109 const std::vector<InternalCalibration::LockMass>& ref_masses,
111 bool lock_require_mono,
112 bool lock_require_iso,
154 Size fillCalibrants(
const std::vector<PeptideIdentification>& pep_ids,
double tol_ppm);
195 double post_ppm_median,
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");
211 static void applyTransformation(std::vector<Precursor>& pcs,
const MZTrafoModel& trafo);
259 void fillIDs_(
const std::vector<PeptideIdentification>& pep_ids,
double tol_ppm );
A more convenient string class.
Definition: String.h:58
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
CalibrationData cal_data_
Definition: InternalCalibration.h:269
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
A container for features.
Definition: FeatureMap.h:95
MODELTYPE
Definition: MZTrafoModel.h:98
helper class, describing a lock mass
Definition: InternalCalibration.h:73
unsigned int ms_level
MS level where it occurs.
Definition: InternalCalibration.h:76
~InternalCalibration()
Destructor.
Definition: InternalCalibration.h:70
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
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
int charge
charge of the ion (to find isotopes)
Definition: InternalCalibration.h:77
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:66
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:79
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