|
OpenMS
2.5.0
|
Go to the documentation of this file.
48 namespace OptimizationFunctions
130 penalties_(opt.penalties_),
131 charge_(opt.charge_){}
160 penalties_ = penalties;
161 param_.setValue(
"penalties:left_width", penalties_.lWidth);
162 param_.setValue(
"penalties:right_width", penalties_.rWidth);
163 param_.setValue(
"penalties:height", penalties_.height);
164 param_.setValue(
"penalties:position", penalties_.pos);
175 bool optimize(std::vector<PeakShape> & peaks, Data & data);
176 Size getNumberOfPeaks_(
Int charge, std::vector<PeakShape> & temp_shapes, Data & data);
189 void setNumberOfPeaks_(
Data & data,
const std::vector<PeakShape> & temp_shapes,
Int charge);
191 void updateMembers_()
override;
Int charge_
Charge state of the current isotope pattern.
Definition: OptimizePeakDeconvolution.h:183
OptimizationFunctions::PenaltyFactorsIntensity penalties
Definition: OptimizePeakDeconvolution.h:115
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
PenaltyFactorsIntensity & operator=(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:64
OptimizationFunctions::PenaltyFactorsIntensity penalties_
Definition: OptimizePeakDeconvolution.h:180
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Class for the penalty factors used during the optimization.
Definition: OptimizePick.h:62
~OptimizePeakDeconvolution() override
Destructor.
Definition: OptimizePeakDeconvolution.h:134
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Class containing the data needed for optimization.
Definition: OptimizePeakDeconvolution.h:110
std::vector< double > signal
Definition: OptimizePeakDeconvolution.h:114
Int charge
Definition: OptimizePeakDeconvolution.h:116
void setPenalties(const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
Mutable access to the penalty parameter.
Definition: OptimizePeakDeconvolution.h:158
void setCharge(const Int charge)
Mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:170
std::vector< Peak1D > RawDataVector
Definition: OptimizePeakDeconvolution.h:103
double pos
Penalty factor for the peak shape's position.
Definition: OptimizePick.h:80
This class provides the deconvolution of peak regions using non-linear optimization.
Definition: OptimizePeakDeconvolution.h:96
std::vector< double > positions
Definition: OptimizePeakDeconvolution.h:113
PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:60
OptimizePeakDeconvolution(const OptimizePeakDeconvolution &opt)
Copy-Constructor.
Definition: OptimizePeakDeconvolution.h:128
double height
Definition: OptimizePeakDeconvolution.h:76
static const double dist_
distance between two isotopic peaks
Definition: OptimizePeakDeconvolution.h:186
PenaltyFactorsIntensity(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:62
~PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:74
Class for the penalty factors used during the optimization.
Definition: OptimizePeakDeconvolution.h:57
OptimizePeakDeconvolution & operator=(const OptimizePeakDeconvolution &opt)
Definition: OptimizePeakDeconvolution.h:140
double lWidth
Penalty factor for the peak shape's left width parameter.
Definition: OptimizePick.h:82
std::vector< PeakShape > peaks
Definition: OptimizePeakDeconvolution.h:112
double rWidth
Penalty factor for the peak shape's right width parameter.
Definition: OptimizePick.h:84
RawDataVector::iterator PeakIterator
Definition: OptimizePeakDeconvolution.h:104
Int getCharge() const
Non-mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:168