| OpenMS 2.5.0

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:

## Public Member Functions

| ExtendedIsotopeFitter1D ()
| Default constructor. More...
| ExtendedIsotopeFitter1D (const ExtendedIsotopeFitter1D &source)
| copy constructor More...
| ~ExtendedIsotopeFitter1D () override
| destructor More...
virtual ExtendedIsotopeFitter1D & | operator= (const ExtendedIsotopeFitter1D &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 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...

## 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

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< 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

Extended isotope 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.
charge | int | 1 |  | Charge state of the model.
statistics:mean | float | 1.0 |  | Centroid position of the model.
statistics:variance | float | 1.0 |  | Variance of the model.
isotope:stdev | float | 0.1 |  | Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
isotope:monoisotopic_mz | float | 1.0 |  | Monoisotopic m/z of the model.
isotope:maximum | int | 100 |  | Maximum isotopic rank to be considered.

Note:

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

## Constructor & Destructor Documentation

## ◆ ExtendedIsotopeFitter1D() [1/2]

ExtendedIsotopeFitter1D | ( |  | ) |

Default constructor.

## ◆ ExtendedIsotopeFitter1D() [2/2]

ExtendedIsotopeFitter1D | ( | const ExtendedIsotopeFitter1D & | source | ) |

copy constructor

## ◆ ~ExtendedIsotopeFitter1D()

~ExtendedIsotopeFitter1D | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static Fitter1D* create | ( |  | ) |

inline static

create new ExtendedIsotopeFitter1D 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 ExtendedIsotopeFitter1D& operator= | ( | const ExtendedIsotopeFitter1D & | 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

## ◆ 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