FeatureFinderAlgorithmPicked.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/FEATUREFINDER/TraceFitter.h>
#include <OpenMS/DATASTRUCTURES/IsotopeCluster.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/CONCEPT/GlobalExceptionHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
 
#include <fstream>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI FeatureFinderDefs
  {
    typedef IsotopeCluster::IndexPair IndexPair;
 
    typedef IsotopeCluster::ChargedIndexSet ChargedIndexSet;
 
    typedef IsotopeCluster::IndexSet IndexSet;
 
    enum Flag {UNUSED, USED};
 
    class OPENMS_DLLAPI NoSuccessor :
      public Exception::BaseException
    {
public:
      NoSuccessor(const char * file, int line, const char * function, const IndexPair & index) :
        BaseException(file, line, function, "NoSuccessor", String("there is no successor/predecessor for the given Index: ") + String(index.first) + "/" + String(index.second)),
        index_(index)
      {
        Exception::GlobalExceptionHandler::setMessage(what());
      }
 
      ~NoSuccessor() noexcept override = default;
 
protected:
      IndexPair index_; // index without successor/predecessor
    };
  };
 
 
  class OPENMS_DLLAPI FeatureFinderAlgorithmPicked :
    public DefaultParamHandler, public ProgressLogger
  {
public:
 
    typedef MSExperiment MapType;
    typedef MapType::SpectrumType SpectrumType;
    typedef SpectrumType::FloatDataArrays FloatDataArrays;
 
protected:
    typedef Peak1D PeakType;
    typedef FeatureFinderAlgorithmPickedHelperStructs::Seed Seed;
    typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace;
    typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces;
    typedef FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern;
    typedef FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern IsotopePattern;
 
public:
    FeatureFinderAlgorithmPicked();
 
    void setSeeds(const FeatureMap& seeds);
 
    void setData(const MSExperiment& map, FeatureMap& features);
 
    void run(PeakMap& input_map, 
      FeatureMap& features, 
      const Param& param, 
      const FeatureMap& seeds);
 
    virtual Param getDefaultParameters() const
    {
      return defaults_;
    }
protected:
    void run();
 
    MapType map_;
 
    FeatureMap* features_;
 
    mutable std::ofstream log_;
    bool debug_;
    std::map<String, UInt> aborts_;
    std::map<Seed, String> abort_reasons_;
    FeatureMap seeds_;
 
 
    double pattern_tolerance_; 
    double trace_tolerance_; 
    UInt min_spectra_; 
    UInt max_missing_trace_peaks_; 
    double slope_bound_; 
    double intensity_percentage_; 
    double intensity_percentage_optional_; 
    double optional_fit_improvement_; 
    double mass_window_width_; 
    UInt intensity_bins_; 
    double min_isotope_fit_; 
    double min_trace_score_; 
    double min_rt_span_; 
    double max_rt_span_; 
    double max_feature_intersection_; 
    String reported_mz_; 
 
 
    double intensity_rt_step_;
    double intensity_mz_step_;
    std::vector<std::vector<std::vector<double> > > intensity_thresholds_;
 
    std::vector<TheoreticalIsotopePattern> isotope_distributions_;
 
    // Docu in base class
    void updateMembers_() override;
 
    void abort_(const Seed& seed, const String& reason);
 
    double intersection_(const Feature& f1, const Feature& f2) const;
 
    const TheoreticalIsotopePattern& getIsotopeDistribution_(double mass) const;
 
    double findBestIsotopeFit_(const Seed& center, UInt charge, IsotopePattern& best_pattern) const;
 
    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;
 
    Size nearest_(double pos, const MSSpectrum& spec, Size start) const;
 
    void findIsotope_(double pos, Size spectrum_index, IsotopePattern& pattern, Size pattern_index, Size& peak_index) const;
 
    double positionScore_(double pos1, double pos2, double allowed_deviation) const;
 
    double isotopeScore_(const TheoreticalIsotopePattern& isotopes, IsotopePattern& pattern, bool consider_mz_distances) const;
 
    double intensityScore_(Size spectrum, Size peak) const;
 
    std::unique_ptr<TraceFitter> chooseTraceFitter_(double& tau);
 
    double intensityScore_(Size rt_bin, Size mz_bin, double intensity) const;
 
 
    void cropFeature_(const std::shared_ptr<TraceFitter>& fitter,
                      const MassTraces& traces,
                      MassTraces& new_traces);
 
    bool checkFeatureQuality_(const 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);
 
    void writeFeatureDebugInfo_(const 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/");
 
private:
 
    FeatureFinderAlgorithmPicked& operator=(const FeatureFinderAlgorithmPicked&);
    FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked&);
  };
 
} // namespace OpenMS