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template<typename SpectrumT , typename TransitionT > |
void | pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group) |
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void | pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &smoothed_chrom, RichPeakChromatogram &picked_chrom) |
| Finds peaks in a chromatogram and annotates left/right borders. More...
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template<typename SpectrumT , typename TransitionT > |
MRMFeature | createMRMFeature (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, int &chr_idx, int &peak_idx) |
| Create feature from a vector of chromatograms and a specified peak. More...
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template<typename SpectrumT > |
void | remove_overlapping_features (std::vector< SpectrumT > &picked_chroms, double best_left, double best_right) |
| Remove overlaping features that are within the current seed feature or overlap with it. More...
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void | findLargestPeak (std::vector< RichPeakChromatogram > &picked_chroms, int &chr_idx, int &peak_idx) |
| Find largest peak in a vector of chromatograms. More...
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| MRMTransitionGroupPicker () |
| Constructor. More...
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| ~MRMTransitionGroupPicker () |
| Destructor. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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double | calculateBgEstimation_ (const RichPeakChromatogram &smoothed_chromat, double best_left, double best_right) |
| Will use the smoothed chromatograms. More...
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void | updateMembers_ () |
| Synchronize members with param class. More...
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MRMTransitionGroupPicker & | operator= (const MRMTransitionGroupPicker &rhs) |
| Assignment operator is private for algorithm. More...
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template<typename SpectrumT , typename TransitionT > |
void | prepareMasterContainer_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, SpectrumT &master_peak_container, int chr_idx, double best_left, double best_right) |
| create an empty master peak container that has the correct mz / RT values set More...
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template<typename SpectrumT > |
SpectrumT | resampleChromatogram_ (const SpectrumT &chromatogram, SpectrumT &master_peak_container, double best_left, double best_right) |
| use the master container from above to resample a chromatogram at those points stored in the master container More...
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Protected Member Functions inherited from DefaultParamHandler |
void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More...
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The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors.
It is called through pickTransitionGroup which will accept an MRMTransitionGroup filled with n chromatograms and perform the following steps:
- Step 1: find features (peaks) in individual chromatograms
- Step 2: merge these features to consensus features that span multiple chromatograms
Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.
Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.