// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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//    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.
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// 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,
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//
// --------------------------------------------------------------------------
// $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_LCMSCDATA_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMSCDATA_H

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

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

namespace OpenMS
{

  class SUPERHIRN_DLLAPI LCMSCData
  {
public:
    typedef std::map<int, LCElutionPeak> elution_peak_list;
    typedef std::map<int, LCElutionPeak>::iterator elution_peak_list_ITERATOR;
    typedef std::map<double, elution_peak_list> MZ_LIST;
    typedef MZ_LIST::iterator MZ_LIST_ITERATOR;

    LCMSCData();
    LCMSCData(const LCMSCData &);
    LCMSCData(const LCMSCData *);
    virtual ~LCMSCData();

    //////////////////////////////////////////////////
    // overload operators:
    LCMSCData & operator=(const LCMSCData &);

    ///////////////////////////////
    // start here all the get / set
    // function to access the
    // variables of the class

    // start / end of the mz list:
    MZ_LIST_ITERATOR get_DATA_start();
    MZ_LIST_ITERATOR get_DATA_end();

    // find data of a specific m/z:
    MZ_LIST_ITERATOR get_MZ_by_iterator(double);
    // add data into the structure:
    void add_LC_elution_peak(double, LCElutionPeak *);

    // get a list of m/z observed in a scan +/- scan_tolerance:
    // return the area of the LC elution peaks
    std::vector<LCElutionPeak> get_MZ_list(int);
    std::vector<LCElutionPeak> get_MZ_list(int, int);

    // get all extracted LC peaks:
    std::vector<LCElutionPeak *> get_ALL_peak();
    // get a vector with all LC peaks ordered by their score:
    std::vector<LCElutionPeak *> get_ALL_peak_ordered();


    /*
    //////////////////////////////////////////////
    // operator which compares LC elution peaks
    // by their score:
    struct OPERATOR_LC_PEAK{
      bool operator()(LCElutionPeak* A,LCElutionPeak* B) const{
        return A->get_LC_score() < B->get_LC_score();
      }
    };
  */

    // minimal MS peak intensity allowed:
    //  static float intensity_min_threshold;



protected:

    // main data structure:
    MZ_LIST DATA;


  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMSCDATA_H
