Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Protected Attributes | List of all members
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>

Public Types

typedef std::vector< MRMFeatureMRMFeatureListType
 Type definitions. More...
 
typedef std::vector< TransitionType > TransitionsType
 List of Reaction Monitoring transitions (meta data) type. More...
 
typedef SpectrumType::PeakType PeakType
 Peak type. More...
 

Public Member Functions

 MRMTransitionGroup ()
 Constructor. More...
 
 MRMTransitionGroup (const MRMTransitionGroup &rhs)
 Copy Constructor. More...
 
virtual ~MRMTransitionGroup ()
 Destructor. More...
 
MRMTransitionGroupoperator= (const MRMTransitionGroup &rhs)
 
Size size () const
 
const StringgetTransitionGroupID () 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
 
void addPrecursorChromatogram (SpectrumType &chromatogram, String key)
 
SpectrumType & getPrecursorChromatogram (String key)
 
bool hasPrecursorChromatogram (String key) const
 
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) More...
 
TransitionsType transitions_
 transition list More...
 
std::vector< SpectrumType > chromatograms_
 chromatogram list More...
 
std::vector< SpectrumType > precursor_chromatograms_
 precursor chromatogram list More...
 
MRMFeatureListType cons_features_
 feature list More...
 
std::map< String, int > chromatogram_map_
 
std::map< String, int > precursor_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 (containing 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 ( )
inlinevirtual

Destructor.

Member Function Documentation

void addChromatogram ( SpectrumType &  chromatogram,
String  key 
)
inline
void addFeature ( MRMFeature feature)
inline
void addPrecursorChromatogram ( SpectrumType &  chromatogram,
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
chromatogramChromatographic traces from the MS1 map to be added
keyIdentifier for this trace, please use use consistent naming like "Precursor_i0", "Precursor_i1", "Precursor_i2" ...
void addTransition ( const TransitionType &  transition,
String  key 
)
inline
SpectrumType& getChromatogram ( String  key)
inline
const std::vector<SpectrumType>& getChromatograms ( ) const
inline
std::vector<SpectrumType>& getChromatograms ( )
inline
const std::vector<MRMFeature>& getFeatures ( ) const
inline
std::vector<MRMFeature>& getFeaturesMuteable ( )
inline
void getLibraryIntensity ( std::vector< double > &  result) const
inline
SpectrumType& getPrecursorChromatogram ( String  key)
inline
const TransitionType& getTransition ( String  key)
inline
const String& getTransitionGroupID ( ) const
inline
const std::vector<TransitionType>& getTransitions ( ) const
inline
std::vector<TransitionType>& getTransitionsMuteable ( )
inline
bool hasChromatogram ( String  key) const
inline
bool hasPrecursorChromatogram ( String  key) const
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

Member Data Documentation

std::map<String, int> chromatogram_map_
protected
std::vector<SpectrumType> chromatograms_
protected
MRMFeatureListType cons_features_
protected
std::map<String, int> precursor_chromatogram_map_
protected
std::vector<SpectrumType> precursor_chromatograms_
protected
String tr_gr_id_
protected
std::map<String, int> transition_map_
protected
TransitionsType transitions_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:57 using doxygen 1.8.9.1