Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

LmaIsotopeFitter1D Class Reference
[FeatureFinder]

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

Inheritance diagram for LmaIsotopeFitter1D:

LevMarqFitter1D Fitter1D FactoryProduct FeatureFinderDefs DefaultParamHandler

List of all members.


Detailed Description

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

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 LmaIsotopeFitter1Doperator= (const LmaIsotopeFitter1D &source)
 assignment operator
QualityType fit1d (const RawDataArrayType &range, InterpolationModel *&model)
 return interpolation model

Static Public Member Functions

static Fitter1Dcreate ()
 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...


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

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

assignment operator

static Fitter1D* create (  )  [inline, static]

create new BiGaussModel object (function needed by Factory)

static const String getProductName (  )  [inline, static]

name of the model (needed by Factory)

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

return interpolation model

Implements Fitter1D.

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.


Member Data Documentation

UInt charge_ [protected]

isotope charge

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).


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1