PeakPickerMaxima.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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) const;
 
    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