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FeatureFinderAlgorithmPicked< PeakType, FeatureType > Class Template Reference
[FeatureFinder]

FeatureFinderAlgorithm for picked peaks. More...

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

Inheritance diagram for FeatureFinderAlgorithmPicked< PeakType, FeatureType >:
FeatureFinderAlgorithm< PeakType, FeatureType > FeatureFinderDefs DefaultParamHandler

List of all members.

Public Types

Type definitions

typedef FeatureFinderAlgorithm
< PeakType, FeatureType >
::MapType 		MapType
typedef FeatureFinderAlgorithm
< PeakType, FeatureType >
::FeatureMapType 		FeatureMapType
typedef MapType::SpectrumType SpectrumType
typedef
SpectrumType::FloatDataArrays 		FloatDataArrays

Public Member Functions

 FeatureFinderAlgorithmPicked ()
 default constructor
virtual void setSeeds (const FeatureMapType &seeds)
virtual void run ()
 Main method for actual FeatureFinder.

Static Public Member Functions

static FeatureFinderAlgorithm
< PeakType, FeatureType > * 		create ()
static const String getProductName ()

Protected Types

typedef
FeatureFinderAlgorithmPickedHelperStructs::Seed 		Seed
typedef
FeatureFinderAlgorithmPickedHelperStructs::MassTrace
< PeakType > 		MassTrace
typedef
FeatureFinderAlgorithmPickedHelperStructs::MassTraces
< PeakType > 		MassTraces
typedef
FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern 		TheoreticalIsotopePattern
typedef
FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern 		IsotopePattern

Protected Member Functions

virtual void updateMembers_ ()
void abort_ (const Seed &seed, const String &reason)
 Writes the abort reason to the log file and counts occurrences for each reason.
DoubleReal intersection_ (const Feature &f1, const Feature &f2) const
const TheoreticalIsotopePattern & getIsotopeDistribution_ (DoubleReal mass) const
 Returns the isotope distribution for a certain mass window.
DoubleReal findBestIsotopeFit_ (const Seed &center, UInt charge, IsotopePattern &best_pattern) const
 Finds the best fitting position of the isotopic pattern estimate defined by center.
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.
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).
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.
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.
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.
DoubleReal intensityScore_ (Size spectrum, Size peak) const
 Compute the intensity score for the peak peak in spectrum spectrum.
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).
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.
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.
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.

Protected Attributes

MapType map_
 editable copy of the map
std::ofstream log_
 Output stream for log/debug info.
bool debug_
 debug flag
std::map< String, UInt > aborts_
 Array of abort reasons.
std::map< Seed, String > abort_reasons_
 Array of abort reasons.
FeatureMapType seeds_
 User-specified seed list.
std::vector
< TheoreticalIsotopePattern > 		isotope_distributions_
 Vector of precalculated isotope distributions for several mass windows.
Members for parameters often needed in methods

DoubleReal pattern_tolerance_
 Stores mass_trace:mz_tolerance.
DoubleReal trace_tolerance_
 Stores isotopic_pattern:mz_tolerance.
UInt min_spectra_
 Number of spectra that have to show the same mass (for finding a mass trace).
UInt max_missing_trace_peaks_
 Stores mass_trace:max_missing.
DoubleReal slope_bound_
 Max slope of mass trace intensities.
DoubleReal intensity_percentage_
 Isotope pattern intensity contribution of required peaks.
DoubleReal intensity_percentage_optional_
 Isotope pattern intensity contribution of optional peaks.
DoubleReal optional_fit_improvement_
 Minimal imrovment for leaving out optional isotope.
DoubleReal mass_window_width_
 Width of the isotope pattern mass bins.
UInt intensity_bins_
 Number of bins (in RT and MZ) for intensity significance estimation.
DoubleReal min_isotope_fit_
 Mimimum isotope pattern fit for a feature.
DoubleReal min_trace_score_
 Minimum quality of a traces.
DoubleReal min_rt_span_
 Minimum RT range that has to be left after the fit.
DoubleReal max_rt_span_
 Maximum RT range the model is allowed to span.
DoubleReal max_feature_intersection_
 Maximum allowed feature intersection (if larger, that one of the feature is removed).
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.
Members for intensity significance estimation

DoubleReal intensity_rt_step_
 RT bin width.
DoubleReal intensity_mz_step_
 m/z bin width
std::vector< std::vector
< std::vector< DoubleReal > > > 		intensity_thresholds_
 Precalculated intensity 20-quantiles (binned).

