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OptimizePeakDeconvolution Class Reference
[PeakPicking]

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

Inheritance diagram for OptimizePeakDeconvolution:

DefaultParamHandler

List of all members.


Detailed Description

This class provides the deconvolution of peak regions using non-linear optimization.

Given a vector of peak shapes, this class optimizes all peak shapes parameters using a non-linear optimization. For the non-linear optimization we use the Levenberg-Marquardt algorithm provided by the gsl. There are a few constraints for the parameters: the positions are equidistant according to the peptide mass rule, e.g. two consecutive isotopic peaks are 1.003/charge away from each other. Besides the peaks have all the same left and right width, respectively.

OptimizePeakDeconvolution Parameters are explained on a separate page.

Public Types

Type definitions
typedef std::vector
< DRawDataPoint< 1 > > 
RawDataVector
typedef RawDataVector::iterator RawDataPointIterator

Public Member Functions

bool optimize (std::vector< PeakShape > &peaks, int failure)
 Performs a nonlinear optimization of the peaks that belong to the current isotope pattern.
Constructors and Destructor
 OptimizePeakDeconvolution ()
 Constructor.
 OptimizePeakDeconvolution (const OptimizePeakDeconvolution &opt)
 Copy-Constructor.
virtual ~OptimizePeakDeconvolution ()
 Destructor.
Assignment
OptimizePeakDeconvolutionoperator= (const OptimizePeakDeconvolution &opt)
const
OptimizationFunctions::PenaltyFactorsIntensity
getPenalties () const
 Non-mutable access to the penalty parameter.
void setPenalties (const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
 Mutable access to the penalty parameter.
const int getCharge () const
 Non-mutable access to the charge.
void setCharge (const int charge)
 Mutable access to the charge.

Protected Member Functions

int getNumberOfPeaks_ (int charge, std::vector< PeakShape > &temp_shapes)
 A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state.
bool checkFWHM_ (std::vector< PeakShape > &peaks, gsl_multifit_fdfsolver *&fit)
void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParam() method.

Protected Attributes

OptimizationFunctions::PenaltyFactorsIntensity penalties_
int charge_
 Charge state of the current isotope pattern.

Static Protected Attributes

static const double dist_
 distance between two isotopic peaks


Member Typedef Documentation

typedef std::vector<DRawDataPoint<1> > RawDataVector

typedef RawDataVector::iterator RawDataPointIterator


Constructor & Destructor Documentation

OptimizePeakDeconvolution (  ) 

Constructor.

OptimizePeakDeconvolution ( const OptimizePeakDeconvolution opt  )  [inline]

Copy-Constructor.

virtual ~OptimizePeakDeconvolution (  )  [inline, virtual]

Destructor.


Member Function Documentation

OptimizePeakDeconvolution& operator= ( const OptimizePeakDeconvolution opt  )  [inline]

const OptimizationFunctions::PenaltyFactorsIntensity& getPenalties (  )  const [inline]

Non-mutable access to the penalty parameter.

Accessors

void setPenalties ( const OptimizationFunctions::PenaltyFactorsIntensity penalties  )  [inline]

Mutable access to the penalty parameter.

const int getCharge (  )  const [inline]

Non-mutable access to the charge.

void setCharge ( const int  charge  )  [inline]

Mutable access to the charge.

bool optimize ( std::vector< PeakShape > &  peaks,
int  failure 
)

Performs a nonlinear optimization of the peaks that belong to the current isotope pattern.

int getNumberOfPeaks_ ( int  charge,
std::vector< PeakShape > &  temp_shapes 
) [protected]

A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state.

bool checkFWHM_ ( std::vector< PeakShape > &  peaks,
gsl_multifit_fdfsolver *&  fit 
) [protected]

void updateMembers_ (  )  [protected, virtual]

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

OptimizationFunctions::PenaltyFactorsIntensity penalties_ [protected]

int charge_ [protected]

Charge state of the current isotope pattern.

const double dist_ [static, protected]

distance between two isotopic peaks


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:48 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1