OpenMS
CalibrationData.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 
36 #pragma once
37 
40 
41 #include <vector>
42 #include <set>
43 
44 namespace OpenMS
45 {
46 
64  class OPENMS_DLLAPI CalibrationData
65  {
66  public:
67 
69  typedef std::vector<CalDataType>::const_iterator const_iterator;
70  typedef std::vector<CalDataType>::value_type value_type;
71 
76 
81 
86 
91 
96 
101 
105  Size size() const;
106 
110  bool empty() const;
111 
115  void clear();
116 
120  void setUsePPM(bool usePPM);
121 
125  bool usePPM() const;
126 
138  CalDataType::CoordinateType mz_ref, double weight,
139  int group = -1);
140 
145 
150 
155 
160 
167  int getGroup(Size i) const;
168 
173 
194  CalibrationData median(double rt_left, double rt_right) const;
195 
199  void sortByRT();
200 
201 
202  private:
203  std::vector<RichPeak2D> data_;
204  bool use_ppm_;
205  std::set<int> groups_;
206  };
207 
208 } // namespace OpenMS
209 
A helper class, holding all calibration points.
Definition: CalibrationData.h:65
bool usePPM() const
Current error unit (ppm or Th)
void setUsePPM(bool usePPM)
When calling getError(), should ppm error or m/z error be returned?
CalDataType::CoordinateType getWeight(Size i) const
Retrieve the weight of the i'th calibration point.
std::vector< CalDataType >::const_iterator const_iterator
Definition: CalibrationData.h:69
static StringList getMetaValues()
List of meta-values which are used internally (for conversion to PeakMap).
void sortByRT()
Sort calibration points by RT, to allow for valid RT chunking.
bool use_ppm_
return ppm values as y-values for the model instead of absolute delta in [Th]
Definition: CalibrationData.h:204
const_iterator begin() const
Begin iterator for calibration points.
CalibrationData()
Default constructor.
int getGroup(Size i) const
Retrieve the group of the i'th calibration point.
std::vector< CalDataType >::value_type value_type
Definition: CalibrationData.h:70
bool empty() const
Do we have any calibration points.
Size getNrOfGroups() const
Number of peak groups (can be 0).
std::vector< RichPeak2D > data_
calibration points
Definition: CalibrationData.h:203
CalDataType::CoordinateType getRefMZ(Size i) const
Retrieve the theoretical m/z of the i'th calibration point.
std::set< int > groups_
peak groups present in this data
Definition: CalibrationData.h:205
CalDataType::CoordinateType getError(Size i) const
Retrieve the error for i'th calibrant in either ppm or Th (depending on usePPM())
CalDataType::CoordinateType getRT(Size i) const
Retrieve the observed RT of the i'th calibration point.
void insertCalibrationPoint(CalDataType::CoordinateType rt, CalDataType::CoordinateType mz_obs, CalDataType::IntensityType intensity, CalDataType::CoordinateType mz_ref, double weight, int group=-1)
Add a new calibration point.
void clear()
Remove all calibration points.
RichPeak2D CalDataType
Definition: CalibrationData.h:68
Size size() const
Number of calibration points.
const_iterator end() const
Past-the-end iterator for calibration points.
CalibrationData median(double rt_left, double rt_right) const
Compute the median in the given RT range for every peak group.
CalDataType::CoordinateType getIntensity(Size i) const
Retrieve the intensity of the i'th calibration point.
CalDataType::CoordinateType getMZ(Size i) const
Retrieve the observed m/z of the i'th calibration point.
float IntensityType
Intensity type.
Definition: Peak2D.h:62
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:56
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48