PeakPickerMaxima.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 2002-2018.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

#include <OpenMS/config.h>
#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI PeakPickerMaxima 
  {
public:

    PeakPickerMaxima(double signal_to_noise, double spacing_difference = 1.5,
        double spacing_difference_gap = 4.0, double sn_window_length = 200,
        unsigned missing = 2);

    virtual ~PeakPickerMaxima() {}

    struct OPENMS_DLLAPI PeakCandidate 
    {
      int pos;
      int left_boundary;
      int right_boundary;
      double mz_max;
      double int_max;
    };

    void findMaxima(const std::vector<double>& mz_array,
        const std::vector<double>& int_array,
        std::vector<PeakCandidate>& pc,
        bool check_spacings = true);

    void pick(std::vector<double>& mz_array, 
        std::vector<double>& int_array, 
        std::vector<PeakCandidate>& pc,
        bool check_spacings = true);

protected:

    // signal-to-noise parameter
    double signal_to_noise_;

    // signal-to-noise window length 
    double sn_window_length_;

    // maximal spacing difference defining a missing data point
    double spacing_difference_;

    // maximal spacing difference defining a large gap
    double spacing_difference_gap_;

    // maximum number of missing points
    unsigned missing_;

  }; // end PeakPickerMaxima

} // namespace OpenMS