Linear Resampling of raw data with alignment. More...
#include <OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h>
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... | |
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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... | |
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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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () 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... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (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 | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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double | spacing_ |
Spacing of the resampled data. More... | |
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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< String > | subsections_ |
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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
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.
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inline |
Applies the resampling algorithm to an MSSpectrum.
References LinearResampler::spacing_.
Referenced by LinearResamplerAlign::raster_align(), and MRMTransitionGroupPicker::resampleChromatogram_().
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inline |
Applies the resampling algorithm to an MSSpectrum.
Applies the resampling algorithm to an MSSpectrum but it will be aligned between start_pos and end_pos.
References LinearResamplerAlign::raster(), and LinearResampler::spacing_.
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inline |
Applies the resampling algorithm using a linear interpolation.
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |