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LmaIsotopeFitter1D Class Reference

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:
LevMarqFitter1D Fitter1D DefaultParamHandler FeatureFinderDefs

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 Types inherited from LevMarqFitter1D
typedef std::vector< doubleContainerType
 
- Public Types inherited from Fitter1D
typedef IsotopeCluster::IndexSet IndexSet
 IndexSet. More...
 
typedef
IsotopeCluster::ChargedIndexSet 
ChargedIndexSet
 IndexSet with charge information. More...
 
typedef Feature::CoordinateType CoordinateType
 Single coordinate. More...
 
typedef Feature::QualityType QualityType
 Quality of a feature. More...
 
typedef Peak1D PeakType
 Raw data point type. More...
 
typedef std::vector< PeakTypeRawDataArrayType
 Raw data container type using for the temporary storage of the input data. More...
 
typedef RawDataArrayType::iterator PeakIterator
 Raw data iterator. More...
 
- Public Types inherited from FeatureFinderDefs
enum  Flag { UNUSED, USED }
 Flags that indicate if a peak is already used in a feature. More...
 
typedef IsotopeCluster::IndexPair IndexPair
 Index to peak consisting of two UInts (scan index / peak index) More...
 
typedef
IsotopeCluster::ChargedIndexSet 
ChargedIndexSet
 Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
 
typedef IsotopeCluster::IndexSet IndexSet
 A set of peak indices. More...
 

Public Member Functions

 LmaIsotopeFitter1D ()
 Default constructor. More...
 
 LmaIsotopeFitter1D (const LmaIsotopeFitter1D &source)
 copy constructor More...
 
virtual ~LmaIsotopeFitter1D ()
 destructor More...
 
virtual LmaIsotopeFitter1Doperator= (const LmaIsotopeFitter1D &source)
 assignment operator More...
 
QualityType fit1d (const RawDataArrayType &range, InterpolationModel *&model)
 return interpolation model More...
 
- Public Member Functions inherited from LevMarqFitter1D
 LevMarqFitter1D ()
 Default constructor. More...
 
 LevMarqFitter1D (const LevMarqFitter1D &source)
 copy constructor More...
 
virtual ~LevMarqFitter1D ()
 destructor More...
 
virtual LevMarqFitter1Doperator= (const LevMarqFitter1D &source)
 assignment operator More...
 
- Public Member Functions inherited from Fitter1D
 Fitter1D ()
 Default constructor. More...
 
 Fitter1D (const Fitter1D &source)
 copy constructor More...
 
virtual ~Fitter1D ()
 destructor More...
 
virtual Fitter1Doperator= (const Fitter1D &source)
 assignment operator More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Static Public Member Functions

static Fitter1Dcreate ()
 create new LmaIsotopeFitter1D object (function needed by Factory) More...
 
static const String getProductName ()
 name of the model (needed by Factory) More...
 
- Static Public Member Functions inherited from Fitter1D
static void registerChildren ()
 register all derived classes here More...
 

Protected Member Functions

void setInitialParameters_ ()
 Compute start parameter. More...
 
void printState_ (Int iter, gsl_multifit_fdfsolver *s)
 
void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from LevMarqFitter1D
const String getGslStatus_ ()
 Return GSL status as string. More...
 
void optimize_ (const RawDataArrayType &set, Int num_params, CoordinateType x_init[], Int(*residual)(const gsl_vector *x, void *params, gsl_vector *f), Int(*jacobian)(const gsl_vector *x, void *params, gsl_matrix *J), Int(*evaluate)(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J), void *advanced_params)
 Optimize start parameter. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Static Protected Member Functions

static Int residual_ (const gsl_vector *x, void *params, gsl_vector *f)
 Evaluation of the target function for nonlinear optimization. More...
 
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. More...
 
static Int evaluate_ (const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
 Driver function for the evaluation of function and jacobian. More...
 

Protected Attributes

UInt charge_
 isotope charge More...
 
CoordinateType isotope_stdev_
 standard derivation in isotope More...
 
CoordinateType total_intensity_
 total intensity (area under curve) More...
 
CoordinateType monoisotopic_mz_
 monoisotopic mass More...
 
Int max_isotope_
 maximum isotopic rank to be considered More...
 
DoubleReal trim_right_cutoff_
 cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered More...
 
DoubleReal isotope_distance_
 distance between consecutive isotopic peaks More...
 
CoordinateType mean_
 Centroid m/z (as opposed to monoisotopic m/z) More...
 
DoubleReal averagine_ [AVERAGINE_NUM]
 number of an atom per Dalton of mass More...
 
ContainerType isotopes_exact_
 relative abundance of i-th isotopic peak More...
 
bool monoisotopic_mass_known_
 The position of the monoisotopic mass is known(=1) or unknown(=0). More...
 
- Protected Attributes inherited from LevMarqFitter1D
Int gsl_status_
 GSL status. More...
 
bool symmetric_
 Parameter indicates symmetric peaks. More...
 
Int max_iteration_
 Maximum number of iterations. More...
 
CoordinateType abs_error_
 Absolute error. More...
 
CoordinateType rel_error_
 Relative error. More...
 
- Protected Attributes inherited from Fitter1D
CoordinateType tolerance_stdev_box_
 standard derivation in bounding box More...
 
CoordinateType min_
 minimum of the bounding box More...
 
CoordinateType max_
 maximum of the bounding box More...
 
CoordinateType stdev1_
 standard derivation More...
 
CoordinateType stdev2_
 standard derivation More...
 
Math::BasicStatistics statistics_
 basic statistics More...
 
CoordinateType interpolation_step_
 interpolation step size More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

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

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
interpolation_step float0.1  Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box float3  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 int500  Maximum number of iterations using by Levenberg-Marquardt algorithm.
deltaAbsError float0.0001  Absolute error used by the Levenberg-Marquardt algorithm.
deltaRelError float0.0001  Relative error used by the Levenberg-Marquardt algorithm.
charge int1  Charge state of the model.
total_intensity float100  Total intensity under the curve in mz dimension.
monoisotopic_mass float0  Monoisotopic mz of the model.
statistics:mean float0  Centroid m/z (as opposed to monoisotopic m/z).
statistics:variance float1  Variance of the model.
averagines:C float0.0444398894906044  Number of C atoms per Dalton of mass.
averagines:H float0.0698157176375389  Number of H atoms per Dalton of mass.
averagines:N float0.0122177302837372  Number of N atoms per Dalton of mass.
averagines:O float0.0132939899340272  Number of O atoms per Dalton of mass.
averagines:S float0.000375250005163252  Number of S atoms per Dalton of mass.
isotope:trim_right_cutoff float0.001  Cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered.
isotope:maximum int100  Maximum isotopic rank to be considered.
isotope:distance float1.000495  Distance between consecutive isotopic peaks.
isotope:stdev float0.1  Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.

Note:

Member Enumeration Documentation

enum Averagines
Enumerator
C 
H 
N 
O 
S 
AVERAGINE_NUM 

Constructor & Destructor Documentation

Default constructor.

copy constructor

virtual ~LmaIsotopeFitter1D ( )
virtual

destructor

Member Function Documentation

static Fitter1D* create ( )
inlinestatic

create new LmaIsotopeFitter1D object (function needed by Factory)

static Int evaluate_ ( const gsl_vector *  x,
void *  params,
gsl_vector *  f,
gsl_matrix *  J 
)
staticprotected

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 ( )
inlinestatic

name of the model (needed by Factory)

static Int jacobian_ ( const gsl_vector *  x,
void *  params,
gsl_matrix *  J 
)
staticprotected

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 
)
protectedvirtual

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.

static Int residual_ ( const gsl_vector *  x,
void *  params,
gsl_vector *  f 
)
staticprotected

Evaluation of the target function for nonlinear optimization.

void setInitialParameters_ ( )
protected

Compute start parameter.

void updateMembers_ ( )
protectedvirtual

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 LevMarqFitter1D.

Member Data Documentation

DoubleReal averagine_[AVERAGINE_NUM]
protected

number of an atom per Dalton of mass

UInt charge_
protected

isotope charge

DoubleReal isotope_distance_
protected

distance between consecutive isotopic peaks

CoordinateType isotope_stdev_
protected

standard derivation in isotope

ContainerType isotopes_exact_
protected

relative abundance of i-th isotopic peak

Int max_isotope_
protected

maximum isotopic rank to be considered

CoordinateType mean_
protected

Centroid m/z (as opposed to monoisotopic m/z)

bool monoisotopic_mass_known_
protected

The position of the monoisotopic mass is known(=1) or unknown(=0).

CoordinateType monoisotopic_mz_
protected

monoisotopic mass

CoordinateType total_intensity_
protected

total intensity (area under curve)

DoubleReal trim_right_cutoff_
protected

cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5