| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
Fitter1D Class Reference
Analysis » FeatureFinder

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

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

Inheritance diagram for Fitter1D:

## 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
| 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...

## Public Member Functions

| Fitter1D ()
| Default constructor. More...
| Fitter1D (const Fitter1D &source)
| copy constructor More...
| ~Fitter1D () override
| destructor More...
virtual Fitter1D & | operator= (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 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 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 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< 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...

## 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:

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.

Note:

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

## Member Typedef Documentation

## ◆ ChargedIndexSet

typedef IsotopeCluster::ChargedIndexSet ChargedIndexSet

IndexSet with charge information.

## ◆ CoordinateType

typedef Feature::CoordinateType CoordinateType

Single coordinate.

## ◆ IndexSet

typedef IsotopeCluster::IndexSet IndexSet

IndexSet.

## ◆ PeakIterator

typedef RawDataArrayType::iterator PeakIterator

Peak type data iterator.

## ◆ PeakType

typedef Peak1D PeakType

Peak type data point type.

## ◆ QualityType

typedef Feature::QualityType QualityType

Quality of a feature.

## ◆ RawDataArrayType

typedef std::vector<PeakType> RawDataArrayType

Peak type 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()

~Fitter1D | ( |  | ) |

inline override

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_()

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.

Reimplemented in MaxLikeliFitter1D, LevMarqFitter1D, IsotopeFitter1D, and GaussFitter1D.

Referenced by MaxLikeliFitter1D::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