FeatureFinderAlgorithm for picked peaks. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h>
Public Types | |
Type definitions | |
typedef FeatureFinderAlgorithm < PeakType, FeatureType > ::MapType | MapType |
typedef FeatureFinderAlgorithm < PeakType, FeatureType > ::FeatureMapType | FeatureMapType |
typedef MapType::SpectrumType | SpectrumType |
typedef SpectrumType::FloatDataArrays | FloatDataArrays |
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typedef MSExperiment< PeakType > | MapType |
Input map type. More... | |
typedef MapType::CoordinateType | CoordinateType |
Coordinate/Position type of peaks. More... | |
typedef MapType::IntensityType | IntensityType |
Intensity type of peaks. More... | |
typedef FeatureMap< FeatureType > | FeatureMapType |
Output feature 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 | |
FeatureFinderAlgorithmPicked () | |
default constructor More... | |
virtual void | setSeeds (const FeatureMapType &seeds) |
Sets a reference to the calling FeatureFinder. More... | |
virtual void | run () |
Main method for actual FeatureFinder. More... | |
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FeatureFinderAlgorithm () | |
default constructor More... | |
virtual | ~FeatureFinderAlgorithm () |
destructor More... | |
virtual Param | getDefaultParameters () const |
Returns the default parameters. Reimplment. More... | |
void | setData (const MapType &map, FeatureMapType &features, FeatureFinder &ff) |
Sets a reference to the calling FeatureFinder. 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... | |
Static Public Member Functions | |
static FeatureFinderAlgorithm < PeakType, FeatureType > * | create () |
static const String | getProductName () |
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static void | registerChildren () |
register all derived classes here (see FeatureFinderAlgorithm_impl.h) More... | |
Protected Member Functions | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | abort_ (const Seed &seed, const String &reason) |
Writes the abort reason to the log file and counts occurrences for each reason. More... | |
DoubleReal | intersection_ (const Feature &f1, const Feature &f2) const |
const TheoreticalIsotopePattern & | getIsotopeDistribution_ (DoubleReal mass) const |
Returns the isotope distribution for a certain mass window. More... | |
DoubleReal | findBestIsotopeFit_ (const Seed ¢er, UInt charge, IsotopePattern &best_pattern) const |
Finds the best fitting position of the isotopic pattern estimate defined by center . More... | |
void | extendMassTraces_ (const IsotopePattern &pattern, MassTraces &traces, Size meta_index_overall) const |
void | extendMassTrace_ (MassTrace &trace, SignedSize spectrum_index, DoubleReal mz, bool increase_rt, Size meta_index_overall, DoubleReal min_rt=0.0, DoubleReal max_rt=0.0) const |
Extends a single mass trace in one RT direction. More... | |
template<typename SpectrumType > | |
Size | nearest_ (DoubleReal pos, const SpectrumType &spec, Size start) const |
Returns the index of the peak nearest to m/z pos in spectrum spec (linear search starting from index start ) More... | |
void | findIsotope_ (DoubleReal pos, Size spectrum_index, IsotopePattern &pattern, Size pattern_index, Size &peak_index) const |
Searches for an isotopic peak in the current spectrum and the adjacent spectra. More... | |
DoubleReal | positionScore_ (DoubleReal pos1, DoubleReal pos2, DoubleReal allowed_deviation) const |
Calculates a score between 0 and 1 for the m/z deviation of two peaks. More... | |
DoubleReal | isotopeScore_ (const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances) const |
Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern. More... | |
DoubleReal | intensityScore_ (Size spectrum, Size peak) const |
Compute the intensity score for the peak peak in spectrum spectrum . More... | |
TraceFitter< PeakType > * | chooseTraceFitter_ (double &tau) |
Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto) More... | |
DoubleReal | intensityScore_ (Size rt_bin, Size mz_bin, DoubleReal intensity) const |
Handling of fitted mass traces | |
Methods to handle the results of the mass trace fitting process. | |
void | cropFeature_ (TraceFitter< PeakType > *fitter, const MassTraces &traces, MassTraces &new_traces) |
Creates new mass traces new_traces based on the fitting result and the original traces traces . More... | |
