| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
MRMTransitionGroup< ChromatogramType, TransitionType > Class Template Reference

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

`#include <OpenMS/KERNEL/MRMTransitionGroup.h>`

## 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

MRMTransitionGroup & | operator= (const MRMTransitionGroup &rhs)
Size | size () const
const String & | getTransitionGroupID () const
void | setTransitionGroupID (const String &tr_gr_id)
const MRMFeature & | getBestFeature () const
| Returns the best feature by overall quality. More...
Constructors and Destructor
| MRMTransitionGroup ()
| Default constructor. More...
| MRMTransitionGroup (const MRMTransitionGroup &rhs)
| Copy Constructor. More...
virtual | ~MRMTransitionGroup ()
| Destructor. More...
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
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

## Protected Member Functions

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

## Protected Attributes

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_

## 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 | ( |  | ) |

inline virtual

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

inline protected

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

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

## ◆ chromatograms_

std::vector<ChromatogramType> chromatograms_

protected

chromatogram list

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

## ◆ 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

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