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MRMTransitionGroupPicker Class Reference

The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>

Inheritance diagram for MRMTransitionGroupPicker:
DefaultParamHandler

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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
MRMTransitionGroupPickeroperator= (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< RichPeakChromatogrampicked_chroms_
 
std::vector< RichPeakChromatogramsmoothed_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< Stringsubsections_
 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...
 

Detailed Description

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.

Member Typedef Documentation

Constructor & Destructor Documentation

Constructor.

Destructor.

Member Function Documentation

double calculateBgEstimation_ ( const RichPeakChromatogram smoothed_chromat,
double  best_left,
double  best_right 
)
protected

Will use the smoothed chromatograms.

MRMFeature createMRMFeature ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group,
std::vector< SpectrumT > &  picked_chroms,
int &  chr_idx,
int &  peak_idx 
)
inline
void findLargestPeak ( std::vector< RichPeakChromatogram > &  picked_chroms,
int &  chr_idx,
int &  peak_idx 
)

Find largest peak in a vector of chromatograms.

MRMTransitionGroupPicker& operator= ( const MRMTransitionGroupPicker rhs)
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.

void pickTransitionGroup ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group)
inline
void prepareMasterContainer_ ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group,
SpectrumT &  master_peak_container,
int  chr_idx,
double  best_left,
double  best_right 
)
inlineprotected

create an empty master peak container that has the correct mz / RT values set

References MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms().

void remove_overlapping_features ( std::vector< SpectrumT > &  picked_chroms,
double  best_left,
double  best_right 
)
inline

Remove overlaping features that are within the current seed feature or overlap with it.

References OpenMS::Constants::k.

SpectrumT resampleChromatogram_ ( const SpectrumT &  chromatogram,
SpectrumT &  master_peak_container,
double  best_left,
double  best_right 
)
inlineprotected

use the master container from above to resample a chromatogram at those points stored in the master container

References LinearResamplerAlign::raster().

void updateMembers_ ( )
protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

String background_subtraction_
protected
DoubleReal gauss_width_
protected
DoubleReal peak_width_
protected
std::vector<RichPeakChromatogram> picked_chroms_
protected
UInt sgolay_frame_length_
protected
UInt sgolay_polynomial_order_
protected
DoubleReal signal_to_noise_
protected
std::vector<RichPeakChromatogram> smoothed_chroms_
protected
UInt sn_bin_count_
protected
DoubleReal sn_win_len_
protected
int stop_after_feature_
protected
DoubleReal stop_after_intensity_ratio_
protected
bool use_gauss_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5