MultiplexFiltering.h

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// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H

#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilterResult.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SplineSpectrum.h>

#include <vector>
#include <algorithm>
#include <iostream>

namespace OpenMS
{
  class OPENMS_DLLAPI MultiplexFiltering :
    public ProgressLogger
  {
public:
    struct PeakReference
    {
      int index_in_previous_spectrum;
      int index_in_next_spectrum;
    };

    struct BlackListEntry
    {
      bool black;
      int black_exception_mass_shift_index;
      int black_exception_charge;
      int black_exception_mz_position;
    };

    MultiplexFiltering(const PeakMap& exp_picked, const std::vector<MultiplexIsotopicPeakPattern> patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");

protected:
    int positionsAndBlacklistFilter_(const MultiplexIsotopicPeakPattern& pattern, int spectrum,
                                    const std::vector<double>& peak_position, int peak, std::vector<double>& mz_shifts_actual,
                                    std::vector<int>& mz_shifts_actual_indices) const;

    bool monoIsotopicPeakIntensityFilter_(const MultiplexIsotopicPeakPattern& pattern, int spectrum_index, const std::vector<int>& mz_shifts_actual_indices) const;

    bool zerothPeakFilter_(const MultiplexIsotopicPeakPattern& pattern, const std::vector<double>& intensities_actual) const;

    bool peptideSimilarityFilter_(const MultiplexIsotopicPeakPattern& pattern, const std::vector<double>& intensities_actual, int peaks_found_in_all_peptides_spline) const;

    bool averagineSimilarityFilter_(const MultiplexIsotopicPeakPattern& pattern, const std::vector<double>& intensities_actual, int peaks_found_in_all_peptides_spline, double mz) const;

    void blacklistPeaks_(const MultiplexIsotopicPeakPattern& pattern, int spectrum, const std::vector<int>& mz_shifts_actual_indices, int peaks_found_in_all_peptides_spline);

    int getPeakIndex_(const std::vector<double>& peak_position, int start, double mz, double scaling) const;

    double getPatternSimilarity_(const std::vector<double>& pattern1, const std::vector<double>& pattern2) const;

    double getAveragineSimilarity_(const std::vector<double>& pattern, double m) const;

    PeakMap exp_picked_;

    std::vector<std::vector<PeakReference> > registry_;
    std::vector<std::vector<BlackListEntry> > blacklist_;

    std::vector<MultiplexIsotopicPeakPattern> patterns_;

    int peaks_per_peptide_min_;

    int peaks_per_peptide_max_;

    bool missing_peaks_;

    double intensity_cutoff_;

    double mz_tolerance_;

    bool mz_tolerance_unit_;

    double peptide_similarity_;

    double averagine_similarity_;

    double averagine_similarity_scaling_;

    String averagine_type_;

  };

}

#endif /* MULTIPLEXFILTERING_H_ */