Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

InternalCalibration Class Reference

#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>

Inheritance diagram for InternalCalibration:

DefaultParamHandler ProgressLogger

List of all members.


Detailed Description

A simple calibration method using linear interpolation of given reference masses.

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.
InternalCalibrationoperator= (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< PickedPeakTypeexp_peaks_
std::vector< std::vector< UInt > > monoiso_peaks_


Member Typedef Documentation

typedef RawDataPoint1D RawDataPointType

Raw data point type.

typedef PickedPeak1D PickedPeakType

Picked Peak type.


Constructor & Destructor Documentation

InternalCalibration (  ) 

Default constructor.

~InternalCalibration (  )  [inline]

Destructor.

InternalCalibration ( InternalCalibration obj  ) 

Copy c'tor.


Member Function Documentation

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.


Member Data Documentation

DoubleReal window_length_ [protected]

MSExperiment<PickedPeakType> exp_peaks_ [protected]

std::vector<std::vector<UInt> > monoiso_peaks_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1