OpenMS: ExtendedIsotopeModel Class Reference

| OpenMS 2.5.0

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

Extended isotope distribution approximated using linear interpolation. More...

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

Inheritance diagram for ExtendedIsotopeModel:

## Public Types

enum | Averagines { C = 0, H, N, O, S, AVERAGINE_NUM }
typedef InterpolationModel::CoordinateType | CoordinateType
typedef InterpolationModel::CoordinateType | IntensityType
Public Types inherited from InterpolationModel
typedef double | IntensityType
typedef DPosition< 1 > | PositionType
typedef double | CoordinateType
typedef Math::LinearInterpolation< double > | LinearInterpolation
Public Types inherited from BaseModel< 1 >
typedef double | IntensityType
typedef double | CoordinateType
typedef DPosition< D > | PositionType
typedef DPeak< D >::Type | PeakType
typedef std::vector< PeakType > | SamplesType

## Public Member Functions

| ExtendedIsotopeModel ()
| Default constructor. More...
| ExtendedIsotopeModel (const ExtendedIsotopeModel &source)
| copy constructor More...
| ~ExtendedIsotopeModel () override
| destructor More...
virtual ExtendedIsotopeModel & | operator= (const ExtendedIsotopeModel &source)
| assignment operator More...
UInt | getCharge ()
void | setOffset (CoordinateType offset) override
| set the offset of the model More...
CoordinateType | getOffset ()
void | setSamples () override
| set sample/supporting points of interpolation More...
CoordinateType | getCenter () const override
| get the monoisotopic mass of the Isotope model More...
Public Member Functions inherited from InterpolationModel
| InterpolationModel ()
| Default constructor. More...
| InterpolationModel (const InterpolationModel &source)
| copy constructor More...
| ~InterpolationModel () override
| destructor More...
virtual InterpolationModel & | operator= (const InterpolationModel &source)
| assignment operator More...
IntensityType | getIntensity (const PositionType &pos) const override
| access model predicted intensity at position `pos` More...
IntensityType | getIntensity (CoordinateType coord) const
| access model predicted intensity at position `pos` More...
const LinearInterpolation & | getInterpolation () const
| Returns the interpolation class. More...
CoordinateType | getScalingFactor () const
| get the scaling for the model More...
void | getSamples (SamplesType &cont) const override
| get reasonable set of samples from the model (i.e. for printing) More...
void | setInterpolationStep (CoordinateType interpolation_step)
| Set the interpolation step for the linear interpolation of the model. More...
void | setScalingFactor (CoordinateType scaling)
Public Member Functions inherited from BaseModel< 1 >
| BaseModel ()
| Default constructor. More...
| BaseModel (const BaseModel &source)
| copy constructor More...
| ~BaseModel () override
| Destructor. More...
virtual BaseModel & | operator= (const BaseModel &source)
| assignment operator More...
void | registerChildren ()
void | registerChildren ()
virtual IntensityType | getIntensity (const PositionType &pos) const=0
| access model predicted intensity at position `pos` More...
virtual bool | isContained (const PositionType &pos) const
| check if position `pos` is part of the model regarding the models cut-off. More...
void | fillIntensity (PeakType &peak) const
| Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity(). More...
void | fillIntensities (PeakIterator begin, PeakIterator end) const
| Convenience function that applies fillIntensity() to an iterator range. More...
virtual IntensityType | getCutOff () const
| get cutoff value More...
virtual void | setCutOff (IntensityType cut_off)
| set cutoff value More...
virtual void | getSamples (std::ostream &os)
| fill stream with reasonable set of samples from the model (i.e. for printing) 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 BaseModel< 1 > * | create ()
| create new ExtendedIsotopeModel object (needed by Factory) More...
static const String | getProductName ()
| name of the model (needed by Factory) More...
Static Public Member Functions inherited from BaseModel< 1 >
static void | registerChildren ()
| register all derived classes here (implemented in file BaseModel_impl.h) 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 InterpolationModel
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 BaseModel< 1 >
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 | isotope_stdev_
UInt | charge_
CoordinateType | monoisotopic_mz_
double | averagine_ [AVERAGINE_NUM]
Int | max_isotope_
double | trim_right_cutoff_
double | isotope_distance_
Protected Attributes inherited from InterpolationModel
LinearInterpolation | interpolation_
CoordinateType | interpolation_step_
CoordinateType | scaling_
Protected Attributes inherited from BaseModel< 1 >
IntensityType | cut_off_
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

Extended isotope distribution approximated using linear interpolation.

