This class represents the abstract base class of a signal to noise estimator. More...

#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimator.h>

Inheritance diagram for SignalToNoiseEstimator< Container >:

Classes
struct	GaussianEstimate
	protected struct to store parameters my, sigma for a Gaussian distribution More...
Public Types
Type definitions

typedef Container::const_iterator	PeakIterator
typedef PeakIterator::value_type	PeakType
Public Member Functions
	SignalToNoiseEstimator ()
	Constructor.
	SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
	Copy constructor.
SignalToNoiseEstimator &	operator= (const SignalToNoiseEstimator &source)
	Assignment operator.
virtual	~SignalToNoiseEstimator ()
	Destructor.
virtual void	init (const PeakIterator &it_begin, const PeakIterator &it_end)
	Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.
virtual void	init (const Container &c)
	Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.
virtual double	getSignalToNoise (const PeakIterator &data_point)
virtual double	getSignalToNoise (const PeakType &data_point)
Protected Member Functions
virtual void	computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_)=0
	computes the S/N values when init() is called
GaussianEstimate	estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
	calculate mean & stdev of intensities of a spectrum
Protected Attributes
std::map< PeakType, double, typename PeakType::PositionLess >	stn_estimates_
	stores the noise estimate for each peak
PeakIterator	first_
	points to the first raw data point in the interval
PeakIterator	last_
	points to the right position next to the last raw data point in the interval
bool	is_result_valid_
	flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.

Detailed Description

template<typename Container = MSSpectrum<>>
class OpenMS::SignalToNoiseEstimator< Container >

This class represents the abstract base class of a signal to noise estimator.

A signal to noise estimator should provide the signal to noise ratio of all raw data points in a given interval [first_,last_).

Member Typedef Documentation

typedef Container::const_iterator PeakIterator

Reimplemented in SignalToNoiseEstimatorMeanIterative< Container >, SignalToNoiseEstimatorMedian< Container >, and SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >.

typedef PeakIterator::value_type PeakType

Reimplemented in SignalToNoiseEstimatorMeanIterative< Container >, SignalToNoiseEstimatorMedian< Container >, and SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >.

Constructor & Destructor Documentation

SignalToNoiseEstimator ( ) [inline]

Constructor.

SignalToNoiseEstimator ( const SignalToNoiseEstimator< Container > & source ) [inline]

Copy constructor.

virtual ~SignalToNoiseEstimator ( ) [inline, virtual]

Destructor.

Member Function Documentation

virtual void computeSTN_	(	const PeakIterator &	scan_first_,
		const PeakIterator &	scan_last_
	)			`[protected, pure virtual]`

computes the S/N values when init() is called

Exceptions:

Throws

Exception::InvalidValue

Implemented in SignalToNoiseEstimatorMeanIterative< Container >, SignalToNoiseEstimatorMedian< Container >, and SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >.

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::init().

GaussianEstimate estimate_	(	const PeakIterator &	scan_first_,
		const PeakIterator &	scan_last_
	)			const `[inline, protected]`

calculate mean & stdev of intensities of a spectrum

Referenced by SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_().

virtual double getSignalToNoise ( const PeakType & data_point ) [inline, virtual]

virtual double getSignalToNoise ( const PeakIterator & data_point ) [inline, virtual]

Return to signal/noise estimate for data point data_point

Note:: the first query to this function will take longer, as all SignalToNoise values are calculated; you will get a warning to stderr if more than 20% of the noise estimates used sparse windows

Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), PeakPickerHiRes::pick(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

virtual void init ( const Container & c ) [inline, virtual]

Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.

virtual void init	(	const PeakIterator &	it_begin,
		const PeakIterator &	it_end
	)			`[inline, virtual]`

Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::init(), SimpleSeeder< PeakType, FeatureType >::initialize_(), PeakPickerHiRes::pick(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

SignalToNoiseEstimator& operator= ( const SignalToNoiseEstimator< Container > & source ) [inline]

Assignment operator.

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::operator=().

Member Data Documentation

PeakIterator first_ [protected]

points to the first raw data point in the interval

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::init(), and SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::operator=().

bool is_result_valid_ [mutable, protected]

flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::init(), SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >::updateMembers_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().

PeakIterator last_ [protected]

points to the right position next to the last raw data point in the interval

Referenced by SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::init(), and SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::operator=().

std::map<PeakType, double, typename PeakType::PositionLess> stn_estimates_ [protected]

stores the noise estimate for each peak

Referenced by SignalToNoiseEstimatorMedian< OpenMS::MSSpectrum< PeakT > >::computeSTN_(), SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), and SignalToNoiseEstimator< OpenMS::MSSpectrum< PeakT > >::operator=().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1

SignalToNoiseEstimator< Container > Class Template Reference

Classes

Public Types

Public Member Functions

Protected Member Functions