// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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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//    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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h>

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h>

namespace OpenMS
{
  /**
    @brief TMT 6plex quantitation to be used with the IsobaricQuantitation.

    @htmlinclude OpenMS_TMTSixPlexQuantitationMethod.parameters
  */
  class OPENMS_DLLAPI TMTSixPlexQuantitationMethod :
    public IsobaricQuantitationMethod
  {
public:
    /// Default c'tor
    TMTSixPlexQuantitationMethod();

    /// d'tor
    ~TMTSixPlexQuantitationMethod() override;

    /// Copy c'tor
    TMTSixPlexQuantitationMethod(const TMTSixPlexQuantitationMethod& other);

    /// Assignment operator
    TMTSixPlexQuantitationMethod & operator=(const TMTSixPlexQuantitationMethod& rhs);

    /// @brief Methods to implement from IsobaricQuantitationMethod
    /// @{

    const String& getName() const override;

    const IsobaricChannelList& getChannelInformation() const override;

    Size getNumberOfChannels() const override;

    Matrix<double> getIsotopeCorrectionMatrix() const override;

    Size getReferenceChannel() const override;

    /// @}

  private:
    /// the actual information on the different tmt 6plex channels.
    IsobaricChannelList channels_;

    /// The name of the quantitation method.
    static const String name_;

    /// The reference channel for this experiment.
    Size reference_channel_;

  protected:
    /// implemented for DefaultParamHandler
    void setDefaultParams_();

    /// implemented for DefaultParamHandler
    void updateMembers_() override;

  };
} // namespace

