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SimpleSeeder< PeakType, FeatureType > Class Template Reference

Simple seeding class that uses the strongest peak as next seed. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleSeeder.h>

Inheritance diagram for SimpleSeeder< PeakType, FeatureType >:
FeaFiModule< PeakType, FeatureType > FeatureFinderDefs DefaultParamHandler

Public Types

typedef FeaFiModule< PeakType,
FeatureType > 
Base
 
typedef MSExperiment< PeakTypeMapType
 
- Public Types inherited from FeaFiModule< PeakType, FeatureType >
typedef FeatureMap< FeatureType > FeatureMapType
 Output feature map type. More...
 
typedef MSExperiment< PeakTypeMapType
 Input map type. More...
 
typedef MapType::SpectrumType SpectrumType
 Input spectrum type. More...
 
typedef PeakType::IntensityType IntensityType
 Input intensity type. More...
 
typedef PeakType::CoordinateType CoordinateType
 Input coordinate type. More...
 
- Public Types inherited from FeatureFinderDefs
enum  Flag { UNUSED, USED }
 Flags that indicate if a peak is already used in a feature. More...
 
typedef IsotopeCluster::IndexPair IndexPair
 Index to peak consisting of two UInts (scan index / peak index) More...
 
typedef
IsotopeCluster::ChargedIndexSet 
ChargedIndexSet
 Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
 
typedef IsotopeCluster::IndexSet IndexSet
 A set of peak indices. More...
 

Public Member Functions

 SimpleSeeder (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)
 Constructor. More...
 
virtual ~SimpleSeeder ()
 destructor More...
 
IndexPair nextSeed ()
 return the next seed More...
 
- Public Member Functions inherited from FeaFiModule< PeakType, FeatureType >
 FeaFiModule (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)
 Constructor. More...
 
virtual ~FeaFiModule ()
 destructor More...
 
IntensityType getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const
 Returns the intensity of a peak. More...
 
CoordinateType getPeakMz (const FeatureFinderDefs::IndexPair &index) const
 Returns the m/z of a peak. More...
 
CoordinateType getPeakRt (const FeatureFinderDefs::IndexPair &index) const
 Returns the retention time of a peak. More...
 
void getNextMz (FeatureFinderDefs::IndexPair &index) const
 fills index with the index of next peak in m/z dimension More...
 
void getPrevMz (FeatureFinderDefs::IndexPair &index) const
 fills index with the index of previous peak in m/z dimension More...
 
void getNextRt (FeatureFinderDefs::IndexPair &index)
 fills index with the index of the nearest peak in the next scan More...
 
void getPrevRt (FeatureFinderDefs::IndexPair &index)
 fills index with the index of the nearest peak in the previous scan More...
 
void addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const
 Calculates the convex hull of a index set and adds it to the feature. 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...
 

Protected Member Functions

void initialize_ ()
 
- 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::vector< IndexPairindices_
 contains the indizes More...
 
std::vector< IndexPair >
::const_iterator 
current_peak_
 Points to the next peak in the peak vector. More...
 
bool initialized_
 Flag that indicates of the indices are initialized. More...
 
- Protected Attributes inherited from FeaFiModule< PeakType, FeatureType >
const MapTypemap_
 Input data pointer. More...
 
FeatureMapTypefeatures_
 Output data pointer. More...
 
FeatureFinderff_
 Pointer to the calling FeatureFinder that is used to access the feature flags and report progress. 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...
 

Private Member Functions

 SimpleSeeder ()
 Not implemented. More...
 
SimpleSeederoperator= (const SimpleSeeder &)
 Not implemented. More...
 
 SimpleSeeder (const SimpleSeeder &)
 Not implemented. More...
 

Detailed Description

template<class PeakType, class FeatureType>
class OpenMS::SimpleSeeder< PeakType, FeatureType >

Simple seeding class that uses the strongest peak as next seed.

This class simply sorts the peaks according to intensity and proposes the highest peak, which is not yet included in a feature, as next seed.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
min_intensity float0 min: 0Absolute value for the minimum intensity required for a seed.
signal_to_noise float10 min: 0Minimal required SignalToNoise (S/N) ratio for a seed.
SignalToNoiseEstimationParameter:max_intensity int-1 min: -1maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.
SignalToNoiseEstimationParameter:auto_max_stdev_factor float3 min: 0 max: 999parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
SignalToNoiseEstimationParameter:auto_max_percentile int95 min: 0 max: 100parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
SignalToNoiseEstimationParameter:auto_mode int0 min: -1 max: 1method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
SignalToNoiseEstimationParameter:win_len float200 min: 1window length in Thomson
SignalToNoiseEstimationParameter:bin_count int30 min: 3number of bins for intensity values
SignalToNoiseEstimationParameter:min_required_elements int10 min: 1minimum number of elements required in a window (otherwise it is considered sparse)
SignalToNoiseEstimationParameter:noise_for_empty_window float1e+20  noise value used for sparse windows

Note:

Member Typedef Documentation

typedef FeaFiModule<PeakType, FeatureType> Base

Constructor & Destructor Documentation

SimpleSeeder ( const MSExperiment< PeakType > *  map,
FeatureMap< FeatureType > *  features,
FeatureFinder ff 
)
inline
virtual ~SimpleSeeder ( )
inlinevirtual

destructor

SimpleSeeder ( )
private

Not implemented.

SimpleSeeder ( const SimpleSeeder< PeakType, FeatureType > &  )
private

Not implemented.

Member Function Documentation

void initialize_ ( )
inlineprotected
IndexPair nextSeed ( )
inline
SimpleSeeder& operator= ( const SimpleSeeder< PeakType, FeatureType > &  )
private

Not implemented.

Member Data Documentation

std::vector<IndexPair>::const_iterator current_peak_
protected
std::vector<IndexPair> indices_
protected
bool initialized_
protected

Flag that indicates of the indices are initialized.

Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), and SimpleSeeder< PeakType, FeatureType >::nextSeed().


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5