Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaIsotopeFitter1D.h>

Inheritance diagram for LmaIsotopeFitter1D:

List of all members.

Classes
struct	Data
	Helper struct (contains the size of an area, a raw data container, the relative abundance of i-th isotopic peak and the distance between consecutive isotopic peaks). More...
Public Types
enum	Averagines { C = 0, H, N, O, S, AVERAGINE_NUM }
Public Member Functions
	LmaIsotopeFitter1D ()
	Default constructor.
	LmaIsotopeFitter1D (const LmaIsotopeFitter1D &source)
	copy constructor
virtual	~LmaIsotopeFitter1D ()
	destructor
virtual LmaIsotopeFitter1D &	operator= (const LmaIsotopeFitter1D &source)
	assignment operator
QualityType	fit1d (const RawDataArrayType &range, InterpolationModel *&model)
	return interpolation model
Static Public Member Functions
static Fitter1D *	create ()
	create new LmaIsotopeFitter1D object (function needed by Factory)
static const String	getProductName ()
	name of the model (needed by Factory)
Protected Member Functions
void	setInitialParameters_ ()
	Compute start parameter.
void	printState_ (Int iter, gsl_multifit_fdfsolver *s)
void	updateMembers_ ()
Static Protected Member Functions
static Int	residual_ (const gsl_vector x, void params, gsl_vector *f)
	Evaluation of the target function for nonlinear optimization.
static Int	jacobian_ (const gsl_vector x, void params, gsl_matrix *J)
	Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data.
static Int	evaluate_ (const gsl_vector x, void params, gsl_vector f, gsl_matrix J)
	Driver function for the evaluation of function and jacobian.
Protected Attributes
UInt	charge_
	isotope charge
CoordinateType	isotope_stdev_
	standard derivation in isotope
CoordinateType	total_intensity_
	total intensity (area under curve)
CoordinateType	monoisotopic_mz_
	monoisotopic mass
Int	max_isotope_
	maximum isotopic rank to be considered
DoubleReal	trim_right_cutoff_
	cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered
DoubleReal	isotope_distance_
	distance between consecutive isotopic peaks
CoordinateType	mean_
	Centroid m/z (as opposed to monoisotopic m/z).
DoubleReal	averagine_ [AVERAGINE_NUM]
	number of an atom per Dalton of mass
ContainerType	isotopes_exact_
	relative abundance of i-th isotopic peak
bool	monoisotopic_mass_known_
	The position of the monoisotopic mass is known(=1) or unknown(=0).

Detailed Description

Isotope distribution fitter (1-dim.) approximated using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization.

Parameters of this class are:

Name	Type	Default	Description
interpolation_step	float	0.1	Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box	float	3	Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
max_iteration	int	500	Maximum number of iterations using by Levenberg-Marquardt algorithm.
deltaAbsError	float	0.0001	Absolute error used by the Levenberg-Marquardt algorithm.
deltaRelError	float	0.0001	Relative error used by the Levenberg-Marquardt algorithm.
charge	int	1	Charge state of the model.
total_intensity	float	100	Total intensity under the curve in mz dimension.
monoisotopic_mass	float	0	Monoisotopic mz of the model.
statistics:mean	float	0	Centroid m/z (as opposed to monoisotopic m/z).
statistics:variance	float	1	Variance 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.

Note:

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

Member Enumeration Documentation

enum Averagines

Enumerator:

C
H
N
O
S
AVERAGINE_NUM

Constructor & Destructor Documentation

LmaIsotopeFitter1D ( )

Default constructor.

LmaIsotopeFitter1D ( const LmaIsotopeFitter1D & source )

copy constructor

virtual ~LmaIsotopeFitter1D ( ) [virtual]

destructor

Member Function Documentation

static Fitter1D* create ( ) [inline, static]

create new LmaIsotopeFitter1D object (function needed by Factory)

static Int evaluate_	(	const gsl_vector *	x,
		void *	params,
		gsl_vector *	f,
		gsl_matrix *	J
	)			`[static, protected]`

Driver function for the evaluation of function and jacobian.

QualityType fit1d	(	const RawDataArrayType &	range,
		InterpolationModel *&	model
	)			`[virtual]`

return interpolation model

Reimplemented from Fitter1D.

static const String getProductName ( ) [inline, static]

name of the model (needed by Factory)

static Int jacobian_	(	const gsl_vector *	x,
		void *	params,
		gsl_matrix *	J
	)			`[static, protected]`

Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data.

virtual LmaIsotopeFitter1D& operator= ( const LmaIsotopeFitter1D & source ) [virtual]

assignment operator

void printState_	(	Int	iter,
		gsl_multifit_fdfsolver *	s
	)			`[protected, virtual]`

Display the intermediate state of the solution. The solver state contains the vector s->x which is the current position, and the vector s->f with corresponding function values

Implements LevMarqFitter1D.