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.
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inline |
Copy constructor.
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inlinevirtual |
Destructor.
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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().
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inlineprotected |
calculate mean & stdev of intensities of a spectrum
Referenced by SignalToNoiseEstimatorMedian< OpenMS::OpenMS::MSSpectrum< PeakT > >::computeSTN_(), and SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_().
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inlinevirtual |
Return to signal/noise estimate for data point data_point
Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), PeakPickerHiRes::pick(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().
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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().
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inlinevirtual |
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.
|
inline |
Assignment operator.
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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=().
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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_().
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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=().
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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 |