The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>
 
  
 | Public Types | |
| typedef MSSpectrum < ChromatogramPeak > | RichPeakChromatogram | 
| Public Member Functions | |
| template<typename SpectrumT , typename TransitionT > | |
| void | pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group) | 
| void | pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &smoothed_chrom, RichPeakChromatogram &picked_chrom) | 
| Finds peaks in a chromatogram and annotates left/right borders.  More... | |
| 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... | |
| 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... | |
| void | findLargestPeak (std::vector< RichPeakChromatogram > &picked_chroms, int &chr_idx, int &peak_idx) | 
| Find largest peak in a vector of chromatograms.  More... | |
| MRMTransitionGroupPicker () | |
| Constructor.  More... | |
| ~MRMTransitionGroupPicker () | |
| Destructor.  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Protected Member Functions | |
| double | calculateBgEstimation_ (const RichPeakChromatogram &smoothed_chromat, double best_left, double best_right) | 
| Will use the smoothed chromatograms.  More... | |
| void | updateMembers_ () | 
| Synchronize members with param class.  More... | |
| MRMTransitionGroupPicker & | operator= (const MRMTransitionGroupPicker &rhs) | 
| Assignment operator is private for algorithm.  More... | |
| Resampling methods | |
| 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... | |
| 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... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Protected Attributes | |
| UInt | sgolay_frame_length_ | 
| UInt | sgolay_polynomial_order_ | 
| DoubleReal | gauss_width_ | 
| bool | use_gauss_ | 
| String | background_subtraction_ | 
| DoubleReal | peak_width_ | 
| DoubleReal | signal_to_noise_ | 
| DoubleReal | sn_win_len_ | 
| UInt | sn_bin_count_ | 
| int | stop_after_feature_ | 
| DoubleReal | stop_after_intensity_ratio_ | 
| std::vector< RichPeakChromatogram > | picked_chroms_ | 
| std::vector< RichPeakChromatogram > | smoothed_chroms_ | 
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
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 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.
Constructor.
Destructor.
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 | protected | 
Will use the smoothed chromatograms.
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 | inline | 
Create feature from a vector of chromatograms and a specified peak.
References MRMFeature::addFeature(), MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), Feature::getConvexHulls(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitionGroupID(), OpenMS::Constants::k, ConvexHull2D::setHullPoints(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), Peak2D::setMZ(), Feature::setOverallQuality(), Feature::setQuality(), and Peak2D::setRT().
| void findLargestPeak | ( | std::vector< RichPeakChromatogram > & | picked_chroms, | 
| int & | chr_idx, | ||
| int & | peak_idx | ||
| ) | 
Find largest peak in a vector of chromatograms.
| 
 | protected | 
Assignment operator is private for algorithm.
| void pickChromatogram | ( | const RichPeakChromatogram & | chromatogram, | 
| RichPeakChromatogram & | smoothed_chrom, | ||
| RichPeakChromatogram & | picked_chrom | ||
| ) | 
Finds peaks in a chromatogram and annotates left/right borders.
| 
 | inline | 
This function will accept a MRMTransitionGroup with raw chromatograms, create features on it and add the features back to the MRMTransitionGroup.
References MRMTransitionGroup< SpectrumType, TransitionType >::addFeature(), MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), Peak2D::getIntensity(), MetaInfoInterface::getMetaValue(), MSSpectrum< PeakT >::isSorted(), OpenMS::Constants::k, MSSpectrum< PeakT >::sortByIntensity(), and MSSpectrum< PeakT >::sortByPosition().
Referenced by MRMFeatureFinderScoring::pickExperiment().
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 | inlineprotected | 
create an empty master peak container that has the correct mz / RT values set
References MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms().
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 | inline | 
Remove overlaping features that are within the current seed feature or overlap with it.
References OpenMS::Constants::k.
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 | inlineprotected | 
use the master container from above to resample a chromatogram at those points stored in the master container
References LinearResamplerAlign::raster().
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Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |