Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ModelFitter.h>
Public Types | |
enum | { RT = Peak2D::RT, MZ = Peak2D::MZ } |
typedef IndexSet::const_iterator | IndexSetIter |
IndexSet iterator. More... | |
typedef Feature::QualityType | QualityType |
Quality of a feature. More... | |
typedef Feature::CoordinateType | CoordinateType |
Single coordinate. More... | |
typedef Feature::IntensityType | IntensityType |
Single intensity. More... | |
typedef Feature::ChargeType | ChargeType |
Isotope charge. More... | |
typedef FeaFiModule< PeakType, FeatureType > | Base |
FeaFiModule. More... | |
typedef std::vector< PeakType > | RawDataArrayType |
Raw data container type using for the temporary storage of the input data. More... | |
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typedef FeatureMap< FeatureType > | FeatureMapType |
Output feature map type. More... | |
typedef MSExperiment< PeakType > | MapType |
Input map type. More... | |
typedef MapType::SpectrumType | SpectrumType |
Input spectrum type. More... | |
typedef PeakType::IntensityType | IntensityType |
Input intensity type. More... | |
typedef PeakType::CoordinateType | CoordinateType |
Input coordinate type. More... | |
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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 | |
ModelFitter (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff) | |
Constructor. More... | |
virtual | ~ModelFitter () |
Destructor. More... | |
void | setMonoIsotopicMass (CoordinateType mz) |
Sets or fixed the monoisotopic m/z at a specific position. More... | |
Feature | fit (const ChargedIndexSet &index_set) |
Return next feature. More... | |
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FeaFiModule (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff) | |
Constructor. More... | |
virtual | ~FeaFiModule () |
destructor More... | |
IntensityType | getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const |
Returns the intensity of a peak. More... | |
CoordinateType | getPeakMz (const FeatureFinderDefs::IndexPair &index) const |
Returns the m/z of a peak. More... | |
CoordinateType | getPeakRt (const FeatureFinderDefs::IndexPair &index) const |
Returns the retention time of a peak. More... | |
void | getNextMz (FeatureFinderDefs::IndexPair &index) const |
fills index with the index of next peak in m/z dimension More... | |
void | getPrevMz (FeatureFinderDefs::IndexPair &index) const |
fills index with the index of previous peak in m/z dimension More... | |
void | getNextRt (FeatureFinderDefs::IndexPair &index) |
fills index with the index of the nearest peak in the next scan More... | |
void | getPrevRt (FeatureFinderDefs::IndexPair &index) |
fills index with the index of the nearest peak in the previous scan More... | |
void | addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const |
Calculates the convex hull of a index set and adds it to the feature . More... | |
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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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () 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... | |
Protected Member Functions | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
QualityType | fitMZLoop_ (const ChargedIndexSet &set, const ChargeType &charge) |
main fit loop More... | |
QualityType | evaluate_ (const IndexSet &set) const |
evaluate 2d-model More... | |
QualityType | fitRT_ (InterpolationModel *&model) const |
1d fit in RT More... | |
QualityType | fitMZ_ (InterpolationModel *&model, const ChargeType &charge) const |
1d fit in MZ More... | |
void | doProjectionDim_ (const Int dim, const ChargedIndexSet &index_set, RawDataArrayType &set) const |
Project the raw data into 1-dim array. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
ProductModel< 2 > | model2D_ |
2D model More... | |
Math::BasicStatistics | mz_stat_ |
statistics for mz More... | |
Math::AsymmetricStatistics | rt_stat_ |
statistics for rt More... | |
RawDataArrayType | mz_input_data_ |
mz raw data More... | |
RawDataArrayType | rt_input_data_ |
rt raw data More... | |
CoordinateType | tolerance_stdev_box_ |
tolerance used for bounding box More... | |
CoordinateType | monoisotopic_mz_ |
monoistopic mass More... | |
CoordinateType | interpolation_step_mz_ |
interpolation step size (in m/z) More... | |
CoordinateType | interpolation_step_rt_ |
interpolation step size (in retention time) More... | |
Int | max_isotope_ |
maximum isotopic rank to be considered More... | |
CoordinateType | iso_stdev_first_ |
first stdev More... | |
CoordinateType | iso_stdev_last_ |
last stdev More... | |
CoordinateType | iso_stdev_stepsize_ |
step size More... | |
Int | first_mz_model_ |
first mz model (0=Gaussian, 1....n = charge ) More... | |
Int | last_mz_model_ |
last mz model More... | |
CoordinateType | isotope_stdev_ |
isotope stdev More... | |
String | algorithm_ |
algorithm More... | |
Int | max_iteration_ |
Maximum number of iterations. More... | |
CoordinateType | deltaAbsError_ |
Absolute error. More... | |
CoordinateType | deltaRelError_ |
Relative error. More... | |
Math::BasicStatistics | basic_stat_ |
statistics More... | |
QualityType | quality_rt_ |
fit quality in RT dimension More... | |
QualityType | quality_mz_ |
fit quality in MZ dimension More... | |
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const MapType * | map_ |
Input data pointer. More... | |
FeatureMapType * | features_ |
Output data pointer. More... | |
FeatureFinder * | ff_ |
Pointer to the calling FeatureFinder that is used to access the feature flags and report progress. More... | |
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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< String > | subsections_ |
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... | |
Private Member Functions | |
ModelFitter () | |
Not implemented. More... | |
ModelFitter & | operator= (const ModelFitter &) |
Not implemented. More... | |
ModelFitter (const ModelFitter &) | |
Not implemented. More... | |
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 (exponentially modified Gaussian with lma optimized parameters) in retention time.