bool | checkFeatureQuality_ (TraceFitter< PeakType > *fitter, MassTraces &feature_traces, const DoubleReal &seed_mz, const DoubleReal &min_feature_score, String &error_msg, DoubleReal &fit_score, DoubleReal &correlation, DoubleReal &final_score) |
Checks the feature based on different score thresholds and model constraints. More... | |
void | writeFeatureDebugInfo_ (TraceFitter< PeakType > *fitter, const MassTraces &traces, const MassTraces &new_traces, bool feature_ok, const String error_msg, const DoubleReal final_score, const Int plot_nr, const PeakType &peak, const String path="debug/features/") |
Creates several files containing plots and viewable data of the fitted mass trace. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
MapType | map_ |
editable copy of the map More... | |
std::ofstream | log_ |
Output stream for log/debug info. More... | |
bool | debug_ |
debug flag More... | |
std::map< String, UInt > | aborts_ |
Array of abort reasons. More... | |
std::map< Seed, String > | abort_reasons_ |
Array of abort reasons. More... | |
FeatureMapType | seeds_ |
User-specified seed list. More... | |
std::vector < TheoreticalIsotopePattern > | isotope_distributions_ |
Vector of precalculated isotope distributions for several mass windows. More... | |
Members for parameters often needed in methods | |
DoubleReal | pattern_tolerance_ |
Stores mass_trace:mz_tolerance. More... | |
DoubleReal | trace_tolerance_ |
Stores isotopic_pattern:mz_tolerance. More... | |
UInt | min_spectra_ |
Number of spectra that have to show the same mass (for finding a mass trace) More... | |
UInt | max_missing_trace_peaks_ |
Stores mass_trace:max_missing. More... | |
DoubleReal | slope_bound_ |
Max slope of mass trace intensities. More... | |
DoubleReal | intensity_percentage_ |
Isotope pattern intensity contribution of required peaks. More... | |
DoubleReal | intensity_percentage_optional_ |
Isotope pattern intensity contribution of optional peaks. More... | |
DoubleReal | optional_fit_improvement_ |
Minimal imrovment for leaving out optional isotope. More... | |
DoubleReal | mass_window_width_ |
Width of the isotope pattern mass bins. More... | |
UInt | intensity_bins_ |
Number of bins (in RT and MZ) for intensity significance estimation. More... | |
DoubleReal | min_isotope_fit_ |
Mimimum isotope pattern fit for a feature. More... | |
DoubleReal | min_trace_score_ |
Minimum quality of a traces. More... | |
DoubleReal | min_rt_span_ |
Minimum RT range that has to be left after the fit. More... | |
DoubleReal | max_rt_span_ |
Maximum RT range the model is allowed to span. More... | |
DoubleReal | max_feature_intersection_ |
Maximum allowed feature intersection (if larger, that one of the feature is removed) More... | |
String | reported_mz_ |
The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model. More... | |
Members for intensity significance estimation | |
DoubleReal | intensity_rt_step_ |
RT bin width. More... | |
DoubleReal | intensity_mz_step_ |
m/z bin width More... | |
std::vector< std::vector < std::vector< DoubleReal > > > | intensity_thresholds_ |
Precalculated intensity 20-quantiles (binned) 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. 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 | |
FeatureFinderAlgorithmPicked & | operator= (const FeatureFinderAlgorithmPicked &) |
Not implemented. More... | |
FeatureFinderAlgorithmPicked (const FeatureFinderAlgorithmPicked &) | |
Not implemented. More... | |
FeatureFinderAlgorithm for picked peaks.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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debug | string | false | true, false | When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode). |
intensity:bins | int | 10 | min: 1 | Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is. This parameter should be decreased, if the algorithm is used on small regions of a map. |
mass_trace:mz_tolerance | float | 0.03 | min: 0 | Tolerated m/z deviation of peaks belonging to the same mass trace. It should be larger than the m/z resolution of the instument. This value must be smaller than that 1/charge_high! |
mass_trace:min_spectra | int | 10 | min: 1 | Number of spectra that have to show a similar peak mass in a mass trace. |
mass_trace:max_missing | int | 1 | min: 0 | Number of consecutive spectra where a high mass deviation or missing peak is acceptable. This parameter should be well below 'min_spectra'! |
