// --------------------------------------------------------------------------
//                   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:
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//  * 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;
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// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/ID/ConsensusIDAlgorithmSimilarity.h>
#include <OpenMS/ANALYSIS/SEQUENCE/NeedlemanWunsch.h>

namespace OpenMS
{
  /**
    @brief Calculates a consensus from multiple ID runs based on PEPs and sequence similarities.

    @note The similarity scoring is based on an amino acid substitution matrix. Therefore only the raw amino acid sequences, without post-translational modifications (PTMs), can be considered for similarity scoring - PTMs are ignored during this step. However, PTMs on peptides are retained and separate results are produced for differently-modified peptides.

    @htmlinclude OpenMS_ConsensusIDAlgorithmPEPMatrix.parameters
    
    @ingroup Analysis_ID
  */
  class OPENMS_DLLAPI ConsensusIDAlgorithmPEPMatrix :
    public ConsensusIDAlgorithmSimilarity
  {
  public:
    /// Default constructor
    ConsensusIDAlgorithmPEPMatrix();


  private:

    /// object for alignment score calculation
    NeedlemanWunsch alignment_;

    /// Not implemented
    ConsensusIDAlgorithmPEPMatrix(const ConsensusIDAlgorithmPEPMatrix&);

    /// Not implemented
    ConsensusIDAlgorithmPEPMatrix& operator=(const ConsensusIDAlgorithmPEPMatrix&);

    /// Sequence similarity based on substitution matrix (ignores PTMs)
    double getSimilarity_(AASequence seq1, AASequence seq2) override;

    // Docu in base class
    void updateMembers_() override;
  };

} // namespace OpenMS

