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ModelFitter Class Template Reference
[FeatureFinder]

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

Inheritance diagram for ModelFitter:

FeaFiModule FeatureFinderDefs DefaultParamHandler

List of all members.


Detailed Description

template<class PeakType, class FeatureType>
class OpenMS::ModelFitter< PeakType, FeatureType >

Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model.

The ModelFitter class uses a gaussian or isotope model in m/z and bigauss, lmagauss (bigauss with Levenberg-Marquardt) or emg (exponent. modified Gaussian with lma aproximized arameters) in retention time.

For the isotope model, we test different charge states and peaks widths.

ModelFitter Parameters are explained on a separate page.

Public Types

enum  { RT = RawDataPoint2D::RT, MZ = RawDataPoint2D::MZ }
typedef IndexSet::const_iterator IndexSetIter
 IndexSet iterator.
typedef Feature::QualityType QualityType
 Quality of a feature.
typedef Feature::CoordinateType CoordinateType
 Single coordinate.
typedef Feature::IntensityType IntensityType
 Single intensity.
typedef Feature::ChargeType ChargeType
 Isotope charge.
typedef FeaFiModule< PeakType,
FeatureType > 
Base
 FeaFiModule.
typedef RawDataPoint1D RawDataPointType
 Raw data point type.
typedef DPeakArray
< RawDataPointType
RawDataArrayType
 Raw data container type using for the temporary storage of the input data.

Public Member Functions

 ModelFitter (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)
 Constructor.
virtual ~ModelFitter ()
 Destructor.
void setMonoIsotopicMass (CoordinateType mz)
 Sets or fixed the monoisotopic m/z at a specific position.
Feature fit (const ChargedIndexSet &index_set) throw (UnableToFit)
 Return next feature.

Protected Member Functions

virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParam() method.
QualityType fitLoop_ (const ChargedIndexSet &set, Int &first_mz, Int &last_mz, ProductModel< 2 > *&final)
 main fit loop
QualityType evaluate_ (const IndexSet &set, ProductModel< 2 > *&final, String algorithm)
 evaluate 2d-model
QualityType fitDim_ (Int dim, String algorithm)
 1d fit
CoordinateType doProjectionDim_ (const ChargedIndexSet &index_set, RawDataArrayType &set, Int dim, String algorithm)
 copy the raw data into 1-dim. DPeakArray

Protected Attributes

ProductModel< 2 > model2D_
 2D model
Math::BasicStatistics mz_stat_
 statistics for mz
Math::AsymmetricStatistics rt_stat_
 statistics for rt
RawDataArrayType mz_input_data_
 mz raw data
RawDataArrayType rt_input_data_
 rt raw data
CoordinateType tolerance_stdev_box_
 tolerance used for bounding box
CoordinateType monoisotopic_mz_
 monoistopic mass
UInt counter_
 counts features (used for debug output only)
CoordinateType interpolation_step_mz_
 interpolation step size (in m/z)
CoordinateType interpolation_step_rt_
 interpolation step size (in retention time)
Int max_isotope_
 maximum isotopic rank to be considered
CoordinateType iso_stdev_first_
 first stdev
CoordinateType iso_stdev_last_
 last stdev
CoordinateType iso_stdev_stepsize_
 step size
Int first_mz_model_
 first mz model (0=Gaussian, 1....n = charge )
Int last_mz_model_
 last mz model
ChargeType charge_
 isotope charge
CoordinateType isotope_stdev_
 isotope stdev
String algorithm_
 algorithm
Int max_iteration_
 Maximum number of iterations.
CoordinateType deltaAbsError_
 Absolute error.
CoordinateType deltaRelError_
 Relative error.
Math::BasicStatistics basic_stat_
 statistics
CoordinateType total_intensity_mz_
 area under mz curve

Private Member Functions

 ModelFitter ()
 Not implemented.
ModelFitteroperator= (const ModelFitter &)
 Not implemented.
 ModelFitter (const ModelFitter &)
 Not implemented.


Member Typedef Documentation

typedef IndexSet::const_iterator IndexSetIter

IndexSet iterator.

typedef Feature::QualityType QualityType

Quality of a feature.

typedef Feature::CoordinateType CoordinateType

Single coordinate.

