OpenMS  2.5.0
InternalCalibration.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
43 
44 #include <vector>
45 
46 namespace OpenMS
47 {
48 
49  class FeatureMap;
50 
61  class OPENMS_DLLAPI InternalCalibration
62  : public ProgressLogger
63  {
64  public:
65 
68 
71 
73  struct LockMass
74  {
75  double mz;
76  unsigned int ms_level;
77  int charge;
78 
79  LockMass(double mz_, int lvl_, int charge_)
80  : mz(mz_),
81  ms_level(lvl_),
82  charge(charge_)
83  {}
84  };
85 
108  Size fillCalibrants(const PeakMap exp,
109  const std::vector<InternalCalibration::LockMass>& ref_masses,
110  double tol_ppm,
111  bool lock_require_mono,
112  bool lock_require_iso,
113  CalibrationData& failed_lock_masses,
114  bool verbose = true);
115 
137  Size fillCalibrants(const FeatureMap& fm, double tol_ppm);
138 
154  Size fillCalibrants(const std::vector<PeptideIdentification>& pep_ids, double tol_ppm);
155 
164  const CalibrationData& getCalibrationPoints() const;
165 
190  bool calibrate(PeakMap& exp,
191  const IntList& target_mslvl,
192  MZTrafoModel::MODELTYPE model_type,
193  double rt_chunk,
194  bool use_RANSAC,
195  double post_ppm_median,
196  double post_ppm_MAD,
197  const String& file_models = "",
198  const String& file_models_plot = "",
199  const String& file_residuals = "",
200  const String& file_residuals_plot = "",
201  const String& rscript_executable = "Rscript");
202 
203  /*
204  @brief Transform a precursor's m/z
205 
206  Calibrate m/z of precursors.
207 
208  @param pcs Uncalibrated Precursors
209  @param trafo The calibration function to apply
210  */
211  static void applyTransformation(std::vector<Precursor>& pcs, const MZTrafoModel& trafo);
212 
213  /*
214  @brief Transform a spectrum (data+precursor)
215 
216  See applyTransformation(MSExperiment, ...) for details.
217 
218  @param spec Uncalibrated MSSpectrum
219  @param target_mslvl List (can be unsorted) of MS levels to calibrate
220  @param trafo The calibration function to apply
221  */
222  static void applyTransformation(PeakMap::SpectrumType& spec, const IntList& target_mslvl, const MZTrafoModel& trafo);
223 
224  /*
225  @brief Transform spectra from a whole map (data+precursor)
226 
227  All data peaks and precursor information (if present) are calibrated in m/z.
228 
229  Only spectra whose MS-level is contained in 'target_mslvl' are calibrated.
230  In addition, if a fragmentation spectrum's precursor information originates from an MS level in 'target_mslvl',
231  the precursor (not the spectrum itself) is also subjected to calibration.
232  E.g., If we only have MS and MS/MS spectra: for 'target_mslvl' = {1} then all MS1 spectra and MS2 precursors are calibrated.
233  If 'target_mslvl' = {2}, only MS2 spectra (not their precursors) are calibrated.
234  If 'target_mslvl' = {1,2} all spectra and precursors are calibrated.
235 
236 
237  @param exp Uncalibrated peak map
238  @param target_mslvl List (can be unsorted) of MS levels to calibrate
239  @param trafo The calibration function to apply
240  */
241  static void applyTransformation(PeakMap& exp, const IntList& target_mslvl, const MZTrafoModel& trafo);
242 
243  protected:
259  void fillIDs_( const std::vector<PeptideIdentification>& pep_ids, double tol_ppm );
260 
261  /*
262  @brief Calibrate m/z of a spectrum, ignoring precursors!
263 
264  This method is not exposed as public, because its easy to be misused on spectra while forgetting about the precursors of high-level spectra.
265  */
266  static void applyTransformation_(PeakMap::SpectrumType& spec, const MZTrafoModel& trafo);
267 
268  private:
270 
271 
272  }; // class InternalCalibration
273 
274 } // namespace OpenMS
275 
helper class, describing a lock mass
Definition: InternalCalibration.h:73
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:79
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
unsigned int ms_level
MS level where it occurs.
Definition: InternalCalibration.h:76
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double mz
m/z of the lock mass (incl. adducts)
Definition: InternalCalibration.h:75
~InternalCalibration()
Destructor.
Definition: InternalCalibration.h:70
int charge
charge of the ion (to find isotopes)
Definition: InternalCalibration.h:77
A container for features.
Definition: FeatureMap.h:95
CalibrationData cal_data_
Definition: InternalCalibration.h:269
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
A helper class, holding all calibration points.
Definition: CalibrationData.h:64
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:61
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A more convenient string class.
Definition: String.h:58
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
MODELTYPE
Definition: MZTrafoModel.h:98
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:66
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46