OpenMS
CalibrationData.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 
10 #pragma once
11 
14 
15 #include <vector>
16 #include <set>
17 
18 namespace OpenMS
19 {
20 
38  class OPENMS_DLLAPI CalibrationData
39  {
40  public:
41 
43  typedef std::vector<CalDataType>::const_iterator const_iterator;
44  typedef std::vector<CalDataType>::value_type value_type;
45 
50 
55 
60 
65 
70 
75 
79  Size size() const;
80 
84  bool empty() const;
85 
89  void clear();
90 
94  void setUsePPM(bool usePPM);
95 
99  bool usePPM() const;
100 
112  CalDataType::CoordinateType mz_ref, double weight,
113  int group = -1);
114 
119 
124 
129 
134 
141  int getGroup(Size i) const;
142 
147 
168  CalibrationData median(double rt_left, double rt_right) const;
169 
173  void sortByRT();
174 
175 
176  private:
177  std::vector<RichPeak2D> data_;
178  bool use_ppm_;
179  std::set<int> groups_;
180  };
181 
182 } // namespace OpenMS
183 
A helper class, holding all calibration points.
Definition: CalibrationData.h:39
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:43
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:178
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:44
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:177
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:179
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:42
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:36
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:38
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:30
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19