mass_trace:slope_bound | float | 0.1 | min: 0 | The maximum slope of mass trace intensities when extending from the highest peak. This parameter is important to seperate overlapping elution peaks. It should be increased if feature elution profiles fluctuate a lot. |
isotopic_pattern:charge_low | int | 1 | min: 1 | Lowest charge to search for. |
isotopic_pattern:charge_high | int | 4 | min: 1 | Highest charge to search for. |
isotopic_pattern:mz_tolerance | float | 0.03 | min: 0 | Tolerated m/z deviation from the theoretical isotopic pattern. It should be larger than the m/z resolution of the instument. This value must be smaller than that 1/charge_high! |
isotopic_pattern:intensity_percentage | float | 10 | min: 0 max: 100 | Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present. |
isotopic_pattern:intensity_percentage_optional | float | 0.1 | min: 0 max: 100 | Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing. |
isotopic_pattern:optional_fit_improvement | float | 2 | min: 0 max: 100 | Minimal percental improvement of isotope fit to allow leaving out an optional peak. |
isotopic_pattern:mass_window_width | float | 25 | min: 1 max: 200 | Window width in Dalton for precalculation of estimated isotope distributions. |
isotopic_pattern:abundance_12C | float | 98.93 | min: 0 max: 100 | Rel. abundance of the light carbon. Modify if labeled. |
isotopic_pattern:abundance_14N | float | 99.632 | min: 0 max: 100 | Rel. abundance of the light nitrogen. Modify if labeled. |
seed:min_score | float | 0.8 | min: 0 max: 1 | Minimum seed score a peak has to reach to be used as seed. The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score. |
fit:epsilon_abs | float | 0.0001 | min: 0 | Absolute epsilon used for convergence of the fit. |
fit:epsilon_rel | float | 0.0001 | min: 0 | Relative epsilon used for convergence of the fit. |
fit:max_iterations | int | 500 | min: 1 | Maximum number of iterations of the fit. |
feature:min_score | float | 0.7 | min: 0 max: 1 | Feature score threshold for a feature to be reported. The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks. |
feature:min_isotope_fit | float | 0.8 | min: 0 max: 1 | Minimum isotope fit of the feature before model fitting. |
feature:min_trace_score | float | 0.5 | min: 0 max: 1 | Trace score threshold. Traces below this threshold are removed after the model fitting. This parameter is important for features that overlap in m/z dimension. |
feature:min_rt_span | float | 0.333 | min: 0 max: 1 | Minimum RT span in relation to extended area that has to remain after model fitting. |
feature:max_rt_span | float | 2.5 | min: 0.5 | Maximum RT span in relation to extended area that the model is allowed to have. |
feature:rt_shape | string | symmetric | symmetric, asymmetric | Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used. |
feature:max_intersection | float | 0.35 | min: 0 max: 1 | Maximum allowed intersection of features. |
feature:reported_mz | string | monoisotopic | maximum, average, monoisotopic | The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model. |
user-seed:rt_tolerance | float | 5 | min: 0 | Allowed RT deviation of seeds from the user-specified seed position. |
user-seed:mz_tolerance | float | 1.1 | min: 0 | Allowed m/z deviation of seeds from the user-specified seed position. |
user-seed:min_score | float | 0.5 | min: 0 max: 1 | Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case. |
debug:pseudo_rt_shift | float | 500 | min: 1 | Pseudo RT shift used when . |
RT model with tailing/fronting (Marc)
More general MZ model - e.g. based on co-elution or with sulfur-averagines (Marc)
Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)
Implement user-specified seed lists support (Marc)
typedef FeatureFinderAlgorithm<PeakType, FeatureType>::FeatureMapType FeatureMapType |
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typedef FeatureFinderAlgorithm<PeakType, FeatureType>::MapType MapType |
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typedef MapType::SpectrumType SpectrumType |
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inline |
default constructor
References StringList::create(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMinFloat(), Param::setMinInt(), Param::setSectionDescription(), Param::setValidStrings(), and Param::setValue().
