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. More... | |
Size | getNumberOfPeaks_ (Int charge, std::vector< PeakShape > &temp_shapes, Data &data) |
Constructors and Destructor | |
OptimizePeakDeconvolution () | |
Constructor. More... | |
OptimizePeakDeconvolution (const OptimizePeakDeconvolution &opt) | |
Copy-Constructor. More... | |
virtual | ~OptimizePeakDeconvolution () |
Destructor. More... | |
Assignment | |
OptimizePeakDeconvolution & | operator= (const OptimizePeakDeconvolution &opt) |
const OptimizationFunctions::PenaltyFactorsIntensity & | getPenalties () const |
Non-mutable access to the penalty parameter. More... | |
void | setPenalties (const OptimizationFunctions::PenaltyFactorsIntensity &penalties) |
Mutable access to the penalty parameter. More... | |
Int | getCharge () const |
Non-mutable access to the charge. More... | |
void | setCharge (const Int charge) |
Mutable access to the charge. More... | |
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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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () 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 | |
void | setNumberOfPeaks_ (Data &data, const std::vector< PeakShape > &temp_shapes, Int charge) |
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. More... | |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
OptimizationFunctions::PenaltyFactorsIntensity | penalties_ |
Int | charge_ |
Charge state of the current isotope pattern. More... | |
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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< String > | subsections_ |
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... | |
Static Protected Attributes | |
static const double | dist_ |
distance between two isotopic peaks More... | |
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. 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.
typedef RawDataVector::iterator PeakIterator |
typedef std::vector<Peak1D> RawDataVector |
Constructor.
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inline |
Copy-Constructor.
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inlinevirtual |
Destructor.
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inline |
Non-mutable access to the charge.
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inline |
Non-mutable access to the penalty parameter.
Accessors
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inline |
Performs a nonlinear optimization of the peaks that belong to the current isotope pattern.
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inline |
Mutable access to the charge.
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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.
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inline |
Mutable access to the penalty parameter.
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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.
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protected |
Charge state of the current isotope pattern.
Referenced by OptimizePeakDeconvolution::operator=().
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staticprotected |
distance between two isotopic peaks
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protected |
Referenced by OptimizePeakDeconvolution::operator=().
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11 |