Private Member Functions

FeatureFinderAlgorithmPicked & operator= (const FeatureFinderAlgorithmPicked &)
 Not implemented.
 FeatureFinderAlgorithmPicked (const FeatureFinderAlgorithmPicked &)
 Not implemented.

Detailed Description

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

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: 0Tolerated 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 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: 0The 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 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: 0Tolerated 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 float10 min: 0 max: 100Isotopic 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 max: 100Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.
isotopic_pattern:optional_fit_improvement float2 min: 0 max: 100Minimal percental improvement of isotope fit to allow leaving out an optional peak.
isotopic_pattern:mass_window_width float25 min: 1 max: 200Window width in Dalton for precalculation of estimated isotope distributions.
isotopic_pattern:abundance_12C float98.93 min: 0 max: 100Rel. abundance of the light carbon. Modify if labeled.
isotopic_pattern:abundance_14N float99.632 min: 0 max: 100Rel. abundance of the light nitrogen. Modify if labeled.
seed:min_score float0.8 min: 0 max: 1Minimum 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 float0.0001 min: 0Absolute epsilon used for convergence of the fit.
fit:epsilon_rel float0.0001 min: 0Relative epsilon used for convergence of the fit.
fit:max_iterations int500 min: 1Maximum number of iterations of the fit.
feature:min_score float0.7 min: 0 max: 1Feature 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 max: 1Minimum isotope fit of the feature before model fitting.
feature:min_trace_score float0.5 min: 0 max: 1Trace 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 max: 1Minimum 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 max: 1Maximum 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 min: 0Allowed RT deviation of seeds from the user-specified seed position.
user-seed:mz_tolerance float1.1 min: 0Allowed m/z deviation of seeds from the user-specified seed position.
user-seed:min_score float0.5 min: 0 max: 1Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.
debug:pseudo_rt_shift float500 min: 1Pseudo RT shift used when .

Note:
Improvement:
RT model with tailing/fronting (Marc)
Improvement:
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

typedef FeatureFinderAlgorithm<PeakType, FeatureType>::FeatureMapType FeatureMapType
typedef SpectrumType::FloatDataArrays FloatDataArrays
typedef FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern IsotopePattern [protected]
typedef FeatureFinderAlgorithm<PeakType, FeatureType>::MapType MapType
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace<PeakType> MassTrace [protected]
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces<PeakType> MassTraces [protected]
typedef FeatureFinderAlgorithmPickedHelperStructs::Seed Seed [protected]
typedef MapType::SpectrumType SpectrumType
typedef FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern [protected]

Constructor & Destructor Documentation

FeatureFinderAlgorithmPicked (  )  [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().

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

Not implemented.

Member Function Documentation

void abort_ ( const Seed &  seed,
const String &  reason 
) [inline, protected]

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().

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 
) [inline, 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:
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
Returns:
true if the feature is valid

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().

TraceFitter<PeakType>* chooseTraceFitter_ ( double &  tau  )  [inline, 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.

References Param::getValue(), LOG_DEBUG, and DefaultParamHandler::param_.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

static FeatureFinderAlgorithm<PeakType, FeatureType>* create (  )  [inline, static]

References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::FeatureFinderAlgorithmPicked().

void cropFeature_ ( TraceFitter< PeakType > *  fitter,
const MassTraces &  traces,
MassTraces &  new_traces 
) [inline, protected]

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

Parameters:
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().

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 [inline, 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:
trace 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.
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.

