MRMTransitionGroup< ChromatogramType, TransitionType > Class Template Reference

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, const String &key)
bool	hasTransition (const String &key) const
const TransitionType &	getTransition (const 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

Add a chromatogram

Chromatograms are internally mapped using the provided key. The ChromatogramType::getNativeID is a good choice.

When querying for a chromatogram, make sure to use this key.

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

addFeature() [1/2]

void addFeature ( const MRMFeature &  feature )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_.

Referenced by MRMTransitionGroupPicker::pickTransitionGroup(), MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

addFeature() [2/2]

void addFeature ( MRMFeature &&  feature )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_.

addPrecursorChromatogram()

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

inline

Add a precursor chromatogram (extracted from an MS1 map)

Precursor chromatograms are internally mapped using the provided key, i.e. ChromatogramType::getNativeID.

When querying for a chromatogram, make sure to use this key.

Parameters

chromatogram

Chromatographic traces from the MS1 map to be added

References MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::subset().

addTransition()

void addTransition ( const TransitionType &  transition, const String &  key  )

inline

Add a transition

Transitions are internally mapped using their nativeID, i.e. TransitionType::getNativeID.

When querying for a transition, make sure to use this key.

References MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

chromatogramIdsMatch()

bool chromatogramIdsMatch ( ) const

inline

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

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), ChromatogramSettings::getNativeID(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatogram(), and MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_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.

References MRMTransitionGroup< ChromatogramType, TransitionType >::getFeatures(), and OPENMS_PRECONDITION.

getChromatogram() [1/2]

ChromatogramType& getChromatogram ( const String &  key )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), and OPENMS_PRECONDITION.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::selectChromHelper_().

getChromatogram() [2/2]

const ChromatogramType& getChromatogram ( const String &  key ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), and OPENMS_PRECONDITION.

getChromatograms() [1/2]

std::vector<ChromatogramType>& getChromatograms ( )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_.

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

getChromatograms() [2/2]

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_.

getFeatures()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::getBestFeature().

getFeaturesMuteable()

std::vector<MRMFeature>& getFeaturesMuteable ( )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_.

getLibraryIntensity()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

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

getPrecursorChromatogram() [1/2]

ChromatogramType& getPrecursorChromatogram ( const String &  key )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::hasPrecursorChromatogram(), OPENMS_PRECONDITION, MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), and MRMTransitionGroupPicker::selectChromHelper_().

getPrecursorChromatogram() [2/2]

const ChromatogramType& getPrecursorChromatogram ( const String &  key ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::hasPrecursorChromatogram(), OPENMS_PRECONDITION, MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_.

getPrecursorChromatograms() [1/2]

std::vector<ChromatogramType>& getPrecursorChromatograms ( )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_.

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

getPrecursorChromatograms() [2/2]

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_.

getTransition()

const TransitionType& getTransition ( const String &  key )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::hasTransition(), OPENMS_PRECONDITION, MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

getTransitionGroupID()

const String& getTransitionGroupID ( ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::tr_gr_id_.

Referenced by MRMTransitionGroupPicker::createMRMFeature().

getTransitions()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

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

getTransitionsMuteable()

std::vector<TransitionType>& getTransitionsMuteable ( )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

hasChromatogram()

bool hasChromatogram ( const String &  key ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), MRMTransitionGroupPicker::selectChromHelper_(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subset().

hasPrecursorChromatogram()

bool hasPrecursorChromatogram ( const String &  key ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_map_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatogram(), and MRMTransitionGroupPicker::selectChromHelper_().

hasTransition()

bool hasTransition ( const String &  key ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::getTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::isMappingConsistent_(), MRMTransitionGroupPicker::pickTransitionGroup(), and MRMTransitionGroup< ChromatogramType, TransitionType >::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)

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, MRMTransitionGroup< ChromatogramType, TransitionType >::isMappingConsistent_(), OPENMS_PRECONDITION, MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

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

isMappingConsistent_()

bool isMappingConsistent_ ( ) const

inlineprotected

Checks that the mapping between chromatograms and transitions is consistent.

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::hasTransition(), and MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent().

operator=()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_, MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_, MRMTransitionGroup< ChromatogramType, TransitionType >::tr_gr_id_, MRMTransitionGroup< ChromatogramType, TransitionType >::transition_map_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

setTransitionGroupID()

void setTransitionGroupID ( const String &  tr_gr_id )

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::tr_gr_id_.

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

size()

Size size ( ) const

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_.

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

subset()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::addChromatogram(), MRMFeature::addFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::addFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::addPrecursorChromatogram(), MRMFeature::addPrecursorFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::addTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, seqan::find(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_, MRMTransitionGroup< ChromatogramType, TransitionType >::precursor_chromatograms_, Peak2D::setIntensity(), Peak2D::setRT(), MRMTransitionGroup< ChromatogramType, TransitionType >::setTransitionGroupID(), MRMTransitionGroup< ChromatogramType, TransitionType >::tr_gr_id_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

subsetDependent()

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

inline

References MRMTransitionGroup< ChromatogramType, TransitionType >::addChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::addFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::addTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogram_map_, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatograms_, seqan::find(), MRMTransitionGroup< ChromatogramType, TransitionType >::mrm_features_, MRMTransitionGroup< ChromatogramType, TransitionType >::setTransitionGroupID(), MRMTransitionGroup< ChromatogramType, TransitionType >::tr_gr_id_, and MRMTransitionGroup< ChromatogramType, TransitionType >::transitions_.

Member Data Documentation

chromatogram_map_

std::map<String, int> chromatogram_map_

protected

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::addChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), MRMTransitionGroup< ChromatogramType, TransitionType >::isMappingConsistent_(), MRMTransitionGroup< ChromatogramType, TransitionType >::operator=(), MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

chromatograms_

std::vector<ChromatogramType> chromatograms_

protected

chromatogram list

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::addChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatograms(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), MRMTransitionGroup< ChromatogramType, TransitionType >::operator=(), MRMTransitionGroup< ChromatogramType, TransitionType >::size(), MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

mrm_features_

MRMFeatureListType mrm_features_

protected

feature list

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

precursor_chromatogram_map_

std::map<String, int> precursor_chromatogram_map_

protected

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

precursor_chromatograms_

std::vector<ChromatogramType> precursor_chromatograms_

protected

precursor chromatogram list

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

tr_gr_id_

String tr_gr_id_

protected

transition group id (peak group id)

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

transition_map_

std::map<String, int> transition_map_

protected

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

transitions_

TransitionsType transitions_

protected

transition list

Referenced by MRMTransitionGroup< ChromatogramType, TransitionType >::addTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::getLibraryIntensity(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitions(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitionsMuteable(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), MRMTransitionGroup< ChromatogramType, TransitionType >::operator=(), MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().