score. Requires the feature list to not be empty.

◆ getChromatogram() [1/2]

ChromatogramType& getChromatogram ( const String & key )

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::selectChromHelper_().

◆ getChromatogram() [2/2]

const ChromatogramType& getChromatogram ( const String & key ) const

inline

◆ getChromatograms() [1/2]

std::vector<ChromatogramType>& getChromatograms ( )

inline

Referenced by EmgScoring::calcElutionFitScore(), TransitionGroupOpenMS< SpectrumT, TransitionT >::getNativeIDs(), MRMTransitionGroupPicker::pickPrecursorChromatograms(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ getChromatograms() [2/2]

const std::vector<ChromatogramType>& getChromatograms ( ) const

inline

◆ getFeatures()

const std::vector<MRMFeature>& getFeatures ( ) const

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getBestFeature().

◆ getFeaturesMuteable()

std::vector<MRMFeature>& getFeaturesMuteable ( )

inline

◆ getLibraryIntensity()

void getLibraryIntensity ( std::vector< double > & result ) const

inline

Referenced by TransitionGroupOpenMS< SpectrumT, TransitionT >::getLibraryIntensities().

◆ getPrecursorChromatogram() [1/2]

ChromatogramType& getPrecursorChromatogram ( const String & key )

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::selectChromHelper_().

◆ getPrecursorChromatogram() [2/2]

const ChromatogramType& getPrecursorChromatogram ( const String & key ) const

inline

◆ getPrecursorChromatograms() [1/2]

std::vector<ChromatogramType>& getPrecursorChromatograms ( )

inline

Referenced by MRMTransitionGroupPicker::pickPrecursorChromatograms(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ getPrecursorChromatograms() [2/2]

const std::vector<ChromatogramType>& getPrecursorChromatograms ( ) const

inline

◆ getTransition()

const TransitionType& getTransition ( String key )

inline

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

◆ getTransitionGroupID()

const String& getTransitionGroupID ( ) const

inline

Referenced by MRMTransitionGroupPicker::createMRMFeature().

◆ getTransitions()

const std::vector<TransitionType>& getTransitions ( ) const

inline

Referenced by MRMTransitionGroupPicker::pickFragmentChromatograms(), MRMTransitionGroupPicker::pickPrecursorChromatograms(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ getTransitionsMuteable()

std::vector<TransitionType>& getTransitionsMuteable ( )

inline

◆ hasChromatogram()

bool hasChromatogram ( const String & key ) const

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getChromatogram(), MRMTransitionGroupPicker::selectChromHelper_(), and MRMTransitionGroup< SpectrumT, TransitionT >::subset().

◆ hasPrecursorChromatogram()

bool hasPrecursorChromatogram ( const String & key ) const

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatogram(), and MRMTransitionGroupPicker::selectChromHelper_().

◆ hasTransition()

bool hasTransition ( String key ) const

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::isMappingConsistent_(), MRMTransitionGroupPicker::pickTransitionGroup(), and MRMTransitionGroup< SpectrumT, TransitionT >::subset().

◆ isInternallyConsistent()

bool isInternallyConsistent ( ) const

inline

Check whether internal state is consistent, e.g. same number of chromatograms and transitions are present (no runtime overhead in release mode)

Referenced by MRMTransitionGroupPicker::createMRMFeature(), and MRMTransitionGroupPicker::pickTransitionGroup().

◆ isMappingConsistent_()

bool isMappingConsistent_ ( ) const

inlineprotected

Checks that the mapping between chromatograms and transitions is consistent.

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::isInternallyConsistent().

◆ operator=()

MRMTransitionGroup& operator= ( const MRMTransitionGroup< ChromatogramType, TransitionType > & rhs )

inline

◆ setTransitionGroupID()

void setTransitionGroupID ( const String & tr_gr_id )

inline

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ size()

Size size ( ) const

inline

Referenced by EmgScoring::calcElutionFitScore(), and TransitionGroupOpenMS< SpectrumT, TransitionT >::size().

