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< MRMFeature > | MRMFeatureListType |
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... | |
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 |
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_ |
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.
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.
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Constructor.
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Copy Constructor.
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Destructor.
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Referenced by MRMTransitionGroupPicker::pickTransitionGroup().
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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" ... |
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Referenced by MRMTransitionGroupPicker::createMRMFeature().
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Referenced by MRMTransitionGroupPicker::createMRMFeature().
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Referenced by MRMTransitionGroupPicker::computeQuality_().
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Referenced by MRMTransitionGroupPicker::createMRMFeature().
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Referenced by EmgScoring::calcElutionFitScore().
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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().
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precursor chromatogram list
Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::addPrecursorChromatogram(), MRMTransitionGroup< SpectrumT, TransitionT >::getPrecursorChromatogram(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().
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transition group id (peak group id)
Referenced by MRMTransitionGroup< SpectrumT, TransitionT >::getTransitionGroupID(), MRMTransitionGroup< SpectrumT, TransitionT >::operator=(), and MRMTransitionGroup< SpectrumT, TransitionT >::setTransitionGroupID().
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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(), and MRMTransitionGroup< SpectrumT, TransitionT >::operator=().
OpenMS / TOPP release 2.0.0 | Documentation generated on Fri May 29 2015 17:20:40 using doxygen 1.8.9.1 |