#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>
This class implements a simle calibration method: given a list of reference masses, the relative errors of the peaks in the data are approximated by linear interpolation and subtracted from the data. If the input data is raw data peak picking is done first.
InternalCalibration Parameters are explained on a separate page.
Public Types | |
typedef RawDataPoint1D | RawDataPointType |
Raw data point type. | |
typedef PickedPeak1D | PickedPeakType |
Picked Peak type. | |
Public Member Functions | |
InternalCalibration () | |
Default constructor. | |
~InternalCalibration () | |
Destructor. | |
InternalCalibration (InternalCalibration &obj) | |
Copy c'tor. | |
InternalCalibration & | operator= (const InternalCalibration &obj) |
Assignment operator. | |
template<typename InputPeakType> | |
void | calibrate (MSExperiment< InputPeakType > &exp, std::vector< double > &ref_masses, bool peak_data=false) |
const DoubleReal | getWindowLength () const |
Non-mutable access to the picked peaks. | |
void | setWindowLength (const DoubleReal window_length) |
Mutable access to the peaks. | |
const MSExperiment < PickedPeakType > & | getPeaks () const |
Non-mutable access to the picked peaks. | |
void | setPeaks (const MSExperiment< PickedPeakType > &exp_peaks) |
Mutable access to the peaks. | |
const std::vector< std::vector < UInt > > & | getMonoisotopicPeaks () const |
Non-mutable access to the monoisotopic peaks. | |
void | setMonoisotopicPeaks (const std::vector< std::vector< UInt > > &monoiso_peaks) |
Mutable access to the calibrant spectra. | |
Protected Member Functions | |
void | getMonoisotopicPeaks_ () |
Determines the monoisotopic peaks. | |
template<typename InputPeakType> | |
void | calibrate_ (MSExperiment< InputPeakType > &exp, std::vector< double > &ref_masses) |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParam() method. | |
Protected Attributes | |
DoubleReal | window_length_ |
MSExperiment< PickedPeakType > | exp_peaks_ |
std::vector< std::vector< UInt > > | monoiso_peaks_ |
typedef RawDataPoint1D RawDataPointType |
Raw data point type.
typedef PickedPeak1D PickedPeakType |
Picked Peak type.
Default constructor.
~InternalCalibration | ( | ) | [inline] |
Destructor.
InternalCalibration | ( | InternalCalibration & | obj | ) |
Copy c'tor.
InternalCalibration& operator= | ( | const InternalCalibration & | obj | ) |
Assignment operator.
void calibrate | ( | MSExperiment< InputPeakType > & | exp, | |
std::vector< double > & | ref_masses, | |||
bool | peak_data = false | |||
) | [inline] |
Calibrate a map using given reference masses. Set the flag peak data if you want to calibrate already picked data.
const DoubleReal getWindowLength | ( | ) | const [inline] |
Non-mutable access to the picked peaks.
void setWindowLength | ( | const DoubleReal | window_length | ) | [inline] |
Mutable access to the peaks.
const MSExperiment<PickedPeakType>& getPeaks | ( | ) | const [inline] |
Non-mutable access to the picked peaks.
void setPeaks | ( | const MSExperiment< PickedPeakType > & | exp_peaks | ) | [inline] |
Mutable access to the peaks.
const std::vector<std::vector<UInt> >& getMonoisotopicPeaks | ( | ) | const [inline] |
Non-mutable access to the monoisotopic peaks.
void setMonoisotopicPeaks | ( | const std::vector< std::vector< UInt > > & | monoiso_peaks | ) | [inline] |
Mutable access to the calibrant spectra.
void getMonoisotopicPeaks_ | ( | ) | [protected] |
Determines the monoisotopic peaks.
void calibrate_ | ( | MSExperiment< InputPeakType > & | exp, | |
std::vector< double > & | ref_masses | |||
) | [inline, protected] |
void updateMembers_ | ( | ) | [protected, virtual] |
This method is used to update extra member variables at the end of the setParam() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
DoubleReal window_length_ [protected] |
MSExperiment<PickedPeakType> exp_peaks_ [protected] |
std::vector<std::vector<UInt> > monoiso_peaks_ [protected] |
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |