Isotope distribution approximated using linear interpolation. More...

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

Inheritance diagram for IsotopeModel:

Collaboration diagram for IsotopeModel:

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
	IsotopeModel ()
	Default constructor. More...

	IsotopeModel (const IsotopeModel &source)
	copy constructor More...

	~IsotopeModel () override
	destructor More...

virtual IsotopeModel &	operator= (const IsotopeModel &source)
	assignment operator More...

UInt	getCharge ()

void	setOffset (CoordinateType offset) override
	set the offset of the model More...

CoordinateType	getOffset ()

EmpiricalFormula	getFormula ()
	return the Averagine peptide formula (mass calculated from mean mass and charge – use .setParameters() to set them) More...

virtual void	setSamples (const EmpiricalFormula &formula)
	set sample/supporting points of interpolation More...

CoordinateType	getCenter () const override
	get the center of the Isotope model More...

const IsotopeDistribution &	getIsotopeDistribution () const
	the Isotope distribution (without widening) from the last setSamples() call More...

virtual void	setSamples ()
	set sample/supporting points of interpolation (from base class) 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...

virtual void	setSamples ()
	set sample/supporting points of interpolation wrt params. 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 IsotopeModel 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...

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 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_

CoordinateType	isotope_lorentz_fwhm_

UInt	charge_

CoordinateType	mean_

CoordinateType	monoisotopic_mz_

double	averagine_ [AVERAGINE_NUM]

Int	max_isotope_

double	trim_right_cutoff_

double	isotope_distance_

IsotopeDistribution	isotope_distribution_

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

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 either a Gaussian or Lorentzian 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	1.0e-03		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:mode:mode	string	Gaussian	Gaussian, Lorentzian	Peak Shape used around each isotope peak.
isotope:mode:LorentzFWHM	float	0.3		Full width of the Lorentzian (Cauchy) function applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
isotope:mode:GaussianSD	float	0.1		Standard deviation of Gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
statistics:mean	float	0.0		Centroid m/z (as opposed to monoisotopic m/z).

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

◆ IsotopeModel() [1/2]

IsotopeModel ( )

Default constructor.

◆ IsotopeModel() [2/2]

IsotopeModel ( const IsotopeModel & source )

copy constructor

◆ ~IsotopeModel()

~IsotopeModel ( )

override

destructor

Member Function Documentation

◆ create()

static BaseModel<1>* create ( )

inlinestatic

create new IsotopeModel object (needed by Factory)

◆ getCenter()

CoordinateType getCenter ( ) const

overridevirtual

get the center of the Isotope model

This is a m/z-value not necessarily the monoisotopic mass.

Reimplemented from InterpolationModel.

◆ getCharge()

UInt getCharge ( )

◆ getFormula()

EmpiricalFormula getFormula ( )

return the Averagine peptide formula (mass calculated from mean mass and charge – use .setParameters() to set them)

◆ getIsotopeDistribution()

const IsotopeDistribution& getIsotopeDistribution ( ) const

the Isotope distribution (without widening) from the last setSamples() call

Useful to determine the number of isotopes that the model contains and their position

◆ getOffset()

CoordinateType getOffset ( )

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

◆ operator=()

virtual IsotopeModel& operator= ( const IsotopeModel & 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() [1/2]

virtual void setSamples

inline

set sample/supporting points of interpolation (from base class)

◆ setSamples() [2/2]

virtual void setSamples ( const EmpiricalFormula & formula )

virtual

set sample/supporting points of interpolation

◆ 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 InterpolationModel.

Member Data Documentation

◆ averagine_

double averagine_[AVERAGINE_NUM]

protected

◆ charge_

UInt charge_

protected

◆ isotope_distance_

double isotope_distance_

protected

◆ isotope_distribution_

IsotopeDistribution isotope_distribution_

protected

◆ isotope_lorentz_fwhm_

CoordinateType isotope_lorentz_fwhm_

protected

◆ isotope_stdev_

CoordinateType isotope_stdev_

protected

◆ max_isotope_

Int max_isotope_

protected

◆ mean_

CoordinateType mean_

protected

◆ monoisotopic_mz_

CoordinateType monoisotopic_mz_

protected

◆ trim_right_cutoff_

double trim_right_cutoff_

protected

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ CoordinateType

◆ IntensityType

Member Enumeration Documentation

◆ Averagines

Constructor & Destructor Documentation

◆ IsotopeModel() [1/2]

◆ IsotopeModel() [2/2]

◆ ~IsotopeModel()

Member Function Documentation

◆ create()

◆ getCenter()

◆ getCharge()

◆ getFormula()

◆ getIsotopeDistribution()

◆ getOffset()

◆ getProductName()

◆ operator=()

◆ setOffset()

◆ setSamples() [1/2]

◆ setSamples() [2/2]

◆ updateMembers_()

Member Data Documentation

◆ averagine_

◆ charge_

◆ isotope_distance_

◆ isotope_distribution_

◆ isotope_lorentz_fwhm_

◆ isotope_stdev_

◆ max_isotope_

◆ mean_

◆ monoisotopic_mz_

◆ trim_right_cutoff_