OpenMS
InternalCalibration.h
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1 // Copyright (c) 2002-2023, 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 #pragma once
10 
18 
19 #include <vector>
20 
21 namespace OpenMS
22 {
23 
24  class FeatureMap;
25 
36  class OPENMS_DLLAPI InternalCalibration
37  : public ProgressLogger
38  {
39  public:
40 
43 
45  ~InternalCalibration() override{}
46 
48  struct LockMass
49  {
50  double mz;
51  unsigned int ms_level;
52  int charge;
53 
54  LockMass(double mz_, int lvl_, int charge_)
55  : mz(mz_),
56  ms_level(lvl_),
57  charge(charge_)
58  {}
59  };
60 
84  const std::vector<InternalCalibration::LockMass>& ref_masses,
85  double tol_ppm,
86  bool lock_require_mono,
87  bool lock_require_iso,
88  CalibrationData& failed_lock_masses,
89  bool verbose = true);
90 
112  Size fillCalibrants(const FeatureMap& fm, double tol_ppm);
113 
129  Size fillCalibrants(const std::vector<PeptideIdentification>& pep_ids, double tol_ppm);
130 
140 
165  bool calibrate(PeakMap& exp,
166  const IntList& target_mslvl,
167  MZTrafoModel::MODELTYPE model_type,
168  double rt_chunk,
169  bool use_RANSAC,
170  double post_ppm_median,
171  double post_ppm_MAD,
172  const String& file_models = "",
173  const String& file_models_plot = "",
174  const String& file_residuals = "",
175  const String& file_residuals_plot = "",
176  const String& rscript_executable = "Rscript");
177 
186  static void applyTransformation(std::vector<Precursor>& pcs, const MZTrafoModel& trafo);
187 
197  static void applyTransformation(PeakMap::SpectrumType& spec, const IntList& target_mslvl, const MZTrafoModel& trafo);
198 
216  static void applyTransformation(PeakMap& exp, const IntList& target_mslvl, const MZTrafoModel& trafo);
217 
218  protected:
219 
222  {
223  CalibrantStats_(const double tol_ppm)
224  : tol_ppm_(tol_ppm)
225  {};
226  Size cnt_empty = 0;
227  Size cnt_nomz = 0;
228  Size cnt_nort = 0;
229  Size cnt_decal = 0;
230  Size cnt_total = 0;
231 
232  void print() const
233  {
234  if (cnt_empty > 0) OPENMS_LOG_WARN << "Warning: " << cnt_empty << "/" << cnt_total << " calibrations points were skipped, since they have no peptide sequence!" << std::endl;
235  if (cnt_nomz > 0) OPENMS_LOG_WARN << "Warning: " << cnt_nomz << "/" << cnt_total << " calibrations points were skipped, since they have no m/z value!" << std::endl;
236  if (cnt_nort > 0) OPENMS_LOG_WARN << "Warning: " << cnt_nort << "/" << cnt_total << " calibrations points were skipped, since they have no RT value!" << std::endl;
237  if (cnt_decal > 0) OPENMS_LOG_WARN << "Warning: " << cnt_decal << "/" << cnt_total << " calibrations points were skipped, since their theoretical weight is more than " << tol_ppm_ << " ppm away from their measured mass!" << std::endl;
238  }
239 
240  private:
241  const double tol_ppm_;
242  };
243 
260  void fillID_( const PeptideIdentification& pep_id, const double tol_ppm, CalibrantStats_& stats);
261 
263  void fillIDs_(const std::vector<PeptideIdentification>& pep_ids, const double tol_ppm, CalibrantStats_& stats);
264 
266  bool isDecalibrated_(const PeptideIdentification& pep_id, const double mz_obs, const double tol_ppm, CalibrantStats_& stats, double& mz_ref);
267 
273  static void applyTransformation_(PeakMap::SpectrumType& spec, const MZTrafoModel& trafo);
274 
275  private:
277  }; // class InternalCalibration
278 
279 } // namespace OpenMS
280 
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:444
A helper class, holding all calibration points.
Definition: CalibrationData.h:39
A container for features.
Definition: FeatureMap.h:80
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:38
static void applyTransformation_(PeakMap::SpectrumType &spec, const MZTrafoModel &trafo)
Calibrate m/z of a spectrum, ignoring precursors!
Size fillCalibrants(const FeatureMap &fm, double tol_ppm)
Extract calibrants from identifications.
static void applyTransformation(PeakMap::SpectrumType &spec, const IntList &target_mslvl, const MZTrafoModel &trafo)
Transform a spectrum (data+precursor)
CalibrationData cal_data_
Definition: InternalCalibration.h:276
~InternalCalibration() override
Destructor.
Definition: InternalCalibration.h:45
Size fillCalibrants(const PeakMap &exp, const std::vector< InternalCalibration::LockMass > &ref_masses, double tol_ppm, bool lock_require_mono, bool lock_require_iso, CalibrationData &failed_lock_masses, bool verbose=true)
Extract calibrants from Raw data (mzML)
bool calibrate(PeakMap &exp, const IntList &target_mslvl, MZTrafoModel::MODELTYPE model_type, double rt_chunk, bool use_RANSAC, double post_ppm_median, double post_ppm_MAD, const String &file_models="", const String &file_models_plot="", const String &file_residuals="", const String &file_residuals_plot="", const String &rscript_executable="Rscript")
Apply calibration to data.
static void applyTransformation(std::vector< Precursor > &pcs, const MZTrafoModel &trafo)
Transform a precursor's m/z.
InternalCalibration()
Default constructor.
const CalibrationData & getCalibrationPoints() const
Get container of calibration points.
bool isDecalibrated_(const PeptideIdentification &pep_id, const double mz_obs, const double tol_ppm, CalibrantStats_ &stats, double &mz_ref)
determine if sequence is within tol_ppm and update stats; fills mz_ref with the theoretical m/z of th...
void fillID_(const PeptideIdentification &pep_id, const double tol_ppm, CalibrantStats_ &stats)
Add(no prior clear) calibrants to internal list.
Size fillCalibrants(const std::vector< PeptideIdentification > &pep_ids, double tol_ppm)
Extract calibrants from identifications.
static void applyTransformation(PeakMap &exp, const IntList &target_mslvl, const MZTrafoModel &trafo)
Transform spectra from a whole map (data+precursor)
void fillIDs_(const std::vector< PeptideIdentification > &pep_ids, const double tol_ppm, CalibrantStats_ &stats)
calls fillID_ on all PeptideIDs
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:39
MODELTYPE
Definition: MZTrafoModel.h:71
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:39
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:29
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
statistics when adding peptide calibrants
Definition: InternalCalibration.h:222
const double tol_ppm_
tolerance used for counting cnt_decal
Definition: InternalCalibration.h:241
void print() const
Definition: InternalCalibration.h:232
CalibrantStats_(const double tol_ppm)
Definition: InternalCalibration.h:223
helper class, describing a lock mass
Definition: InternalCalibration.h:49
double mz
m/z of the lock mass (incl. adducts)
Definition: InternalCalibration.h:50
unsigned int ms_level
MS level where it occurs.
Definition: InternalCalibration.h:51
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:54
int charge
charge of the ion (to find isotopes)
Definition: InternalCalibration.h:52