MultiplexFilteringProfile.h

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// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERINGPROFILE_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERINGPROFILE_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/MultiplexFiltering.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 MultiplexFilteringProfile :
    public MultiplexFiltering
  {
public:
    MultiplexFilteringProfile(const PeakMap& exp_profile, const PeakMap& exp_picked, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries, 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");

    std::vector<MultiplexFilterResult> filter();

private:
    int nonLocalIntensityFilter_(const MultiplexIsotopicPeakPattern& pattern, const std::vector<double>& mz_shifts_actual, const std::vector<int>& mz_shifts_actual_indices, SplineSpectrum::Navigator nav, std::vector<double>& intensities_actual, int peaks_found_in_all_peptides, double mz) const;

    int findNearest_(int spectrum_index, double mz, double scaling) const;

    PeakMap exp_profile_;
    std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_;

  };

}

#endif /* MULTIPLEXFILTERINGPROFILE_H_ */