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Fitter1D Class Reference

Abstract base class for all 1D-dimensional model fitter. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h>

Inheritance diagram for Fitter1D:
DefaultParamHandler FeatureFinderDefs LevMarqFitter1D MaxLikeliFitter1D EGHFitter1D EmgFitter1D BiGaussFitter1D ExtendedIsotopeFitter1D GaussFitter1D IsotopeFitter1D

Public Types

typedef IsotopeCluster::IndexSet IndexSet
 IndexSet. More...
 
typedef IsotopeCluster::ChargedIndexSet ChargedIndexSet
 IndexSet with charge information. More...
 
typedef Feature::CoordinateType CoordinateType
 Single coordinate. More...
 
typedef Feature::QualityType QualityType
 Quality of a feature. More...
 
typedef Peak1D PeakType
 Raw data point type. More...
 
typedef std::vector< PeakTypeRawDataArrayType
 Raw data container type using for the temporary storage of the input data. More...
 
typedef RawDataArrayType::iterator PeakIterator
 Raw data iterator. 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

 Fitter1D ()
 Default constructor. More...
 
 Fitter1D (const Fitter1D &source)
 copy constructor More...
 
virtual ~Fitter1D ()
 destructor More...
 
virtual Fitter1Doperator= (const Fitter1D &source)
 assignment operator More...
 
virtual QualityType fit1d (const RawDataArrayType &, InterpolationModel *&)
 return interpolation model 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...
 

Static Public Member Functions

static void registerChildren ()
 register all derived classes here More...
 

Protected Member Functions

virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

CoordinateType tolerance_stdev_box_
 standard derivation in bounding box More...
 
Math::BasicStatistics statistics_
 basic statistics More...
 
CoordinateType interpolation_step_
 interpolation step size 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...
 

Detailed Description

Abstract base class for all 1D-dimensional model fitter.

Every derived class has to implement the static functions "T* create()" and "const String getProductName()" (see DefaultParamHandler for details)

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
interpolation_step float0.2  Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box float3  Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
statistics:mean float1  Centroid position of the model.
statistics:variance float1  The variance of the model.

Note:

Member Typedef Documentation

◆ ChargedIndexSet

IndexSet with charge information.

◆ CoordinateType

Single coordinate.

◆ IndexSet

IndexSet.

◆ PeakIterator

typedef RawDataArrayType::iterator PeakIterator

Raw data iterator.

◆ PeakType

typedef Peak1D PeakType

Raw data point type.

◆ QualityType

Quality of a feature.

◆ RawDataArrayType

typedef std::vector<PeakType> RawDataArrayType

Raw data container type using for the temporary storage of the input data.

Constructor & Destructor Documentation

◆ Fitter1D() [1/2]

Fitter1D ( )

Default constructor.

◆ Fitter1D() [2/2]

Fitter1D ( const Fitter1D source)

copy constructor

◆ ~Fitter1D()

virtual ~Fitter1D ( )
inlinevirtual

destructor

Member Function Documentation

◆ fit1d()

virtual QualityType fit1d ( const RawDataArrayType ,
InterpolationModel *&   
)
virtual

return interpolation model

Reimplemented in EGHFitter1D, EmgFitter1D, ExtendedIsotopeFitter1D, IsotopeFitter1D, BiGaussFitter1D, and GaussFitter1D.

◆ operator=()

virtual Fitter1D& operator= ( const Fitter1D source)
virtual

assignment operator

Referenced by MaxLikeliFitter1D::operator=(), and LevMarqFitter1D::operator=().

◆ registerChildren()

static void registerChildren ( )
static

register all derived classes here

◆ updateMembers_()

virtual void updateMembers_ ( )
protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Reimplemented in LevMarqFitter1D, MaxLikeliFitter1D, EmgFitter1D, EGHFitter1D, ExtendedIsotopeFitter1D, BiGaussFitter1D, IsotopeFitter1D, and GaussFitter1D.

Referenced by MaxLikeliFitter1D::updateMembers_(), and LevMarqFitter1D::updateMembers_().

Member Data Documentation

◆ interpolation_step_

CoordinateType interpolation_step_
protected

interpolation step size

◆ statistics_

Math::BasicStatistics statistics_
protected

basic statistics

◆ tolerance_stdev_box_

CoordinateType tolerance_stdev_box_
protected

standard derivation in bounding box


OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:09 using doxygen 1.8.13