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 Member Functions
	ExtendedIsotopeModel ()
	Default constructor.
	ExtendedIsotopeModel (const ExtendedIsotopeModel &source)
	copy constructor
virtual	~ExtendedIsotopeModel ()
	destructor
virtual ExtendedIsotopeModel &	operator= (const ExtendedIsotopeModel &source)
	assignment operator
UInt	getCharge ()
void	setOffset (CoordinateType offset)
	set the offset of the model
CoordinateType	getOffset ()
void	setSamples ()
	set sample/supporting points of interpolation
CoordinateType	getCenter () const
	get the monoisotopic mass of the Isotope model
Static Public Member Functions
static BaseModel< 1 > *	create ()
	create new ExtendedIsotopeModel 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_
UInt	charge_
CoordinateType	monoisotopic_mz_
DoubleReal	averagine_ [AVERAGINE_NUM]
Int	max_isotope_
DoubleReal	trim_right_cutoff_
DoubleReal	isotope_distance_

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	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: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	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

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

ExtendedIsotopeModel ( )

Default constructor.

ExtendedIsotopeModel ( const ExtendedIsotopeModel & source )

copy constructor

virtual ~ExtendedIsotopeModel ( ) [virtual]

destructor

Member Function Documentation

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

create new ExtendedIsotopeModel object (needed by Factory)

CoordinateType getCenter ( ) const [virtual]

get the monoisotopic mass of the Isotope model

Reimplemented from InterpolationModel.

UInt getCharge ( )

CoordinateType getOffset ( )

static const String getProductName ( ) [inline, static]

name of the model (needed by Factory)

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

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

assignment operator

void setOffset ( CoordinateType offset )

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.

void setSamples ( ) [virtual]

set sample/supporting points of interpolation

Reimplemented from InterpolationModel.

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.