// --------------------------------------------------------------------------
//                   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
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//    documentation and/or other materials provided with the distribution.
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//    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"
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXISOTOPICPEAKPATTERN_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXISOTOPICPEAKPATTERN_H

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

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

namespace OpenMS
{
  /**
   * @brief data structure for pattern of isotopic peaks
   * 
   * Groups of peptides appear as characteristic patterns of isotopic peaks
   * in MS1 spectra. For example, for an Arg6 labeled SILAC peptide pair
   * of charge 2+ with three isotopic peaks we expect peaks
   * at relative m/z shifts of 0, 0.5, 1, 3, 3.5 and 4 Th.
   */
  class OPENMS_DLLAPI MultiplexIsotopicPeakPattern
  {
    public:

    /**
     * @brief constructor
     */
    MultiplexIsotopicPeakPattern(int c, int ppp, MultiplexDeltaMasses ms, int msi);
    
    /**
     * @brief returns charge
     */
    int getCharge() const;
     
    /**
     * @brief returns peaks per peptide
     */
    int getPeaksPerPeptide() const;
    
    /**
     * @brief returns mass shifts
     */
    MultiplexDeltaMasses getMassShifts() const;
    
    /**
     * @brief returns mass shift index
     */
    int getMassShiftIndex() const;
    
    /**
     * @brief returns number of mass shifts
     */
    unsigned getMassShiftCount() const;
   
    /**
     * @brief returns mass shift at position i
     */
    double getMassShiftAt(int i) const;
    
    /**
     * @brief returns m/z shift at position i
     */
    double getMZShiftAt(int i) const;
    
    /**
     * @brief returns number of m/z shifts
     */
    unsigned getMZShiftCount() const;
    
    private:

    /**
     * @brief m/z shifts between isotopic peaks
     * (number of mz_shifts_ = peaks_per_peptide_ * number of mass_shifts_)
     */
    std::vector<double> mz_shifts_;

    /**
     * @brief charge
     */
    int charge_;

    /**
     * @brief number of isotopic peaks in each peptide
     */
    int peaks_per_peptide_;
   
    /**
     * @brief mass shifts between peptides
     * (including zero mass shift for first peptide)
     */
    MultiplexDeltaMasses mass_shifts_;

    /**
     * @brief index in mass shift list
     */
    int mass_shift_index_;
      
 };
  
}

#endif /* MULTIPLEXISOTOPICPEAKPATTERN_H */