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::create().
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private |
Not implemented.
Writes the abort reason to the log file and counts occurrences for each reason.
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_reasons_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::aborts_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Checks the feature based on different score thresholds and model constraints.
Feature can get invalid for following reasons:
fitter | The TraceFitter containing the results from the rt profile fitting step. |
feature_traces | Cropped feature mass traces. |
seed_mz | Mz of the seed |
min_feature_score | Minimal required feature score |
error_msg | Will be filled with the error message, if the feature is invalid |
fit_score | Will be filled with the fit score |
correlation | Will be filled with correlation between feature and model |
final_score | Will be filled with the final score |
References FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline, TraceFitter< PeakType >::checkMaximalRTSpan(), TraceFitter< PeakType >::checkMinimalRTSpan(), TraceFitter< PeakType >::computeTheoretical(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, TraceFitter< PeakType >::getCenter(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getPeakCount(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getRTBounds(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::isValid(), OpenMS::Constants::k, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_rt_span_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_rt_span_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, OpenMS::Math::pearsonCorrelationCoefficient(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto)
References Param::getValue(), LOG_DEBUG, and DefaultParamHandler::param_.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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inlinestatic |
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Creates new mass traces new_traces
based on the fitting result and the original traces traces
.
fitter | The TraceFitter containing the results from the rt profile fitting step. |
traces | Original mass traces found in the experiment. |
new_traces | Mass traces created by cropping the original mass traces. |
References FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline, TraceFitter< PeakType >::computeTheoretical(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, TraceFitter< PeakType >::getLowerRTBound(), TraceFitter< PeakType >::getUpperRTBound(), FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::isValid(), OpenMS::Constants::k, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_trace_score_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, OpenMS::Math::pearsonCorrelationCoefficient(), and FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::theoretical_int.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Extends a single mass trace in one RT direction.
How to use this method:
trace
increase_rt
whether to extend in downstream or upstream directiontrace | The trace that should be extended |
spectrum_index | The index of the spectrum from which on the mass trace should be extended |
mz | The mz location (center) of the trace |
increase_rt | Indicator whether the extension is done in forward or backward direction (with respect to the current spectrum) |
meta_index_overall | The index of the overall score |
min_rt | The rt minimum up to which the trace will be extended. |
max_rt | The rt maximum up to which the trace will be extended. |
min_rt
or max_rt
are set to 0.0 no boundary is assumed in the respective direction. References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_(), MSExperiment< PeakT, ChromatogramPeakT >::size(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::slope_bound_, and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_().
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Extends all mass traces of an isotope pattern in one step
pattern | The IsotopePattern that should be extended. |
traces | The MassTraces datastructure where the extended mass traces will be stored in. |
meta_index_overall | The index of the data array where the qualtiy scores for the given charge are stored. |
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), Peak2D::getIntensity(), Peak2D::getMZ(), FeatureFinderAlgorithmPickedHelperStructs::Seed::intensity, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::isValid(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_, FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_, FeatureFinderAlgorithmPickedHelperStructs::Seed::peak, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak, FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks, MSExperiment< PeakT, ChromatogramPeakT >::size(), FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum, and FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Finds the best fitting position of the isotopic pattern estimate defined by center
.
center | the maximum peak of the isotope distribution (contains charge as well) |
charge | The charge of the pattern |
best_pattern | Returns the indices of the isotopic peaks. If a isopopic peak is missing -1 is returned. |
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, FeatureFinderAlgorithmPickedHelperStructs::Seed::peak, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size(), FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum, and FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Searches for an isotopic peak in the current spectrum and the adjacent spectra.
