// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------

#pragma once

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

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

namespace OpenMS
{
    /**
     * @brief data structure storing all peaks (and optionally their raw data points)
     * of an experiment corresponding to one specific peak pattern
     * 
     * @see MultiplexPeakPattern
     */
    class OPENMS_DLLAPI MultiplexFilteredMSExperiment
    {
        public:
        /**
         * @brief constructor
         */
        MultiplexFilteredMSExperiment();
        
        /**
         * @brief adds a single peak to the results
         */
        void addPeak(const MultiplexFilteredPeak& peak);
        
        /**
         * @brief returns a single peak from the results
         */
        MultiplexFilteredPeak getPeak(size_t i) const;
               
        /**
         * @brief returns m/z of a single peak
         */
        double getMZ(size_t i) const;
        
        /**
         * @brief returns m/z positions of all peaks
         */
        std::vector<double> getMZ() const;
        
        /**
         * @brief returns RT of a single peak
         */
        double getRT(size_t i) const;
        
        /**
         * @brief returns RT of all peaks
         */
        std::vector<double> getRT() const;
        
        /**
         * @brief returns number of peaks in the result
         */
        size_t size() const;
        
        /**
         * @brief write all peaks to a consensusXML file
         * 
         * @param exp_picked   original (i.e. not white) centroided experimental data
         * @param debug_out    file name of the debug output
         */
        void writeDebugOutput(const MSExperiment& exp_picked, const String& debug_out) const;
        
        private:
        /**
         * @brief peaks which passed the peak pattern filter
         */
        std::vector<MultiplexFilteredPeak> result_;

   };
  
}