For the isotope model, we test different charge states and peaks widths.
Name | Type | Default | Restrictions | Description |
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fit_algorithm | string | simple | simple, simplest, wavelet | Fitting algorithm type (internal parameter). |
max_iteration | int | 500 | min: 1 | Maximum number of iterations for fitting with Levenberg-Marquardt algorithm. |
deltaAbsError | float | 0.0001 | min: 0 | Absolute error used by the Levenberg-Marquardt algorithm. |
deltaRelError | float | 0.0001 | min: 0 | Relative error used by the Levenberg-Marquardt algorithm. |
tolerance_stdev_bounding_box | float | 3 | min: 0 | Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data |
intensity_cutoff_factor | float | 0.0500000007450581 | min: 0 max: 1 | Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model |
feature_intensity_sum | int | 1 | min: 0 max: 1 | Determines what is reported as feature intensity. 1: the sum of peak intensities; 0: the maximum intensity of all peaks |
min_num_peaks:final | int | 5 | min: 1 | Minimum number of peaks left after cutoff. If smaller, feature will be discarded. |
min_num_peaks:extended | int | 10 | min: 1 | Minimum number of peaks after extension. If smaller, feature will be discarded. |
rt:interpolation_step | float | 0.200000002980232 | min: 0 | Step size in seconds used to interpolate model for RT. |
mz:interpolation_step | float | 0.0299999993294477 | min: 0.001 | Interpolation step size for m/z. |
mz:model_type:first | int | 1 | min: 0 | Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian). |
mz:model_type:last | int | 4 | min: 0 | Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian). |
quality:type | string | Correlation | Correlation, RankCorrelation | Type of the quality measure used to assess the fit of model vs data. |
quality:minimum | float | 0.649999976158142 | min: 0 max: 1 | Minimum quality of fit, features below this threshold are discarded. |
isotope_model:stdev:first | float | 0.0399999991059303 | min: 0 | First standard deviation to be considered for isotope model. |
isotope_model:stdev:last | float | 0.119999997317791 | min: 0 | Last standard deviation to be considered for isotope model. |
isotope_model:stdev:step | float | 0.0399999991059303 | min: 0 | Step size for standard deviations considered for isotope model. |
isotope_model:averagines:C | float | 0.0444398894906044 | min: 0 | Number of C atoms per Dalton of the mass. |
isotope_model:averagines:H | float | 0.0698157176375389 | min: 0 | Number of H atoms per Dalton of the mass. |
isotope_model:averagines:N | float | 0.0122177302837372 | min: 0 | Number of N atoms per Dalton of the mass. |
isotope_model:averagines:O | float | 0.0132939899340272 | min: 0 | Number of O atoms per Dalton of the mass. |
isotope_model:averagines:S | float | 0.000375250005163252 | min: 0 | Number of S atoms per Dalton of the mass. |
isotope_model:isotope:trim_right_cutoff | float | 0.00100000004749745 | min: 0 | Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered. |
isotope_model:isotope:maximum | int | 100 | min: 1 | Maximum number of isotopes being used for the IsotopeModel. |
isotope_model:isotope:distance | float | 1.00049495697021 | min: 0 | Distance between consecutive isotopic peaks. |
typedef FeaFiModule<PeakType, FeatureType> Base |
typedef Feature::ChargeType ChargeType |
Isotope charge.
typedef Feature::CoordinateType CoordinateType |
Single coordinate.
typedef IndexSet::const_iterator IndexSetIter |
IndexSet iterator.
typedef Feature::IntensityType IntensityType |
Single intensity.
typedef Feature::QualityType QualityType |
Quality of a feature.
typedef std::vector<PeakType> RawDataArrayType |
Raw data container type using for the temporary storage of the input data.
