OpenMS  2.7.0
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ExtendedIsotopeFitter1D Class Reference

Extended isotope distribution fitter (1-dim.) approximated using linear interpolation. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ExtendedIsotopeFitter1D.h>

Inheritance diagram for ExtendedIsotopeFitter1D:
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Collaboration diagram for ExtendedIsotopeFitter1D:
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Public Member Functions

 ExtendedIsotopeFitter1D ()
 Default constructor. More...
 
 ExtendedIsotopeFitter1D (const ExtendedIsotopeFitter1D &source)
 copy constructor More...
 
 ~ExtendedIsotopeFitter1D () override
 destructor More...
 
virtual ExtendedIsotopeFitter1Doperator= (const ExtendedIsotopeFitter1D &source)
 assignment operator More...
 
QualityType fit1d (const RawDataArrayType &range, std::unique_ptr< InterpolationModel > &model) override
 return interpolation model More...
 
- Public Member Functions inherited from MaxLikeliFitter1D
 MaxLikeliFitter1D ()
 default constructor More...
 
 MaxLikeliFitter1D (const MaxLikeliFitter1D &source)
 copy constructor More...
 
 ~MaxLikeliFitter1D () override
 destructor More...
 
virtual MaxLikeliFitter1Doperator= (const MaxLikeliFitter1D &source)
 assignment operator More...
 
- Public Member Functions inherited from Fitter1D
 Fitter1D ()
 Default constructor. More...
 
 Fitter1D (const Fitter1D &source)
 copy constructor More...
 
 ~Fitter1D () override
 destructor More...
 
virtual Fitter1Doperator= (const Fitter1D &source)
 assignment operator 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 Fitter1Dcreate ()
 create new ExtendedIsotopeFitter1D object (function needed by Factory) More...
 
static const String getProductName ()
 name of the model (needed by Factory) More...
 
- Static Public Member Functions inherited from Fitter1D
static void registerChildren ()
 register all derived classes here More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
 Writes all parameters to meta values. More...
 

Protected Member Functions

void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from MaxLikeliFitter1D
QualityType fitOffset_ (std::unique_ptr< InterpolationModel > &model, const RawDataArrayType &set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step) const
 fit an offset on the basis of the Pearson correlation coefficient More...
 
void updateMembers_ () override
 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 charge_
 isotope charge More...
 
CoordinateType isotope_stdev_
 standard derivation in isotope More...
 
CoordinateType monoisotopic_mz_
 monoisotopic mass More...
 
Int max_isotope_
 maximum isotopic rank to be considered More...
 
- Protected Attributes inherited from Fitter1D
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...
 

Additional Inherited Members

- Public Types inherited from Fitter1D
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
 Peak type data point type. More...
 
typedef std::vector< PeakTypeRawDataArrayType
 Peak type data container type using for the temporary storage of the input data. More...
 
typedef RawDataArrayType::iterator PeakIterator
 Peak type 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...
 

Detailed Description

Extended isotope distribution fitter (1-dim.) approximated using linear interpolation.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
interpolation_step float0.2  Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box float3.0  Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
charge int1  Charge state of the model.
statistics:mean float1.0  Centroid position of the model.
statistics:variance float1.0  Variance of the model.
isotope:stdev float0.1  Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
isotope:monoisotopic_mz float1.0  Monoisotopic m/z of the model.
isotope:maximum int100  Maximum isotopic rank to be considered.

Note:

Constructor & Destructor Documentation

◆ ExtendedIsotopeFitter1D() [1/2]

Default constructor.

◆ ExtendedIsotopeFitter1D() [2/2]

copy constructor

◆ ~ExtendedIsotopeFitter1D()

~ExtendedIsotopeFitter1D ( )
override

destructor

Member Function Documentation

◆ create()

static Fitter1D* create ( )
inlinestatic

create new ExtendedIsotopeFitter1D object (function needed by Factory)

◆ fit1d()

QualityType fit1d ( const RawDataArrayType range,
std::unique_ptr< InterpolationModel > &  model 
)
overridevirtual

return interpolation model

Reimplemented from Fitter1D.

◆ getProductName()

static const String getProductName ( )
inlinestatic

name of the model (needed by Factory)

◆ operator=()

virtual ExtendedIsotopeFitter1D& operator= ( const ExtendedIsotopeFitter1D source)
virtual

assignment operator

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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.

Member Data Documentation

◆ charge_

CoordinateType charge_
protected

isotope charge

◆ isotope_stdev_

CoordinateType isotope_stdev_
protected

standard derivation in isotope

◆ max_isotope_

Int max_isotope_
protected

maximum isotopic rank to be considered

◆ monoisotopic_mz_

CoordinateType monoisotopic_mz_
protected

monoisotopic mass