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OpenMS
2.5.0
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85 void pickAndCalibrate(
PeakMap & calib_spectra,
PeakMap & exp, std::vector<double> & exp_masses);
93 void calibrate(
PeakMap & calib_spectra,
PeakMap & exp, std::vector<double> & exp_masses);
96 inline const std::vector<double> &
getML1s()
const {
return ml1s_; }
98 inline void setML1s(
const std::vector<double> & ml1s)
104 inline const std::vector<double> &
getML2s()
const {
return ml2s_; }
106 inline void setML2s(
const std::vector<double> & ml2s)
112 inline const std::vector<double> &
getML3s()
const {
return ml3s_; }
114 inline void setML3s(
const std::vector<double> & ml3s)
128 std::map<double, std::vector<double> >
errors_;
149 void calculateCalibCoeffs_(
PeakMap & calib_peaks_ft);
153 void getMonoisotopicPeaks_(
PeakMap & calib_peaks, std::vector<std::vector<unsigned int> > & monoiso_peaks);
165 void applyTOFConversion_(
PeakMap & calib_spectra);
168 void matchMasses_(
PeakMap & calib_peaks,
169 std::vector<std::vector<unsigned int> > & monoiso_peaks,
170 std::vector<unsigned int> & obs_masses,
171 std::vector<double> & exp_masses,
175 inline double mQ_(
double ft,
unsigned int spec)
177 return coeff_quad_fit_[3 * spec] + ft * coeff_quad_fit_[3 * spec + 1] + ft * ft * coeff_quad_fit_[3 * spec + 2];
183 return a_ + ft * b_ + ft * ft * c_;
187 void averageErrors_();
190 void averageCoefficients_();
Base class for TOPP applications.
Definition: TOPPBase.h:144
ConstIterator end() const
Gives access to the underlying text buffer.
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void setML2s(const std::vector< double > &ml2s)
mutable access to the second calibration constant
Definition: TOFCalibration.h:106
double mQ_(double ft, unsigned int spec)
Calculate the mass value for a given flight time using the coefficients of the quadratic fit in a spe...
Definition: TOFCalibration.h:175
std::map< double, std::vector< double > > errors_
error in ppm after quadratic fit
Definition: TOFCalibration.h:128
This class implements a peak picking algorithm using wavelet techniques.
Definition: PeakPickerCWT.h:78
void setML1s(const std::vector< double > &ml1s)
mutable access to the first calibration constant
Definition: TOFCalibration.h:98
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
std::vector< double > calib_masses_
Definition: TOFCalibration.h:134
std::vector< double > ml3s_
Definition: TOFCalibration.h:139
Size size() const
Definition: MSExperiment.h:127
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void pickAndCalibrate(PeakMap &calib_spectra, PeakMap &exp, std::vector< double > &exp_masses)
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
double c_
Definition: TOFCalibration.h:145
void setParameters(const Param ¶m)
Sets the parameters.
void setML3s(const std::vector< double > &ml3s)
mutable access to the third calibration constant
Definition: TOFCalibration.h:114
void calibrate(PeakMap &calib_spectra, PeakMap &exp, std::vector< double > &exp_masses)
Calibration of m/z positions.
Definition: DataProcessing.h:69
std::vector< double > coeff_quad_fit_
all coefficients of the quadratic fit
Definition: TOFCalibration.h:142
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ConstIterator begin() const
Gives access to the underlying text buffer.
PeakMap calib_peaks_ft_
the calibrant spectra still using flight times instead of m/z-values
Definition: TOFCalibration.h:121
const std::vector< double > & getML1s() const
Non-mutable access to the first calibration constant.
Definition: TOFCalibration.h:96
std::vector< double > ml2s_
Definition: TOFCalibration.h:138
std::vector< double > error_medians_
median errors
Definition: TOFCalibration.h:131
This class implements an external calibration for TOF data using external calibrant spectra.
Definition: TOFCalibration.h:66
std::vector< double > exp_masses_
the expected calibrant masses
Definition: TOFCalibration.h:125
Management and storage of parameters / INI files.
Definition: Param.h:73
double mQAv_(double ft)
Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit...
Definition: TOFCalibration.h:181
std::vector< double > ml1s_
calibration constants from the instrument needed for the conversion of the calibrant spectra
Definition: TOFCalibration.h:137
const std::vector< double > & getML3s() const
Non-mutable access to the third calibration constant.
Definition: TOFCalibration.h:112
const std::vector< double > & getML2s() const
Non-mutable access to the second calibration constant.
Definition: TOFCalibration.h:104
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
void insert(const String &prefix, const Param ¶m)
void load(const String &filename, bool trim_lines=false, Int first_n=-1, bool skip_empty_lines=false)
Loads data from a text file.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!