OpenMS  3.0.0
FeatureDistance.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Clemens Groepl, Hendrik Weisser, Chris Bielow $
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34 
35 #pragma once
36 
39 
40 #include <limits>
41 
42 namespace OpenMS
43 {
89  class OPENMS_DLLAPI FeatureDistance :
90  public DefaultParamHandler
91  {
92 public:
94  static const double infinity;
95 
102  FeatureDistance(double max_intensity = 1.0,
103  bool force_constraints = false);
104 
106  ~FeatureDistance() override;
107 
109  FeatureDistance & operator=(const FeatureDistance & other);
110 
118  std::pair<bool, double> operator()(const BaseFeature & left,
119  const BaseFeature & right);
120 
121 protected:
122 
125  {
127 
128  DistanceParams_(const String & what, const Param & global)
129  {
130  Param param = global.copy("distance_" + what + ":", true);
131  if (what == "MZ")
132  {
133  max_diff_ppm = (param.getValue("unit") == "ppm");
134  }
135  else
136  {
137  max_diff_ppm = false;
138  }
139 
140  max_difference = param.getValue("max_difference");
141  exponent = param.getValue("exponent");
142  weight = param.getValue("weight");
143  norm_factor = 1 / max_difference;
144 
145  relevant = (weight != 0.0) && (exponent != 0.0);
146  if (!relevant)
147  {
148  weight = 0.0;
149  }
150  }
151 
152  double max_difference, exponent, weight, norm_factor;
153  bool max_diff_ppm, relevant;
154  };
155 
157  void updateMembers_() override;
158 
160  inline double distance_(double diff, const DistanceParams_ & params) const;
161 
163  DistanceParams_ params_rt_, params_mz_, params_intensity_;
164 
167 
170 
173 
176 
179 
182  };
183 
184 } // namespace OpenMS
185 
DefaultParamHandler.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FeatureDistance::DistanceParams_::weight
double weight
Definition: FeatureDistance.h:152
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:58
OpenMS::FeatureDistance::DistanceParams_::relevant
bool relevant
Definition: FeatureDistance.h:153
OpenMS::FeatureDistance::log_transform_
bool log_transform_
Log-transform intensities when computing intensity distance?
Definition: FeatureDistance.h:181
OpenMS::FeatureDistance::force_constraints_
bool force_constraints_
Always return infinity if "max. difference" constraints are not met?
Definition: FeatureDistance.h:178
OpenMS::FeatureDistance::DistanceParams_
Structure for storing distance parameters.
Definition: FeatureDistance.h:124
OpenMS::FeatureDistance::ignore_charge_
bool ignore_charge_
Compute a distance even if charge states don't match?
Definition: FeatureDistance.h:172
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::FeatureDistance::DistanceParams_::DistanceParams_
DistanceParams_(const String &what, const Param &global)
Definition: FeatureDistance.h:128
OpenMS::FeatureDistance::DistanceParams_::DistanceParams_
DistanceParams_()
Definition: FeatureDistance.h:126
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
BaseFeature.h
OpenMS::FeatureDistance::ignore_adduct_
bool ignore_adduct_
Compute a distance even if adducts don't match?
Definition: FeatureDistance.h:175
OpenMS::FeatureDistance
A functor class for the calculation of distances between features or consensus features.
Definition: FeatureDistance.h:89
OpenMS::FeatureDistance::max_intensity_
double max_intensity_
Maximum intensity of features (for normalization)
Definition: FeatureDistance.h:169
OpenMS::FeatureDistance::params_rt_
DistanceParams_ params_rt_
Storage of parameters for the individual distance components.
Definition: FeatureDistance.h:163
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::FeatureDistance::infinity
static const double infinity
Value to return if max. difference is exceeded or if charge states don't match.
Definition: FeatureDistance.h:94
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::FeatureDistance::total_weight_reciprocal_
double total_weight_reciprocal_
Reciprocal value of the total weight in the distance function.
Definition: FeatureDistance.h:166