◆ subset()

MRMTransitionGroup subset ( std::vector< std::string > tr_ids ) const

inline

◆ subsetDependent()

MRMTransitionGroup subsetDependent ( std::vector< std::string > tr_ids ) const

inline

Member Data Documentation

◆ chromatogram_map_

std::map<String, int> chromatogram_map_

protected

◆ chromatograms_

std::vector<ChromatogramType> chromatograms_

protected

chromatogram list

◆ mrm_features_

MRMFeatureListType mrm_features_

protected

feature list

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addFeature(), MRMTransitionGroup< SpectrumT, TransitionT >::getFeatures(), MRMTransitionGroup< SpectrumT, TransitionT >::getFeaturesMuteable(), MRMTransitionGroup< SpectrumT, TransitionT >::operator=(), MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ precursor_chromatogram_map_

std::map<String, int> precursor_chromatogram_map_

protected

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::hasPrecursorChromatogram(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().

◆ precursor_chromatograms_

std::vector<ChromatogramType> precursor_chromatograms_

protected

precursor chromatogram list

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatograms(), MRMTransitionGroup< SpectrumT, TransitionT >::operator=(), and MRMTransitionGroup< SpectrumT, TransitionT >::subset().

◆ tr_gr_id_

String tr_gr_id_

protected

transition group id (peak group id)

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getTransitionGroupID(), MRMTransitionGroup< SpectrumT, TransitionT >::operator=(), MRMTransitionGroup< SpectrumT, TransitionT >::setTransitionGroupID(), MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ transition_map_

std::map<String, int> transition_map_

protected

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::getTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::hasTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::isInternallyConsistent(), MRMTransitionGroup< SpectrumT, TransitionT >::isMappingConsistent_(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().

◆ transitions_

TransitionsType transitions_

protected

transition list

Public Types

Public Member Functions

Helper functions

Detailed Description

template<typename ChromatogramType, typename TransitionType> class OpenMS::MRMTransitionGroup< ChromatogramType, TransitionType >

Member Typedef Documentation

◆ MRMFeatureListType

◆ PeakType

◆ TransitionsType

Constructor & Destructor Documentation

◆ MRMTransitionGroup() [1/2]

◆ MRMTransitionGroup() [2/2]

◆ ~MRMTransitionGroup()

Member Function Documentation

◆ addChromatogram()

◆ addFeature() [1/2]

◆ addFeature() [2/2]

◆ addPrecursorChromatogram()

◆ addTransition()

◆ chromatogramIdsMatch()

◆ getBestFeature()

◆ getChromatogram() [1/2]

◆ getChromatogram() [2/2]

◆ getChromatograms() [1/2]

◆ getChromatograms() [2/2]

◆ getFeatures()

◆ getFeaturesMuteable()

◆ getLibraryIntensity()

◆ getPrecursorChromatogram() [1/2]

◆ getPrecursorChromatogram() [2/2]

◆ getPrecursorChromatograms() [1/2]

◆ getPrecursorChromatograms() [2/2]

◆ getTransition()

◆ getTransitionGroupID()

◆ getTransitions()

◆ getTransitionsMuteable()

◆ hasChromatogram()

◆ hasPrecursorChromatogram()

◆ hasTransition()

◆ isInternallyConsistent()

◆ isMappingConsistent_()

◆ operator=()

◆ setTransitionGroupID()

◆ size()

◆ subset()

◆ subsetDependent()

Member Data Documentation

◆ chromatogram_map_

◆ chromatograms_

◆ mrm_features_

◆ precursor_chromatogram_map_

◆ precursor_chromatograms_

◆ tr_gr_id_

◆ transition_map_

◆ transitions_

template<typename ChromatogramType, typename TransitionType>
class OpenMS::MRMTransitionGroup< ChromatogramType, TransitionType >