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PeakPickerHiRes Class Reference

This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>

Inheritance diagram for PeakPickerHiRes:
DefaultParamHandler ProgressLogger

Public Member Functions

 PeakPickerHiRes ()
 Constructor. More...
 
virtual ~PeakPickerHiRes ()
 Destructor. More...
 
template<typename PeakType >
void pick (const MSSpectrum< PeakType > &input, MSSpectrum< PeakType > &output) const
 Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. More...
 
template<typename PeakType >
void pick (const MSChromatogram< PeakType > &input, MSChromatogram< PeakType > &output) const
 
template<typename PeakType , typename ChromatogramPeakT >
void pickExperiment (const MSExperiment< PeakType, ChromatogramPeakT > &input, MSExperiment< PeakType, ChromatogramPeakT > &output) const
 Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. 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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

Protected Member Functions

void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

double signal_to_noise_
 
- 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width.

This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline.

So far, this peak picker was mainly tested on high resolution data. With appropriate preprocessing steps (e.g. noise reduction and baseline subtraction), it might be also applied to low resolution data.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
signal_to_noise float1 min: 0Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)
ms1_only stringfalse true, falseIf true, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes.

Note:
Note
The peaks must be sorted according to ascending m/z!

Constructor & Destructor Documentation

Constructor.

virtual ~PeakPickerHiRes ( )
virtual

Destructor.

Member Function Documentation

void pick ( const MSSpectrum< PeakType > &  input,
MSSpectrum< PeakType > &  output 
) const
inline
void pick ( const MSChromatogram< PeakType > &  input,
MSChromatogram< PeakType > &  output 
) const
inline
void pickExperiment ( const MSExperiment< PeakType, ChromatogramPeakT > &  input,
MSExperiment< PeakType, ChromatogramPeakT > &  output 
) const
inline

Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.

References MSExperiment< PeakT, ChromatogramPeakT >::addChromatogram(), MSExperiment< PeakT, ChromatogramPeakT >::clear(), MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::resize(), and MSExperiment< PeakT, ChromatogramPeakT >::size().

void updateMembers_ ( )
protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

double signal_to_noise_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5