// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2016.
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// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERRESULTPEAK_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERRESULTPEAK_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilterResultRaw.h>

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

namespace OpenMS
{
  /**
   * @brief data structure storing a single peak that passed all filters
   * 
   * Each peak filter result corresponds to a successful search for a particular
   * peak pattern in the centroided data. The actual m/z shifts seen in the filter
   * result might differ from the theoretical shifts listed in the peak pattern.
   * 
   * @see MultiplexPeakPattern
   */
  class OPENMS_DLLAPI MultiplexFilterResultPeak
  {
    public:
    /**
     * @brief constructor
     */
    MultiplexFilterResultPeak(double mz, double rt, std::vector<double> mz_shifts,
                              std::vector<double> intensities, std::vector<MultiplexFilterResultRaw> rawDataPoints);

     /**
     * @brief returns m/z of the peak
     */
     double getMZ() const;
     
     /**
     * @brief returns RT of the peak
     */
     double getRT() const;
     
    /**
     * @brief returns m/z shifts
     */
    std::vector<double> getMZShifts() const;

    /**
     * @brief returns intensities
     */
    std::vector<double> getIntensities() const;
    
    /**
     * @brief returns the number of raw data points belonging to the peak
     */
     int size() const;
     
     /**
     * @brief returns a single raw data point belonging to the peak
     */
     MultiplexFilterResultRaw getFilterResultRaw(int i) const;
     
     private:
    /**
     * @brief position of the peak
     */
    double mz_;
    double rt_;

    /**
     * @brief m/z shifts at which peaks corresponding to a pattern were found
     */
    std::vector<double> mz_shifts_;

    /**
     * @brief peak intensities at mz_ + mz_shifts_
     */
    std::vector<double> intensities_;

    /**
     * @brief (optional) raw data points corresponding to the peak
     */
    std::vector<MultiplexFilterResultRaw> raw_data_points_;
 
  };
  
}

#endif /* MULTIPLEXFILTERRESULTPEAK_H */
