#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaIsotopeFitter1D.h>
LmaIsotopeFitter1D Parameters are explained on a separate page.
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 BiGaussModel 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_ () |
This method is used to update extra member variables at the end of the setParam() method. | |
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 Daton 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). | |
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... |
enum Averagines |
Default constructor.
LmaIsotopeFitter1D | ( | const LmaIsotopeFitter1D & | source | ) |
copy constructor
virtual ~LmaIsotopeFitter1D | ( | ) | [virtual] |
destructor
virtual LmaIsotopeFitter1D& operator= | ( | const LmaIsotopeFitter1D & | source | ) | [virtual] |
assignment operator
static Fitter1D* create | ( | ) | [inline, static] |
create new BiGaussModel object (function needed by Factory)
QualityType fit1d | ( | const RawDataArrayType & | range, | |
InterpolationModel *& | model | |||
) | [virtual] |
void setInitialParameters_ | ( | ) | [protected] |
Compute start parameter.
static Int residual_ | ( | const gsl_vector * | x, | |
void * | params, | |||
gsl_vector * | f | |||
) | [static, protected] |
Evaluation of the target function for nonlinear optimization.
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.
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.
void printState_ | ( | Int | iter, | |
gsl_multifit_fdfsolver * | s | |||
) | [protected, virtual] |
Diplay 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.
void updateMembers_ | ( | ) | [protected, virtual] |
This method is used to update extra member variables at the end of the setParam() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from LevMarqFitter1D.
CoordinateType isotope_stdev_ [protected] |
standard derivation in isotope
CoordinateType total_intensity_ [protected] |
total intensity (area under curve)
CoordinateType monoisotopic_mz_ [protected] |
monoisotopic mass
Int max_isotope_ [protected] |
maximum isotopic rank to be considered
DoubleReal trim_right_cutoff_ [protected] |
cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered
DoubleReal isotope_distance_ [protected] |
distance between consecutive isotopic peaks
CoordinateType mean_ [protected] |
Centroid m/z (as opposed to monoisotopic m/z).
DoubleReal averagine_[AVERAGINE_NUM] [protected] |
number of an atom per Daton of mass
ContainerType isotopes_exact_ [protected] |
relative abundance of i-th isotopic peak
bool monoisotopic_mass_known_ [protected] |
The position of the monoisotopic mass is known(=1) or unknown(=0).
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |