Isotope distribution approximated using linear interpolation. More...

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

Inheritance diagram for LmaIsotopeModel:

Public Types
enum	Averagines { C = 0, H, N, O, S, AVERAGINE_NUM }
typedef InterpolationModel::CoordinateType	CoordinateType
typedef InterpolationModel::CoordinateType	IntensityType
Public Member Functions
	LmaIsotopeModel ()
	Default constructor.
	LmaIsotopeModel (const LmaIsotopeModel &source)
	copy constructor
virtual	~LmaIsotopeModel ()
	destructor
virtual LmaIsotopeModel &	operator= (const LmaIsotopeModel &source)
	assignment operator
UInt	getCharge ()
	returns the charge
void	setOffset (CoordinateType offset)
	set the offset of the model
CoordinateType	getOffset ()
	returns the offset
void	setSamples ()
	set sample/supporting points of interpolation
CoordinateType	getCenter () const
	get the monoisotopic mass of the Isotope model This is a m/z-value not necessarily the monoisotopic mass.
Static Public Member Functions
static BaseModel< 1 > *	create ()
	create new LmaIsotopeModel 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	total_intensity_
	total intensity (area under curve)
CoordinateType	min_
CoordinateType	max_
CoordinateType	isotope_stdev_
UInt	charge_
CoordinateType	mean_
CoordinateType	monoisotopic_mz_
DoubleReal	averagine_ [AVERAGINE_NUM]
Int	max_isotope_
DoubleReal	trim_right_cutoff_
DoubleReal	isotope_distance_

Detailed Description

Isotope distribution approximated using linear interpolation.

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.
total_intensity	float	100	Total intensity under isotope curve.
monoisotopic_mz	float	0	Position (mz) of the monoisotopic peak.
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.
statistics:mean	float	0	Centroid m/z (as opposed to monoisotopic m/z).
bounding_box:min	float	0	Lower end of bounding box enclosing the data used to fit the model.
bounding_box:max	float	1	Upper end of bounding box enclosing the data used to fit 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

LmaIsotopeModel ( )

Default constructor.

LmaIsotopeModel ( const LmaIsotopeModel & source )

copy constructor

virtual ~LmaIsotopeModel ( ) [virtual]

destructor

Member Function Documentation

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

create new LmaIsotopeModel object (needed by Factory)

CoordinateType getCenter ( ) const [virtual]

get the monoisotopic mass of the Isotope model This is a m/z-value not necessarily the monoisotopic mass.

Reimplemented from InterpolationModel.

UInt getCharge ( )

returns the charge

CoordinateType getOffset ( )

returns the offset

static const String getProductName ( ) [inline, static]

name of the model (needed by Factory)

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

virtual LmaIsotopeModel& operator= ( const LmaIsotopeModel & 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 ( ) [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.