Isotope distribution approximated using linear interpolation. More...

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

Inheritance diagram for IsotopeModel:

Public Types
enum	Averagines { C = 0, H, N, O, S, AVERAGINE_NUM }
typedef InterpolationModel::CoordinateType	CoordinateType
typedef InterpolationModel::CoordinateType	IntensityType
Public Member Functions
	IsotopeModel ()
	Default constructor.
	IsotopeModel (const IsotopeModel &source)
	copy constructor
virtual	~IsotopeModel ()
	destructor
virtual IsotopeModel &	operator= (const IsotopeModel &source)
	assignment operator
UInt	getCharge ()
void	setOffset (CoordinateType offset)
	set the offset of the model
CoordinateType	getOffset ()
EmpiricalFormula	getFormula ()
	return the Averagine peptide formula (mass calculated from mean mass and charge -- use .setParameters() to set them)
void	setSamples (const EmpiricalFormula &formula)
	set sample/supporting points of interpolation
CoordinateType	getCenter () const
	get the center of the Isotope model
const IsotopeDistribution &	getIsotopeDistribution () const
	the Isotope distribution (without widening) from the last setSamples() call
Static Public Member Functions
static BaseModel< 1 > *	create ()
	create new IsotopeModel object (needed by Factory)
static const String	getProductName ()
	name of the model (needed by Factory)
Protected Member Functions
void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
Protected Attributes
CoordinateType	isotope_stdev_
CoordinateType	isotope_lorentz_fwhm_
UInt	charge_
CoordinateType	mean_
CoordinateType	monoisotopic_mz_
DoubleReal	averagine_ [AVERAGINE_NUM]
Int	max_isotope_
DoubleReal	trim_right_cutoff_
DoubleReal	isotope_distance_
IsotopeDistribution	isotope_distribution_

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		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		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	0.0444398894906044		Number of C atoms per Dalton of mass.
averagines:H	float	0.0698157176375389		Number of H atoms per Dalton of mass.
averagines:N	float	0.0122177302837372		Number of N atoms per Dalton of mass.
averagines:O	float	0.0132939899340272		Number of O atoms per Dalton of mass.
averagines:S	float	0.000375250005163252		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: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		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

typedef InterpolationModel::CoordinateType CoordinateType

Reimplemented from InterpolationModel.

typedef InterpolationModel::CoordinateType IntensityType

Reimplemented from InterpolationModel.

Member Enumeration Documentation

enum Averagines

Enumerator:

C
H
N
O
S
AVERAGINE_NUM

Constructor & Destructor Documentation

IsotopeModel ( )

Default constructor.

IsotopeModel ( const IsotopeModel & source )

copy constructor

virtual ~IsotopeModel ( ) [virtual]

destructor

Member Function Documentation

static BaseModel<1>* create ( ) [inline, static]

create new IsotopeModel object (needed by Factory)

CoordinateType getCenter ( ) const [virtual]

get the center of the Isotope model

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

Reimplemented from InterpolationModel.

UInt getCharge ( )

EmpiricalFormula getFormula ( )

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

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

CoordinateType getOffset ( )

static const String getProductName ( ) [inline, static]

name of the model (needed by Factory)

Referenced by BaseModel< D >::registerChildren().

virtual IsotopeModel& operator= ( const IsotopeModel & source ) [virtual]

assignment operator

void setOffset ( CoordinateType offset ) [virtual]

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.

void setSamples ( const EmpiricalFormula & formula )

set sample/supporting points of interpolation

void updateMembers_ ( ) [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 InterpolationModel.