This models a smoothed (widened) distribution, i.e. can be used to sample actual raw peaks (depending on the points you query). If you only want the distribution (no widening), use either EmpiricalFormula::getIsotopeDistribution() // for a certain sum formula or IsotopeDistribution::estimateFromPeptideWeight (double average_weight) // for averagine

Peak widening is achieved by a Gaussian shape.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
cutoff | float | 0.0 |  | Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.
interpolation_step | float | 0.1 |  | Sampling rate for the interpolation of the model function
intensity_scaling | float | 1.0 |  | Scaling factor used to adjust the model distribution to the intensities of the data
charge | int | 1 |  | Charge state of the model.
averagines:C | float | 0.044439889490604 |  | Number of C atoms per Dalton of mass.
averagines:H | float | 0.069815717637539 |  | Number of H atoms per Dalton of mass.
averagines:N | float | 0.012217730283737 |  | Number of N atoms per Dalton of mass.
averagines:O | float | 0.013293989934027 |  | Number of O atoms per Dalton of mass.
averagines:S | float | 3.752500051632524e-04 |  | Number of S atoms per Dalton of mass.
isotope:trim_right_cutoff | float | 0.001 |  | Cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered.
isotope:maximum | int | 100 |  | Maximum isotopic rank to be considered.
isotope:distance | float | 1.000495 |  | Distance between consecutive isotopic peaks.
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.

Note:

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

## Member Typedef Documentation

## ◆ CoordinateType

typedef InterpolationModel::CoordinateType CoordinateType

## ◆ IntensityType

typedef InterpolationModel::CoordinateType IntensityType

## Member Enumeration Documentation

## ◆ Averagines

enum Averagines

Enumerator
C |
H |
N |
O |
S |
AVERAGINE_NUM |

## Constructor & Destructor Documentation

## ◆ ExtendedIsotopeModel() [1/2]

ExtendedIsotopeModel | ( |  | ) |

Default constructor.

## ◆ ExtendedIsotopeModel() [2/2]

ExtendedIsotopeModel | ( | const ExtendedIsotopeModel & | source | ) |

copy constructor

## ◆ ~ExtendedIsotopeModel()

~ExtendedIsotopeModel | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static BaseModel<1>* create | ( |  | ) |

inlinestatic

create new ExtendedIsotopeModel object (needed by Factory)

## ◆ getCenter()

CoordinateType getCenter | ( |  | ) | const

overridevirtual

get the monoisotopic mass of the Isotope model

Reimplemented from InterpolationModel.

## ◆ getCharge()

UInt getCharge | ( |  | ) |

## ◆ getOffset()

CoordinateType getOffset | ( |  | ) |

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inlinestatic

name of the model (needed by Factory)

## ◆ operator=()

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

virtual

assignment operator

## ◆ setOffset()

void setOffset | ( | CoordinateType | offset | ) |

overridevirtual

set the offset of the model

The whole model will be shifted to the new offset without being computing all over. This leaves a discrepancy which is minor in small shifts (i.e. shifting by one or two standard deviations) but can get significant otherwise. In that case use setParameters() which enforces a recomputation of the model.

Reimplemented from InterpolationModel.

## ◆ setSamples()

void setSamples | ( |  | ) |

overridevirtual

set sample/supporting points of interpolation

Reimplemented from InterpolationModel.

## ◆ 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

## ◆ averagine_

double averagine_[AVERAGINE_NUM]

protected

## ◆ charge_

UInt charge_

protected

## ◆ isotope_distance_

double isotope_distance_

protected

## ◆ isotope_stdev_

CoordinateType isotope_stdev_

protected

## ◆ max_isotope_

Int max_isotope_

protected

## ◆ monoisotopic_mz_

CoordinateType monoisotopic_mz_

protected

## ◆ trim_right_cutoff_

double trim_right_cutoff_

protected