Reimplemented from FeaFiModule.

typedef Feature::IntensityType IntensityType

Single intensity.

Reimplemented from FeaFiModule.

typedef Feature::ChargeType ChargeType

Isotope charge.

typedef FeaFiModule<PeakType,FeatureType> Base

FeaFiModule.

typedef RawDataPoint1D RawDataPointType

Raw data point type.

typedef DPeakArray<RawDataPointType > RawDataArrayType

Raw data container type using for the temporary storage of the input data.


Member Enumeration Documentation

anonymous enum

Enumerator:
RT 
MZ 


Constructor & Destructor Documentation

ModelFitter ( const MSExperiment< PeakType > *  map,
FeatureMap< FeatureType > *  features,
FeatureFinder ff 
) [inline]

Constructor.

virtual ~ModelFitter (  )  [inline, virtual]

Destructor.

ModelFitter (  )  [private]

Not implemented.

ModelFitter ( const ModelFitter< PeakType, FeatureType > &   )  [private]

Not implemented.


Member Function Documentation

void setMonoIsotopicMass ( CoordinateType  mz  )  [inline]

Sets or fixed the monoisotopic m/z at a specific position.

Parameters:
mz The monoisotopic m/z that occures in the current data set.

Feature fit ( const ChargedIndexSet index_set  )  throw (UnableToFit) [inline]

Return next feature.

virtual void updateMembers_ (  )  [inline, 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 DefaultParamHandler.

QualityType fitLoop_ ( const ChargedIndexSet set,
Int first_mz,
Int last_mz,
ProductModel< 2 > *&  final 
) [inline, protected]

main fit loop

QualityType evaluate_ ( const IndexSet set,
ProductModel< 2 > *&  final,
String  algorithm 
) [inline, protected]

evaluate 2d-model

QualityType fitDim_ ( Int  dim,
String  algorithm 
) [inline, protected]

1d fit

CoordinateType doProjectionDim_ ( const ChargedIndexSet index_set,
RawDataArrayType set,
Int  dim,
String  algorithm 
) [inline, protected]

copy the raw data into 1-dim. DPeakArray

ModelFitter& operator= ( const ModelFitter< PeakType, FeatureType > &   )  [private]

Not implemented.


Member Data Documentation

ProductModel<2> model2D_ [protected]

2D model

Math::BasicStatistics mz_stat_ [protected]

statistics for mz

Math::AsymmetricStatistics rt_stat_ [protected]

statistics for rt

RawDataArrayType mz_input_data_ [protected]

mz raw data

RawDataArrayType rt_input_data_ [protected]

rt raw data

CoordinateType tolerance_stdev_box_ [protected]

tolerance used for bounding box

CoordinateType monoisotopic_mz_ [protected]

monoistopic mass

UInt counter_ [protected]

counts features (used for debug output only)

CoordinateType interpolation_step_mz_ [protected]

interpolation step size (in m/z)

CoordinateType interpolation_step_rt_ [protected]

interpolation step size (in retention time)

Int max_isotope_ [protected]

maximum isotopic rank to be considered

CoordinateType iso_stdev_first_ [protected]

first stdev

CoordinateType iso_stdev_last_ [protected]

last stdev

CoordinateType iso_stdev_stepsize_ [protected]

step size

Int first_mz_model_ [protected]

first mz model (0=Gaussian, 1....n = charge )

Int last_mz_model_ [protected]

last mz model

ChargeType charge_ [protected]

isotope charge

CoordinateType isotope_stdev_ [protected]

isotope stdev

String algorithm_ [protected]

algorithm

Int max_iteration_ [protected]

Maximum number of iterations.

CoordinateType deltaAbsError_ [protected]

Absolute error.

Test for the convergence of the sequence by comparing the last iteration step dx with the absolute error epsabs and relative error epsrel to the current position x

CoordinateType deltaRelError_ [protected]

Relative error.

Math::BasicStatistics basic_stat_ [protected]

statistics

CoordinateType total_intensity_mz_ [protected]

area under mz curve


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