// --------------------------------------------------------------------------
//                   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: $
// --------------------------------------------------------------------------

#pragma once

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

#include <OpenMS/KERNEL/ConversionHelper.h>

namespace OpenMS
{
  /**
      @brief A map feature grouping algorithm for unlabeled data.

      It takes multiple maps and searches for corresponding features.
      The corresponding features must be aligned, but may have small position deviations.

      There are two ways to run the algorithm:

      - a) Simply call "group" with all maps in memory.
      - b) Call "setReference", "addToGroup" (n times), "getResultMap" in that order.
      
      The second way is more memory efficient because at all times, only the
      reference map and the current map need to be in memory

      @htmlinclude OpenMS_FeatureGroupingAlgorithmUnlabeled.parameters

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

    /// Destructor
    ~FeatureGroupingAlgorithmUnlabeled() override;

    /**
        @brief Sets the reference map for the algorithm
        
        This will store the input map in the first argument of the pairfinder_input_ vector.

        Note that map_id needs to be unique (see addToGroup docu).
    */
    template <typename MapType>
    void setReference(int map_id, const MapType & map)
    {
      MapConversion::convert(map_id, map, pairfinder_input_[0]);
    }

    /**
        @brief Returns the computed consensus map (after calling addToGroup with all maps)
    */
    ConsensusMap & getResultMap()
    {
      return pairfinder_input_[0];
    }

    /**
        @brief Applies the algorithm

        @exception IllegalArgument is thrown if less than two input maps are given.
    */
    void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) override;

    /**
        @brief Adds one map to the group

        This assumes that setReference has been called before. It is the callers
        responsibility to provide a valid map_id. Note that all calls to
        addToGroup _must_ use different map_ids and they all need to be
        different from the one used to call setReference!

        @exception IllegalArgument is thrown if the map_id has been used before
    */
    void addToGroup(int map_id, const FeatureMap & feature_map);

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

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

private:

    // This vector should always have 2 elements
    // - the first element is the currently computed consensus map.
    //   After initialization of the algorithm, it will consist of the reference
    //   map alone, after adding all maps through addToGroup it will contain the
    //   final result (e.g. the consensus result of all maps).
    // - the second element is the map which was last added to the consensus map
    std::vector<ConsensusMap> pairfinder_input_;

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

  };

} // namespace OpenMS

