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EGHTraceFitter.h
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34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_EGHTRACEFITTER_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_EGHTRACEFITTER_H
37 
39 
40 namespace OpenMS
41 {
42 
55  class OPENMS_DLLAPI EGHTraceFitter :
56  public TraceFitter
57  {
58 public:
62  {
63 public:
64 
65  EGHTraceFunctor(int dimensions,
66  const TraceFitter::ModelData* data);
67 
68  virtual ~EGHTraceFunctor();
69 
70  int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec);
71 
72  // compute Jacobian matrix for the different parameters
73  int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J);
74 
75 protected:
77  };
78 
80 
81  EGHTraceFitter(const EGHTraceFitter& other);
82 
83  EGHTraceFitter& operator=(const EGHTraceFitter& source);
84 
85  virtual ~EGHTraceFitter();
86 
87  // override important methods
89 
90  double getLowerRTBound() const;
91 
92  double getTau() const;
93 
94  double getUpperRTBound() const;
95 
96  double getHeight() const;
97 
98  double getSigma() const;
99 
100  double getCenter() const;
101 
102  bool checkMaximalRTSpan(const double max_rt_span);
103 
104  bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span);
105 
106  double getValue(double rt) const;
107 
108  double getArea();
109 
110  double getFWHM() const;
111 
112  String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift);
113 
114 protected:
115  double apex_rt_;
116  double height_;
117 
118  double sigma_;
119  double tau_;
120 
121  std::pair<double, double> sigma_5_bound_;
122 
124 
126  static const double EPSILON_COEFS_[];
127 
128  static const Size NUM_PARAMS_;
129 
135  std::pair<double, double> getAlphaBoundaries_(const double alpha) const;
136 
137  void getOptimizedParameters_(const Eigen::VectorXd& x_init);
138 
139  void setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);
140 
141  virtual void updateMembers_();
142  };
143 
144 } // namespace OpenMS
145 
146 #endif // #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKEDTRACEFITTERGAUSS_H
Definition: TraceFitter.h:63
A more convenient string class.
Definition: String.h:57
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:110
Abstract fitter for RT profile fitting.
Definition: TraceFitter.h:56
static const Size NUM_PARAMS_
Definition: EGHTraceFitter.h:128
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
const TraceFitter::ModelData * m_data
Definition: EGHTraceFitter.h:76
Definition: EGHTraceFitter.h:60
double apex_rt_
Definition: EGHTraceFitter.h:115
double region_rt_span_
Definition: EGHTraceFitter.h:123
double sigma_
Definition: EGHTraceFitter.h:118
Definition: TraceFitter.h:168
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
A RT Profile fitter using an Exponential Gaussian Hybrid background model.
Definition: EGHTraceFitter.h:55
double height_
Definition: EGHTraceFitter.h:116
double tau_
Definition: EGHTraceFitter.h:119
std::pair< double, double > sigma_5_bound_
Definition: EGHTraceFitter.h:121
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:80

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:00 using doxygen 1.8.13