#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h>
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 | |
OptimizePeakDeconvolution & | operator= (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 |
typedef std::vector<DRawDataPoint<1> > RawDataVector |
typedef RawDataVector::iterator RawDataPointIterator |
Constructor.
OptimizePeakDeconvolution | ( | const OptimizePeakDeconvolution & | opt | ) | [inline] |
Copy-Constructor.
virtual ~OptimizePeakDeconvolution | ( | ) | [inline, virtual] |
Destructor.
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.
int charge_ [protected] |
Charge state of the current isotope pattern.
const double dist_ [static, protected] |
distance between two isotopic peaks
Generated Tue Apr 1 15:36:48 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |