OpenMS  3.0.0
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FeatureFinderAlgorithmPicked Class Reference

FeatureFinderAlgorithm for picked peaks. More...

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

Inheritance diagram for FeatureFinderAlgorithmPicked:
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Collaboration diagram for FeatureFinderAlgorithmPicked:
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Protected Attributes

Members for parameters often needed in methods
double pattern_tolerance_
 Stores mass_trace:mz_tolerance. More...
 
double 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...
 
double slope_bound_
 Max slope of mass trace intensities. More...
 
double intensity_percentage_
 Isotope pattern intensity contribution of required peaks. More...
 
double intensity_percentage_optional_
 Isotope pattern intensity contribution of optional peaks. More...
 
double optional_fit_improvement_
 Minimal improvement for leaving out optional isotope. More...
 
double 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...
 
double min_isotope_fit_
 Minimum isotope pattern fit for a feature. More...
 
double min_trace_score_
 Minimum quality of a traces. More...
 
double min_rt_span_
 Minimum RT range that has to be left after the fit. More...
 
double max_rt_span_
 Maximum RT range the model is allowed to span. More...
 
double 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...
 
- Protected Attributes inherited from FeatureFinderAlgorithm
const MapTypemap_
 Input data pointer. More...
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 Pointer to the calling FeatureFinder that is used to access the feature flags. 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...
 

Type definitions

typedef FeatureFinderAlgorithm::MapType MapType
 
typedef MapType::SpectrumType SpectrumType
 
typedef SpectrumType::FloatDataArrays FloatDataArrays
 
typedef Peak1D PeakType
 
typedef FeatureFinderAlgorithmPickedHelperStructs::Seed Seed
 
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
 
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
 
typedef FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern
 
typedef FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern IsotopePattern
 
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, UIntaborts_
 Array of abort reasons. More...
 
std::map< Seed, Stringabort_reasons_
 Array of abort reasons. More...
 
FeatureMap seeds_
 User-specified seed list. More...
 
 FeatureFinderAlgorithmPicked ()
 default constructor More...
 
void setSeeds (const FeatureMap &seeds) override
 Sets a reference to the calling FeatureFinder. More...
 
void run () override
 Main method for actual FeatureFinder. More...
 
static FeatureFinderAlgorithmcreate ()
 
static const String getProductName ()
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 Pointer to the calling FeatureFinder that is used to access the feature flags. More...
 

Members for intensity significance estimation

double intensity_rt_step_
 RT bin width. More...
 
double intensity_mz_step_
 m/z bin width More...
 
std::vector< std::vector< std::vector< double > > > intensity_thresholds_
 Precalculated intensity 20-quantiles (binned) More...
 
std::vector< TheoreticalIsotopePatternisotope_distributions_
 Vector of precalculated isotope distributions for several mass windows. More...
 
void updateMembers_ () override
 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...
 
double intersection_ (const Feature &f1, const Feature &f2) const
 
const TheoreticalIsotopePatterngetIsotopeDistribution_ (double mass) const
 Returns the isotope distribution for a certain mass window. More...
 
double findBestIsotopeFit_ (const Seed &center, 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, double mz, bool increase_rt, Size meta_index_overall, double min_rt=0.0, double max_rt=0.0) const
 Extends a single mass trace in one RT direction. More...
 
Size nearest_ (double pos, const MSSpectrum &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_ (double 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...
 
double positionScore_ (double pos1, double pos2, double allowed_deviation) const
 Calculates a score between 0 and 1 for the m/z deviation of two peaks. More...
 
double 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...
 
double intensityScore_ (Size spectrum, Size peak) const
 Compute the intensity score for the peak peak in spectrum spectrum. More...
 
std::unique_ptr< TraceFitterchooseTraceFitter_ (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...
 
double intensityScore_ (Size rt_bin, Size mz_bin, double intensity) const
 

Handling of fitted mass traces

Methods to handle the results of the mass trace fitting process.

void cropFeature_ (std::shared_ptr< TraceFitter > 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_ (std::shared_ptr< TraceFitter > fitter, MassTraces &feature_traces, const double &seed_mz, const double &min_feature_score, String &error_msg, double &fit_score, double &correlation, double &final_score)
 Checks the feature based on different score thresholds and model constraints. More...
 
void writeFeatureDebugInfo_ (std::shared_ptr< TraceFitter > fitter, const MassTraces &traces, const MassTraces &new_traces, bool feature_ok, const String error_msg, const double 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...
 
FeatureFinderAlgorithmPickedoperator= (const FeatureFinderAlgorithmPicked &)
 Not implemented. More...
 
 FeatureFinderAlgorithmPicked (const FeatureFinderAlgorithmPicked &)
 Not implemented. More...
 

Additional Inherited Members

- Public Types inherited from FeatureFinderAlgorithm
typedef PeakMap MapType
 Input map type. More...
 
typedef MapType::CoordinateType CoordinateType
 Coordinate/Position type of peaks. More...
 
typedef MapType::IntensityType IntensityType
 Intensity type of peaks. 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 inherited from FeatureFinderAlgorithm
 FeatureFinderAlgorithm ()
 default constructor More...
 
 ~FeatureFinderAlgorithm () override
 destructor More...
 
virtual Param getDefaultParameters () const
 Returns the default parameters. Reimplement. More...
 
void setData (const MapType &map, FeatureMap &features, FeatureFinder &ff)
 Sets a reference to the calling FeatureFinder. 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 inherited from FeatureFinderAlgorithm
static void registerChildren ()
 register all derived classes here (see FeatureFinderAlgorithm_impl.h) More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Detailed Description

FeatureFinderAlgorithm for picked peaks.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
debug stringfalse true, falseWhen debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).
intensity:bins int10 min: 1Number 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 float0.03 min: 0.0Tolerated m/z deviation of peaks belonging to the same mass trace.
It should be larger than the m/z resolution of the instrument.
This value must be smaller than that 1/charge_high!
mass_trace:min_spectra int10 min: 1Number of spectra that have to show a similar peak mass in a mass trace.
mass_trace:max_missing int1 min: 0Number 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 float0.1 min: 0.0The maximum slope of mass trace intensities when extending from the highest peak.
This parameter is important to separate overlapping elution peaks.
It should be increased if feature elution profiles fluctuate a lot.
isotopic_pattern:charge_low int1 min: 1Lowest charge to search for.
isotopic_pattern:charge_high int4 min: 1Highest charge to search for.
isotopic_pattern:mz_tolerance float0.03 min: 0.0Tolerated m/z deviation from the theoretical isotopic pattern.
It should be larger than the m/z resolution of the instrument.
This value must be smaller than that 1/charge_high!
isotopic_pattern:intensity_percentage float10.0 min: 0.0 max: 100.0Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.
isotopic_pattern:intensity_percentage_optional float0.1 min: 0.0 max: 100.0Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.
isotopic_pattern:optional_fit_improvement float2.0 min: 0.0 max: 100.0Minimal percental improvement of isotope fit to allow leaving out an optional peak.
isotopic_pattern:mass_window_width float25.0 min: 1.0 max: 200.0Window width in Dalton for precalculation of estimated isotope distributions.
isotopic_pattern:abundance_12C float98.930000000000007 min: 0.0 max: 100.0Rel. abundance of the light carbon. Modify if labeled.
isotopic_pattern:abundance_14N float99.632000000000005 min: 0.0 max: 100.0Rel. abundance of the light nitrogen. Modify if labeled.
seed:min_score float0.8 min: 0.0 max: 1.0Minimum 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:max_iterations int500 min: 1Maximum number of iterations of the fit.
feature:min_score float0.7 min: 0.0 max: 1.0Feature 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 float0.8 min: 0.0 max: 1.0Minimum isotope fit of the feature before model fitting.
feature:min_trace_score float0.5 min: 0.0 max: 1.0Trace 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 float0.333 min: 0.0 max: 1.0Minimum RT span in relation to extended area that has to remain after model fitting.
feature:max_rt_span float2.5 min: 0.5Maximum RT span in relation to extended area that the model is allowed to have.
feature:rt_shape stringsymmetric symmetric, asymmetricChoose 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 float0.35 min: 0.0 max: 1.0Maximum allowed intersection of features.
feature:reported_mz stringmonoisotopic maximum, average, monoisotopicThe 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 float5.0 min: 0.0Allowed RT deviation of seeds from the user-specified seed position.
user-seed:mz_tolerance float1.1 min: 0.0Allowed m/z deviation of seeds from the user-specified seed position.
user-seed:min_score float0.5 min: 0.0 max: 1.0Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.
debug:pseudo_rt_shift float500.0 min: 1.0Pseudo RT shift used when .

Note:
Improvement:

RT model with tailing/fronting (Marc)

More general MZ model - e.g. based on co-elution or with sulfur-averagines (Marc)

Todo:

Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)

Implement user-specified seed lists support (Marc)

Member Typedef Documentation

◆ FloatDataArrays

◆ IsotopePattern

◆ MapType

◆ MassTrace

◆ MassTraces

◆ PeakType

typedef Peak1D PeakType
protected

◆ Seed

◆ SpectrumType

◆ TheoreticalIsotopePattern

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmPicked() [1/2]

default constructor

◆ FeatureFinderAlgorithmPicked() [2/2]

Not implemented.

Member Function Documentation

◆ abort_()

void abort_ ( const Seed seed,
const String reason 
)
protected

Writes the abort reason to the log file and counts occurrences for each reason.

◆ checkFeatureQuality_()

bool checkFeatureQuality_ ( std::shared_ptr< TraceFitter fitter,
MassTraces feature_traces,
const double seed_mz,
const double min_feature_score,
String error_msg,
double fit_score,
double correlation,
double final_score 
)
protected

Checks the feature based on different score thresholds and model constraints.

Feature can get invalid for following reasons:

  • Invalid fit: Fitted model is bigger than 'max_rt_span'
  • Invalid feature after fit - too few traces or peaks left
  • Invalid fit: Center outside of feature bounds
  • Invalid fit: Less than 'min_rt_span' left after fit
  • Feature quality too low after fit
Parameters
fitterThe TraceFitter containing the results from the rt profile fitting step.
feature_tracesCropped feature mass traces.
seed_mzMz of the seed
min_feature_scoreMinimal required feature score
error_msgWill be filled with the error message, if the feature is invalid
fit_scoreWill be filled with the fit score
correlationWill be filled with correlation between feature and model
final_scoreWill be filled with the final score
Returns
true if the feature is valid

◆ chooseTraceFitter_()

std::unique_ptr<TraceFitter> chooseTraceFitter_ ( double tau)
protected

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)

Returns
A pointer to the trace fitter that should be used.

◆ create()

static FeatureFinderAlgorithm* create ( )
static

◆ cropFeature_()

void cropFeature_ ( std::shared_ptr< TraceFitter fitter,
const MassTraces traces,
MassTraces new_traces 
)
protected

Creates new mass traces new_traces based on the fitting result and the original traces traces.

Parameters
fitterThe TraceFitter containing the results from the rt profile fitting step.
tracesOriginal mass traces found in the experiment.
new_tracesMass traces created by cropping the original mass traces.

◆ extendMassTrace_()

void extendMassTrace_ ( MassTrace trace,
SignedSize  spectrum_index,
double  mz,
bool  increase_rt,
Size  meta_index_overall,
double  min_rt = 0.0,
double  max_rt = 0.0 
) const
protected

Extends a single mass trace in one RT direction.

How to use this method:

  • Add the starting peak to the trace
  • Indicate using increase_rt whether to extend in downstream or upstream direction
Parameters
traceThe trace that should be extended
spectrum_indexThe index of the spectrum from which on the mass trace should be extended
mzThe mz location (center) of the trace
increase_rtIndicator whether the extension is done in forward or backward direction (with respect to the current spectrum)
meta_index_overallThe index of the overall score
min_rtThe rt minimum up to which the trace will be extended.
max_rtThe rt maximum up to which the trace will be extended.
Note
This method assumes that it extends from a local maximum.
If min_rt or max_rt are set to 0.0 no boundary is assumed in the respective direction.

◆ extendMassTraces_()

void extendMassTraces_ ( const IsotopePattern pattern,
MassTraces traces,
Size  meta_index_overall 
) const
protected

Extends all mass traces of an isotope pattern in one step

Parameters
patternThe IsotopePattern that should be extended.
tracesThe MassTraces datastructure where the extended mass traces will be stored in.
meta_index_overallThe index of the data array where the quality scores for the given charge are stored.

◆ findBestIsotopeFit_()

double findBestIsotopeFit_ ( const Seed center,
UInt  charge,
IsotopePattern best_pattern 
) const
protected

Finds the best fitting position of the isotopic pattern estimate defined by center.

Parameters
centerthe maximum peak of the isotope distribution (contains charge as well)
chargeThe charge of the pattern
best_patternReturns the indices of the isotopic peaks. If a isotopic peak is missing -1 is returned.

◆ findIsotope_()

void findIsotope_ ( double  pos,
Size  spectrum_index,
IsotopePattern pattern,
Size  pattern_index,
Size peak_index 
) const
protected

Searches for an isotopic peak in the current spectrum and the adjacent spectra.

Parameters
posm/z position of the searched for peak
spectrum_indexindex of the central spectrum
patternIsotopePattern to store found peaks
pattern_indexindex of the isotope in the pattern
peak_indexstarting index of the search (to avoid multiple binary searches)

◆ getIsotopeDistribution_()

const TheoreticalIsotopePattern& getIsotopeDistribution_ ( double  mass) const
protected

Returns the isotope distribution for a certain mass window.

◆ getProductName()

static const String getProductName ( )
static

◆ intensityScore_() [1/2]

double intensityScore_ ( Size  rt_bin,
Size  mz_bin,
double  intensity 
) const
protected

◆ intensityScore_() [2/2]

double intensityScore_ ( Size  spectrum,
Size  peak 
) const
protected

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.

Parameters
spectrumIndex of the spectrum we are currently looking at
peakIndex of the peak that should be scored inside the spectrum spectrum

◆ intersection_()

double intersection_ ( const Feature f1,
const Feature f2 
) const
protected

Calculates the intersection between features. The value is normalized by the size of the smaller feature, so it ranges from 0 to 1.