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_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::slope_bound_, and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_().

void extendMassTraces_ ( const IsotopePattern &  pattern,
MassTraces &  traces,
Size  meta_index_overall 
) const [inline, protected]

Extends all mass traces of an isotope pattern in one step

Parameters:
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, FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum, FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum, and FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

DoubleReal findBestIsotopeFit_ ( const Seed &  center,
UInt  charge,
IsotopePattern &  best_pattern 
) const [inline, protected]

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

Parameters:
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().

void findIsotope_ ( DoubleReal  pos,
Size  spectrum_index,
IsotopePattern &  pattern,
Size  pattern_index,
Size &  peak_index 
) const [inline, protected]

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

Parameters:
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_, 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_(), FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum, and FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_mz.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

const TheoreticalIsotopePattern& getIsotopeDistribution_ ( DoubleReal  mass  )  const [inline, protected]

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().

static const String getProductName (  )  [inline, static]
DoubleReal intensityScore_ ( Size  spectrum,
Size  peak 
) const [inline, 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:
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().

DoubleReal intensityScore_ ( Size  rt_bin,
Size  mz_bin,
DoubleReal  intensity 
) const [inline, protected]

References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_thresholds_.

DoubleReal intersection_ ( const Feature &  f1,
const Feature &  f2 
) const [inline, protected]

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().

DoubleReal isotopeScore_ ( const TheoreticalIsotopePattern &  isotopes,
IsotopePattern &  pattern,
bool  consider_mz_distances 
) const [inline, protected]

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().

Size nearest_ ( DoubleReal  pos,
const SpectrumType &  spec,
Size  start 
) const [inline, protected]

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_().

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

Not implemented.

DoubleReal positionScore_ ( DoubleReal  pos1,
DoubleReal  pos2,
DoubleReal  allowed_deviation 
) const [inline, protected]

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().

virtual void run (  )  [inline, virtual]

Main method for actual FeatureFinder.

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::IsotopePattern::peak, FeatureFinderAlgorithmPickedHelperStructs::Seed::peak, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_(), OpenMS::Constants::PROTON_MASS_U, FeatureFinderAlgorithmPicked< PeakType, FeatureType >::reported_mz_, 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(), FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size(), IsotopeDistribution::size(), FeatureMap< FeatureT >::sortByIntensity(), FeatureMap< FeatureT >::sortByMZ(), FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum, ProgressLogger::startProgress(), 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_().

virtual void setSeeds ( const FeatureMapType &  seeds  )  [inline, virtual]

References FeatureFinderAlgorithmPicked< PeakType, FeatureType >::seeds_.

virtual void updateMembers_ (  )  [inline, protected, virtual]

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_.

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/" 
) [inline, protected]

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

Parameters:
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().

Member Data Documentation

std::map<Seed, String> abort_reasons_ [protected]

Array of abort reasons.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

std::map<String, UInt> aborts_ [protected]

Array of abort reasons.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

bool debug_ [protected]

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().

UInt intensity_bins_ [protected]

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_().

DoubleReal intensity_mz_step_ [protected]

m/z bin width

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

DoubleReal intensity_percentage_ [protected]

Isotope pattern intensity contribution of required peaks.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal intensity_percentage_optional_ [protected]

Isotope pattern intensity contribution of optional peaks.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal intensity_rt_step_ [protected]

RT bin width.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

std::vector<std::vector<std::vector<DoubleReal> > > intensity_thresholds_ [protected]

Precalculated intensity 20-quantiles (binned).

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

std::vector<TheoreticalIsotopePattern> isotope_distributions_ [protected]

Vector of precalculated isotope distributions for several mass windows.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

std::ofstream log_ [mutable, protected]

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().

MapType map_ [protected]

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().

DoubleReal mass_window_width_ [protected]

Width of the isotope pattern mass bins.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal max_feature_intersection_ [protected]

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

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

UInt max_missing_trace_peaks_ [protected]

Stores mass_trace:max_missing.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal max_rt_span_ [protected]

Maximum RT range the model is allowed to span.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal min_isotope_fit_ [protected]

Mimimum isotope pattern fit for a feature.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal min_rt_span_ [protected]

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

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

UInt min_spectra_ [protected]

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_().

DoubleReal min_trace_score_ [protected]

Minimum quality of a traces.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal optional_fit_improvement_ [protected]

Minimal imrovment for leaving out optional isotope.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal pattern_tolerance_ [protected]

Stores mass_trace:mz_tolerance.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

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.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

FeatureMapType seeds_ [protected]

User-specified seed list.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::setSeeds().

DoubleReal slope_bound_ [protected]

Max slope of mass trace intensities.

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_().

DoubleReal trace_tolerance_ [protected]

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 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1