36 #ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H 37 #define OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H 49 namespace OptimizationFunctions
131 penalties_(opt.penalties_),
132 charge_(opt.charge_){}
161 penalties_ = penalties;
162 param_.setValue(
"penalties:left_width", penalties_.lWidth);
163 param_.setValue(
"penalties:right_width", penalties_.rWidth);
164 param_.setValue(
"penalties:height", penalties_.height);
165 param_.setValue(
"penalties:position", penalties_.pos);
176 bool optimize(std::vector<PeakShape> & peaks,
Data & data);
177 Size getNumberOfPeaks_(
Int charge, std::vector<PeakShape> & temp_shapes,
Data & data);
190 void setNumberOfPeaks_(
Data & data,
const std::vector<PeakShape> & temp_shapes,
Int charge);
192 void updateMembers_();
This class provides the deconvolution of peak regions using non-linear optimization.
Definition: OptimizePeakDeconvolution.h:97
~PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:75
OptimizePeakDeconvolution & operator=(const OptimizePeakDeconvolution &opt)
Definition: OptimizePeakDeconvolution.h:141
Int getCharge() const
Non-mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:169
RawDataVector::iterator PeakIterator
Definition: OptimizePeakDeconvolution.h:105
void setPenalties(const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
Mutable access to the penalty parameter.
Definition: OptimizePeakDeconvolution.h:159
OptimizationFunctions::PenaltyFactorsIntensity penalties
Definition: OptimizePeakDeconvolution.h:116
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double lWidth
Penalty factor for the peak shape's left width parameter.
Definition: OptimizePick.h:83
std::vector< Peak1D > RawDataVector
Definition: OptimizePeakDeconvolution.h:104
void setCharge(const Int charge)
Mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:171
std::vector< double > signal
Definition: OptimizePeakDeconvolution.h:115
std::vector< PeakShape > peaks
Definition: OptimizePeakDeconvolution.h:113
double pos
Penalty factor for the peak shape's position.
Definition: OptimizePick.h:81
double rWidth
Penalty factor for the peak shape's right width parameter.
Definition: OptimizePick.h:85
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Class containing the data needed for optimization.
Definition: OptimizePeakDeconvolution.h:111
Class for the penalty factors used during the optimization.
Definition: OptimizePick.h:63
virtual ~OptimizePeakDeconvolution()
Destructor.
Definition: OptimizePeakDeconvolution.h:135
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Int charge
Definition: OptimizePeakDeconvolution.h:117
OptimizePeakDeconvolution(const OptimizePeakDeconvolution &opt)
Copy-Constructor.
Definition: OptimizePeakDeconvolution.h:129
Int charge_
Charge state of the current isotope pattern.
Definition: OptimizePeakDeconvolution.h:184
PenaltyFactorsIntensity & operator=(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:65
int Int
Signed integer type.
Definition: Types.h:103
double height
Definition: OptimizePeakDeconvolution.h:77
std::vector< double > positions
Definition: OptimizePeakDeconvolution.h:114
static const double dist_
distance between two isotopic peaks
Definition: OptimizePeakDeconvolution.h:187
OptimizationFunctions::PenaltyFactorsIntensity penalties_
Definition: OptimizePeakDeconvolution.h:181
Class for the penalty factors used during the optimization.
Definition: OptimizePeakDeconvolution.h:58
PenaltyFactorsIntensity(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:63
PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:61