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inline |
Constructor.
References StringList::create(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMaxInt(), Param::setMinFloat(), Param::setMinInt(), DefaultParamHandler::setName(), Param::setSectionDescription(), Param::setValidStrings(), and Param::setValue().
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Destructor.
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private |
Not implemented.
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Not implemented.
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Project the raw data into 1-dim array.
References ModelFitter< PeakType, FeatureType >::algorithm_, FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakMz(), FeaFiModule< PeakType, FeatureType >::getPeakRt(), and ModelFitter< PeakType, FeatureType >::MZ.
Referenced by ModelFitter< PeakType, FeatureType >::fit().
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evaluate 2d-model
References ModelFitter< PeakType, FeatureType >::algorithm_, ProductModel< 2 >::getIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakMz(), Param::getValue(), ModelFitter< PeakType, FeatureType >::model2D_, DefaultParamHandler::param_, OpenMS::Math::pearsonCorrelationCoefficient(), and OpenMS::Math::rankCorrelationCoefficient().
Referenced by ModelFitter< PeakType, FeatureType >::fitMZLoop_().
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Return next feature.
Exception::UnableToFit | is thrown if fitting cannot be performed |
Exception::InvalidParameter | if first and last charge to test do not define a range (first<=last) |
References FeaFiModule< PeakType, FeatureType >::addConvexHull(), IsotopeCluster::ChargedIndexSet::charge, ModelDescription< D >::createModel(), ModelFitter< PeakType, FeatureType >::doProjectionDim_(), Feature::encloses(), FeaFiModule< PeakType, FeatureType >::ff_, ModelFitter< PeakType, FeatureType >::first_mz_model_, ModelFitter< PeakType, FeatureType >::fitMZLoop_(), ModelFitter< PeakType, FeatureType >::fitRT_(), ConvexHull2D::getBoundingBox(), BaseFeature::getCharge(), Feature::getConvexHull(), ProductModel< 2 >::getIntensity(), ProductModel< 2 >::getModel(), Feature::getModelDescription(), Peak2D::getMZ(), DefaultParamHandler::getName(), Feature::getOverallQuality(), FeatureFinder::getPeakFlag(), FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakMz(), FeaFiModule< PeakType, FeatureType >::getPeakRt(), Feature::getQuality(), Peak2D::getRT(), Feature::getSubordinates(), Param::getValue(), BaseModel< D >::isContained(), ModelFitter< PeakType, FeatureType >::last_mz_model_, ModelFitter< PeakType, FeatureType >::model2D_, ModelFitter< PeakType, FeatureType >::MZ, ModelFitter< PeakType, FeatureType >::mz_input_data_, ModelFitter< PeakType, FeatureType >::mz_stat_, DefaultParamHandler::param_, ModelFitter< PeakType, FeatureType >::quality_mz_, ModelFitter< PeakType, FeatureType >::quality_rt_, ModelFitter< PeakType, FeatureType >::RT, ModelFitter< PeakType, FeatureType >::rt_input_data_, ModelFitter< PeakType, FeatureType >::rt_stat_, BaseFeature::setCharge(), BaseModel< D >::setCutOff(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), ProductModel< 2 >::setModel(), Feature::setModelDescription(), Peak2D::setMZ(), Feature::setOverallQuality(), Feature::setQuality(), Peak2D::setRT(), ProductModel< 2 >::setScale(), FeatureFinderDefs::UNUSED, AsymmetricStatistics< Real >::update(), and BasicStatistics< RealT >::update().
Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run().
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1d fit in MZ
References ModelFitter< PeakType, FeatureType >::algorithm_, Factory< FactoryProduct >::create(), ModelFitter< PeakType, FeatureType >::deltaAbsError_, ModelFitter< PeakType, FeatureType >::deltaRelError_, Fitter1D::fit1d(), ModelFitter< PeakType, FeatureType >::interpolation_step_mz_, ModelFitter< PeakType, FeatureType >::isotope_stdev_, ModelFitter< PeakType, FeatureType >::max_isotope_, ModelFitter< PeakType, FeatureType >::max_iteration_, BasicStatistics< RealT >::mean(), ModelFitter< PeakType, FeatureType >::monoisotopic_mz_, ModelFitter< PeakType, FeatureType >::mz_input_data_, ModelFitter< PeakType, FeatureType >::mz_stat_, DefaultParamHandler::setParameters(), Param::setValue(), ModelFitter< PeakType, FeatureType >::tolerance_stdev_box_, and BasicStatistics< RealT >::variance().
Referenced by ModelFitter< PeakType, FeatureType >::fitMZLoop_().
