#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ModelFitter.h>
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. | |
ModelFitter & | operator= (const ModelFitter &) |
Not implemented. | |
ModelFitter (const ModelFitter &) | |
Not implemented. |
typedef IndexSet::const_iterator IndexSetIter |
IndexSet iterator.
typedef Feature::QualityType QualityType |
Quality of a feature.
typedef Feature::IntensityType IntensityType |
typedef Feature::ChargeType ChargeType |
Isotope charge.
typedef FeaFiModule<PeakType,FeatureType> Base |
typedef RawDataPoint1D RawDataPointType |
Raw data point type.
typedef DPeakArray<RawDataPointType > RawDataArrayType |
Raw data container type using for the temporary storage of the input data.
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.
void setMonoIsotopicMass | ( | CoordinateType | mz | ) | [inline] |
Sets or fixed the monoisotopic m/z at a specific position.
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.
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
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
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |