This class provides the deconvolution of peak regions using non-linear optimization. More...
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h>
Classes | |
| struct | Data |
| Class containing the data needed for optimization. More... | |
Public Types | |
Type definitions | |
| typedef std::vector< Peak1D > | RawDataVector |
| typedef RawDataVector::iterator | PeakIterator |
Public Member Functions | |
| bool | optimize (std::vector< PeakShape > &peaks, Data &data) |
| 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. | |
| Int | getCharge () const |
| Non-mutable access to the charge. | |
| void | setCharge (const Int charge) |
| Mutable access to the charge. | |
Protected Member Functions | |
| Size | getNumberOfPeaks_ (Int charge, std::vector< PeakShape > &temp_shapes, Data &data) |
| 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 setParameters() method. | |
Protected Attributes | |
| OptimizationFunctions::PenaltyFactorsIntensity | penalties_ |
| Int | charge_ |
| Charge state of the current isotope pattern. | |
Static Protected Attributes | |
| static const DoubleReal | dist_ |
| distance between two isotopic peaks | |
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.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| max_iteration | int | 10 | maximal number of iterations for the fitting step | |
| eps_abs | float | 0.0001 | if the absolute error gets smaller than this value the fitting is stopped | |
| eps_rel | float | 0.0001 | if the relative error gets smaller than this value the fitting is stopped | |
| fwhm_threshold | float | 1 | If a peaks is broader than fwhm_threshold, it is assumed that it contains another peaks and an additional peak is added. | |
| penalties:left_width | float | 0 | penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized. | |
| penalties:right_width | float | 0 | penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized. | |
| penalties:height | float | 0 | penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized. | |
| penalties:position | float | 0 | penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
| typedef RawDataVector::iterator PeakIterator |
| typedef std::vector<Peak1D> RawDataVector |
Constructor & Destructor Documentation
Constructor.
| OptimizePeakDeconvolution | ( | const OptimizePeakDeconvolution & | opt | ) | [inline] |
Copy-Constructor.
| virtual ~OptimizePeakDeconvolution | ( | ) | [inline, virtual] |
Destructor.
Member Function Documentation
| bool checkFWHM_ | ( | std::vector< PeakShape > & | peaks, | |
| gsl_multifit_fdfsolver *& | fit | |||
| ) | [protected] |
| Int getCharge | ( | ) | const [inline] |
Non-mutable access to the charge.
| Size getNumberOfPeaks_ | ( | Int | charge, | |
| std::vector< PeakShape > & | temp_shapes, | |||
| Data & | data | |||
| ) | [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.
| const OptimizationFunctions::PenaltyFactorsIntensity& getPenalties | ( | ) | const [inline] |
Non-mutable access to the penalty parameter.
Accessors
| OptimizePeakDeconvolution& operator= | ( | const OptimizePeakDeconvolution & | opt | ) | [inline] |
Performs a nonlinear optimization of the peaks that belong to the current isotope pattern.
| void setCharge | ( | const Int | charge | ) | [inline] |
Mutable access to the charge.
| void setPenalties | ( | const OptimizationFunctions::PenaltyFactorsIntensity & | penalties | ) | [inline] |
Mutable access to the penalty parameter.
| void updateMembers_ | ( | ) | [protected, virtual] |
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
Charge state of the current isotope pattern.
Referenced by OptimizePeakDeconvolution::operator=().
const DoubleReal dist_ [static, protected] |
distance between two isotopic peaks
Referenced by OptimizePeakDeconvolution::operator=().
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:57 using doxygen 1.7.1 |