// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2016.
//
// 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: Timo Sachsenberg $
// $Authors: Lukas Mueller, Markus Mueller $
// --------------------------------------------------------------------------
//
///////////////////////////////////////////////////////////////////////////
//
//  PEAK DETECTION OF FOURIER TRANSFORME MS INSTRUMENT DATA
//
//  written by Markus Mueller, markus.mueller@imsb.biol.ethz.ch
//  ( and Lukas Mueller, Lukas.Mueller@imsb.biol.ethz.ch)
//  October 2005
//
//  Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
//  December 2010
//
//  Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
//
//

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_BACKGROUNDINTENSITYBIN_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_BACKGROUNDINTENSITYBIN_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>

#include <vector>
#include <map>

namespace OpenMS
{

  class MSPeak;

  class SUPERHIRN_DLLAPI BackgroundIntensityBin
  {

private:

    // do not allow default constructor
    BackgroundIntensityBin()
    {
    }

    // mz and tr coordinates of the bin:
    double mzCoord_;
    double trCoord_;
    double zCoord_;

    std::vector<double> intensityMap_;
    std::map<double, double> intensityHist_;

    double mean_;
    void computeIntensityHist();

public:

    virtual ~BackgroundIntensityBin();

    // copy constructor
    BackgroundIntensityBin(const BackgroundIntensityBin &);

    // assignment operator
    BackgroundIntensityBin & operator=(const BackgroundIntensityBin &);

    BackgroundIntensityBin(double, double);

    /*
     * @brief Check if a peak belongs to this intensity bin
     */
    bool checkBelonging(MSPeak *);

    /*
     * @brief Add intensity to BackgroundIntensityBin
     */
    void addIntensity(double);

    /*
     * @brief add peak to BackgroundIntensityBin
     */
    void addMSPeak(MSPeak *);
    /*
     * @brief Process collected intensities in the map
     */
    void processIntensities();

    std::vector<double> * getIntensityMap();
    std::map<double, double> * getIntensityHist();
    double getMean();
  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_BACKGROUNDINTENSITYBIN_H