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main fit loop
References ModelFitter< PeakType, FeatureType >::evaluate_(), ModelFitter< PeakType, FeatureType >::fitMZ_(), ModelFitter< PeakType, FeatureType >::iso_stdev_first_, ModelFitter< PeakType, FeatureType >::iso_stdev_last_, ModelFitter< PeakType, FeatureType >::iso_stdev_stepsize_, ModelFitter< PeakType, FeatureType >::isotope_stdev_, ModelFitter< PeakType, FeatureType >::model2D_, ModelFitter< PeakType, FeatureType >::MZ, ModelFitter< PeakType, FeatureType >::quality_mz_, and ProductModel< 2 >::setModel().
Referenced by ModelFitter< PeakType, FeatureType >::fit().
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1d fit in RT
References ModelFitter< PeakType, FeatureType >::algorithm_, Factory< FactoryProduct >::create(), ModelFitter< PeakType, FeatureType >::deltaAbsError_, ModelFitter< PeakType, FeatureType >::deltaRelError_, Fitter1D::fit1d(), ModelFitter< PeakType, FeatureType >::interpolation_step_rt_, ModelFitter< PeakType, FeatureType >::max_iteration_, BasicStatistics< RealT >::mean(), ModelFitter< PeakType, FeatureType >::rt_input_data_, ModelFitter< PeakType, FeatureType >::rt_stat_, DefaultParamHandler::setParameters(), Param::setValue(), ModelFitter< PeakType, FeatureType >::tolerance_stdev_box_, BasicStatistics< RealT >::variance(), AsymmetricStatistics< Real >::variance1(), and AsymmetricStatistics< Real >::variance2().
Referenced by ModelFitter< PeakType, FeatureType >::fit().
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Not implemented.
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Sets or fixed the monoisotopic m/z at a specific position.
mz | The monoisotopic m/z that occurres in the current data set. |
References ModelFitter< PeakType, FeatureType >::monoisotopic_mz_.
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inlineprotectedvirtual |
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 DefaultParamHandler.
References ModelFitter< PeakType, FeatureType >::algorithm_, ModelFitter< PeakType, FeatureType >::deltaAbsError_, ModelFitter< PeakType, FeatureType >::deltaRelError_, ModelFitter< PeakType, FeatureType >::first_mz_model_, Param::getValue(), ModelFitter< PeakType, FeatureType >::interpolation_step_mz_, ModelFitter< PeakType, FeatureType >::interpolation_step_rt_, ModelFitter< PeakType, FeatureType >::iso_stdev_first_, ModelFitter< PeakType, FeatureType >::iso_stdev_last_, ModelFitter< PeakType, FeatureType >::iso_stdev_stepsize_, ModelFitter< PeakType, FeatureType >::last_mz_model_, ModelFitter< PeakType, FeatureType >::max_isotope_, ModelFitter< PeakType, FeatureType >::max_iteration_, DefaultParamHandler::param_, and ModelFitter< PeakType, FeatureType >::tolerance_stdev_box_.
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statistics
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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
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), ModelFitter< PeakType, FeatureType >::fitRT_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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Relative error.
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), ModelFitter< PeakType, FeatureType >::fitRT_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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first mz model (0=Gaussian, 1....n = charge )
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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interpolation step size (in m/z)
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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interpolation step size (in retention time)
Referenced by ModelFitter< PeakType, FeatureType >::fitRT_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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first stdev
Referenced by ModelFitter< PeakType, FeatureType >::fitMZLoop_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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last stdev
Referenced by ModelFitter< PeakType, FeatureType >::fitMZLoop_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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step size
Referenced by ModelFitter< PeakType, FeatureType >::fitMZLoop_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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isotope stdev
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), and ModelFitter< PeakType, FeatureType >::fitMZLoop_().
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last mz model
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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maximum isotopic rank to be considered
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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Maximum number of iterations.
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), ModelFitter< PeakType, FeatureType >::fitRT_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
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monoistopic mass
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), and ModelFitter< PeakType, FeatureType >::setMonoIsotopicMass().
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mz raw data
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::fitMZ_().
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statistics for mz
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::fitMZ_().
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fit quality in MZ dimension
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::fitMZLoop_().
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fit quality in RT dimension
Referenced by ModelFitter< PeakType, FeatureType >::fit().
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rt raw data
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::fitRT_().
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statistics for rt
Referenced by ModelFitter< PeakType, FeatureType >::fit(), and ModelFitter< PeakType, FeatureType >::fitRT_().
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tolerance used for bounding box
Referenced by ModelFitter< PeakType, FeatureType >::fitMZ_(), ModelFitter< PeakType, FeatureType >::fitRT_(), and ModelFitter< PeakType, FeatureType >::updateMembers_().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |