OpenMS  2.4.0
MZTrafoModel.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 
36 #pragma once
37 
41 
42 #include <vector>
43 
44 namespace OpenMS
45 {
46 
66  class OPENMS_DLLAPI MZTrafoModel
67  {
68 
69  private:
70  std::vector<double> coeff_;
71  bool use_ppm_;
72  double rt_;
73 
75  static double limit_offset_;
76  static double limit_scale_;
77  static double limit_power_;
78 
79  public:
80 
84  MZTrafoModel();
85 
96  MZTrafoModel(bool ppm_model);
97 
98  enum MODELTYPE { LINEAR, LINEAR_WEIGHTED, QUADRATIC, QUADRATIC_WEIGHTED, SIZE_OF_MODELTYPE };
99  static const std::string names_of_modeltype[];
100 
107  static MODELTYPE nameToEnum(const std::string& name);
114  static const std::string& enumToName(MODELTYPE mt);
115 
116 
126  static void setRANSACParams(const Math::RANSACParam& p);
127 
136  static void setCoefficientLimits(double offset, double scale, double power);
147  static bool isValidModel(const MZTrafoModel& trafo);
148 
155  bool isTrained() const;
156 
160  double getRT() const;
161 
174  double predict(double mz) const;
175 
187  static Size findNearest(const std::vector<MZTrafoModel>& tms, double rt);
188 
189 
191  struct RTLess :
192  public std::binary_function<MZTrafoModel, MZTrafoModel, bool>
193  {
194  inline bool operator()(const double& left, const MZTrafoModel& right) const
195  {
196  return left < right.rt_;
197  }
198  inline bool operator()(const MZTrafoModel& left, const double& right) const
199  {
200  return left.rt_ < right;
201  }
202  inline bool operator()(const MZTrafoModel& left, const MZTrafoModel& right) const
203  {
204  return left.rt_ < right.rt_;
205  }
206  };
228  bool train(const CalibrationData& cd, MODELTYPE md, bool use_RANSAC,
229  double rt_left = -std::numeric_limits<double>::max(),
230  double rt_right = std::numeric_limits<double>::max()
231  );
232 
257  bool train(std::vector<double> error_mz,
258  std::vector<double> theo_mz,
259  std::vector<double> weights,
260  MODELTYPE md,
261  bool use_RANSAC);
262 
274  void getCoefficients(double& intercept, double& slope, double& power);
275 
279  void setCoefficients(const MZTrafoModel& rhs);
280 
292  void setCoefficients(double intercept, double slope, double power);
293 
300  String toString() const;
301 
302  }; // MZTrafoModel
303 
304 } // namespace OpenMS
305 
static double limit_offset_
acceptable boundary for the estimated offset; if estimated offset is larger (absolute) the model does...
Definition: MZTrafoModel.h:75
static double limit_scale_
acceptable boundary for the estimated scale; if estimated scale is larger (absolute) the model does n...
Definition: MZTrafoModel.h:76
A more convenient string class.
Definition: String.h:57
Comparator by position. As this class has dimension 1, this is basically an alias for MZLess...
Definition: MZTrafoModel.h:191
MODELTYPE
Definition: MZTrafoModel.h:98
std::vector< double > coeff_
Model coefficients (for both linear and quadratic models), estimated from the data.
Definition: MZTrafoModel.h:70
static double limit_power_
acceptable boundary for the estimated power; if estimated power is larger (absolute) the model does n...
Definition: MZTrafoModel.h:77
A simple struct to carry all the parameters required for a RANSAC run.
Definition: RANSAC.h:58
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:66
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool use_ppm_
during training, model is build on absolute or relative(ppm) predictions. predict(), i.e. applying the model, requires this information too
Definition: MZTrafoModel.h:71
bool operator()(const MZTrafoModel &left, const double &right) const
Definition: MZTrafoModel.h:198
double rt_
retention time associated to the model (i.e. where the calibrant data was taken from) ...
Definition: MZTrafoModel.h:72
A helper class, holding all calibration points.
Definition: CalibrationData.h:64
bool operator()(const MZTrafoModel &left, const MZTrafoModel &right) const
Definition: MZTrafoModel.h:202
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool operator()(const double &left, const MZTrafoModel &right) const
Definition: MZTrafoModel.h:194
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68
static Math::RANSACParam * ransac_params_
global pointer, init to NULL at startup; set class-global RANSAC params
Definition: MZTrafoModel.h:74