◆ isotopeScore_()

double isotopeScore_ ( const TheoreticalIsotopePattern isotopes,
IsotopePattern pattern,
bool  consider_mz_distances 
) const
protected

Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern.

◆ nearest_()

Size nearest_ ( double  pos,
const MSSpectrum spec,
Size  start 
) const
protected

Returns the index of the peak nearest to m/z pos in spectrum spec (linear search starting from index start)

◆ operator=()

Not implemented.

◆ positionScore_()

double positionScore_ ( double  pos1,
double  pos2,
double  allowed_deviation 
) const
protected

Calculates a score between 0 and 1 for the m/z deviation of two peaks.

◆ run()

void run ( )
overridevirtual

Main method for actual FeatureFinder.

Implements FeatureFinderAlgorithm.

◆ setSeeds()

void setSeeds ( const FeatureMap seeds)
overridevirtual

Sets a reference to the calling FeatureFinder.

Exceptions
Exception::IllegalArgumentis thrown if the algorithm does not support user-specified seed lists

Reimplemented from FeatureFinderAlgorithm.

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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.

◆ writeFeatureDebugInfo_()

void writeFeatureDebugInfo_ ( std::shared_ptr< TraceFitter fitter,
const MassTraces traces,
const MassTraces new_traces,
bool  feature_ok,
const String  error_msg,
const double  final_score,
const Int  plot_nr,
const PeakType peak,
const String  path = "debug/features/" 
)
protected

Creates several files containing plots and viewable data of the fitted mass trace.

Parameters
fitterThe TraceFitter containing the results from the rt profile fitting step.
tracesOriginal mass traces found in the spectra
new_tracesCropped feature mass traces
feature_okStatus of the feature
error_msgIf the feature is invalid, error_msg contains the reason
final_scoreFinal score of the feature
plot_nrIndex of the feature
peakThe Seed Peak
pathThe path where to put the debug files (default is debug/features)

Member Data Documentation

◆ abort_reasons_

std::map<Seed, String> abort_reasons_
protected

Array of abort reasons.

◆ aborts_

std::map<String, UInt> aborts_
protected

Array of abort reasons.

◆ debug_

bool debug_
protected

debug flag

◆ features_

FeatureMap* features_

Output data pointer.

◆ ff_

Pointer to the calling FeatureFinder that is used to access the feature flags.

◆ intensity_bins_

UInt intensity_bins_
protected

Number of bins (in RT and MZ) for intensity significance estimation.

◆ intensity_mz_step_

double intensity_mz_step_
protected

m/z bin width

◆ intensity_percentage_

double intensity_percentage_
protected

Isotope pattern intensity contribution of required peaks.

◆ intensity_percentage_optional_

double intensity_percentage_optional_
protected

Isotope pattern intensity contribution of optional peaks.

◆ intensity_rt_step_

double intensity_rt_step_
protected

RT bin width.

◆ intensity_thresholds_

std::vector<std::vector<std::vector<double> > > intensity_thresholds_
protected

Precalculated intensity 20-quantiles (binned)

◆ isotope_distributions_

std::vector<TheoreticalIsotopePattern> isotope_distributions_
protected

Vector of precalculated isotope distributions for several mass windows.

◆ log_

std::ofstream log_
mutableprotected

Output stream for log/debug info.

◆ map_

MapType map_
protected

editable copy of the map

◆ mass_window_width_

double mass_window_width_
protected

Width of the isotope pattern mass bins.

◆ max_feature_intersection_

double max_feature_intersection_
protected

Maximum allowed feature intersection (if larger, that one of the feature is removed)

◆ max_missing_trace_peaks_

UInt max_missing_trace_peaks_
protected

Stores mass_trace:max_missing.

◆ max_rt_span_

double max_rt_span_
protected

Maximum RT range the model is allowed to span.

◆ min_isotope_fit_

double min_isotope_fit_
protected

Minimum isotope pattern fit for a feature.

◆ min_rt_span_

double min_rt_span_
protected

Minimum RT range that has to be left after the fit.

◆ min_spectra_

UInt min_spectra_
protected

Number of spectra that have to show the same mass (for finding a mass trace)

◆ min_trace_score_

double min_trace_score_
protected

Minimum quality of a traces.

◆ optional_fit_improvement_

double optional_fit_improvement_
protected

Minimal improvement for leaving out optional isotope.

◆ pattern_tolerance_

double pattern_tolerance_
protected

Stores mass_trace:mz_tolerance.

◆ reported_mz_

String reported_mz_
protected

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.

◆ seeds_

FeatureMap seeds_
protected

User-specified seed list.

◆ slope_bound_

double slope_bound_
protected

Max slope of mass trace intensities.

◆ trace_tolerance_

double trace_tolerance_
protected

Stores isotopic_pattern:mz_tolerance.