pos | m/z position of the searched for peak |
spectrum_index | index of the central spectrum |
pattern | IsotopePattern to store found peaks |
pattern_index | index of the isotope in the pattern |
peak_index | starting index of the search (to avoid multiple binary searches) |
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, MSExperiment< PeakT, ChromatogramPeakT >::empty(), MSSpectrum< PeakT >::findNearest(), FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::intensity, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::mz_score, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::nearest_(), String::number(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_(), MSExperiment< PeakT, ChromatogramPeakT >::size(), FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum, and FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_mz.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Returns the isotope distribution for a certain mass window.
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotope_distributions_, and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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inlinestatic |
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Compute the intensity score for the peak peak
in spectrum spectrum
.
The intensity score is computed by interpolating the score between the 4 nearest intensity bins. The scores from the different bins are weighted by the distance of the bin center to the peak.
spectrum | Index of the spectrum we are currently looking at |
peak | Index of the peak that should be scored inside the spectrum spectrum |
References MSExperiment< PeakT, ChromatogramPeakT >::getMinMZ(), MSExperiment< PeakT, ChromatogramPeakT >::getMinRT(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_mz_step_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_rt_step_, OpenMS::Math::isOdd(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, and OPENMS_POSTCONDITION.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Calculates the intersection between features. The value is normalized by the size of the smaller feature, so it ranges from 0 to 1.
References Feature::getConvexHulls(), DBoundingBox< D >::intersects(), DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), and DIntervalBase< D >::width().
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern.
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::intensity, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::mz_score, OPENMS_POSTCONDITION, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_begin, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_end, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::optional_fit_improvement_, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak, OpenMS::Math::pearsonCorrelationCoefficient(), and FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size().
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Returns the index of the peak nearest to m/z pos
in spectrum spec
(linear search starting from index start
)
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_().
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Not implemented.
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Calculates a score between 0 and 1 for the m/z deviation of two peaks.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Main method for actual FeatureFinder.
Implements FeatureFinderAlgorithm< PeakType, FeatureType >.
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_reasons_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::aborts_, MSExperiment< PeakT, ChromatogramPeakT >::areaBeginConst(), MSExperiment< PeakT, ChromatogramPeakT >::areaEndConst(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline, IsotopeDistribution::begin(), OpenMS::Constants::c, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::chooseTraceFitter_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_, DefaultParamHandler::defaults_, Feature::encloses(), DBoundingBox< D >::encloses(), IsotopeDistribution::end(), ProgressLogger::endProgress(), IsotopeDistribution::estimateFromPeptideWeight(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithm< PeakType, FeatureType >::features_, FeatureFinderAlgorithm< PeakType, FeatureType >::ff_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), MSSpectrum< PeakT >::findNearest(), TraceFitter< PeakType >::fit(), ConvexHull2D::getBoundingBox(), TraceFitter< PeakType >::getCenter(), BaseFeature::getCharge(), Feature::getConvexHull(), Feature::getConvexHulls(), ElementDB::getElement(), TraceFitter< PeakType >::getFeatureIntensityContribution(), TraceFitter< PeakType >::getFWHM(), TraceFitter< PeakType >::getHeight(), ElementDB::getInstance(), Peak2D::getIntensity(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), MSExperiment< PeakT, ChromatogramPeakT >::getMaxMZ(), MSExperiment< PeakT, ChromatogramPeakT >::getMaxRT(), MSExperiment< PeakT, ChromatogramPeakT >::getMinMZ(), MSExperiment< PeakT, ChromatogramPeakT >::getMinRT(), Peak2D::getMZ(), Feature::getOverallQuality(), MSSpectrum< PeakT >::getRT(), Feature::getSubordinates(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getTheoreticalmaxPosition(), Param::getValue(), IF_MASTERTHREAD, FeatureFinderAlgorithmPickedHelperStructs::Seed::intensity, FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_mz_step_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_optional_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_rt_step_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_thresholds_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intersection_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotope_distributions_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::isValid(), OpenMS::Constants::k, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_, LOG_DEBUG, LOG_INFO, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_feature_intersection_, FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_, DefaultParamHandler::param_, FeatureFinderAlgorithmPickedHelperStructs::Seed::peak, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_(), OpenMS::Constants::PROTON_MASS_U, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::reported_mz_, MSExperiment< PeakT, ChromatogramPeakT >::resize(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::seeds_, IsotopeDistribution::set(), BaseFeature::setCharge(), Peak2D::setIntensity(), Element::setIsotopeDistribution(), IsotopeDistribution::setMaxIsotope(), MetaInfoInterface::setMetaValue(), Peak2D::setMZ(), Feature::setOverallQuality(), DefaultParamHandler::setParameters(), ProgressLogger::setProgress(), Peak2D::setRT(), UniqueIdInterface::setUniqueId(), Param::setValue(), BaseFeature::setWidth(), MSExperiment< PeakT, ChromatogramPeakT >::size(), IsotopeDistribution::size(), FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size(), FeatureMap< FeatureT >::sortByIntensity(), FeatureMap< FeatureT >::sortByMZ(), FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum, ProgressLogger::startProgress(), FeatureXMLFile::store(), MzMLFile::store(), FeatureMap< FeatureT >::swapFeaturesOnly(), FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_, IsotopeDistribution::trimLeft(), FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::trimmed_left, IsotopeDistribution::trimRight(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::updateBaseline(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_().
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Sets a reference to the calling FeatureFinder.
Exception::IllegalArgument | is thrown if the algorithm does not support user-specified seed lists |
Reimplemented from FeatureFinderAlgorithm< PeakType, FeatureType >.
References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::seeds_.
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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 Param::getValue(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_optional_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_feature_intersection_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_rt_span_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_rt_span_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_trace_score_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::optional_fit_improvement_, DefaultParamHandler::param_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::reported_mz_, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::slope_bound_, and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_.
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Creates several files containing plots and viewable data of the fitted mass trace.
fitter | The TraceFitter containing the results from the rt profile fitting step. |
traces | Original mass traces found in the spectra |
new_traces | Cropped feature mass traces |
feature_ok | Status of the feature |
error_msg | If the feature is invalid, error_msg contains the reason |
final_score | Final score of the feature |
plot_nr | Index of the feature |
peak | The Seed Peak |
path | The path where to put the debug files (default is debug/features) |
References FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline, FeatureFinderAlgorithm< PeakType, FeatureType >::features_, TraceFitter< PeakType >::getCenter(), TraceFitter< PeakType >::getGnuplotFormula(), Peak2D::getMZ(), FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getPeakCount(), Param::getValue(), OpenMS::Constants::k, String::number(), DefaultParamHandler::param_, and TextFile::store().
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
Array of abort reasons.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
Array of abort reasons.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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debug flag
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Number of bins (in RT and MZ) for intensity significance estimation.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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m/z bin width
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Isotope pattern intensity contribution of required peaks.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Isotope pattern intensity contribution of optional peaks.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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RT bin width.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Precalculated intensity 20-quantiles (binned)
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Vector of precalculated isotope distributions for several mass windows.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Output stream for log/debug info.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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editable copy of the map
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Width of the isotope pattern mass bins.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Maximum allowed feature intersection (if larger, that one of the feature is removed)
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Maximum RT range the model is allowed to span.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Mimimum isotope pattern fit for a feature.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Minimum RT range that has to be left after the fit.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Number of spectra that have to show the same mass (for finding a mass trace)
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Minimum quality of a traces.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Minimal imrovment for leaving out optional isotope.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Stores mass_trace:mz_tolerance.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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User-specified seed list.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::setSeeds().
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Max slope of mass trace intensities.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
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Stores isotopic_pattern:mz_tolerance.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |