This class represents the abstract base class of a signal to noise estimator. More...
#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimator.h>
 
  
 | 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 Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } | 
| Possible log types.  More... | |
| Public Member Functions | |
| SignalToNoiseEstimator () | |
| Constructor.  More... | |
| SignalToNoiseEstimator (const SignalToNoiseEstimator &source) | |
| Copy constructor.  More... | |
| SignalToNoiseEstimator & | operator= (const SignalToNoiseEstimator &source) | 
| Assignment operator.  More... | |
| virtual | ~SignalToNoiseEstimator () | 
| Destructor.  More... | |
| 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.  More... | |
| 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.  More... | |
| virtual double | getSignalToNoise (const PeakIterator &data_point) | 
| virtual double | getSignalToNoise (const PeakType &data_point) | 
|  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 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... | |
|  Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor.  More... | |
| ~ProgressLogger () | |
| Destructor.  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... | |
| Protected Member Functions | |
| virtual void | computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_)=0 | 
| computes the S/N values when init() is called  More... | |
| GaussianEstimate | estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const | 
| calculate mean & stdev of intensities of a spectrum  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Protected Attributes | |
| std::map< PeakType, double, typename PeakType::PositionLess > | stn_estimates_ | 
| stores the noise estimate for each peak  More... | |
| PeakIterator | first_ | 
| points to the first raw data point in the interval  More... | |
| PeakIterator | last_ | 
| points to the right position next to the last raw data point in the interval  More... | |
| bool | is_result_valid_ | 
| flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.  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< 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... | |
|  Protected Attributes inherited from ProgressLogger | |
| LogType | type_ | 
| SignedSize | begin_ | 
| SignedSize | end_ | 
| SignedSize | value_ | 
| QProgressDialog * | dlg_ | 
| StopWatch | stop_watch_ | 
| time_t | last_invoke_ | 
| Additional Inherited Members | |
|  Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ | 
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_).
| typedef Container::const_iterator PeakIterator | 
| typedef PeakIterator::value_type PeakType | 
| 
 | inline | 
Constructor.
| 
 | inline | 
Copy constructor.
| 
 | inlinevirtual | 
Destructor.
| 
 | protectedpure virtual | 
computes the S/N values when init() is called
| Throws | Exception::InvalidValue | 
Implemented in SignalToNoiseEstimatorMeanIterative< Container >, SignalToNoiseEstimatorMedian< Container >, and SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >.
Referenced by SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::init().
| 
 | inlineprotected | 
calculate mean & stdev of intensities of a spectrum
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_().
| 
 | inlinevirtual | 
Return to signal/noise estimate for data point data_point 
Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), PeakPickerHiRes::pick(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().
| 
 | inlinevirtual | 
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.
Referenced by SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::init(), SimpleSeeder< PeakType, FeatureType >::initialize_(), PeakPickerHiRes::pick(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().
| 
 | inlinevirtual | 
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.
| 
 | inline | 
Assignment operator.
| 
 | protected | 
points to the first raw data point in the interval
Referenced by SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::init(), and SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::operator=().
| 
 | mutableprotected | 
flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.
Referenced by SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::init(), SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::updateMembers_(), and SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_().
| 
 | protected | 
points to the right position next to the last raw data point in the interval
Referenced by SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::init(), and SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::operator=().
| 
 | protected | 
stores the noise estimate for each peak
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::getSignalToNoise(), and SignalToNoiseEstimator< OpenMS::OpenMS::MSSpectrum< PeakT > >::operator=().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |