OpenMS
InternalCalibration.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 #pragma once
36 
44 
45 #include <vector>
46 
47 namespace OpenMS
48 {
49 
50  class FeatureMap;
51 
62  class OPENMS_DLLAPI InternalCalibration
63  : public ProgressLogger
64  {
65  public:
66 
69 
71  ~InternalCalibration() override{}
72 
74  struct LockMass
75  {
76  double mz;
77  unsigned int ms_level;
78  int charge;
79 
80  LockMass(double mz_, int lvl_, int charge_)
81  : mz(mz_),
82  ms_level(lvl_),
83  charge(charge_)
84  {}
85  };
86 
110  const std::vector<InternalCalibration::LockMass>& ref_masses,
111  double tol_ppm,
112  bool lock_require_mono,
113  bool lock_require_iso,
114  CalibrationData& failed_lock_masses,
115  bool verbose = true);
116 
138  Size fillCalibrants(const FeatureMap& fm, double tol_ppm);
139 
155  Size fillCalibrants(const std::vector<PeptideIdentification>& pep_ids, double tol_ppm);
156 
166 
191  bool calibrate(PeakMap& exp,
192  const IntList& target_mslvl,
193  MZTrafoModel::MODELTYPE model_type,
194  double rt_chunk,
195  bool use_RANSAC,
196  double post_ppm_median,
197  double post_ppm_MAD,
198  const String& file_models = "",
199  const String& file_models_plot = "",
200  const String& file_residuals = "",
201  const String& file_residuals_plot = "",
202  const String& rscript_executable = "Rscript");
203 
212  static void applyTransformation(std::vector<Precursor>& pcs, const MZTrafoModel& trafo);
213 
223  static void applyTransformation(PeakMap::SpectrumType& spec, const IntList& target_mslvl, const MZTrafoModel& trafo);
224 
242  static void applyTransformation(PeakMap& exp, const IntList& target_mslvl, const MZTrafoModel& trafo);
243 
244  protected:
245 
248  {
249  CalibrantStats_(const double tol_ppm)
250  : tol_ppm_(tol_ppm)
251  {};
252  Size cnt_empty = 0;
253  Size cnt_nomz = 0;
254  Size cnt_nort = 0;
255  Size cnt_decal = 0;
256  Size cnt_total = 0;
257 
258  void print() const
259  {
260  if (cnt_empty > 0) OPENMS_LOG_WARN << "Warning: " << cnt_empty << "/" << cnt_total << " calibrations points were skipped, since they have no peptide sequence!" << std::endl;
261  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;
262  if (cnt_nort > 0) OPENMS_LOG_WARN << "Warning: " << cnt_nort << "/" << cnt_total << " calibrations points were skipped, since they have no RT value!" << std::endl;
263  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;
264  }
265 
266  private:
267  const double tol_ppm_;
268  };
269 
286  void fillID_( const PeptideIdentification& pep_id, const double tol_ppm, CalibrantStats_& stats);
287 
289  void fillIDs_(const std::vector<PeptideIdentification>& pep_ids, const double tol_ppm, CalibrantStats_& stats);
290 
292  bool isDecalibrated_(const PeptideIdentification& pep_id, const double mz_obs, const double tol_ppm, CalibrantStats_& stats, double& mz_ref);
293 
299  static void applyTransformation_(PeakMap::SpectrumType& spec, const MZTrafoModel& trafo);
300 
301  private:
303  }; // class InternalCalibration
304 
305 } // namespace OpenMS
306 
#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:470
A helper class, holding all calibration points.
Definition: CalibrationData.h:65
A container for features.
Definition: FeatureMap.h:106
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:64
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:302
~InternalCalibration() override
Destructor.
Definition: InternalCalibration.h:71
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:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:65
MODELTYPE
Definition: MZTrafoModel.h:97
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
statistics when adding peptide calibrants
Definition: InternalCalibration.h:248
const double tol_ppm_
tolerance used for counting cnt_decal
Definition: InternalCalibration.h:267
void print() const
Definition: InternalCalibration.h:258
CalibrantStats_(const double tol_ppm)
Definition: InternalCalibration.h:249
helper class, describing a lock mass
Definition: InternalCalibration.h:75
double mz
m/z of the lock mass (incl. adducts)
Definition: InternalCalibration.h:76
unsigned int ms_level
MS level where it occurs.
Definition: InternalCalibration.h:77
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:80
int charge
charge of the ion (to find isotopes)
Definition: InternalCalibration.h:78