35 #ifndef OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H 36 #define OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H 112 const std::vector<InternalCalibration::LockMass>& ref_masses,
114 bool lock_require_mono,
115 bool lock_require_iso,
157 Size fillCalibrants(
const std::vector<PeptideIdentification>& pep_ids,
double tol_ppm);
198 double post_ppm_median,
200 const String& file_models =
"",
201 const String& file_models_plot =
"",
202 const String& file_residuals =
"",
203 const String& file_residuals_plot =
"",
204 const String& rscript_executable =
"Rscript");
214 static void applyTransformation(std::vector<Precursor>& pcs,
const MZTrafoModel& trafo);
262 void fillIDs_(
const std::vector<PeptideIdentification>& pep_ids,
double tol_ppm );
279 #endif // OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H
A more convenient string class.
Definition: String.h:57
MODELTYPE
Definition: MZTrafoModel.h:99
A container for features.
Definition: FeatureMap.h:94
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:62
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:59
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
int charge
Definition: InternalCalibration.h:78
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
~InternalCalibration()
Destructor.
Definition: InternalCalibration.h:71
helper class, describing a lock mass
Definition: InternalCalibration.h:74
A helper class, holding all calibration points.
Definition: CalibrationData.h:65
unsigned int ms_level
Definition: InternalCalibration.h:77
double mz
Definition: InternalCalibration.h:76
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
CalibrationData cal_data_
Definition: InternalCalibration.h:272
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:80
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )