// --------------------------------------------------------------------------
//                   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
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// 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: Timo Sachsenberg $
// $Authors: Katharina Albers $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/ConsensusMap.h>

namespace OpenMS
{

  /**
      @brief Base class for all Caap evaluation algorithms

      These algorithms evaluates alignment results against a ground truth.
  */
  class OPENMS_DLLAPI MapAlignmentEvaluationAlgorithm
  {

protected:
    typedef ConsensusFeature::HandleSetType::const_iterator HandleIterator;

public:

    /// Default constructor
    MapAlignmentEvaluationAlgorithm();

    /// Destructor
    virtual ~MapAlignmentEvaluationAlgorithm();


    ///Applies the algorithm. The input consensus map is compared to the ground truth.
    virtual void evaluate(const ConsensusMap & conensus_map_in, const ConsensusMap & consensus_map_gt, const double & rt_dev, const double & mz_dev, const Peak2D::IntensityType & int_dev, const bool use_charge, double & out) = 0;

    ///Decides if two features are the same, based on maximum allowed deviations for retention time, m/z and intensity.
    bool isSameHandle(const FeatureHandle & lhs, const FeatureHandle & rhs, const double & rt_dev, const double & mz_dev, const Peak2D::IntensityType & int_dev, const bool use_charge);

    /// Register all derived classes in this method
    static void registerChildren();

private:
    ///Copy constructor is not implemented -> private
    MapAlignmentEvaluationAlgorithm(const MapAlignmentEvaluationAlgorithm &);
    ///Assignment operator is not implemented -> private
    MapAlignmentEvaluationAlgorithm & operator=(const MapAlignmentEvaluationAlgorithm &);

  };

} // namespace OpenMS

