| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
BiGaussFitter1D Class Reference

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

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/BiGaussFitter1D.h>`

Inheritance diagram for BiGaussFitter1D:

## Public Member Functions

| BiGaussFitter1D ()
| Default constructor. More...
| BiGaussFitter1D (const BiGaussFitter1D &source)
| copy constructor More...
| ~BiGaussFitter1D () override
| destructor More...
virtual BiGaussFitter1D & | operator= (const BiGaussFitter1D &source)
| assignment operator More...
QualityType | fit1d (const RawDataArrayType &range, 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 MaxLikeliFitter1D & | operator= (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 Fitter1D & | operator= (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 DefaultParamHandler & | operator= (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 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...

## Static Public Member Functions

static Fitter1D * | create ()
| create new BiGaussModel 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...

## 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_ (InterpolationModel *model, const RawDataArrayType &set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step)
| 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

Math::BasicStatistics | statistics1_
| statistics for first peak site More...
Math::BasicStatistics | statistics2_
| statistics for second peak site 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< 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...

## 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< PeakType > | RawDataArrayType
| 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

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

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
interpolation_step | float | 0.2 |  | Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box | float | 3.0 |  | 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 | float | 1.0 |  | Centroid position of the model.
statistics:variance | float | 1.0 |  | The variance of the model.
statistics:variance1 | float | 1.0 |  | Variance of the first gaussian, used for the lower half of the model.
statistics:variance2 | float | 1.0 |  | Variance of the second gaussian, used for the upper half of the model.

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ BiGaussFitter1D() [1/2]

BiGaussFitter1D | ( |  | ) |

Default constructor.

## ◆ BiGaussFitter1D() [2/2]

BiGaussFitter1D | ( | const BiGaussFitter1D & | source | ) |

copy constructor

## ◆ ~BiGaussFitter1D()

~BiGaussFitter1D | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static Fitter1D* create | ( |  | ) |

inline static

create new BiGaussModel object (function needed by Factory)

## ◆ fit1d()

QualityType fit1d | ( | const RawDataArrayType & | range,
|  | InterpolationModel *& | model
| ) |  |

override virtual

return interpolation model

Reimplemented from Fitter1D.

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

name of the model (needed by Factory)

## ◆ operator=()

virtual BiGaussFitter1D& operator= | ( | const BiGaussFitter1D & | source | ) |

virtual

assignment operator

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

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

## ◆ statistics1_

Math::BasicStatistics statistics1_

protected

statistics for first peak site

## ◆ statistics2_

Math::BasicStatistics statistics2_

protected

statistics for second peak site