OpenMS
2.4.0
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The representation of a group of transitions in a targeted proteomics experiment. More...
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
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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) |
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_ |
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.
typedef std::vector<MRMFeature> MRMFeatureListType |
Type definitions.
List of MRM Features type
typedef ChromatogramType::PeakType PeakType |
Peak type.
typedef std::vector<TransitionType> TransitionsType |
List of Reaction Monitoring transitions (meta data) type.
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Default constructor.
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Copy Constructor.
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Destructor.
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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.
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().
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Ensure that chromatogram native ids match their keys in the map.
Referenced by MRMTransitionGroupPicker::createMRMFeature(), and MRMTransitionGroupPicker::pickTransitionGroup().
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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.
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Referenced by MRMTransitionGroupPicker::pickTransitionGroup().
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Referenced by MRMTransitionGroupPicker::createMRMFeature().
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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().
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Checks that the mapping between chromatograms and transitions is consistent.
Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::isInternallyConsistent().
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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().
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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().
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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().
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Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::chromatogramIdsMatch(), MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::hasPrecursorChromatogram(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().
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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().
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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().
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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=().
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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().