// --------------------------------------------------------------------------
//                   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
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>

namespace OpenMS
{
  /**
      @brief A map feature grouping algorithm for labeling techniques with two labels.

      It takes one maps and searches for corresponding features with a defined distance in RT and m/z.

    @htmlinclude OpenMS_FeatureGroupingAlgorithmLabeled.parameters

      @ingroup FeatureGrouping
  */
  class OPENMS_DLLAPI FeatureGroupingAlgorithmLabeled :
    public FeatureGroupingAlgorithm
  {
public:
    /// Default constructor
    FeatureGroupingAlgorithmLabeled();

    /// Destructor
    ~FeatureGroupingAlgorithmLabeled() override;

    /**
        @brief Applies the algorithm

        @note Exactly one @em input map has to be provided.
        @note The @em output map has to have two file descriptions, containing
        the same file name. The file descriptions have to be labeled 'heavy' and 'light'.

        @exception Exception::IllegalArgument is thrown if the input data is not valid.
    */
    void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) override;

    ///Creates a new instance of this class (for Factory)
    static FeatureGroupingAlgorithm * create()
    {
      return new FeatureGroupingAlgorithmLabeled();
    }

    ///Returns the product name (for the Factory)
    static String getProductName()
    {
      return "labeled";
    }

private:

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

  };

} // namespace OpenMS

