FeatureFinderAlgorithmPicked.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/TraceFitter.h>

#include <fstream>

namespace OpenMS
{
  class OPENMS_DLLAPI FeatureFinderAlgorithmPicked :
    public FeatureFinderAlgorithm,
    public FeatureFinderDefs
  {
public:

    typedef FeatureFinderAlgorithm::MapType MapType;
    typedef MapType::SpectrumType SpectrumType;
    typedef SpectrumType::FloatDataArrays FloatDataArrays;

    using FeatureFinderAlgorithm::param_;
    using FeatureFinderAlgorithm::features_;
    using FeatureFinderAlgorithm::ff_;
    using FeatureFinderAlgorithm::defaults_;

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();

    // docu in base class
    virtual void setSeeds(const FeatureMap& seeds);

    virtual void run();

    static FeatureFinderAlgorithm* create();

    static const String getProductName();

protected:
    MapType map_;
    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
    virtual void updateMembers_();

    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;

    TraceFitter* chooseTraceFitter_(double& tau);

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


    void cropFeature_(TraceFitter* fitter,
                      const MassTraces& traces,
                      MassTraces& new_traces);

    bool checkFeatureQuality_(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_(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

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_H