OpenMS
BaseModel.h
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34 
35 #pragma once
36 
38 #include <OpenMS/KERNEL/DPeak.h>
39 
40 namespace OpenMS
41 {
42 
49  template<UInt D>
51  {
52  public:
53  typedef double IntensityType;
54  typedef double CoordinateType;
56  typedef typename DPeak<D>::Type PeakType;
57  typedef std::vector<PeakType> SamplesType;
58 
59 
61  BaseModel() : DefaultParamHandler("BaseModel")
62  {
63  defaults_.setValue("cutoff", 0.0, "Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.");
64  }
65 
67  BaseModel(const BaseModel& source) : DefaultParamHandler(source), cut_off_(source.cut_off_)
68  {
69  }
70 
72  ~BaseModel() override
73  {
74  }
75 
77  BaseModel& operator=(const BaseModel& source)
78  {
79  if (&source == this)
80  return *this;
81 
83  cut_off_ = source.cut_off_;
84 
85  return *this;
86  }
87 
89  static void registerChildren();
90 
92  virtual IntensityType getIntensity(const PositionType& pos) const = 0;
93 
95  virtual bool isContained(const PositionType& pos) const
96  {
97  return getIntensity(pos) >= cut_off_;
98  }
99 
104  template<typename PeakType>
105  void fillIntensity(PeakType& peak) const
106  {
107  peak.setIntensity(getIntensity(peak.getPosition()));
108  }
109 
113  template<class PeakIterator>
115  {
116  for (PeakIterator it = begin; it != end; ++it)
117  {
118  fillIntensity(*it);
119  }
120  }
121 
123  virtual IntensityType getCutOff() const
124  {
125  return cut_off_;
126  }
127 
129  virtual void setCutOff(IntensityType cut_off)
130  {
131  cut_off_ = cut_off;
132  param_.setValue("cutoff", cut_off_);
133  }
134 
136  virtual void getSamples(SamplesType& cont) const = 0;
137 
139  virtual void getSamples(std::ostream& os)
140  {
141  SamplesType samples;
142  getSamples(samples);
143  for (typename SamplesType::const_iterator it = samples.begin(); it != samples.end(); ++it)
144  {
145  os << *it << std::endl;
146  }
147  }
148 
149  protected:
151 
152  void updateMembers_() override
153  {
154  cut_off_ = (double)param_.getValue("cutoff");
155  }
156  };
157 } // namespace OpenMS
Abstract base class for all D-dimensional models.
Definition: BaseModel.h:51
virtual IntensityType getIntensity(const PositionType &pos) const =0
access model predicted intensity at position pos
DPeak< D >::Type PeakType
Definition: BaseModel.h:56
BaseModel(const BaseModel &source)
copy constructor
Definition: BaseModel.h:67
BaseModel & operator=(const BaseModel &source)
assignment operator
Definition: BaseModel.h:77
double CoordinateType
Definition: BaseModel.h:54
BaseModel()
Default constructor.
Definition: BaseModel.h:61
virtual void setCutOff(IntensityType cut_off)
set cutoff value
Definition: BaseModel.h:129
DPosition< D > PositionType
Definition: BaseModel.h:55
void fillIntensities(PeakIterator begin, PeakIterator end) const
Convenience function that applies fillIntensity() to an iterator range.
Definition: BaseModel.h:114
static void registerChildren()
register all derived classes here (implemented in file BaseModel_impl.h)
~BaseModel() override
Destructor.
Definition: BaseModel.h:72
virtual bool isContained(const PositionType &pos) const
check if position pos is part of the model regarding the models cut-off.
Definition: BaseModel.h:95
virtual IntensityType getCutOff() const
get cutoff value
Definition: BaseModel.h:123
std::vector< PeakType > SamplesType
Definition: BaseModel.h:57
void fillIntensity(PeakType &peak) const
Convenience function to set the intensity of a peak to the predicted intensity at its current positio...
Definition: BaseModel.h:105
virtual void getSamples(SamplesType &cont) const =0
get reasonable set of samples from the model (i.e. for printing)
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
Definition: BaseModel.h:152
double IntensityType
Definition: BaseModel.h:53
IntensityType cut_off_
Definition: BaseModel.h:150
virtual void getSamples(std::ostream &os)
fill stream with reasonable set of samples from the model (i.e. for printing)
Definition: BaseModel.h:139
Representation of a coordinate in D-dimensional space.
Definition: DPosition.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:165
DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:172
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
RawDataVector::iterator PeakIterator
Profile data iterator type.
Definition: OptimizePick.h:58
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Metafunction to choose among Peak1D respectively Peak2D through a template argument.
Definition: DPeak.h:61