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LinearResamplerAlign Class Reference

Linear Resampling of raw data with alignment. More...

#include <OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h>

Inheritance diagram for LinearResamplerAlign:
LinearResampler DefaultParamHandler ProgressLogger

Public Member Functions

template<template< typename > class SpecT, typename PeakType >
void raster (SpecT< PeakType > &spectrum)
 Applies the resampling algorithm to an MSSpectrum. More...
 
template<template< typename > class SpecT, typename PeakType >
void raster_align (SpecT< PeakType > &spectrum, double start_pos, double end_pos)
 Applies the resampling algorithm to an MSSpectrum but it will be aligned between start_pos and end_pos. More...
 
template<typename PeakTypeIterator , typename ConstPeakTypeIterator >
void raster (ConstPeakTypeIterator raw_it, ConstPeakTypeIterator raw_end, PeakTypeIterator resample_it, PeakTypeIterator resample_end)
 Applies the resampling algorithm to an MSSpectrum. More...
 
template<typename PeakTypeIterator >
void raster_interpolate (PeakTypeIterator raw_it, PeakTypeIterator raw_end, PeakTypeIterator it, PeakTypeIterator resampled_end)
 Applies the resampling algorithm using a linear interpolation. More...
 
- Public Member Functions inherited from LinearResampler
 LinearResampler ()
 Constructor. More...
 
 ~LinearResampler ()
 Destructor. More...
 
template<typename PeakType >
void raster (MSSpectrum< PeakType > &spectrum)
 Applies the resampling algorithm to an MSSpectrum. More...
 
template<typename PeakType >
void rasterExperiment (MSExperiment< PeakType > &exp)
 Resamples the data in an MSExperiment. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Member Functions inherited from LinearResampler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. More...
 
- Protected Attributes inherited from LinearResampler
double spacing_
 Spacing of the resampled data. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

Linear Resampling of raw data with alignment.

This class can be used to generate uniform data from non-uniform raw data (e.g. ESI-TOF or MALDI-TOF experiments). Therefore the intensity at every position x in the input raw data is spread to the two adjacent resampling points. This method preserves the area of the input signal and also the centroid position of a peak. Therefore it is recommended for quantitation as well as for ProteinIdentification experiments.

In addition to the LinearResampler, this class also allows to fix the points at which resampling will occur. This is useful if the resampling points are known in advance, e.g. if one needs to resample a chromatogram at the positions of another chromatogram.

Member Function Documentation

void raster ( SpecT< PeakType > &  spectrum)
inline
void raster ( ConstPeakTypeIterator  raw_it,
ConstPeakTypeIterator  raw_end,
PeakTypeIterator  resample_it,
PeakTypeIterator  resample_end 
)
inline

Applies the resampling algorithm to an MSSpectrum.

void raster_align ( SpecT< PeakType > &  spectrum,
double  start_pos,
double  end_pos 
)
inline

Applies the resampling algorithm to an MSSpectrum but it will be aligned between start_pos and end_pos.

References LinearResamplerAlign::raster(), and LinearResampler::spacing_.

void raster_interpolate ( PeakTypeIterator  raw_it,
PeakTypeIterator  raw_end,
PeakTypeIterator  it,
PeakTypeIterator  resampled_end 
)
inline

Applies the resampling algorithm using a linear interpolation.


OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:36 using doxygen 1.8.9.1