MRMTransitionGroup< SpectrumType, TransitionType > Class Template Reference

The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to. More...

#include <OpenMS/KERNEL/MRMTransitionGroup.h>

List of all members.

Public Types
typedef std::vector< MRMFeature >	MRMFeatureListType
	Type definitions.
typedef std::vector < TransitionType >	TransitionsType
	List of Reaction Monitoring transitions (meta data) type.
typedef SpectrumType::PeakType	PeakType
	Peak type.
Public Member Functions
	MRMTransitionGroup ()
	Constructor.
	MRMTransitionGroup (const MRMTransitionGroup &rhs)
	Copy Constructor.
virtual	~MRMTransitionGroup ()
	Destructor.
MRMTransitionGroup &	operator= (const MRMTransitionGroup &rhs)
Size	size () const
const String &	getTransitionGroupID () const
void	setTransitionGroupID (const String &tr_gr_id)
const std::vector < TransitionType > &	getTransitions () const
std::vector< TransitionType > &	getTransitionsMuteable ()
void	addTransition (const TransitionType &transition, String key)
const TransitionType &	getTransition (String key)
bool	hasTransition (String key)
const std::vector< SpectrumType > &	getChromatograms () const
std::vector< SpectrumType > &	getChromatograms ()
void	addChromatogram (SpectrumType &chromatogram, String key)
SpectrumType &	getChromatogram (String key)
bool	hasChromatogram (String key)
const std::vector< MRMFeature > &	getFeatures () const
std::vector< MRMFeature > &	getFeaturesMuteable ()
void	addFeature (MRMFeature &feature)
void	getLibraryIntensity (std::vector< double > &result) const
Protected Attributes
String	tr_gr_id_
	transition group id (peak group id)
TransitionsType	transitions_
	transition list
std::vector< SpectrumType >	chromatograms_
	chromatogram list
MRMFeatureListType	cons_features_
	feature list
std::map< String, int >	chromatogram_map_
std::map< String, int >	transition_map_

---

Detailed Description

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

The representation of a transition group that has information about the individual chromatograms as well as the transitions it refers to.

This means that the MRM Transition Group establishes the mapping between the individual Transition (containind the meta-data) and the Chromatogram data points (measured data).

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

typedef std::vector<MRMFeature> MRMFeatureListType

Type definitions.

List of MRM Features type

typedef SpectrumType::PeakType PeakType

Peak type.

typedef std::vector<TransitionType> TransitionsType

List of Reaction Monitoring transitions (meta data) type.

---

Constructor & Destructor Documentation

MRMTransitionGroup

(

)

[inline]

Constructor.

MRMTransitionGroup

(

const MRMTransitionGroup< SpectrumType, TransitionType > &

rhs

)

[inline]

Copy Constructor.

virtual ~MRMTransitionGroup

(

)

[inline, virtual]

Destructor.

---

Member Function Documentation

void addChromatogram	(	SpectrumType &	chromatogram,
		String	key
	)			[inline]

void addFeature

(

MRMFeature &

feature

)

[inline]

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

void addTransition	(	const TransitionType &	transition,
		String	key
	)			[inline]

SpectrumType& getChromatogram

(

String

key

)

[inline]

const std::vector<SpectrumType>& getChromatograms

(

)

const [inline]

Referenced by EmgScoring::calcElutionFitScore(), MRMTransitionGroupPicker::createMRMFeature(), MRMFeatureFinderScoring::pickExperiment(), MRMTransitionGroupPicker::pickTransitionGroup(), MRMTransitionGroupPicker::prepareMasterContainer_(), and MRMFeatureFinderScoring::scorePeakgroups_().

std::vector<SpectrumType>& getChromatograms

(

)

[inline]

const std::vector<MRMFeature>& getFeatures

(

)

const [inline]

std::vector<MRMFeature>& getFeaturesMuteable

(

)

[inline]

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

void getLibraryIntensity

(

std::vector< double > &

result

)

const [inline]

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

const TransitionType& getTransition

(

String

key

)

[inline]

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

const String& getTransitionGroupID

(

)

const [inline]

Referenced by MRMTransitionGroupPicker::createMRMFeature(), and MRMFeatureFinderScoring::scorePeakgroups_().

const std::vector<TransitionType>& getTransitions

(

)

const [inline]

Referenced by MRMFeatureFinderScoring::calculateSwathScores_(), MRMFeatureFinderScoring::pickExperiment(), and MRMFeatureFinderScoring::scorePeakgroups_().

std::vector<TransitionType>& getTransitionsMuteable

(

)

[inline]

bool hasChromatogram

(

String

key

)

[inline]

bool hasTransition

(

String

key

)

[inline]

MRMTransitionGroup& operator=

(

const MRMTransitionGroup< SpectrumType, TransitionType > &

rhs

)

[inline]

void setTransitionGroupID

(

const String &

tr_gr_id

)

[inline]

Size size

(

)

const [inline]

Referenced by EmgScoring::calcElutionFitScore(), MRMFeatureFinderScoring::calculateSwathScores_(), and MRMFeatureFinderScoring::scorePeakgroups_().

---

Member Data Documentation

std::map<String, int> chromatogram_map_ [protected]

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::hasChromatogram(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().

std::vector<SpectrumType> chromatograms_ [protected]

chromatogram list

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getChromatograms(), MRMTransitionGroup< SpectrumT, TransitionT >::operator=(), and MRMTransitionGroup< SpectrumT, TransitionT >::size().

MRMFeatureListType cons_features_ [protected]

feature list

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

String tr_gr_id_ [protected]

transition group id (peak group id)

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

std::map<String, int> transition_map_ [protected]

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

TransitionsType transitions_ [protected]

transition list

Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::getLibraryIntensity(), MRMTransitionGroup< SpectrumT, TransitionT >::getTransition(), MRMTransitionGroup< SpectrumT, TransitionT >::getTransitions(), MRMTransitionGroup< SpectrumT, TransitionT >::getTransitionsMuteable(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().